Diff of the two buildlogs:

--
--- b1/build.log	2024-05-16 19:00:15.694617903 +0000
+++ b2/build.log	2024-05-16 19:46:54.711567907 +0000
@@ -1,6 +1,6 @@
 I: pbuilder: network access will be disabled during build
-I: Current time: Wed Jun 18 12:37:00 -12 2025
-I: pbuilder-time-stamp: 1750293420
+I: Current time: Fri May 17 09:00:19 +14 2024
+I: pbuilder-time-stamp: 1715886019
 I: Building the build Environment
 I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz]
 I: copying local configuration
@@ -40,51 +40,83 @@
 dpkg-source: info: applying remove_tests_needing_junitx.patch
 I: Not using root during the build.
 I: Installing the build-deps
-I: user script /srv/workspace/pbuilder/395956/tmp/hooks/D02_print_environment starting
+I: user script /srv/workspace/pbuilder/1102110/tmp/hooks/D01_modify_environment starting
+debug: Running on infom01-amd64.
+I: Changing host+domainname to test build reproducibility
+I: Adding a custom variable just for the fun of it...
+I: Changing /bin/sh to bash
+'/bin/sh' -> '/bin/bash'
+lrwxrwxrwx 1 root root 9 May 16 19:00 /bin/sh -> /bin/bash
+I: Setting pbuilder2's login shell to /bin/bash
+I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other
+I: user script /srv/workspace/pbuilder/1102110/tmp/hooks/D01_modify_environment finished
+I: user script /srv/workspace/pbuilder/1102110/tmp/hooks/D02_print_environment starting
 I: set
-  BUILDDIR='/build/reproducible-path'
-  BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other'
-  BUILDUSERNAME='pbuilder1'
-  BUILD_ARCH='amd64'
-  DEBIAN_FRONTEND='noninteractive'
+  BASH=/bin/sh
+  BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath
+  BASH_ALIASES=()
+  BASH_ARGC=()
+  BASH_ARGV=()
+  BASH_CMDS=()
+  BASH_LINENO=([0]="12" [1]="0")
+  BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:.
+  BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment")
+  BASH_VERSINFO=([0]="5" [1]="2" [2]="21" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu")
+  BASH_VERSION='5.2.21(1)-release'
+  BUILDDIR=/build/reproducible-path
+  BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other'
+  BUILDUSERNAME=pbuilder2
+  BUILD_ARCH=amd64
+  DEBIAN_FRONTEND=noninteractive
   DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 '
-  DISTRIBUTION='unstable'
-  HOME='/root'
-  HOST_ARCH='amd64'
+  DIRSTACK=()
+  DISTRIBUTION=unstable
+  EUID=0
+  FUNCNAME=([0]="Echo" [1]="main")
+  GROUPS=()
+  HOME=/root
+  HOSTNAME=i-capture-the-hostname
+  HOSTTYPE=x86_64
+  HOST_ARCH=amd64
   IFS=' 	
   '
-  INVOCATION_ID='66b3b5e4932443dcbfd20ff9e47c3e8c'
-  LANG='C'
-  LANGUAGE='en_US:en'
-  LC_ALL='C'
-  MAIL='/var/mail/root'
-  OPTIND='1'
-  PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games'
-  PBCURRENTCOMMANDLINEOPERATION='build'
-  PBUILDER_OPERATION='build'
-  PBUILDER_PKGDATADIR='/usr/share/pbuilder'
-  PBUILDER_PKGLIBDIR='/usr/lib/pbuilder'
-  PBUILDER_SYSCONFDIR='/etc'
-  PPID='395956'
-  PS1='# '
-  PS2='> '
+  INVOCATION_ID=e1d0160ceb784bb2a9c6d6b6ea558946
+  LANG=C
+  LANGUAGE=et_EE:et
+  LC_ALL=C
+  MACHTYPE=x86_64-pc-linux-gnu
+  MAIL=/var/mail/root
+  OPTERR=1
+  OPTIND=1
+  OSTYPE=linux-gnu
+  PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path
+  PBCURRENTCOMMANDLINEOPERATION=build
+  PBUILDER_OPERATION=build
+  PBUILDER_PKGDATADIR=/usr/share/pbuilder
+  PBUILDER_PKGLIBDIR=/usr/lib/pbuilder
+  PBUILDER_SYSCONFDIR=/etc
+  PIPESTATUS=([0]="0")
+  POSIXLY_CORRECT=y
+  PPID=1102110
   PS4='+ '
-  PWD='/'
-  SHELL='/bin/bash'
-  SHLVL='2'
-  SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.ul0uXN8T/pbuilderrc_1LmL --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.ul0uXN8T/b1 --logfile b1/build.log biojava6-live_6.1.0+dfsg-4.dsc'
-  SUDO_GID='109'
-  SUDO_UID='104'
-  SUDO_USER='jenkins'
-  TERM='unknown'
-  TZ='/usr/share/zoneinfo/Etc/GMT+12'
-  USER='root'
-  _='/usr/bin/systemd-run'
+  PWD=/
+  SHELL=/bin/bash
+  SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix
+  SHLVL=3
+  SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.ul0uXN8T/pbuilderrc_GeJ3 --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.ul0uXN8T/b2 --logfile b2/build.log biojava6-live_6.1.0+dfsg-4.dsc'
+  SUDO_GID=109
+  SUDO_UID=104
+  SUDO_USER=jenkins
+  TERM=unknown
+  TZ=/usr/share/zoneinfo/Etc/GMT-14
+  UID=0
+  USER=root
+  _='I: set'
 I: uname -a
-  Linux infom02-amd64 6.6.13+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.6.13-1~bpo12+1 (2024-02-15) x86_64 GNU/Linux
+  Linux i-capture-the-hostname 6.1.0-21-cloud-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.90-1 (2024-05-03) x86_64 GNU/Linux
 I: ls -l /bin
-  lrwxrwxrwx 1 root root 7 Jun 18 14:05 /bin -> usr/bin
-I: user script /srv/workspace/pbuilder/395956/tmp/hooks/D02_print_environment finished
+  lrwxrwxrwx 1 root root 7 May 16 07:42 /bin -> usr/bin
+I: user script /srv/workspace/pbuilder/1102110/tmp/hooks/D02_print_environment finished
  -> Attempting to satisfy build-dependencies
  -> Creating pbuilder-satisfydepends-dummy package
 Package: pbuilder-satisfydepends-dummy
@@ -589,7 +621,7 @@
 Get: 407 http://deb.debian.org/debian unstable/main amd64 maven all 3.8.7-2 [19.3 kB]
 Get: 408 http://deb.debian.org/debian unstable/main amd64 maven-repo-helper all 1.11 [142 kB]
 Get: 409 http://deb.debian.org/debian unstable/main amd64 maven-debian-helper all 2.6.4 [108 kB]
-Fetched 339 MB in 5s (65.6 MB/s)
+Fetched 339 MB in 4s (77.6 MB/s)
 debconf: delaying package configuration, since apt-utils is not installed
 Selecting previously unselected package libpipeline1:amd64.
 (Reading database ... 
(Reading database ... 5%
(Reading database ... 10%
(Reading database ... 15%
(Reading database ... 20%
(Reading database ... 25%
(Reading database ... 30%
(Reading database ... 35%
(Reading database ... 40%
(Reading database ... 45%
(Reading database ... 50%
(Reading database ... 55%
(Reading database ... 60%
(Reading database ... 65%
(Reading database ... 70%
(Reading database ... 75%
(Reading database ... 80%
(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 19701 files and directories currently installed.)
@@ -1914,8 +1946,8 @@
 Setting up tzdata (2024a-4) ...
 
 Current default time zone: 'Etc/UTC'
-Local time is now:      Thu Jun 19 00:39:09 UTC 2025.
-Universal Time is now:  Thu Jun 19 00:39:09 UTC 2025.
+Local time is now:      Thu May 16 19:02:14 UTC 2024.
+Universal Time is now:  Thu May 16 19:02:14 UTC 2024.
 Run 'dpkg-reconfigure tzdata' if you wish to change it.
 
 Setting up libgeronimo-annotation-1.3-spec-java (1.3-1) ...
@@ -2448,7 +2480,11 @@
 Building tag database...
  -> Finished parsing the build-deps
 I: Building the package
-I: Running cd /build/reproducible-path/biojava6-live-6.1.0+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S  > ../biojava6-live_6.1.0+dfsg-4_source.changes
+I: user script /srv/workspace/pbuilder/1102110/tmp/hooks/A99_set_merged_usr starting
+Not re-configuring usrmerge for unstable
+I: user script /srv/workspace/pbuilder/1102110/tmp/hooks/A99_set_merged_usr finished
+hostname: Name or service not known
+I: Running cd /build/reproducible-path/biojava6-live-6.1.0+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S  > ../biojava6-live_6.1.0+dfsg-4_source.changes
 dpkg-buildpackage: info: source package biojava6-live
 dpkg-buildpackage: info: source version 6.1.0+dfsg-4
 dpkg-buildpackage: info: source distribution unstable
@@ -2598,30 +2634,30 @@
 [WARNING] Javadoc Warnings
 [WARNING] warning: The -footer option is no longer supported and will be ignored.
 [WARNING] It may be removed in a future release.
+[WARNING] Loading source files for package demo...
+[WARNING] Loading source files for package org.biojava.nbio.core.search.io.blast...
+[WARNING] Loading source files for package org.biojava.nbio.core.search.io...
+[WARNING] Loading source files for package org.biojava.nbio.core.util...
+[WARNING] Loading source files for package org.biojava.nbio.core.alignment.template...
+[WARNING] Loading source files for package org.biojava.nbio.core.alignment...
+[WARNING] Loading source files for package org.biojava.nbio.core.alignment.matrices...
 [WARNING] Loading source files for package org.biojava.nbio.core.exceptions...
-[WARNING] Loading source files for package org.biojava.nbio.core.sequence...
 [WARNING] Loading source files for package org.biojava.nbio.core.sequence.template...
-[WARNING] Loading source files for package org.biojava.nbio.core.sequence.features...
-[WARNING] Loading source files for package org.biojava.nbio.core.sequence.reference...
 [WARNING] Loading source files for package org.biojava.nbio.core.sequence.transcription...
-[WARNING] Loading source files for package org.biojava.nbio.core.sequence.io...
+[WARNING] Loading source files for package org.biojava.nbio.core.sequence...
+[WARNING] Loading source files for package org.biojava.nbio.core.sequence.reference...
+[WARNING] Loading source files for package org.biojava.nbio.core.sequence.edits...
 [WARNING] Loading source files for package org.biojava.nbio.core.sequence.io.template...
+[WARNING] Loading source files for package org.biojava.nbio.core.sequence.io...
 [WARNING] Loading source files for package org.biojava.nbio.core.sequence.io.util...
 [WARNING] Loading source files for package org.biojava.nbio.core.sequence.io.embl...
-[WARNING] Loading source files for package org.biojava.nbio.core.sequence.location...
+[WARNING] Loading source files for package org.biojava.nbio.core.sequence.storage...
 [WARNING] Loading source files for package org.biojava.nbio.core.sequence.location.template...
+[WARNING] Loading source files for package org.biojava.nbio.core.sequence.location...
 [WARNING] Loading source files for package org.biojava.nbio.core.sequence.views...
-[WARNING] Loading source files for package org.biojava.nbio.core.sequence.edits...
 [WARNING] Loading source files for package org.biojava.nbio.core.sequence.compound...
+[WARNING] Loading source files for package org.biojava.nbio.core.sequence.features...
 [WARNING] Loading source files for package org.biojava.nbio.core.sequence.loader...
-[WARNING] Loading source files for package org.biojava.nbio.core.sequence.storage...
-[WARNING] Loading source files for package org.biojava.nbio.core.search.io...
-[WARNING] Loading source files for package org.biojava.nbio.core.search.io.blast...
-[WARNING] Loading source files for package org.biojava.nbio.core.util...
-[WARNING] Loading source files for package org.biojava.nbio.core.alignment...
-[WARNING] Loading source files for package org.biojava.nbio.core.alignment.template...
-[WARNING] Loading source files for package org.biojava.nbio.core.alignment.matrices...
-[WARNING] Loading source files for package demo...
 [WARNING] Constructing Javadoc information...
 [WARNING] Building index for all the packages and classes...
 [WARNING] Standard Doclet version 17.0.11+9-Debian-1
@@ -3187,70 +3223,82 @@
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/util/package-tree.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/constant-values.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/serialized-form.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/demo/class-use/ParseFastaFileDemo.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/demo/class-use/UncompressFile.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/demo/class-use/DemoSixFrameTranslation.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/search/io/blast/class-use/BlastResultBuilder.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/search/io/blast/class-use/BlastTabularParser.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/search/io/blast/class-use/BlastResult.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/search/io/blast/class-use/BlastHitBuilder.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/search/io/blast/class-use/BlastHspBuilder.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/search/io/blast/class-use/BlastXMLParser.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/search/io/class-use/SearchIO.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/search/io/class-use/ResultFactory.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/search/io/class-use/Hsp.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/search/io/class-use/Result.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/search/io/class-use/Hit.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/util/class-use/ConcurrencyTools.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/util/class-use/SequenceTools.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/util/class-use/XMLWriter.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/util/class-use/PrettyXMLWriter.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/util/class-use/SingleLinkageClusterer.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/util/class-use/UncompressInputStream.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/util/class-use/InputStreamProvider.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/util/class-use/FileDownloadUtils.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/util/class-use/FlatFileCache.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/util/class-use/Hashcoder.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/util/class-use/SoftHashMap.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/util/class-use/Equals.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/util/class-use/StringManipulationHelper.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/util/class-use/XMLHelper.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/util/class-use/CRC64Checksum.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/alignment/template/class-use/MutableProfilePair.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/alignment/template/class-use/MutableProfile.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/alignment/template/class-use/AlignedSequence.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/alignment/template/class-use/AlignedSequence.Step.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/alignment/template/class-use/SequencePair.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/alignment/template/class-use/ProfileView.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/alignment/template/class-use/SubstitutionMatrix.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/alignment/template/class-use/ProfilePair.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/alignment/template/class-use/MutableAlignedSequence.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/alignment/template/class-use/Profile.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/alignment/template/class-use/Profile.StringFormat.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/alignment/template/class-use/MutableSequencePair.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/alignment/class-use/SimpleSequencePair.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/alignment/class-use/SimpleProfilePair.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/alignment/class-use/SimpleProfile.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/alignment/class-use/SimpleAlignedSequence.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/alignment/matrices/class-use/AAIndexFileParser.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/alignment/matrices/class-use/ScaledSubstitutionMatrix.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/alignment/matrices/class-use/SubstitutionMatrixHelper.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/alignment/matrices/class-use/SimpleSubstitutionMatrix.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/alignment/matrices/class-use/DefaultAAIndexProvider.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/alignment/matrices/class-use/AAIndexProvider.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/alignment/matrices/class-use/AAindexFactory.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/exceptions/class-use/ParserException.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/exceptions/class-use/TranslationException.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/exceptions/class-use/Messages.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/exceptions/class-use/TranslationException.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/exceptions/class-use/CompoundNotFoundException.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/class-use/ExonSequence.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/class-use/ChromosomeSequence.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/class-use/BasicSequence.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/class-use/GeneSequence.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/class-use/AccessionID.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/class-use/DataSource.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/class-use/CDSSequence.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/class-use/DNASequence.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/class-use/DNASequence.DNAType.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/class-use/RNASequence.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/class-use/StartCodonSequence.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/class-use/CDSComparator.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/class-use/IntronSequence.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/class-use/TranscriptSequence.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/class-use/TaxonomyID.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/class-use/Strand.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/class-use/MultipleSequenceAlignment.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/class-use/ExonComparator.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/class-use/ProteinSequence.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/class-use/StopCodonSequence.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/class-use/SequenceOptimizationHints.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/class-use/SequenceOptimizationHints.SequenceCollection.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/class-use/SequenceOptimizationHints.SequenceUsage.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/class-use/SequenceComparator.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/template/class-use/SequenceReader.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/template/class-use/Compound.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/template/class-use/ProxySequenceReader.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/template/class-use/Accessioned.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/template/class-use/SequenceMixin.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/template/class-use/SequenceMixin.SequenceIterator.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/template/class-use/AbstractCompoundTranslator.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/template/class-use/CompoundSet.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/template/class-use/SequenceProxyView.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/template/class-use/ComplementCompound.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/template/class-use/LightweightProfile.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/template/class-use/LightweightProfile.StringFormat.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/template/class-use/AbstractNucleotideCompoundSet.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/template/class-use/Sequence.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/template/class-use/ComplementCompound.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/template/class-use/ProxySequenceReader.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/template/class-use/Accessioned.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/template/class-use/SequenceProxyView.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/template/class-use/SequenceReader.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/template/class-use/SequenceView.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/template/class-use/AbstractCompound.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/template/class-use/CompoundTranslator.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/template/class-use/AbstractCompoundSet.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/template/class-use/AbstractSequence.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/template/class-use/AbstractSequence.AnnotationType.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/template/class-use/AbstractCompoundTranslator.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/template/class-use/SequenceMixin.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/template/class-use/SequenceMixin.SequenceIterator.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/template/class-use/Compound.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/template/class-use/AbstractCompound.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/template/class-use/SequenceView.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/template/class-use/AbstractNucleotideCompoundSet.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/template/class-use/CompoundTranslator.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/features/class-use/AbstractFeature.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/features/class-use/FeaturesKeyWordInterface.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/features/class-use/DatabaseReferenceInterface.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/features/class-use/Qualifier.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/features/class-use/TextFeature.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/features/class-use/FeatureInterface.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/features/class-use/FeatureRetriever.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/features/class-use/FeatureDbReferenceInfo.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/features/class-use/QuantityFeature.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/features/class-use/QualityFeature.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/features/class-use/DBReferenceInfo.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/reference/class-use/GenbankReference.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/reference/class-use/ReferenceInterface.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/reference/class-use/AbstractReference.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/transcription/class-use/RNAToAminoAcidTranslator.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/transcription/class-use/CaseInsensitiveCompound.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/transcription/class-use/TranscriptionEngine.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/transcription/class-use/TranscriptionEngine.Builder.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/transcription/class-use/Table.html...
@@ -3258,149 +3306,137 @@
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/transcription/class-use/Table.Codon.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/transcription/class-use/DNAToRNATranslator.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/transcription/class-use/Frame.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/class-use/GenericInsdcHeaderFormat.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/class-use/PlainFastaHeaderParser.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/class-use/FastaSequenceParser.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/class-use/GenericFastaHeaderFormat.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/class-use/FileProxyDNASequenceCreator.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/transcription/class-use/RNAToAminoAcidTranslator.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/transcription/class-use/CaseInsensitiveCompound.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/class-use/ExonSequence.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/class-use/SequenceOptimizationHints.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/class-use/SequenceOptimizationHints.SequenceCollection.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/class-use/SequenceOptimizationHints.SequenceUsage.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/class-use/ExonComparator.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/class-use/CDSComparator.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/class-use/GeneSequence.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/class-use/BasicSequence.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/class-use/Strand.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/class-use/StopCodonSequence.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/class-use/AccessionID.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/class-use/DataSource.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/class-use/IntronSequence.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/class-use/SequenceComparator.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/class-use/ChromosomeSequence.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/class-use/TaxonomyID.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/class-use/CDSSequence.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/class-use/MultipleSequenceAlignment.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/class-use/ProteinSequence.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/class-use/RNASequence.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/class-use/TranscriptSequence.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/class-use/StartCodonSequence.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/class-use/DNASequence.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/class-use/DNASequence.DNAType.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/reference/class-use/GenbankReference.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/reference/class-use/AbstractReference.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/reference/class-use/ReferenceInterface.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/edits/class-use/Edit.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/edits/class-use/Edit.Substitute.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/edits/class-use/Edit.Insert.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/edits/class-use/Edit.Delete.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/edits/class-use/Edit.AbstractEdit.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/template/class-use/SequenceCreatorInterface.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/template/class-use/GenbankHeaderFormatInterface.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/template/class-use/SequenceParserInterface.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/template/class-use/FastaHeaderFormatInterface.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/template/class-use/SequenceHeaderParserInterface.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/class-use/DNASequenceCreator.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/class-use/CasePreservingProteinSequenceCreator.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/class-use/FastaReaderHelper.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/class-use/GenbankWriter.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/class-use/FileProxyRNASequenceCreator.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/class-use/GenbankSequenceParser.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/class-use/FastaSequenceParser.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/class-use/GenbankReader.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/class-use/GenbankWriterHelper.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/class-use/FileProxyDNASequenceCreator.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/class-use/GenericGenbankHeaderFormat.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/class-use/GenbankReaderHelper.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/class-use/FastaWriter.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/class-use/GenbankWriter.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/class-use/FileProxyProteinSequenceCreator.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/class-use/GenbankWriterHelper.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/class-use/ProteinSequenceCreator.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/class-use/FastaGeneWriter.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/class-use/FastaReader.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/class-use/ABITrace.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/class-use/GenericFastaHeaderFormat.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/class-use/IUPACParser.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/class-use/IUPACParser.IUPACTable.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/class-use/GenbankReader.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/class-use/FastaWriter.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/class-use/FastaReaderHelper.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/class-use/GenericGenbankHeaderParser.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/class-use/CasePreservingProteinSequenceCreator.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/class-use/FastaWriterHelper.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/class-use/PlainFastaHeaderParser.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/class-use/BufferedReaderBytesRead.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/class-use/GenericInsdcHeaderFormat.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/class-use/FileProxyProteinSequenceCreator.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/class-use/GenericFastaHeaderParser.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/class-use/FastaGeneWriter.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/class-use/RNASequenceCreator.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/class-use/FileProxyRNASequenceCreator.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/class-use/ABITrace.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/class-use/FastaReader.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/class-use/ProteinSequenceCreator.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/class-use/GenericGenbankHeaderParser.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/class-use/BufferedReaderBytesRead.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/template/class-use/SequenceParserInterface.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/template/class-use/GenbankHeaderFormatInterface.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/template/class-use/SequenceCreatorInterface.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/template/class-use/SequenceHeaderParserInterface.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/template/class-use/FastaHeaderFormatInterface.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/util/class-use/IOUtils.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/util/class-use/IOUtils.ReaderProcessor.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/util/class-use/ClasspathResource.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/embl/class-use/EmblReference.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/embl/class-use/EmblId.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/embl/class-use/EmblRecord.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/embl/class-use/EmblReader.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/embl/class-use/EmblRecord.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/embl/class-use/EmblId.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/embl/class-use/EmblReference.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/storage/class-use/FourBitSequenceReader.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/storage/class-use/FourBitSequenceReader.FourBitArrayWorker.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/storage/class-use/BitSequenceReader.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/storage/class-use/BitSequenceReader.BitArrayWorker.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/storage/class-use/ArrayListSequenceReader.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/storage/class-use/SequenceAsStringHelper.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/storage/class-use/SingleCompoundSequenceReader.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/storage/class-use/TwoBitSequenceReader.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/storage/class-use/TwoBitSequenceReader.TwoBitArrayWorker.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/storage/class-use/JoiningSequenceReader.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/location/template/class-use/Location.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/location/template/class-use/Location.Tools.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/location/template/class-use/Point.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/location/template/class-use/Point.Resolver.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/location/template/class-use/AccesionedLocation.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/location/template/class-use/AbstractLocation.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/location/class-use/SimpleLocation.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/location/class-use/FuzzyPoint.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/location/class-use/InsdcParser.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/location/class-use/InsdcLocations.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/location/class-use/InsdcLocations.OneOfLocation.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/location/class-use/InsdcLocations.GroupLocation.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/location/class-use/InsdcLocations.OrderLocation.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/location/class-use/InsdcLocations.BondLocation.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/location/class-use/FuzzyPoint.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/location/class-use/LocationHelper.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/location/class-use/SimpleLocation.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/location/class-use/SimplePoint.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/location/class-use/LocationHelper.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/location/class-use/SequenceLocation.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/location/class-use/InsdcParser.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/location/template/class-use/AbstractLocation.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/location/template/class-use/AccesionedLocation.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/location/template/class-use/Location.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/location/template/class-use/Location.Tools.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/location/template/class-use/Point.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/location/template/class-use/Point.Resolver.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/views/class-use/RnaSequenceView.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/views/class-use/ComplementSequenceView.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/views/class-use/WindowedSequence.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/views/class-use/ReversedSequenceView.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/edits/class-use/Edit.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/edits/class-use/Edit.Substitute.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/edits/class-use/Edit.Insert.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/edits/class-use/Edit.Delete.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/edits/class-use/Edit.AbstractEdit.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/views/class-use/RnaSequenceView.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/views/class-use/ComplementSequenceView.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/compound/class-use/DNACompoundSet.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/compound/class-use/AmbiguityDNARNAHybridCompoundSet.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/compound/class-use/AminoAcidCompoundSet.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/compound/class-use/RNACompoundSet.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/compound/class-use/CodonCompound.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/compound/class-use/NucleotideCompound.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/compound/class-use/AmbiguityRNACompoundSet.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/compound/class-use/AmbiguityDNACompoundSet.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/compound/class-use/CodonCompound.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/compound/class-use/AminoAcidCompoundSet.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/compound/class-use/AmbiguityRNACompoundSet.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/compound/class-use/ABITracerCompoundSet.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/compound/class-use/RNACompoundSet.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/compound/class-use/AminoAcidCompound.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/loader/class-use/SequenceFileProxyLoader.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/loader/class-use/StringProxySequenceReader.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/compound/class-use/AmbiguityDNARNAHybridCompoundSet.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/features/class-use/DBReferenceInfo.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/features/class-use/Qualifier.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/features/class-use/AbstractFeature.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/features/class-use/DatabaseReferenceInterface.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/features/class-use/FeatureRetriever.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/features/class-use/TextFeature.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/features/class-use/QualityFeature.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/features/class-use/FeatureInterface.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/features/class-use/QuantityFeature.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/features/class-use/FeatureDbReferenceInfo.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/features/class-use/FeaturesKeyWordInterface.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/loader/class-use/ArrayListProxySequenceReader.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/loader/class-use/GenbankProxySequenceReader.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/loader/class-use/SequenceFileProxyLoader.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/loader/class-use/StringProxySequenceReader.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/loader/class-use/UniprotProxySequenceReader.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/storage/class-use/SequenceAsStringHelper.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/storage/class-use/FourBitSequenceReader.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/storage/class-use/FourBitSequenceReader.FourBitArrayWorker.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/storage/class-use/SingleCompoundSequenceReader.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/storage/class-use/TwoBitSequenceReader.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/storage/class-use/TwoBitSequenceReader.TwoBitArrayWorker.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/storage/class-use/JoiningSequenceReader.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/storage/class-use/BitSequenceReader.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/storage/class-use/BitSequenceReader.BitArrayWorker.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/storage/class-use/ArrayListSequenceReader.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/search/io/class-use/Result.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/search/io/class-use/Hsp.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/search/io/class-use/Hit.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/search/io/class-use/ResultFactory.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/search/io/class-use/SearchIO.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/search/io/blast/class-use/BlastHitBuilder.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/search/io/blast/class-use/BlastResult.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/search/io/blast/class-use/BlastResultBuilder.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/search/io/blast/class-use/BlastTabularParser.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/search/io/blast/class-use/BlastHspBuilder.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/search/io/blast/class-use/BlastXMLParser.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/util/class-use/SingleLinkageClusterer.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/util/class-use/XMLWriter.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/util/class-use/ConcurrencyTools.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/util/class-use/FileDownloadUtils.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/util/class-use/SequenceTools.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/util/class-use/UncompressInputStream.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/util/class-use/CRC64Checksum.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/util/class-use/SoftHashMap.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/util/class-use/Hashcoder.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/util/class-use/Equals.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/util/class-use/InputStreamProvider.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/util/class-use/StringManipulationHelper.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/util/class-use/PrettyXMLWriter.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/util/class-use/XMLHelper.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/util/class-use/FlatFileCache.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/alignment/class-use/SimpleSequencePair.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/alignment/class-use/SimpleProfile.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/alignment/class-use/SimpleAlignedSequence.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/alignment/class-use/SimpleProfilePair.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/alignment/template/class-use/MutableProfile.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/alignment/template/class-use/MutableAlignedSequence.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/alignment/template/class-use/SubstitutionMatrix.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/alignment/template/class-use/MutableSequencePair.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/alignment/template/class-use/MutableProfilePair.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/alignment/template/class-use/ProfilePair.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/alignment/template/class-use/ProfileView.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/alignment/template/class-use/SequencePair.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/alignment/template/class-use/Profile.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/alignment/template/class-use/Profile.StringFormat.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/alignment/template/class-use/AlignedSequence.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/alignment/template/class-use/AlignedSequence.Step.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/alignment/matrices/class-use/AAIndexFileParser.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/alignment/matrices/class-use/DefaultAAIndexProvider.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/alignment/matrices/class-use/ScaledSubstitutionMatrix.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/alignment/matrices/class-use/SubstitutionMatrixHelper.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/alignment/matrices/class-use/AAIndexProvider.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/alignment/matrices/class-use/AAindexFactory.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/alignment/matrices/class-use/SimpleSubstitutionMatrix.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/demo/class-use/UncompressFile.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/demo/class-use/DemoSixFrameTranslation.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/demo/class-use/ParseFastaFileDemo.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/demo/package-use.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/alignment/package-use.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/alignment/matrices/package-use.html...
@@ -3474,51 +3510,51 @@
 [WARNING] Javadoc Warnings
 [WARNING] warning: The -footer option is no longer supported and will be ignored.
 [WARNING] It may be removed in a future release.
-[WARNING] Loading source files for package org.forester.surfacing...
-[WARNING] Loading source files for package org.forester.tools...
-[WARNING] Loading source files for package org.forester.pccx...
-[WARNING] Loading source files for package org.forester.sequence...
-[WARNING] Loading source files for package org.forester.analysis...
-[WARNING] Loading source files for package org.forester.go...
-[WARNING] Loading source files for package org.forester.go.etc...
 [WARNING] Loading source files for package org.forester.archaeopteryx...
+[WARNING] Loading source files for package org.forester.archaeopteryx.phylogeny.data...
 [WARNING] Loading source files for package org.forester.archaeopteryx.tools...
 [WARNING] Loading source files for package org.forester.archaeopteryx.webservices...
-[WARNING] Loading source files for package org.forester.archaeopteryx.phylogeny.data...
-[WARNING] Loading source files for package org.forester.protein...
-[WARNING] Loading source files for package org.forester.io.parsers.tol...
+[WARNING] Loading source files for package org.forester.evoinference.distance...
+[WARNING] Loading source files for package org.forester.evoinference.parsimony...
+[WARNING] Loading source files for package org.forester.evoinference.tools...
+[WARNING] Loading source files for package org.forester.evoinference.matrix.distance...
+[WARNING] Loading source files for package org.forester.evoinference.matrix.character...
+[WARNING] Loading source files for package org.forester.evoinference...
+[WARNING] Loading source files for package org.forester.phylogeny.factories...
+[WARNING] Loading source files for package org.forester.phylogeny...
+[WARNING] Loading source files for package org.forester.phylogeny.data...
+[WARNING] Loading source files for package org.forester.phylogeny.iterators...
+[WARNING] Loading source files for package org.forester.test...
+[WARNING] Loading source files for package org.forester.test.examples...
+[WARNING] Loading source files for package org.forester.tools...
+[WARNING] Loading source files for package org.forester.io.writers...
+[WARNING] Loading source files for package org.forester.io.parsers.nexus...
 [WARNING] Loading source files for package org.forester.io.parsers...
 [WARNING] Loading source files for package org.forester.io.parsers.util...
 [WARNING] Loading source files for package org.forester.io.parsers.phyloxml...
 [WARNING] Loading source files for package org.forester.io.parsers.phyloxml.data...
-[WARNING] Loading source files for package org.forester.io.parsers.nexus...
 [WARNING] Loading source files for package org.forester.io.parsers.nhx...
-[WARNING] Loading source files for package org.forester.io.writers...
-[WARNING] Loading source files for package org.forester.test...
-[WARNING] Loading source files for package org.forester.test.examples...
-[WARNING] Loading source files for package org.forester.evoinference.tools...
-[WARNING] Loading source files for package org.forester.evoinference.parsimony...
-[WARNING] Loading source files for package org.forester.evoinference.distance...
-[WARNING] Loading source files for package org.forester.evoinference.matrix.character...
-[WARNING] Loading source files for package org.forester.evoinference.matrix.distance...
-[WARNING] Loading source files for package org.forester.evoinference...
-[WARNING] Loading source files for package org.forester.msa...
-[WARNING] Loading source files for package org.forester.ws.seqdb...
-[WARNING] Loading source files for package org.forester.ws.hmmer...
+[WARNING] Loading source files for package org.forester.io.parsers.tol...
 [WARNING] Loading source files for package org.forester.ws.wabi...
-[WARNING] Loading source files for package org.forester.msa_compactor...
-[WARNING] Loading source files for package org.forester.rio...
+[WARNING] Loading source files for package org.forester.ws.hmmer...
+[WARNING] Loading source files for package org.forester.ws.seqdb...
 [WARNING] Loading source files for package org.forester.util...
+[WARNING] Loading source files for package org.forester.surfacing...
+[WARNING] Loading source files for package org.forester.datastructures...
+[WARNING] Loading source files for package org.forester.pccx...
+[WARNING] Loading source files for package org.forester.protein...
+[WARNING] Loading source files for package org.forester.analysis...
+[WARNING] Loading source files for package org.forester.go...
+[WARNING] Loading source files for package org.forester.go.etc...
+[WARNING] Loading source files for package org.forester.species...
+[WARNING] Loading source files for package org.forester.msa...
+[WARNING] Loading source files for package org.forester.sdi...
 [WARNING] Loading source files for package org.forester.application...
 [WARNING] Loading source files for package org.forester.development...
-[WARNING] Loading source files for package org.forester.phylogeny...
-[WARNING] Loading source files for package org.forester.phylogeny.data...
-[WARNING] Loading source files for package org.forester.phylogeny.factories...
-[WARNING] Loading source files for package org.forester.phylogeny.iterators...
+[WARNING] Loading source files for package org.forester.sequence...
+[WARNING] Loading source files for package org.forester.msa_compactor...
 [WARNING] Loading source files for package org.forester.applications...
-[WARNING] Loading source files for package org.forester.datastructures...
-[WARNING] Loading source files for package org.forester.sdi...
-[WARNING] Loading source files for package org.forester.species...
+[WARNING] Loading source files for package org.forester.rio...
 [WARNING] Constructing Javadoc information...
 [WARNING] Building index for all the packages and classes...
 [WARNING] Standard Doclet version 17.0.11+9-Debian-1
@@ -4108,409 +4144,409 @@
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/ws/wabi/package-tree.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/constant-values.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/serialized-form.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/surfacing/class-use/DirectedBinaryDomainCombination.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/surfacing/class-use/PairwiseDomainSimilarity.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/surfacing/class-use/GenomeWideCombinableDomains.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/surfacing/class-use/GenomeWideCombinableDomains.GenomeWideCombinableDomainsSortOrder.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/surfacing/class-use/SurfacingUtil.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/surfacing/class-use/ProteinCountsBasedPairwiseDomainSimilarityCalculator.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/surfacing/class-use/AdjactantDirectedBinaryDomainCombination.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/surfacing/class-use/DomainArchitectureBasedGenomeSimilarityCalculator.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/surfacing/class-use/PairwiseDomainSimilarityCalculator.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/surfacing/class-use/SimpleDomain.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/surfacing/class-use/CountsBasedPairwiseDomainSimilarity.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/surfacing/class-use/DomainCountsBasedPairwiseSimilarityCalculator.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/surfacing/class-use/CombinationsBasedPairwiseDomainSimilarity.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/surfacing/class-use/CombinationsBasedPairwiseDomainSimilarityCalculator.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/surfacing/class-use/TestSurfacing.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/surfacing/class-use/CombinableDomains.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/surfacing/class-use/DomainCountsDifferenceUtil.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/surfacing/class-use/DomainCountsDifferenceUtil.COPY_CALCULATION_MODE.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/surfacing/class-use/DomainLengths.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/surfacing/class-use/SurfacingConstants.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/surfacing/class-use/DomainParsimonyCalculator.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/surfacing/class-use/DomainLengthsTable.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/surfacing/class-use/AdjactantDirectedCombinableDomains.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/surfacing/class-use/DirectedCombinableDomains.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/surfacing/class-use/BasicDomainSimilarityCalculator.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/surfacing/class-use/BasicCombinableDomains.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/surfacing/class-use/DomainSimilarityCalculator.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/surfacing/class-use/DomainSimilarityCalculator.GoAnnotationOutput.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/surfacing/class-use/DomainSimilarityCalculator.Detailedness.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/surfacing/class-use/BasicGenomeWideCombinableDomains.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/surfacing/class-use/MappingResults.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/surfacing/class-use/DomainSimilarity.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/surfacing/class-use/DomainSimilarity.PRINT_OPTION.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/surfacing/class-use/DomainSimilarity.DomainSimilaritySortField.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/surfacing/class-use/DomainSimilarity.DomainSimilarityScoring.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/surfacing/class-use/BasicBinaryDomainCombination.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/surfacing/class-use/PairwiseGenomeComparator.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/tools/class-use/ConfidenceAssessor.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/tools/class-use/TreeSplitMatrix.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/tools/class-use/SupportCount.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/tools/class-use/PhylogenyDecorator.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/tools/class-use/PhylogenyDecorator.FIELD.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/pccx/class-use/CoverageCalculationOptions.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/pccx/class-use/ModelingUtils.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/pccx/class-use/ScoringMethodForExternalNode.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/pccx/class-use/CoverageCalculator.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/pccx/class-use/BasicExternalNodeBasedCoverageExtender.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/pccx/class-use/BranchLengthBasedScoringMethod.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/pccx/class-use/TestPccx.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/pccx/class-use/BranchCountingBasedScoringMethod.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/pccx/class-use/CoverageCalculationMethod.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/pccx/class-use/Coverage.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/pccx/class-use/ExternalNodeBasedCoverageMethod.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/pccx/class-use/LogBranchLengthBasedScoringMethod.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/pccx/class-use/ExternalNodeBasedCoverage.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/pccx/class-use/ExternalNodeBasedCoverageMethodOptions.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/pccx/class-use/CoverageExtender.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/sequence/class-use/BasicSequence.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/sequence/class-use/MolecularSequence.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/sequence/class-use/MolecularSequence.TYPE.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/analysis/class-use/TaxonomyDataManager.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/analysis/class-use/AncestralTaxonomyInference.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/analysis/class-use/AncestralTaxonomyInferenceException.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/go/class-use/GoId.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/go/class-use/PfamToGoMapping.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/go/class-use/GoSubset.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/go/class-use/GoSubset.Type.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/go/class-use/GoUtils.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/go/class-use/GoRelationship.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/go/class-use/GoRelationship.Type.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/go/class-use/BasicGoTerm.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/go/class-use/PfamToGoParser.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/go/class-use/TestGo.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/go/class-use/GoTerm.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/go/class-use/GoXRef.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/go/class-use/GoXRef.Type.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/go/class-use/Mapping.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/go/class-use/OBOparser.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/go/class-use/OBOparser.ReturnType.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/go/class-use/BasicGoXRef.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/go/class-use/BasicGoRelationship.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/go/class-use/GoNameSpace.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/go/class-use/GoNameSpace.GoNamespaceType.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/go/class-use/BasicGoSubset.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/go/etc/class-use/MetaOntologizer.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/go/etc/class-use/OntologizerResult.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/go/etc/class-use/OntologizerResult.TYPE.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/archaeopteryx/class-use/TreeFontSet.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/archaeopteryx/class-use/Configuration.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/archaeopteryx/class-use/Configuration.UI.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/archaeopteryx/class-use/Configuration.EXT_NODE_DATA_RETURN_ON.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/archaeopteryx/class-use/TreePanelUtil.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/archaeopteryx/class-use/ArchaeopteryxE.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/archaeopteryx/class-use/MainFrameApplet.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/archaeopteryx/class-use/Options.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/archaeopteryx/class-use/Options.PHYLOGENY_GRAPHICS_TYPE.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/archaeopteryx/class-use/Options.NODE_LABEL_DIRECTION.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/archaeopteryx/class-use/Options.CLADOGRAM_TYPE.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/archaeopteryx/class-use/MainFrame.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/archaeopteryx/class-use/FontChooser.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/archaeopteryx/class-use/Constants.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/archaeopteryx/class-use/AptxUtil.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/archaeopteryx/class-use/AptxUtil.GraphicsExportType.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/archaeopteryx/class-use/MainFrameApplet.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/archaeopteryx/class-use/TreePanelUtil.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/archaeopteryx/class-use/UrlTreeReader.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/archaeopteryx/class-use/MainFrameApplication.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/archaeopteryx/class-use/Archaeopteryx.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/archaeopteryx/class-use/ArchaeopteryxA.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/archaeopteryx/class-use/FontChooser.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/archaeopteryx/class-use/TreeFontSet.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/archaeopteryx/class-use/Configuration.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/archaeopteryx/class-use/Configuration.UI.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/archaeopteryx/class-use/Configuration.EXT_NODE_DATA_RETURN_ON.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/archaeopteryx/class-use/TreePanel.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/archaeopteryx/class-use/UrlTreeReader.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/archaeopteryx/class-use/MainFrame.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/archaeopteryx/class-use/Constants.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/archaeopteryx/class-use/MainPanel.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/archaeopteryx/class-use/TreeColorSet.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/archaeopteryx/class-use/Archaeopteryx.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/archaeopteryx/class-use/ArchaeopteryxA.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/archaeopteryx/class-use/AptxUtil.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/archaeopteryx/class-use/AptxUtil.GraphicsExportType.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/archaeopteryx/phylogeny/data/class-use/RenderablePhylogenyData.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/archaeopteryx/phylogeny/data/class-use/RenderableVector.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/archaeopteryx/phylogeny/data/class-use/RenderableDomainArchitecture.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/archaeopteryx/phylogeny/data/class-use/RenderableMsaSequence.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/archaeopteryx/tools/class-use/PhylogeneticInferrer.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/archaeopteryx/tools/class-use/PhylogeneticInferrer.MSA_PRG.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/archaeopteryx/tools/class-use/PhylogeneticInferenceOptions.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/archaeopteryx/tools/class-use/ProcessRunning.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/archaeopteryx/tools/class-use/RunnableProcess.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/archaeopteryx/tools/class-use/SequenceDataRetriver.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/archaeopteryx/tools/class-use/ProcessPool.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/archaeopteryx/tools/class-use/AncestralTaxonomyInferrer.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/archaeopteryx/tools/class-use/PhylogeneticInferenceOptions.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/archaeopteryx/tools/class-use/Blast.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/archaeopteryx/tools/class-use/ImageLoader.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/archaeopteryx/tools/class-use/InferenceManager.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/archaeopteryx/tools/class-use/AncestralTaxonomyInferrer.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/archaeopteryx/tools/class-use/ProcessPool.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/archaeopteryx/tools/class-use/RunnableProcess.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/archaeopteryx/tools/class-use/PhyloInferenceDialog.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/archaeopteryx/webservices/class-use/PhylogeniesWebserviceClient.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/archaeopteryx/tools/class-use/ImageLoader.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/archaeopteryx/tools/class-use/ProcessRunning.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/archaeopteryx/webservices/class-use/WebservicesManager.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/archaeopteryx/webservices/class-use/WebservicesManager.WsPhylogenyFormat.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/archaeopteryx/webservices/class-use/WebserviceUtil.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/archaeopteryx/webservices/class-use/PhylogeniesWebserviceClient.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/archaeopteryx/webservices/class-use/BasicPhylogeniesWebserviceClient.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/archaeopteryx/phylogeny/data/class-use/RenderablePhylogenyData.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/archaeopteryx/phylogeny/data/class-use/RenderableVector.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/archaeopteryx/phylogeny/data/class-use/RenderableMsaSequence.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/archaeopteryx/phylogeny/data/class-use/RenderableDomainArchitecture.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/protein/class-use/BasicProtein.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/protein/class-use/BinaryDomainCombination.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/protein/class-use/BinaryDomainCombination.OutputFormat.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/protein/class-use/BinaryDomainCombination.DomainCombinationType.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/protein/class-use/ProteinId.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/protein/class-use/BasicDomain.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/protein/class-use/Domain.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/protein/class-use/Protein.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/tol/class-use/TolXmlHandler.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/tol/class-use/TolXmlMapping.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/tol/class-use/TolParser.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/evoinference/distance/class-use/PairwiseDistanceCalculator.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/evoinference/distance/class-use/PairwiseDistanceCalculator.PWD_DISTANCE_METHOD.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/evoinference/distance/class-use/NeighborJoining.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/evoinference/distance/class-use/NeighborJoiningR.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/evoinference/distance/class-use/NeighborJoiningF.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/evoinference/distance/class-use/Sarray.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/evoinference/distance/class-use/Sset.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/evoinference/parsimony/class-use/DolloParsimony.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/evoinference/parsimony/class-use/FitchParsimony.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/evoinference/parsimony/class-use/SankoffParsimony.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/evoinference/tools/class-use/BootstrapResampler.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/evoinference/matrix/distance/class-use/DistanceMatrix.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/evoinference/matrix/distance/class-use/DistanceMatrix.Format.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/evoinference/matrix/distance/class-use/BasicSymmetricalDistanceMatrix.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/evoinference/matrix/character/class-use/BasicCharacterStateMatrix.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/evoinference/matrix/character/class-use/CharacterStateMatrix.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/evoinference/matrix/character/class-use/CharacterStateMatrix.NucleotideStates.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/evoinference/matrix/character/class-use/CharacterStateMatrix.GainLossStates.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/evoinference/matrix/character/class-use/CharacterStateMatrix.Format.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/evoinference/matrix/character/class-use/CharacterStateMatrix.BinaryStates.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/evoinference/class-use/TestPhylogenyReconstruction.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/phylogeny/factories/class-use/PhylogenyFactory.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/phylogeny/factories/class-use/ParserBasedPhylogenyFactory.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/phylogeny/class-use/PhylogenyMethods.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/phylogeny/class-use/PhylogenyMethods.PhylogenyNodeField.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/phylogeny/class-use/PhylogenyMethods.DESCENDANT_SORT_PRIORITY.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/phylogeny/class-use/PhylogenyBranch.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/phylogeny/class-use/Phylogeny.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/phylogeny/class-use/PhylogenyNode.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/phylogeny/class-use/PhylogenyNode.NH_CONVERSION_SUPPORT_VALUE_STYLE.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/phylogeny/data/class-use/BinaryCharacters.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/phylogeny/data/class-use/Polygon.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/phylogeny/data/class-use/Identifier.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/phylogeny/data/class-use/Event.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/phylogeny/data/class-use/Event.EventType.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/phylogeny/data/class-use/Uri.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/phylogeny/data/class-use/PropertiesMap.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/phylogeny/data/class-use/Accession.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/phylogeny/data/class-use/Accession.Source.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/phylogeny/data/class-use/PhylogenyData.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/phylogeny/data/class-use/Taxonomy.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/phylogeny/data/class-use/NodeData.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/phylogeny/data/class-use/PhylogenyDataUtil.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/phylogeny/data/class-use/NodeDataField.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/phylogeny/data/class-use/SequenceRelation.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/phylogeny/data/class-use/SequenceRelation.SEQUENCE_RELATION_TYPE.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/phylogeny/data/class-use/BranchWidth.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/phylogeny/data/class-use/Date.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/phylogeny/data/class-use/Sequence.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/phylogeny/data/class-use/Annotation.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/phylogeny/data/class-use/BranchColor.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/phylogeny/data/class-use/ProteinDomain.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/phylogeny/data/class-use/Point.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/phylogeny/data/class-use/Distribution.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/phylogeny/data/class-use/DomainArchitecture.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/phylogeny/data/class-use/Confidence.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/phylogeny/data/class-use/BranchData.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/phylogeny/data/class-use/MultipleUris.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/phylogeny/data/class-use/NodeVisualData.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/phylogeny/data/class-use/NodeVisualData.NodeShape.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/phylogeny/data/class-use/NodeVisualData.NodeFill.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/phylogeny/data/class-use/NodeVisualData.FontType.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/phylogeny/data/class-use/Reference.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/phylogeny/data/class-use/Property.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/phylogeny/data/class-use/Property.AppliesTo.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/phylogeny/iterators/class-use/ExternalForwardIterator.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/phylogeny/iterators/class-use/PreorderTreeIterator.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/phylogeny/iterators/class-use/PhylogenyNodeIterator.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/phylogeny/iterators/class-use/PostOrderStackObject.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/phylogeny/iterators/class-use/PostorderTreeIterator.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/phylogeny/iterators/class-use/LevelOrderTreeIterator.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/test/class-use/Test.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/test/examples/class-use/Example1.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/test/examples/class-use/Example2.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/test/examples/class-use/Example3.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/test/examples/class-use/Example5.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/test/examples/class-use/Example4.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/tools/class-use/PhylogenyDecorator.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/tools/class-use/PhylogenyDecorator.FIELD.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/tools/class-use/SupportCount.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/tools/class-use/TreeSplitMatrix.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/tools/class-use/ConfidenceAssessor.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/writers/class-use/SequenceWriter.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/writers/class-use/SequenceWriter.SEQ_FORMAT.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/writers/class-use/PhylogenyWriter.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/writers/class-use/PhylogenyWriter.FORMAT.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/writers/class-use/PhyloXmlNodeWriter.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/nexus/class-use/NexusCharactersParser.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/nexus/class-use/PaupLogParser.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/nexus/class-use/NexusConstants.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/nexus/class-use/NexusPhylogeniesParser.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/nexus/class-use/NexusBinaryStatesMatrixParser.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/nexus/class-use/NexusFormatException.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/class-use/FastaParser.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/class-use/IteratingPhylogenyParser.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/class-use/GeneralMsaParser.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/class-use/PhylogenyParser.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/class-use/HmmscanPerDomainTableParser.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/class-use/HmmscanPerDomainTableParser.ReturnType.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/class-use/HmmscanPerDomainTableParser.INDIVIDUAL_SCORE_CUTOFF.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/class-use/HmmscanPerDomainTableParser.FilterType.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/class-use/SymmetricalDistanceMatrixParser.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/class-use/SymmetricalDistanceMatrixParser.InputMatrixType.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/class-use/HmmPfamOutputParser.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/class-use/HmmPfamOutputParser.ReturnType.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/class-use/HmmPfamOutputParser.FilterType.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/class-use/SymmetricalDistanceMatrixParser.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/class-use/SymmetricalDistanceMatrixParser.InputMatrixType.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/class-use/PhylogenyParser.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/class-use/IteratingPhylogenyParser.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/class-use/FastaParser.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/util/class-use/ParserUtils.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/util/class-use/PhylogenyParserException.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/phyloxml/class-use/PhyloXmlDataFormatException.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/util/class-use/ParserUtils.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/phyloxml/class-use/PhyloXmlException.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/phyloxml/class-use/PhyloXmlHandler.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/phyloxml/class-use/XmlElement.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/phyloxml/class-use/PhyloXmlException.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/phyloxml/class-use/PhyloXmlMapping.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/phyloxml/class-use/PhyloXmlParser.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/phyloxml/class-use/PhyloXmlDataFormatException.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/phyloxml/class-use/PhyloXmlUtil.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/phyloxml/data/class-use/ReferenceParser.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/phyloxml/data/class-use/DistributionParser.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/phyloxml/data/class-use/ConfidenceParser.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/phyloxml/data/class-use/DomainArchitectureParser.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/phyloxml/data/class-use/UriParser.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/phyloxml/data/class-use/IdentifierParser.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/phyloxml/data/class-use/BinaryCharactersParser.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/phyloxml/data/class-use/EventParser.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/phyloxml/data/class-use/DistributionParser.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/phyloxml/data/class-use/BranchWidthParser.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/phyloxml/data/class-use/AccessionParser.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/phyloxml/data/class-use/PropertyParser.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/phyloxml/data/class-use/DateParser.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/phyloxml/data/class-use/PolygonParser.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/phyloxml/data/class-use/DomainArchitectureParser.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/phyloxml/data/class-use/ProteinDomainParser.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/phyloxml/data/class-use/TaxonomyParser.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/phyloxml/data/class-use/ReferenceParser.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/phyloxml/data/class-use/ColorParser.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/phyloxml/data/class-use/DateParser.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/phyloxml/data/class-use/TaxonomyParser.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/phyloxml/data/class-use/ProteinDomainParser.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/phyloxml/data/class-use/SequenceParser.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/phyloxml/data/class-use/EventParser.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/phyloxml/data/class-use/ConfidenceParser.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/phyloxml/data/class-use/AnnotationParser.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/phyloxml/data/class-use/PhylogenyDataPhyloXmlParser.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/phyloxml/data/class-use/SequenceRelationParser.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/phyloxml/data/class-use/PropertyParser.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/phyloxml/data/class-use/AccessionParser.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/phyloxml/data/class-use/PointParser.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/phyloxml/data/class-use/BranchWidthParser.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/phyloxml/data/class-use/PhylogenyDataPhyloXmlParser.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/phyloxml/data/class-use/IdentifierParser.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/phyloxml/data/class-use/AnnotationParser.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/phyloxml/data/class-use/UriParser.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/phyloxml/data/class-use/SequenceParser.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/nexus/class-use/NexusCharactersParser.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/nexus/class-use/PaupLogParser.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/nexus/class-use/NexusConstants.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/nexus/class-use/NexusFormatException.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/nexus/class-use/NexusPhylogeniesParser.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/nexus/class-use/NexusBinaryStatesMatrixParser.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/nhx/class-use/NHXFormatException.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/nhx/class-use/NHXtags.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/nhx/class-use/NHXParser.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/nhx/class-use/NHXParser.TAXONOMY_EXTRACTION.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/writers/class-use/PhyloXmlNodeWriter.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/writers/class-use/SequenceWriter.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/writers/class-use/SequenceWriter.SEQ_FORMAT.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/writers/class-use/PhylogenyWriter.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/writers/class-use/PhylogenyWriter.FORMAT.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/test/class-use/Test.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/test/examples/class-use/Example4.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/test/examples/class-use/Example2.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/test/examples/class-use/Example3.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/test/examples/class-use/Example5.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/test/examples/class-use/Example1.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/evoinference/tools/class-use/BootstrapResampler.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/evoinference/parsimony/class-use/SankoffParsimony.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/evoinference/parsimony/class-use/FitchParsimony.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/evoinference/parsimony/class-use/DolloParsimony.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/evoinference/distance/class-use/PairwiseDistanceCalculator.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/evoinference/distance/class-use/PairwiseDistanceCalculator.PWD_DISTANCE_METHOD.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/evoinference/distance/class-use/NeighborJoining.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/evoinference/distance/class-use/Sarray.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/evoinference/distance/class-use/Sset.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/evoinference/distance/class-use/NeighborJoiningR.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/evoinference/distance/class-use/NeighborJoiningF.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/evoinference/matrix/character/class-use/BasicCharacterStateMatrix.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/evoinference/matrix/character/class-use/CharacterStateMatrix.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/evoinference/matrix/character/class-use/CharacterStateMatrix.NucleotideStates.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/evoinference/matrix/character/class-use/CharacterStateMatrix.GainLossStates.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/evoinference/matrix/character/class-use/CharacterStateMatrix.Format.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/evoinference/matrix/character/class-use/CharacterStateMatrix.BinaryStates.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/evoinference/matrix/distance/class-use/DistanceMatrix.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/evoinference/matrix/distance/class-use/DistanceMatrix.Format.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/evoinference/matrix/distance/class-use/BasicSymmetricalDistanceMatrix.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/evoinference/class-use/TestPhylogenyReconstruction.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/msa/class-use/DeleteableMsa.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/msa/class-use/ClustalOmega.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/msa/class-use/Msa.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/msa/class-use/Msa.MSA_FORMAT.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/msa/class-use/BasicMsa.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/msa/class-use/ResampleableMsa.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/msa/class-use/Mafft.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/msa/class-use/MsaFormatException.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/msa/class-use/MsaInferrer.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/msa/class-use/MsaMethods.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/ws/seqdb/class-use/SequenceDatabaseEntry.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/ws/seqdb/class-use/UniProtTaxonomy.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/ws/seqdb/class-use/EbiDbEntry.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/ws/seqdb/class-use/UniProtEntry.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/ws/seqdb/class-use/SequenceDbWsTools.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/ws/hmmer/class-use/Test.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/tol/class-use/TolXmlMapping.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/tol/class-use/TolXmlHandler.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/tol/class-use/TolParser.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/ws/wabi/class-use/TxSearch.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/ws/wabi/class-use/TxSearch.TAX_RANK.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/ws/wabi/class-use/TxSearch.TAX_NAME_CLASS.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/ws/wabi/class-use/TxSearch.RANKS.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/ws/wabi/class-use/WabiTools.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/ws/wabi/class-use/RestUtil.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/msa_compactor/class-use/MsaCompactor.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/msa_compactor/class-use/Chart.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/msa_compactor/class-use/GapContribution.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/msa_compactor/class-use/MsaProperties.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/rio/class-use/RIO.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/rio/class-use/RIO.REROOTING.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/rio/class-use/TestRIO.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/rio/class-use/RIOException.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/util/class-use/DescriptiveStatistics.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/ws/wabi/class-use/WabiTools.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/ws/hmmer/class-use/Test.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/ws/seqdb/class-use/UniProtTaxonomy.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/ws/seqdb/class-use/SequenceDatabaseEntry.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/ws/seqdb/class-use/UniProtEntry.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/ws/seqdb/class-use/SequenceDbWsTools.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/ws/seqdb/class-use/EbiDbEntry.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/util/class-use/BasicDescriptiveStatistics.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/util/class-use/ExternalProgram.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/util/class-use/TaxonomyColors.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/util/class-use/AsciiHistogram.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/util/class-use/StringInt.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/util/class-use/StringInt.DescendingIntComparator.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/util/class-use/SequenceAccessionTools.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/util/class-use/TaxonomyUtil.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/util/class-use/ForesterConstants.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/util/class-use/ForesterConstants.PhylogeneticTreeFormats.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/util/class-use/BasicTableParser.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/util/class-use/DescriptiveStatistics.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/util/class-use/CommandProcessBuilder.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/util/class-use/ForesterUtil.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/util/class-use/CommandLineArguments.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/util/class-use/WindowsUtils.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/util/class-use/SystemCommandExecutor.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/util/class-use/BasicTable.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/util/class-use/EasyWriter.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/util/class-use/SequenceAccessionTools.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/util/class-use/FailedConditionCheckException.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/util/class-use/ForesterUtil.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/util/class-use/AsciiHistogram.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/util/class-use/BasicTable.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/util/class-use/BasicTableParser.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/util/class-use/IllegalFormatUseException.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/util/class-use/FailedConditionCheckException.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/util/class-use/SystemCommandExecutor.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/util/class-use/ExternalProgram.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/util/class-use/GeneralTable.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/application/class-use/msa_compactor.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/application/class-use/goac.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/application/class-use/pfam2go_extractor.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/application/class-use/confadd.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/util/class-use/ForesterConstants.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/util/class-use/ForesterConstants.PhylogeneticTreeFormats.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/util/class-use/StringInt.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/util/class-use/StringInt.DescendingIntComparator.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/util/class-use/WindowsUtils.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/surfacing/class-use/CountsBasedPairwiseDomainSimilarity.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/surfacing/class-use/PairwiseDomainSimilarityCalculator.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/surfacing/class-use/DomainParsimonyCalculator.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/surfacing/class-use/AdjactantDirectedCombinableDomains.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/surfacing/class-use/AdjactantDirectedBinaryDomainCombination.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/surfacing/class-use/CombinationsBasedPairwiseDomainSimilarity.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/surfacing/class-use/CombinableDomains.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/surfacing/class-use/SimpleDomain.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/surfacing/class-use/BasicCombinableDomains.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/surfacing/class-use/DomainLengths.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/surfacing/class-use/DirectedBinaryDomainCombination.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/surfacing/class-use/DomainCountsDifferenceUtil.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/surfacing/class-use/DomainCountsDifferenceUtil.COPY_CALCULATION_MODE.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/surfacing/class-use/SurfacingConstants.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/surfacing/class-use/BasicDomainSimilarityCalculator.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/surfacing/class-use/DomainLengthsTable.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/surfacing/class-use/DomainSimilarity.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/surfacing/class-use/DomainSimilarity.PRINT_OPTION.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/surfacing/class-use/DomainSimilarity.DomainSimilaritySortField.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/surfacing/class-use/DomainSimilarity.DomainSimilarityScoring.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/surfacing/class-use/BasicBinaryDomainCombination.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/surfacing/class-use/BasicGenomeWideCombinableDomains.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/surfacing/class-use/ProteinCountsBasedPairwiseDomainSimilarityCalculator.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/surfacing/class-use/PairwiseDomainSimilarity.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/surfacing/class-use/DomainSimilarityCalculator.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/surfacing/class-use/DomainSimilarityCalculator.GoAnnotationOutput.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/surfacing/class-use/DomainSimilarityCalculator.Detailedness.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/surfacing/class-use/MappingResults.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/surfacing/class-use/PairwiseGenomeComparator.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/surfacing/class-use/DomainCountsBasedPairwiseSimilarityCalculator.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/surfacing/class-use/GenomeWideCombinableDomains.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/surfacing/class-use/GenomeWideCombinableDomains.GenomeWideCombinableDomainsSortOrder.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/surfacing/class-use/CombinationsBasedPairwiseDomainSimilarityCalculator.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/surfacing/class-use/DomainArchitectureBasedGenomeSimilarityCalculator.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/surfacing/class-use/DirectedCombinableDomains.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/surfacing/class-use/TestSurfacing.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/surfacing/class-use/SurfacingUtil.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/datastructures/class-use/Queue.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/datastructures/class-use/IntMatrix.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/pccx/class-use/ExternalNodeBasedCoverageMethod.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/pccx/class-use/ScoringMethodForExternalNode.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/pccx/class-use/Coverage.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/pccx/class-use/BranchCountingBasedScoringMethod.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/pccx/class-use/CoverageCalculationMethod.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/pccx/class-use/ModelingUtils.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/pccx/class-use/ExternalNodeBasedCoverageMethodOptions.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/pccx/class-use/LogBranchLengthBasedScoringMethod.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/pccx/class-use/BranchLengthBasedScoringMethod.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/pccx/class-use/ExternalNodeBasedCoverage.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/pccx/class-use/CoverageCalculationOptions.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/pccx/class-use/CoverageCalculator.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/pccx/class-use/BasicExternalNodeBasedCoverageExtender.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/pccx/class-use/TestPccx.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/pccx/class-use/CoverageExtender.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/protein/class-use/BasicDomain.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/protein/class-use/BasicProtein.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/protein/class-use/ProteinId.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/protein/class-use/BinaryDomainCombination.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/protein/class-use/BinaryDomainCombination.OutputFormat.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/protein/class-use/BinaryDomainCombination.DomainCombinationType.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/protein/class-use/Protein.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/protein/class-use/Domain.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/analysis/class-use/AncestralTaxonomyInferenceException.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/analysis/class-use/AncestralTaxonomyInference.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/analysis/class-use/TaxonomyDataManager.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/go/class-use/PfamToGoMapping.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/go/class-use/BasicGoSubset.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/go/class-use/PfamToGoParser.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/go/class-use/GoUtils.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/go/class-use/Mapping.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/go/class-use/GoId.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/go/class-use/BasicGoXRef.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/go/class-use/OBOparser.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/go/class-use/OBOparser.ReturnType.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/go/class-use/GoSubset.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/go/class-use/GoSubset.Type.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/go/class-use/GoRelationship.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/go/class-use/GoRelationship.Type.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/go/class-use/GoNameSpace.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/go/class-use/GoNameSpace.GoNamespaceType.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/go/class-use/GoXRef.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/go/class-use/GoXRef.Type.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/go/class-use/BasicGoTerm.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/go/class-use/BasicGoRelationship.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/go/class-use/TestGo.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/go/class-use/GoTerm.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/go/etc/class-use/OntologizerResult.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/go/etc/class-use/OntologizerResult.TYPE.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/go/etc/class-use/MetaOntologizer.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/species/class-use/Species.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/species/class-use/BasicSpecies.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/msa/class-use/ClustalOmega.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/msa/class-use/MsaMethods.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/msa/class-use/Mafft.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/msa/class-use/BasicMsa.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/msa/class-use/Msa.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/msa/class-use/Msa.MSA_FORMAT.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/msa/class-use/ResampleableMsa.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/msa/class-use/DeleteableMsa.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/msa/class-use/MsaFormatException.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/msa/class-use/MsaInferrer.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/sdi/class-use/GSDI.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/sdi/class-use/GSDIR.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/sdi/class-use/SDIException.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/sdi/class-use/GSDII.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/sdi/class-use/TestGSDI.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/sdi/class-use/SDIutil.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/sdi/class-use/SDIutil.TaxonomyComparisonBase.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/sdi/class-use/SDIutil.ALGORITHM.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/sdi/class-use/SDIR.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/sdi/class-use/SDI.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/application/class-use/count_support.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/application/class-use/mcc.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/application/class-use/pfamacc2go.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/application/class-use/decoratorX.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/application/class-use/phylostrip.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/application/class-use/surfacing.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/application/class-use/gene_tree_preprocess.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/application/class-use/pccx.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/application/class-use/obo_tool.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/application/class-use/pfam_go.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/application/class-use/annotator.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/application/class-use/pfamacc2pfamid.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/application/class-use/decorator.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/application/class-use/nj.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/application/class-use/pccx.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/application/class-use/table2fasta.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/application/class-use/support_statistics.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/application/class-use/pfam2go_extractor.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/application/class-use/surfacing.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/application/class-use/rio.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/application/class-use/decoratorX.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/application/class-use/obo_tool.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/application/class-use/confadd.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/application/class-use/check_fasta.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/application/class-use/nj.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/application/class-use/dom_dup.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/application/class-use/msa_compactor.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/application/class-use/support_statistics.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/application/class-use/phyloxml_converter.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/application/class-use/gsdi.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/application/class-use/phylostrip.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/application/class-use/support_transfer.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/application/class-use/gene_tree_preprocess.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/application/class-use/mcc.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/application/class-use/meta_ontologizer.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/application/class-use/rio.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/application/class-use/goac.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/application/class-use/dom_dup.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/application/class-use/pfamacc2pfamid.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/application/class-use/gsdi.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/application/class-use/pfamacc2go.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/application/class-use/fasta_split.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/development/class-use/Test.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/application/class-use/pfam_go.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/application/class-use/annotator.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/development/class-use/MsaRenderer.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/development/class-use/HmmerRest.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/development/class-use/Time.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/development/class-use/neTest.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/development/class-use/neTest.DoublePointer.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/development/class-use/ResidueRenderer.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/development/class-use/Test.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/development/class-use/Hello3d.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/development/class-use/AbstractRenderer.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/development/class-use/DevelopmentTools.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/development/class-use/Hello3d.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/development/class-use/ResidueRenderer.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/development/class-use/HmmerRest.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/development/class-use/RandomThing.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/phylogeny/class-use/PhylogenyNode.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/phylogeny/class-use/PhylogenyNode.NH_CONVERSION_SUPPORT_VALUE_STYLE.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/phylogeny/class-use/PhylogenyBranch.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/phylogeny/class-use/PhylogenyMethods.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/phylogeny/class-use/PhylogenyMethods.PhylogenyNodeField.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/phylogeny/class-use/PhylogenyMethods.DESCENDANT_SORT_PRIORITY.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/phylogeny/class-use/Phylogeny.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/phylogeny/data/class-use/NodeData.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/phylogeny/data/class-use/Uri.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/phylogeny/data/class-use/Sequence.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/phylogeny/data/class-use/Polygon.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/phylogeny/data/class-use/PropertiesMap.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/phylogeny/data/class-use/Identifier.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/phylogeny/data/class-use/PhylogenyDataUtil.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/phylogeny/data/class-use/NodeDataField.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/phylogeny/data/class-use/Accession.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/phylogeny/data/class-use/Accession.Source.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/phylogeny/data/class-use/BranchWidth.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/phylogeny/data/class-use/Event.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/phylogeny/data/class-use/Event.EventType.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/phylogeny/data/class-use/MultipleUris.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/phylogeny/data/class-use/Distribution.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/phylogeny/data/class-use/BinaryCharacters.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/phylogeny/data/class-use/NodeVisualData.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/phylogeny/data/class-use/NodeVisualData.NodeShape.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/phylogeny/data/class-use/NodeVisualData.NodeFill.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/phylogeny/data/class-use/NodeVisualData.FontType.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/phylogeny/data/class-use/Property.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/phylogeny/data/class-use/Property.AppliesTo.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/phylogeny/data/class-use/Reference.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/phylogeny/data/class-use/PhylogenyData.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/phylogeny/data/class-use/Annotation.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/phylogeny/data/class-use/BranchColor.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/phylogeny/data/class-use/Taxonomy.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/phylogeny/data/class-use/Confidence.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/phylogeny/data/class-use/DomainArchitecture.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/phylogeny/data/class-use/ProteinDomain.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/phylogeny/data/class-use/SequenceRelation.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/phylogeny/data/class-use/SequenceRelation.SEQUENCE_RELATION_TYPE.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/phylogeny/data/class-use/BranchData.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/phylogeny/data/class-use/Date.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/phylogeny/data/class-use/Point.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/phylogeny/factories/class-use/PhylogenyFactory.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/phylogeny/factories/class-use/ParserBasedPhylogenyFactory.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/phylogeny/iterators/class-use/LevelOrderTreeIterator.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/phylogeny/iterators/class-use/PreorderTreeIterator.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/phylogeny/iterators/class-use/PostOrderStackObject.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/phylogeny/iterators/class-use/PhylogenyNodeIterator.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/phylogeny/iterators/class-use/PostorderTreeIterator.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/phylogeny/iterators/class-use/ExternalForwardIterator.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/applications/class-use/domainloss_replacement.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/applications/class-use/set_comparator.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/applications/class-use/genome_counts_for_once_appearing_dcs.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/applications/class-use/subtree_feature_count.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/applications/class-use/core_chars.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/development/class-use/neTest.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/development/class-use/neTest.DoublePointer.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/development/class-use/Time.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/sequence/class-use/BasicSequence.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/sequence/class-use/MolecularSequence.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/sequence/class-use/MolecularSequence.TYPE.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/msa_compactor/class-use/MsaProperties.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/msa_compactor/class-use/GapContribution.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/msa_compactor/class-use/MsaCompactor.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/msa_compactor/class-use/Chart.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/applications/class-use/get_distances.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/applications/class-use/phylo2graphics.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/applications/class-use/tax_code_cleaner.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/applications/class-use/get_genome_counts_per_char.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/applications/class-use/phylo2coloredgraphics.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/applications/class-use/reinv_count.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/applications/class-use/aaa.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/applications/class-use/genome_counts_for_once_appearing_dcs.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/applications/class-use/get_genome_counts_per_char.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/applications/class-use/get_loss_nodes.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/applications/class-use/set_comparator.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/applications/class-use/map_lengths.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/applications/class-use/aa.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/applications/class-use/simple_node_processor.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/applications/class-use/tax_code_cleaner.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/applications/class-use/core_chars.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/applications/class-use/shared_chars_in_ext_nodes.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/applications/class-use/get_subtree_specific_chars.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/applications/class-use/get_loss_nodes.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/applications/class-use/get_shared_chars.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/applications/class-use/domainloss_replacement.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/applications/class-use/subtree_feature_count.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/applications/class-use/phylo2graphics.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/applications/class-use/simple_node_processor.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/applications/class-use/wiki_examples.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/applications/class-use/map_lengths.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/applications/class-use/aaa.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/applications/class-use/get_shared_chars.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/applications/class-use/inverted_dcs.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/datastructures/class-use/IntMatrix.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/datastructures/class-use/Queue.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/sdi/class-use/GSDI.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/sdi/class-use/TestGSDI.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/sdi/class-use/SDIR.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/sdi/class-use/SDIutil.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/sdi/class-use/SDIutil.TaxonomyComparisonBase.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/sdi/class-use/SDIutil.ALGORITHM.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/sdi/class-use/SDI.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/sdi/class-use/SDIException.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/sdi/class-use/GSDII.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/sdi/class-use/GSDIR.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/species/class-use/BasicSpecies.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/species/class-use/Species.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/applications/class-use/get_subtree_specific_chars.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/applications/class-use/reinv_count.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/rio/class-use/RIO.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/rio/class-use/RIO.REROOTING.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/rio/class-use/RIOException.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/rio/class-use/TestRIO.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/analysis/package-use.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/application/package-use.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/applications/package-use.html...
@@ -4603,12 +4639,12 @@
 [WARNING] Javadoc Warnings
 [WARNING] warning: The -footer option is no longer supported and will be ignored.
 [WARNING] It may be removed in a future release.
-[WARNING] Loading source files for package org.biojava.nbio.phylo...
-[WARNING] Loading source files for package org.biojava.nbio.alignment...
+[WARNING] Loading source files for package demo...
 [WARNING] Loading source files for package org.biojava.nbio.alignment.template...
+[WARNING] Loading source files for package org.biojava.nbio.alignment...
 [WARNING] Loading source files for package org.biojava.nbio.alignment.io...
 [WARNING] Loading source files for package org.biojava.nbio.alignment.routines...
-[WARNING] Loading source files for package demo...
+[WARNING] Loading source files for package org.biojava.nbio.phylo...
 [WARNING] Constructing Javadoc information...
 [WARNING] Building index for all the packages and classes...
 [WARNING] Standard Doclet version 17.0.11+9-Debian-1
@@ -4811,51 +4847,29 @@
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/phylo/package-tree.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/constant-values.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/serialized-form.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/phylo/class-use/DistanceMatrixCalculator.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/phylo/class-use/DistanceTreeEvaluator.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/phylo/class-use/TreeType.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/phylo/class-use/ForesterWrapper.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/phylo/class-use/TreeConstructor.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/phylo/class-use/Comparison.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/phylo/class-use/TreeConstructorType.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/class-use/SubstitutionMatrixScorer.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/class-use/SmithWaterman.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/class-use/NeedlemanWunsch.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/class-use/SimpleProfileProfileAligner.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/class-use/FractionalSimilarityInProfileScorer.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/class-use/FractionalIdentityScorer.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/class-use/FractionalIdentityInProfileScorer.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/class-use/FractionalSimilarityScorer.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/class-use/Alignments.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/class-use/Alignments.RefinerType.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/class-use/Alignments.ProfileProfileAlignerType.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/class-use/Alignments.PairwiseSequenceScorerType.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/class-use/Alignments.PairwiseSequenceAlignerType.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/class-use/Alignments.PairInProfileScorerType.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/class-use/GuideTree.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/class-use/GuideTree.Node.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/class-use/StandardRescoreRefiner.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/class-use/SimpleGapPenalty.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/template/class-use/AbstractProfileProfileAligner.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/template/class-use/RescoreRefiner.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/template/class-use/GuideTreeNode.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/template/class-use/PairInProfileScorer.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/template/class-use/PairwiseSequenceScorer.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/template/class-use/PairwiseSequenceAligner.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/demo/class-use/DemoDistanceTree.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/demo/class-use/DemoLoadSubstMax.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/demo/class-use/TestDNANeedlemanWunsch.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/demo/class-use/CookbookMSA.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/demo/class-use/DemoAlignProteins.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/template/class-use/AbstractScorer.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/template/class-use/CallablePairwiseSequenceAligner.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/template/class-use/AbstractMatrixAligner.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/template/class-use/MatrixAligner.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/template/class-use/AbstractPairwiseSequenceAligner.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/template/class-use/ProfileProfileAligner.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/template/class-use/HierarchicalClusterer.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/template/class-use/Scorer.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/template/class-use/ProfileProfileScorer.html...
 [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/PartitionRefiner.java:31: warning: Tag @link: reference not found: Profile
 [WARNING] * Defines an algorithm which computes a new alignment {@link Profile} by splitting a current alignment and realigning.
 [WARNING] ^
 [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/ProfileProfileAligner.java:31: warning: Tag @link: reference not found: Profile
 [WARNING] * Defines an {@link Aligner} for a pair of {@link Profile}s.
 [WARNING] ^
-[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/RescoreRefiner.java:32: warning: Tag @link: reference not found: Profile
-[WARNING] * Defines an algorithm which computes a new alignment {@link Profile} by rescoring all pairs in an alignment and
-[WARNING] ^
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/template/class-use/AbstractPairwiseSequenceAligner.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/template/class-use/RescoreRefiner.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/template/class-use/GuideTreeNode.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/template/class-use/CallableProfileProfileAligner.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/template/class-use/PairwiseSequenceScorer.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/template/class-use/CallablePairwiseSequenceScorer.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/template/class-use/Aligner.html...
 [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/PartitionRefiner.java:31: warning: Tag @link: reference not found: Profile
 [WARNING] * Defines an algorithm which computes a new alignment {@link Profile} by splitting a current alignment and realigning.
@@ -4866,39 +4880,61 @@
 [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/RescoreRefiner.java:32: warning: Tag @link: reference not found: Profile
 [WARNING] * Defines an algorithm which computes a new alignment {@link Profile} by rescoring all pairs in an alignment and
 [WARNING] ^
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/template/class-use/ProfileProfileScorer.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/template/class-use/PairInProfileScorer.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/template/class-use/PairwiseSequenceAligner.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/template/class-use/GapPenalty.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/template/class-use/GapPenalty.Type.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/template/class-use/MatrixAligner.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/template/class-use/AbstractProfileProfileAligner.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/template/class-use/PartitionRefiner.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/template/class-use/Scorer.html...
 [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/PartitionRefiner.java:31: warning: Tag @link: reference not found: Profile
 [WARNING] * Defines an algorithm which computes a new alignment {@link Profile} by splitting a current alignment and realigning.
 [WARNING] ^
 [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/ProfileProfileAligner.java:31: warning: Tag @link: reference not found: Profile
 [WARNING] * Defines an {@link Aligner} for a pair of {@link Profile}s.
 [WARNING] ^
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/template/class-use/CallablePairwiseSequenceAligner.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/template/class-use/CallableProfileProfileAligner.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/template/class-use/AbstractScorer.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/template/class-use/ProfileProfileAligner.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/template/class-use/CallablePairwiseSequenceScorer.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/template/class-use/PartitionRefiner.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/template/class-use/GapPenalty.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/template/class-use/GapPenalty.Type.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/io/class-use/StockholmFileAnnotation.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/io/class-use/StockholmFileAnnotation.StockholmFileAnnotationReference.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/io/class-use/StockholmFileParser.html...
+[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/RescoreRefiner.java:32: warning: Tag @link: reference not found: Profile
+[WARNING] * Defines an algorithm which computes a new alignment {@link Profile} by rescoring all pairs in an alignment and
+[WARNING] ^
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/class-use/SimpleGapPenalty.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/class-use/NeedlemanWunsch.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/class-use/FractionalSimilarityScorer.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/class-use/GuideTree.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/class-use/GuideTree.Node.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/class-use/StandardRescoreRefiner.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/class-use/FractionalIdentityScorer.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/class-use/Alignments.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/class-use/Alignments.RefinerType.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/class-use/Alignments.ProfileProfileAlignerType.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/class-use/Alignments.PairwiseSequenceScorerType.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/class-use/Alignments.PairwiseSequenceAlignerType.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/class-use/Alignments.PairInProfileScorerType.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/class-use/SubstitutionMatrixScorer.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/class-use/FractionalSimilarityInProfileScorer.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/class-use/SmithWaterman.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/class-use/SimpleProfileProfileAligner.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/class-use/FractionalIdentityInProfileScorer.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/io/class-use/StockholmStructure.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/io/class-use/StockholmStructure.DatabaseReference.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/io/class-use/StockholmFileParser.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/io/class-use/StockholmFileAnnotation.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/io/class-use/StockholmFileAnnotation.StockholmFileAnnotationReference.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/routines/class-use/AnchoredPairwiseSequenceAligner.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/routines/class-use/GuanUberbacher.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/routines/class-use/AlignerHelper.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/routines/class-use/AlignerHelper.Subproblem.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/routines/class-use/AlignerHelper.Anchor.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/routines/class-use/AlignerHelper.Anchor.QueryIndexComparator.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/routines/class-use/AlignerHelper.Cut.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/routines/class-use/AlignerHelper.Last.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/routines/class-use/AnchoredPairwiseSequenceAligner.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/routines/class-use/GuanUberbacher.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/demo/class-use/CookbookMSA.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/demo/class-use/DemoLoadSubstMax.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/demo/class-use/DemoAlignProteins.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/demo/class-use/DemoDistanceTree.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/demo/class-use/TestDNANeedlemanWunsch.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/phylo/class-use/ForesterWrapper.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/phylo/class-use/DistanceTreeEvaluator.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/phylo/class-use/TreeConstructorType.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/phylo/class-use/TreeConstructor.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/phylo/class-use/DistanceMatrixCalculator.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/phylo/class-use/Comparison.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/phylo/class-use/TreeType.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/demo/package-use.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/package-use.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/io/package-use.html...
@@ -4988,51 +5024,51 @@
 [WARNING] Javadoc Warnings
 [WARNING] warning: The -footer option is no longer supported and will be ignored.
 [WARNING] It may be removed in a future release.
-[WARNING] Loading source files for package org.biojava.nbio.structure.secstruc...
+[WARNING] Loading source files for package demo...
 [WARNING] Loading source files for package org.biojava.nbio.structure...
-[WARNING] Loading source files for package org.biojava.nbio.structure.math...
-[WARNING] Loading source files for package org.biojava.nbio.structure.jama...
-[WARNING] Loading source files for package org.biojava.nbio.structure.cluster...
+[WARNING] Loading source files for package org.biojava.nbio.structure.domain...
+[WARNING] Loading source files for package org.biojava.nbio.structure.domain.pdp...
 [WARNING] Loading source files for package org.biojava.nbio.structure.geometry...
+[WARNING] Loading source files for package org.biojava.nbio.structure.cath...
+[WARNING] Loading source files for package org.biojava.nbio.structure.math...
 [WARNING] Loading source files for package org.biojava.nbio.structure.io...
-[WARNING] Loading source files for package org.biojava.nbio.structure.io.cif...
-[WARNING] Loading source files for package org.biojava.nbio.structure.io.util...
 [WARNING] Loading source files for package org.biojava.nbio.structure.io.mmtf...
+[WARNING] Loading source files for package org.biojava.nbio.structure.io.util...
+[WARNING] Loading source files for package org.biojava.nbio.structure.io.cif...
 [WARNING] Loading source files for package org.biojava.nbio.structure.io.sifts...
-[WARNING] Loading source files for package org.biojava.nbio.structure.domain.pdp...
-[WARNING] Loading source files for package org.biojava.nbio.structure.domain...
+[WARNING] Loading source files for package org.biojava.nbio.structure.jama...
+[WARNING] Loading source files for package org.biojava.nbio.structure.xtal.io...
+[WARNING] Loading source files for package org.biojava.nbio.structure.xtal...
+[WARNING] Loading source files for package org.biojava.nbio.structure.chem...
+[WARNING] Loading source files for package org.biojava.nbio.structure.asa...
+[WARNING] Loading source files for package org.biojava.nbio.structure.scop...
+[WARNING] Loading source files for package org.biojava.nbio.structure.contact...
+[WARNING] Loading source files for package org.biojava.nbio.structure.symmetry.geometry...
+[WARNING] Loading source files for package org.biojava.nbio.structure.symmetry.utils...
+[WARNING] Loading source files for package org.biojava.nbio.structure.symmetry.internal...
+[WARNING] Loading source files for package org.biojava.nbio.structure.symmetry.misc...
+[WARNING] Loading source files for package org.biojava.nbio.structure.symmetry.axis...
+[WARNING] Loading source files for package org.biojava.nbio.structure.symmetry.core...
 [WARNING] Loading source files for package org.biojava.nbio.structure.basepairs...
-[WARNING] Loading source files for package org.biojava.nbio.structure.align.client...
+[WARNING] Loading source files for package org.biojava.nbio.structure.quaternary...
+[WARNING] Loading source files for package org.biojava.nbio.structure.secstruc...
+[WARNING] Loading source files for package org.biojava.nbio.structure.ecod...
+[WARNING] Loading source files for package org.biojava.nbio.structure.cluster...
 [WARNING] Loading source files for package org.biojava.nbio.structure.align...
 [WARNING] Loading source files for package org.biojava.nbio.structure.align.fatcat...
 [WARNING] Loading source files for package org.biojava.nbio.structure.align.fatcat.calc...
 [WARNING] Loading source files for package org.biojava.nbio.structure.align.ce...
-[WARNING] Loading source files for package org.biojava.nbio.structure.align.pairwise...
-[WARNING] Loading source files for package org.biojava.nbio.structure.align.model...
-[WARNING] Loading source files for package org.biojava.nbio.structure.align.seq...
+[WARNING] Loading source files for package org.biojava.nbio.structure.align.client...
 [WARNING] Loading source files for package org.biojava.nbio.structure.align.util...
+[WARNING] Loading source files for package org.biojava.nbio.structure.align.model...
+[WARNING] Loading source files for package org.biojava.nbio.structure.align.xml...
 [WARNING] Loading source files for package org.biojava.nbio.structure.align.helper...
+[WARNING] Loading source files for package org.biojava.nbio.structure.align.seq...
 [WARNING] Loading source files for package org.biojava.nbio.structure.align.quaternary...
 [WARNING] Loading source files for package org.biojava.nbio.structure.align.multiple...
 [WARNING] Loading source files for package org.biojava.nbio.structure.align.multiple.util...
 [WARNING] Loading source files for package org.biojava.nbio.structure.align.multiple.mc...
-[WARNING] Loading source files for package org.biojava.nbio.structure.align.xml...
-[WARNING] Loading source files for package org.biojava.nbio.structure.symmetry.axis...
-[WARNING] Loading source files for package org.biojava.nbio.structure.symmetry.geometry...
-[WARNING] Loading source files for package org.biojava.nbio.structure.symmetry.utils...
-[WARNING] Loading source files for package org.biojava.nbio.structure.symmetry.misc...
-[WARNING] Loading source files for package org.biojava.nbio.structure.symmetry.core...
-[WARNING] Loading source files for package org.biojava.nbio.structure.symmetry.internal...
-[WARNING] Loading source files for package org.biojava.nbio.structure.contact...
-[WARNING] Loading source files for package org.biojava.nbio.structure.asa...
-[WARNING] Loading source files for package org.biojava.nbio.structure.cath...
-[WARNING] Loading source files for package org.biojava.nbio.structure.quaternary...
-[WARNING] Loading source files for package org.biojava.nbio.structure.scop...
-[WARNING] Loading source files for package org.biojava.nbio.structure.xtal...
-[WARNING] Loading source files for package org.biojava.nbio.structure.xtal.io...
-[WARNING] Loading source files for package org.biojava.nbio.structure.chem...
-[WARNING] Loading source files for package org.biojava.nbio.structure.ecod...
-[WARNING] Loading source files for package demo...
+[WARNING] Loading source files for package org.biojava.nbio.structure.align.pairwise...
 [WARNING] Constructing Javadoc information...
 [WARNING] Building index for all the packages and classes...
 [WARNING] Standard Doclet version 17.0.11+9-Debian-1
@@ -5867,447 +5903,447 @@
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/xtal/io/package-tree.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/constant-values.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/serialized-form.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/secstruc/class-use/BridgeType.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/secstruc/class-use/Ladder.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/secstruc/class-use/SecStrucType.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/secstruc/class-use/SecStrucTools.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/secstruc/class-use/HBond.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/secstruc/class-use/DSSPParser.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/secstruc/class-use/SecStrucCalc.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/secstruc/class-use/SecStrucInfo.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/secstruc/class-use/SecStrucElement.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/secstruc/class-use/SecStrucState.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/secstruc/class-use/BetaBridge.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/class-use/PassthroughIdentifier.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/class-use/NucleotideImpl.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/class-use/ExperimentalTechnique.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/class-use/PDBStatus.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/class-use/PDBStatus.Status.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/class-use/AugmentedResidueRange.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/class-use/StructureIO.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/class-use/Author.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/demo/class-use/DemoBioAssemblies.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/demo/class-use/DemoAsa.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/demo/class-use/DemoSCOP.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/demo/class-use/DemoMultipleMC.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/demo/class-use/DemoContacts.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/demo/class-use/DemoMMCIFReader.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/demo/class-use/DemoSecStrucCalc.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/demo/class-use/DemoCrystalInterfaces.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/demo/class-use/DemoDomainsplit.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/demo/class-use/DemoChangeChemCompProvider.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/demo/class-use/DemoLoadSecStruc.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/demo/class-use/DemoMmcifToPdbConverter.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/demo/class-use/DemoCE.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/demo/class-use/DemoMmtfReader.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/demo/class-use/DemoBerkeleyScop.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/demo/class-use/DemoAtomCache.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/demo/class-use/DemoCeSymm.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/demo/class-use/DemoQsAlign.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/demo/class-use/DemoCATH.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/demo/class-use/DemoFATCAT.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/demo/class-use/ChemCompDistribution.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/demo/class-use/DemoCommandLineStartup.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/demo/class-use/DemoSymmetry.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/demo/class-use/DemoLoadStructure.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/demo/class-use/DemoMmtfWriter.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/class-use/Chain.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/class-use/ElementType.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/class-use/BondImpl.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/class-use/SeqMisMatch.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/class-use/AtomImpl.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/class-use/JournalArticle.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/class-use/Model.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/class-use/EntityInfo.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/class-use/GroupType.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/class-use/PDBCrystallographicInfo.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/class-use/BondType.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/class-use/ResidueNumber.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/class-use/Element.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/class-use/StructureIdentifier.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/class-use/SeqMisMatchImpl.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/class-use/StandardAminoAcid.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/class-use/StructureException.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/class-use/DatabasePDBRevRecord.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/class-use/Calc.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/class-use/ResidueRange.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/class-use/AminoAcidImpl.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/class-use/StructureImpl.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/class-use/AtomPositionMap.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/class-use/AtomPositionMap.GroupMatcher.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/class-use/HetatomImpl.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/class-use/HetatomImpl.PerformanceBehavior.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/class-use/Mutator.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/class-use/EntityType.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/class-use/Structure.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/class-use/Site.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/class-use/PdbId.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/class-use/Chain.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/class-use/Bond.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/class-use/ResidueRangeAndLength.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/class-use/SeqMisMatch.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/class-use/AtomImpl.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/class-use/GroupIterator.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/class-use/URLIdentifier.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/class-use/EntityType.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/class-use/AugmentedResidueRange.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/class-use/ResidueRangeAndLength.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/class-use/SubstructureIdentifier.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/class-use/DBRef.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/class-use/BioAssemblyIdentifier.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/class-use/StructureException.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/class-use/AminoAcid.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/class-use/ResidueNumber.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/class-use/Author.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/class-use/Bond.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/class-use/StructureIO.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/class-use/BondType.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/class-use/StructureTools.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/class-use/StandardAminoAcid.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/class-use/ChainImpl.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/class-use/AtomIterator.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/class-use/BondImpl.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/class-use/Structure.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/class-use/SeqMisMatchImpl.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/class-use/Calc.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/class-use/PDBHeader.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/class-use/JournalArticle.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/class-use/StructureIdentifier.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/class-use/PassthroughIdentifier.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/class-use/HetatomImpl.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/class-use/HetatomImpl.PerformanceBehavior.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/class-use/AtomIterator.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/class-use/Mutator.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/class-use/AtomPositionMap.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/class-use/AtomPositionMap.GroupMatcher.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/class-use/GroupType.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/class-use/PDBCrystallographicInfo.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/class-use/Group.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/class-use/DBRef.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/class-use/SubstructureIdentifier.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/class-use/ExperimentalTechnique.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/class-use/Element.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/class-use/Atom.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/class-use/GroupIterator.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/class-use/PDBStatus.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/class-use/PDBStatus.Status.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/class-use/AminoAcid.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/class-use/AminoAcidImpl.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/class-use/ResidueRange.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/class-use/EntityInfo.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/class-use/PDBRecord.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/class-use/ElementType.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/math/class-use/SparseVector.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/math/class-use/SparseSquareMatrix.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/math/class-use/SymbolTable.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/jama/class-use/Matrix.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/jama/class-use/QRDecomposition.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/jama/class-use/LUDecomposition.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/jama/class-use/CholeskyDecomposition.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/jama/class-use/SingularValueDecomposition.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/jama/class-use/Maths.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/jama/class-use/EigenvalueDecomposition.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/cluster/class-use/SubunitClustererParameters.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/cluster/class-use/SubunitClustererMethod.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/cluster/class-use/Subunit.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/cluster/class-use/SubunitCluster.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/cluster/class-use/SubunitExtractor.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/cluster/class-use/SubunitClusterer.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/geometry/class-use/SuperPositionQCP.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/class-use/NucleotideImpl.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/class-use/ChainImpl.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/domain/class-use/SerializableCache.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/domain/class-use/DomainProvider.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/domain/class-use/LocalProteinDomainParser.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/domain/pdp/class-use/CutValues.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/domain/pdp/class-use/Cut.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/domain/pdp/class-use/Segment.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/domain/pdp/class-use/ClusterDomains.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/domain/pdp/class-use/GetDistanceMatrix.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/domain/pdp/class-use/CutDomain.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/domain/pdp/class-use/PDPDistanceMatrix.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/domain/pdp/class-use/ShortSegmentRemover.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/domain/pdp/class-use/SegmentComparator.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/domain/pdp/class-use/CutSites.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/domain/pdp/class-use/Domain.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/domain/pdp/class-use/PDPParameters.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/geometry/class-use/UnitQuaternions.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/geometry/class-use/SuperPosition.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/geometry/class-use/MomentsOfInertia.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/geometry/class-use/MomentsOfInertia.SymmetryClass.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/geometry/class-use/Matrices.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/geometry/class-use/SuperPositionQuat.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/geometry/class-use/SuperPositionSVD.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/geometry/class-use/CalcPoint.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/geometry/class-use/UnitQuaternions.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/geometry/class-use/SuperPositionQuat.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/geometry/class-use/SuperPositions.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/geometry/class-use/SuperPositionQCP.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/geometry/class-use/CalcPoint.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/geometry/class-use/SuperPositionAbstract.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/class-use/CAConverter.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/class-use/StructureSequenceMatcher.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/geometry/class-use/MomentsOfInertia.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/geometry/class-use/MomentsOfInertia.SymmetryClass.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/geometry/class-use/Matrices.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/cath/class-use/CathInstallation.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/cath/class-use/CathCategory.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/cath/class-use/CathFragment.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/cath/class-use/CathSegment.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/cath/class-use/CathDatabase.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/cath/class-use/CathFactory.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/cath/class-use/CathNode.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/cath/class-use/CathDomain.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/math/class-use/SparseSquareMatrix.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/math/class-use/SparseVector.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/math/class-use/SymbolTable.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/class-use/PDBFileReader.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/class-use/SeqRes2AtomAligner.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/class-use/CifFileReader.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/class-use/FileParsingParameters.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/class-use/PDBBioAssemblyParser.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/class-use/StructureFiletype.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/class-use/StructureIOFile.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/class-use/MMTFFileReader.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/class-use/FileConvert.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/class-use/PDBFileParser.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/class-use/SeqRes2AtomAligner.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/class-use/ChargeAdder.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/class-use/StructureProvider.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/class-use/EntityFinder.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/class-use/FileParsingParameters.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/class-use/PDBParseException.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/class-use/LocalPDBDirectory.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/class-use/LocalPDBDirectory.FetchBehavior.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/class-use/LocalPDBDirectory.ObsoleteBehavior.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/class-use/FileConvert.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/class-use/PDBFileParser.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/class-use/CAConverter.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/class-use/EntityFinder.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/class-use/StructureIOFile.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/class-use/GroupToSDF.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/class-use/MMTFFileReader.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/class-use/CifFileReader.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/class-use/PDBBioAssemblyParser.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/class-use/SSBondImpl.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/class-use/BondMaker.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/class-use/StructureSequenceMatcher.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/class-use/FastaAFPChainConverter.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/class-use/FastaStructureParser.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/class-use/ChargeAdder.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/class-use/GroupToSDF.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/class-use/PDBParseException.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/class-use/BcifFileReader.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/class-use/SSBondImpl.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/cif/class-use/CifFileConsumer.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/cif/class-use/ChemCompConsumer.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/class-use/FastaStructureParser.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/mmtf/class-use/MmtfSummaryDataBean.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/mmtf/class-use/MmtfUtils.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/mmtf/class-use/MmtfStructureReader.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/mmtf/class-use/MmtfActions.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/mmtf/class-use/MmtfStructureWriter.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/util/class-use/PDBTemporaryStorageUtils.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/util/class-use/PDBTemporaryStorageUtils.LinkRecord.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/cif/class-use/ChemCompConverter.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/cif/class-use/CifChainSupplierImpl.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/cif/class-use/ChemCompConsumerImpl.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/cif/class-use/ChemCompConsumer.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/cif/class-use/CifFileSupplier.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/cif/class-use/MetalBondConsumerImpl.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/cif/class-use/MetalBondConverter.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/cif/class-use/CifBean.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/cif/class-use/CifStructureConsumerImpl.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/cif/class-use/CifStructureConsumer.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/cif/class-use/CifFileConsumer.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/cif/class-use/MetalBondConsumer.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/cif/class-use/ChemCompConsumerImpl.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/cif/class-use/AbstractCifFileSupplier.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/cif/class-use/AbstractCifFileSupplier.WrappedAtom.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/cif/class-use/MetalBondConverter.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/cif/class-use/ChemCompConverter.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/cif/class-use/MetalBondConsumerImpl.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/cif/class-use/CifStructureSupplierImpl.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/cif/class-use/CifFileSupplier.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/cif/class-use/CifStructureConverter.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/cif/class-use/CifStructureConsumerImpl.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/cif/class-use/MetalBondConsumer.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/util/class-use/PDBTemporaryStorageUtils.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/util/class-use/PDBTemporaryStorageUtils.LinkRecord.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/mmtf/class-use/MmtfStructureReader.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/mmtf/class-use/MmtfStructureWriter.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/mmtf/class-use/MmtfSummaryDataBean.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/mmtf/class-use/MmtfActions.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/mmtf/class-use/MmtfUtils.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/sifts/class-use/SiftsXMLParser.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/sifts/class-use/SiftsSegment.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/sifts/class-use/SiftsMappingProvider.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/cif/class-use/CifStructureSupplierImpl.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/sifts/class-use/SiftsChainToUniprotMapping.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/sifts/class-use/SiftsResidue.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/sifts/class-use/SiftsChainEntry.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/sifts/class-use/SiftsXMLParser.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/sifts/class-use/SiftsEntity.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/domain/pdp/class-use/CutDomain.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/domain/pdp/class-use/Cut.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/domain/pdp/class-use/CutValues.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/domain/pdp/class-use/PDPParameters.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/domain/pdp/class-use/GetDistanceMatrix.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/domain/pdp/class-use/CutSites.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/domain/pdp/class-use/SegmentComparator.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/domain/pdp/class-use/Segment.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/domain/pdp/class-use/PDPDistanceMatrix.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/domain/pdp/class-use/Domain.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/domain/pdp/class-use/ClusterDomains.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/domain/pdp/class-use/ShortSegmentRemover.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/domain/class-use/LocalProteinDomainParser.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/domain/class-use/DomainProvider.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/domain/class-use/SerializableCache.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/sifts/class-use/SiftsResidue.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/sifts/class-use/SiftsMappingProvider.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/sifts/class-use/SiftsSegment.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/jama/class-use/CholeskyDecomposition.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/jama/class-use/SingularValueDecomposition.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/jama/class-use/QRDecomposition.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/jama/class-use/Maths.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/jama/class-use/Matrix.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/jama/class-use/EigenvalueDecomposition.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/jama/class-use/LUDecomposition.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/xtal/io/class-use/TransfAlgebraicAdapter.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/xtal/io/class-use/SpaceGroupMapRoot.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/xtal/io/class-use/SpaceGroupMapElements.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/xtal/io/class-use/TreeMapSpaceGroupWrapper.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/xtal/class-use/CrystalTransform.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/xtal/class-use/UnitCellBoundingBox.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/xtal/class-use/SpaceGroup.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/xtal/class-use/BravaisLattice.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/xtal/class-use/CrystalBuilder.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/xtal/class-use/TransformType.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/xtal/class-use/SymoplibParser.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/xtal/class-use/CrystalCell.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/chem/class-use/AllChemCompProvider.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/chem/class-use/ChemicalComponentDictionary.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/chem/class-use/PolymerType.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/chem/class-use/ChemCompDescriptor.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/chem/class-use/ChemCompAtom.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/chem/class-use/MetalBondDistance.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/chem/class-use/ChemCompGroupFactory.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/chem/class-use/ChemCompTools.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/chem/class-use/ZipChemCompProvider.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/chem/class-use/DownloadChemCompProvider.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/chem/class-use/ResidueType.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/chem/class-use/ChemComp.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/chem/class-use/ReducedChemCompProvider.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/chem/class-use/ChemCompProvider.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/chem/class-use/ChemCompBond.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/asa/class-use/GroupAsa.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/asa/class-use/AsaCalculator.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/scop/class-use/ScopFactory.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/scop/class-use/ScopDescription.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/scop/class-use/ScopMirror.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/scop/class-use/ScopDatabase.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/scop/class-use/BerkeleyScopInstallation.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/scop/class-use/Astral.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/scop/class-use/Astral.AstralSet.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/scop/class-use/ScopInstallation.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/scop/class-use/LocalScopDatabase.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/scop/class-use/ScopNode.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/scop/class-use/ScopCategory.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/scop/class-use/ScopIOException.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/scop/class-use/ScopDomain.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/contact/class-use/AtomContactSet.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/contact/class-use/GroupContact.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/contact/class-use/InterfaceFinder.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/contact/class-use/Pair.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/contact/class-use/GridCell.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/contact/class-use/AtomContact.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/contact/class-use/StructureInterfaceCluster.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/contact/class-use/AtomIdentifier.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/contact/class-use/StructureInterface.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/contact/class-use/GroupContactSet.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/contact/class-use/StructureInterfaceList.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/contact/class-use/Contact.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/contact/class-use/Grid.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/contact/class-use/BoundingBox.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/symmetry/geometry/class-use/Tetrahedron.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/symmetry/geometry/class-use/DistanceBox.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/symmetry/geometry/class-use/Icosahedron.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/symmetry/geometry/class-use/RectangularPrism.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/symmetry/geometry/class-use/Octahedron.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/symmetry/geometry/class-use/Polyhedron.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/symmetry/geometry/class-use/IcosahedralSampler.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/symmetry/geometry/class-use/SphereSampler.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/symmetry/geometry/class-use/Prism.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/symmetry/utils/class-use/PermutationGenerator.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/symmetry/utils/class-use/PowerSet.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/symmetry/utils/class-use/BlastClustReader.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/symmetry/utils/class-use/SymmetryTools.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/symmetry/internal/class-use/SymmOptimizer.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/symmetry/internal/class-use/CeSymmResult.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/symmetry/internal/class-use/GraphComponentOrderDetector.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/symmetry/internal/class-use/SequenceFunctionOrderDetector.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/symmetry/internal/class-use/SequenceFunctionRefiner.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/symmetry/internal/class-use/RefinerFailedException.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/symmetry/internal/class-use/CESymmParameters.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/symmetry/internal/class-use/CESymmParameters.SymmetryType.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/symmetry/internal/class-use/CESymmParameters.RefineMethod.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/symmetry/internal/class-use/CESymmParameters.OrderDetectorMethod.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/symmetry/internal/class-use/CeSymm.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/symmetry/internal/class-use/ResidueGroup.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/symmetry/internal/class-use/SymmetryAxes.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/symmetry/internal/class-use/SymmetryAxes.Axis.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/symmetry/internal/class-use/AngleOrderDetectorPlus.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/symmetry/internal/class-use/CeSymmIterative.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/symmetry/internal/class-use/GraphComponentRefiner.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/symmetry/internal/class-use/SymmetryRefiner.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/symmetry/internal/class-use/OrderDetector.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/symmetry/misc/class-use/ChainSignature.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/symmetry/misc/class-use/ProteinComplexSignature.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/symmetry/axis/class-use/HelixAxisAligner.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/symmetry/axis/class-use/AxisAligner.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/symmetry/axis/class-use/RotationAxisAligner.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/symmetry/core/class-use/SymmetryPerceptionMethod.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/symmetry/core/class-use/QuatSymmetryParameters.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/symmetry/core/class-use/QuatSymmetrySolver.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/symmetry/core/class-use/Stoichiometry.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/symmetry/core/class-use/Stoichiometry.StringOverflowStrategy.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/symmetry/core/class-use/HelixExtender.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/symmetry/core/class-use/QuatSymmetryResults.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/symmetry/core/class-use/QuatSymmetryDetector.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/symmetry/core/class-use/SystematicSolver.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/symmetry/core/class-use/QuatSuperpositionScorer.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/symmetry/core/class-use/HelicalRepeatUnit.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/symmetry/core/class-use/HelixSolver.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/symmetry/core/class-use/Helix.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/symmetry/core/class-use/QuatSymmetrySubunits.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/symmetry/core/class-use/Rotation.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/symmetry/core/class-use/RotationSolver.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/symmetry/core/class-use/RotationGroup.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/symmetry/core/class-use/QuatSymmetryScores.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/symmetry/core/class-use/HelixLayers.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/symmetry/core/class-use/C2RotationSolver.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/symmetry/core/class-use/PermutationGroup.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/basepairs/class-use/TertiaryBasePairParameters.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/basepairs/class-use/BasePairParameters.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/basepairs/class-use/MismatchedBasePairParameters.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/basepairs/class-use/TertiaryBasePairParameters.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/client/class-use/PdbPair.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/client/class-use/StructureName.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/client/class-use/StructureName.Source.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/class-use/CallableStructureAlignment.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/class-use/AFPTwister.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/class-use/ClusterAltAligs.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/quaternary/class-use/CartesianProduct.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/quaternary/class-use/BioAssemblyInfo.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/quaternary/class-use/BioAssemblyTools.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/quaternary/class-use/OperatorResolver.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/quaternary/class-use/BiologicalAssemblyTransformation.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/quaternary/class-use/OrderedPair.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/quaternary/class-use/BiologicalAssemblyBuilder.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/secstruc/class-use/SecStrucTools.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/secstruc/class-use/SecStrucCalc.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/secstruc/class-use/Ladder.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/secstruc/class-use/BetaBridge.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/secstruc/class-use/SecStrucElement.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/secstruc/class-use/SecStrucState.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/secstruc/class-use/HBond.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/secstruc/class-use/DSSPParser.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/secstruc/class-use/SecStrucInfo.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/secstruc/class-use/BridgeType.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/secstruc/class-use/SecStrucType.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/ecod/class-use/EcodInstallation.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/ecod/class-use/EcodInstallation.EcodParser.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/ecod/class-use/EcodDatabase.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/ecod/class-use/EcodFactory.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/ecod/class-use/EcodDomain.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/cluster/class-use/SubunitClustererMethod.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/cluster/class-use/SubunitCluster.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/cluster/class-use/SubunitClusterer.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/cluster/class-use/SubunitExtractor.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/cluster/class-use/Subunit.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/cluster/class-use/SubunitClustererParameters.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/class-use/AbstractStructureAlignment.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/class-use/MultipleStructureAligner.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/class-use/StructurePairAligner.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/class-use/StrucAligParameters.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/class-use/StructureAlignment.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/class-use/StructurePairAligner.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/class-use/MultipleStructureAligner.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/class-use/CallableStructureAlignment.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/class-use/ClusterAltAligs.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/class-use/StructureAlignmentFactory.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/class-use/BioJavaStructureAlignment.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/fatcat/class-use/FatCatFlexible.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/class-use/StructureAlignment.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/class-use/AFPTwister.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/fatcat/class-use/FatCatRigid.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/fatcat/class-use/FatCatUserArgumentProcessor.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/fatcat/class-use/FatCatUserArgumentProcessor.FatCatStartupParams.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/fatcat/class-use/FatCatRigid.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/fatcat/class-use/FatCatFlexible.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/fatcat/class-use/FatCat.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/fatcat/calc/class-use/AFPCalculator.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/fatcat/calc/class-use/AFPPostProcessor.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/fatcat/calc/class-use/StructureAlignmentOptimizer.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/fatcat/calc/class-use/AFPChainer.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/fatcat/calc/class-use/SigEva.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/fatcat/calc/class-use/StructureAlignmentOptimizer.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/fatcat/calc/class-use/FCAlignHelper.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/fatcat/calc/class-use/FatCatAligner.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/fatcat/calc/class-use/SigEva.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/fatcat/calc/class-use/AFPOptimizer.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/fatcat/calc/class-use/AFPCalculator.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/fatcat/calc/class-use/FatCatAligner.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/fatcat/calc/class-use/FatCatParameters.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/ce/class-use/GuiWrapper.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/ce/class-use/CeSideChainMain.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/ce/class-use/OptimalCECPMain.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/fatcat/calc/class-use/AFPPostProcessor.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/ce/class-use/ConfigStrucAligParams.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/ce/class-use/UserArgumentProcessor.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/ce/class-use/CeSideChainUserArgumentProcessor.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/ce/class-use/CeCPUserArgumentProcessor.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/ce/class-use/CeCPUserArgumentProcessor.CeCPStartupParams.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/ce/class-use/GuiWrapper.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/ce/class-use/CeCPMain.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/ce/class-use/CeCPMain.CPRange.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/ce/class-use/OptimalCECPParameters.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/ce/class-use/CECalculator.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/ce/class-use/StartupParameters.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/ce/class-use/CeUserArgumentProcessor.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/ce/class-use/CeUserArgumentProcessor.CeStartupParams.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/ce/class-use/CeSideChainUserArgumentProcessor.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/ce/class-use/CECPParameters.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/ce/class-use/CECPParameters.DuplicationHint.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/ce/class-use/CeCalculatorEnhanced.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/ce/class-use/AbstractUserArgumentProcessor.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/ce/class-use/CeMain.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/ce/class-use/CeUserArgumentProcessor.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/ce/class-use/CeUserArgumentProcessor.CeStartupParams.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/ce/class-use/CeParameters.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/ce/class-use/CeParameters.ScoringStrategy.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/ce/class-use/ConfigStrucAligParams.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/ce/class-use/CeCPUserArgumentProcessor.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/ce/class-use/CeCPUserArgumentProcessor.CeCPStartupParams.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/ce/class-use/CECalculator.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/ce/class-use/AbstractUserArgumentProcessor.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/ce/class-use/MatrixListener.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/pairwise/class-use/AligNPE.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/pairwise/class-use/Alignable.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/pairwise/class-use/StrCompAlignment.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/pairwise/class-use/AlternativeAlignment.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/pairwise/class-use/AlignmentProgressListener.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/pairwise/class-use/FragmentJoiner.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/pairwise/class-use/Gotoh.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/pairwise/class-use/AltAligComparator.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/pairwise/class-use/AlignmentResult.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/pairwise/class-use/FragmentPair.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/model/class-use/AFPChain.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/model/class-use/AfpChainWriter.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/model/class-use/AFP.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/seq/class-use/SmithWaterman3Daligner.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/seq/class-use/SmithWaterman3DParameters.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/seq/class-use/SmithWatermanUserArgumentProcessor.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/seq/class-use/SmithWatermanUserArgumentProcessor.SmithWatermanStartupParams.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/util/class-use/RotationAxis.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/ce/class-use/CeCalculatorEnhanced.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/ce/class-use/StartupParameters.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/ce/class-use/OptimalCECPMain.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/ce/class-use/CeSideChainMain.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/ce/class-use/OptimalCECPParameters.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/ce/class-use/CeMain.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/client/class-use/StructureName.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/client/class-use/StructureName.Source.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/client/class-use/PdbPair.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/util/class-use/CollectionTools.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/util/class-use/AFPChainScorer.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/util/class-use/ConfigurationException.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/util/class-use/AFPAlignmentDisplay.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/util/class-use/RotationAxis.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/util/class-use/URLConnectionTools.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/util/class-use/CliTools.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/util/class-use/AtomCache.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/util/class-use/SynchronizedOutFile.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/util/class-use/UserConfiguration.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/util/class-use/AlignmentTools.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/util/class-use/AlignmentTools.IdentityMap.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/util/class-use/ResourceManager.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/util/class-use/AtomCache.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/util/class-use/UserConfiguration.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/util/class-use/URLConnectionTools.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/util/class-use/AFPAlignmentDisplay.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/util/class-use/AFPChainScorer.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/util/class-use/SynchronizedOutFile.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/util/class-use/ConfigurationException.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/model/class-use/AFPChain.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/model/class-use/AfpChainWriter.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/model/class-use/AFP.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/xml/class-use/MultipleAlignmentXMLConverter.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/xml/class-use/MultipleAlignmentXMLParser.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/xml/class-use/AFPChainXMLParser.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/xml/class-use/AFPChainXMLConverter.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/xml/class-use/AFPChainFlipper.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/xml/class-use/PdbPairsMessage.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/xml/class-use/PdbPairXMLConverter.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/helper/class-use/GapArray.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/helper/class-use/JointFragments.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/helper/class-use/AligMatEl.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/helper/class-use/IndexPair.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/helper/class-use/AlignUtils.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/helper/class-use/IdxComparator.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/quaternary/class-use/QsAlign.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/helper/class-use/AligMatEl.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/helper/class-use/IndexPair.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/helper/class-use/JointFragments.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/seq/class-use/SmithWatermanUserArgumentProcessor.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/seq/class-use/SmithWatermanUserArgumentProcessor.SmithWatermanStartupParams.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/seq/class-use/SmithWaterman3DParameters.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/seq/class-use/SmithWaterman3Daligner.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/quaternary/class-use/QsAlignResult.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/quaternary/class-use/QsAlignParameters.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/quaternary/class-use/QsRelation.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/multiple/class-use/ScoresCache.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/multiple/class-use/BlockSet.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/multiple/class-use/MultipleAlignmentEnsemble.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/multiple/class-use/AbstractScoresCache.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/quaternary/class-use/QsAlign.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/multiple/class-use/BlockImpl.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/multiple/class-use/BlockSetImpl.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/multiple/class-use/MultipleAlignmentImpl.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/multiple/class-use/MultipleAlignment.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/multiple/class-use/AbstractScoresCache.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/multiple/class-use/MultipleAlignmentEnsemble.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/multiple/class-use/Block.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/multiple/class-use/BlockSet.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/multiple/class-use/MultipleAlignmentEnsembleImpl.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/multiple/class-use/MultipleAlignment.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/multiple/class-use/ScoresCache.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/multiple/util/class-use/MultipleAlignmentDisplay.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/multiple/util/class-use/ReferenceSuperimposer.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/multiple/util/class-use/MultipleAlignmentTools.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/multiple/util/class-use/MultipleAlignmentWriter.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/multiple/util/class-use/CoreSuperimposer.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/multiple/util/class-use/MultipleAlignmentScorer.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/multiple/util/class-use/MultipleAlignmentDisplay.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/multiple/util/class-use/MultipleSuperimposer.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/multiple/util/class-use/CoreSuperimposer.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/multiple/util/class-use/MultipleAlignmentWriter.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/multiple/mc/class-use/MultipleMcOptimizer.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/multiple/mc/class-use/MultipleMcMain.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/multiple/mc/class-use/MultipleMcParameters.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/multiple/mc/class-use/MultipleMcOptimizer.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/xml/class-use/AFPChainXMLParser.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/xml/class-use/MultipleAlignmentXMLConverter.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/xml/class-use/MultipleAlignmentXMLParser.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/xml/class-use/AFPChainXMLConverter.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/xml/class-use/PdbPairXMLConverter.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/xml/class-use/AFPChainFlipper.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/xml/class-use/PdbPairsMessage.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/symmetry/axis/class-use/AxisAligner.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/symmetry/axis/class-use/RotationAxisAligner.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/symmetry/axis/class-use/HelixAxisAligner.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/symmetry/geometry/class-use/SphereSampler.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/symmetry/geometry/class-use/Octahedron.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/symmetry/geometry/class-use/RectangularPrism.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/symmetry/geometry/class-use/DistanceBox.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/symmetry/geometry/class-use/IcosahedralSampler.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/symmetry/geometry/class-use/Polyhedron.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/symmetry/geometry/class-use/Tetrahedron.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/symmetry/geometry/class-use/Prism.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/symmetry/geometry/class-use/Icosahedron.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/symmetry/utils/class-use/PermutationGenerator.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/symmetry/utils/class-use/PowerSet.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/symmetry/utils/class-use/BlastClustReader.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/symmetry/utils/class-use/SymmetryTools.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/symmetry/misc/class-use/ChainSignature.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/symmetry/misc/class-use/ProteinComplexSignature.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/symmetry/core/class-use/QuatSymmetrySubunits.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/symmetry/core/class-use/QuatSymmetrySolver.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/symmetry/core/class-use/HelixSolver.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/symmetry/core/class-use/Rotation.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/symmetry/core/class-use/Stoichiometry.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/symmetry/core/class-use/Stoichiometry.StringOverflowStrategy.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/symmetry/core/class-use/PermutationGroup.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/symmetry/core/class-use/QuatSymmetryDetector.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/symmetry/core/class-use/SymmetryPerceptionMethod.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/symmetry/core/class-use/RotationSolver.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/symmetry/core/class-use/QuatSymmetryScores.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/symmetry/core/class-use/SystematicSolver.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/symmetry/core/class-use/HelixLayers.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/symmetry/core/class-use/C2RotationSolver.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/symmetry/core/class-use/Helix.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/symmetry/core/class-use/QuatSymmetryResults.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/symmetry/core/class-use/QuatSymmetryParameters.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/symmetry/core/class-use/HelixExtender.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/symmetry/core/class-use/RotationGroup.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/symmetry/core/class-use/HelicalRepeatUnit.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/symmetry/core/class-use/QuatSuperpositionScorer.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/symmetry/internal/class-use/SequenceFunctionRefiner.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/symmetry/internal/class-use/SymmOptimizer.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/symmetry/internal/class-use/ResidueGroup.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/symmetry/internal/class-use/AngleOrderDetectorPlus.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/symmetry/internal/class-use/OrderDetector.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/symmetry/internal/class-use/CeSymm.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/symmetry/internal/class-use/RefinerFailedException.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/symmetry/internal/class-use/SymmetryAxes.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/symmetry/internal/class-use/SymmetryAxes.Axis.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/symmetry/internal/class-use/CeSymmIterative.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/symmetry/internal/class-use/SequenceFunctionOrderDetector.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/symmetry/internal/class-use/SymmetryRefiner.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/symmetry/internal/class-use/CeSymmResult.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/symmetry/internal/class-use/GraphComponentRefiner.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/symmetry/internal/class-use/CESymmParameters.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/symmetry/internal/class-use/CESymmParameters.SymmetryType.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/symmetry/internal/class-use/CESymmParameters.RefineMethod.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/symmetry/internal/class-use/CESymmParameters.OrderDetectorMethod.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/symmetry/internal/class-use/GraphComponentOrderDetector.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/contact/class-use/GridCell.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/contact/class-use/AtomIdentifier.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/contact/class-use/Contact.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/contact/class-use/InterfaceFinder.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/contact/class-use/AtomContactSet.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/contact/class-use/AtomContact.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/contact/class-use/StructureInterface.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/contact/class-use/GroupContact.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/contact/class-use/Pair.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/contact/class-use/GroupContactSet.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/contact/class-use/BoundingBox.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/contact/class-use/StructureInterfaceList.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/contact/class-use/StructureInterfaceCluster.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/contact/class-use/Grid.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/asa/class-use/AsaCalculator.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/asa/class-use/GroupAsa.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/cath/class-use/CathFactory.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/cath/class-use/CathNode.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/cath/class-use/CathFragment.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/cath/class-use/CathInstallation.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/cath/class-use/CathDomain.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/cath/class-use/CathDatabase.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/cath/class-use/CathSegment.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/cath/class-use/CathCategory.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/quaternary/class-use/OrderedPair.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/quaternary/class-use/OperatorResolver.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/quaternary/class-use/BiologicalAssemblyTransformation.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/quaternary/class-use/CartesianProduct.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/quaternary/class-use/BioAssemblyTools.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/quaternary/class-use/BiologicalAssemblyBuilder.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/quaternary/class-use/BioAssemblyInfo.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/scop/class-use/ScopDescription.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/scop/class-use/BerkeleyScopInstallation.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/scop/class-use/ScopInstallation.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/scop/class-use/LocalScopDatabase.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/scop/class-use/ScopDatabase.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/scop/class-use/ScopMirror.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/scop/class-use/ScopDomain.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/scop/class-use/Astral.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/scop/class-use/Astral.AstralSet.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/scop/class-use/ScopFactory.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/scop/class-use/ScopCategory.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/scop/class-use/ScopIOException.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/scop/class-use/ScopNode.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/xtal/class-use/CrystalTransform.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/xtal/class-use/CrystalCell.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/xtal/class-use/UnitCellBoundingBox.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/xtal/class-use/TransformType.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/xtal/class-use/BravaisLattice.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/xtal/class-use/SymoplibParser.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/xtal/class-use/SpaceGroup.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/xtal/class-use/CrystalBuilder.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/xtal/io/class-use/SpaceGroupMapElements.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/xtal/io/class-use/TransfAlgebraicAdapter.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/xtal/io/class-use/TreeMapSpaceGroupWrapper.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/xtal/io/class-use/SpaceGroupMapRoot.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/chem/class-use/ChemCompTools.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/chem/class-use/ZipChemCompProvider.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/chem/class-use/ChemCompGroupFactory.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/chem/class-use/AllChemCompProvider.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/chem/class-use/ChemComp.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/chem/class-use/ChemicalComponentDictionary.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/chem/class-use/PolymerType.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/chem/class-use/ResidueType.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/chem/class-use/DownloadChemCompProvider.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/chem/class-use/ChemCompAtom.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/chem/class-use/ReducedChemCompProvider.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/chem/class-use/ChemCompBond.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/chem/class-use/ChemCompProvider.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/chem/class-use/MetalBondDistance.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/chem/class-use/ChemCompDescriptor.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/ecod/class-use/EcodFactory.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/ecod/class-use/EcodDatabase.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/ecod/class-use/EcodDomain.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/ecod/class-use/EcodInstallation.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/ecod/class-use/EcodInstallation.EcodParser.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/demo/class-use/DemoCommandLineStartup.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/demo/class-use/ChemCompDistribution.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/demo/class-use/DemoMmtfWriter.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/demo/class-use/DemoCeSymm.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/demo/class-use/DemoAtomCache.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/demo/class-use/DemoSymmetry.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/demo/class-use/DemoLoadSecStruc.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/demo/class-use/DemoBerkeleyScop.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/demo/class-use/DemoLoadStructure.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/demo/class-use/DemoMmcifToPdbConverter.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/demo/class-use/DemoCATH.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/demo/class-use/DemoQsAlign.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/demo/class-use/DemoSecStrucCalc.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/demo/class-use/DemoCE.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/demo/class-use/DemoFATCAT.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/demo/class-use/DemoChangeChemCompProvider.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/demo/class-use/DemoAsa.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/demo/class-use/DemoMMCIFReader.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/demo/class-use/DemoBioAssemblies.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/demo/class-use/DemoSCOP.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/demo/class-use/DemoContacts.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/demo/class-use/DemoCrystalInterfaces.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/demo/class-use/DemoMmtfReader.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/demo/class-use/DemoMultipleMC.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/demo/class-use/DemoDomainsplit.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/pairwise/class-use/AligNPE.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/pairwise/class-use/AlignmentResult.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/pairwise/class-use/AlignmentProgressListener.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/pairwise/class-use/AltAligComparator.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/pairwise/class-use/AlternativeAlignment.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/pairwise/class-use/Gotoh.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/pairwise/class-use/Alignable.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/pairwise/class-use/FragmentPair.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/pairwise/class-use/StrCompAlignment.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/pairwise/class-use/FragmentJoiner.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/demo/package-use.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/package-use.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/package-use.html...
@@ -6424,12 +6460,12 @@
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-jcolorbrewer/target/apidocs/org/jcolorbrewer/ui/package-summary.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-jcolorbrewer/target/apidocs/org/jcolorbrewer/ui/package-tree.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-jcolorbrewer/target/apidocs/serialized-form.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-jcolorbrewer/target/apidocs/org/jcolorbrewer/ui/class-use/PaletteIcon.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-jcolorbrewer/target/apidocs/org/jcolorbrewer/ui/class-use/ColorPanelSelectionModel.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-jcolorbrewer/target/apidocs/org/jcolorbrewer/ui/class-use/QualitativeColorPalettePanel.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-jcolorbrewer/target/apidocs/org/jcolorbrewer/ui/class-use/ColorPaletteChooserDialog.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-jcolorbrewer/target/apidocs/org/jcolorbrewer/ui/class-use/SequentialColorPalettePanel.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-jcolorbrewer/target/apidocs/org/jcolorbrewer/ui/class-use/DivergingColorPalettePanel.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-jcolorbrewer/target/apidocs/org/jcolorbrewer/ui/class-use/ColorPaletteChooserDialog.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-jcolorbrewer/target/apidocs/org/jcolorbrewer/ui/class-use/QualitativeColorPalettePanel.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-jcolorbrewer/target/apidocs/org/jcolorbrewer/ui/class-use/ColorPanelSelectionModel.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-jcolorbrewer/target/apidocs/org/jcolorbrewer/ui/class-use/PaletteIcon.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-jcolorbrewer/target/apidocs/org/jcolorbrewer/class-use/ColorBrewer.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-jcolorbrewer/target/apidocs/org/jcolorbrewer/package-use.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-jcolorbrewer/target/apidocs/org/jcolorbrewer/ui/package-use.html...
@@ -6484,18 +6520,18 @@
 [WARNING] Javadoc Warnings
 [WARNING] warning: The -footer option is no longer supported and will be ignored.
 [WARNING] It may be removed in a future release.
+[WARNING] Loading source files for package demo...
+[WARNING] Loading source files for package org.biojava.nbio.structure.gui...
+[WARNING] Loading source files for package org.biojava.nbio.structure.gui.util...
+[WARNING] Loading source files for package org.biojava.nbio.structure.gui.util.color...
+[WARNING] Loading source files for package org.biojava.nbio.structure.gui.events...
+[WARNING] Loading source files for package org.biojava.nbio.structure.symmetry.gui...
+[WARNING] Loading source files for package org.biojava.nbio.structure.symmetry.jmolScript...
 [WARNING] Loading source files for package org.biojava.nbio.structure.align.gui...
 [WARNING] Loading source files for package org.biojava.nbio.structure.align.gui.aligpanel...
 [WARNING] Loading source files for package org.biojava.nbio.structure.align.gui.autosuggest...
 [WARNING] Loading source files for package org.biojava.nbio.structure.align.gui.jmol...
 [WARNING] Loading source files for package org.biojava.nbio.structure.align.webstart...
-[WARNING] Loading source files for package org.biojava.nbio.structure.symmetry.jmolScript...
-[WARNING] Loading source files for package org.biojava.nbio.structure.symmetry.gui...
-[WARNING] Loading source files for package org.biojava.nbio.structure.gui...
-[WARNING] Loading source files for package org.biojava.nbio.structure.gui.events...
-[WARNING] Loading source files for package org.biojava.nbio.structure.gui.util...
-[WARNING] Loading source files for package org.biojava.nbio.structure.gui.util.color...
-[WARNING] Loading source files for package demo...
 [WARNING] Constructing Javadoc information...
 [WARNING] Building index for all the packages and classes...
 [WARNING] Standard Doclet version 17.0.11+9-Debian-1
@@ -6696,137 +6732,137 @@
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/symmetry/jmolScript/package-tree.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/constant-values.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/serialized-form.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/AlignmentGui.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/demo/class-use/ShowStructureInJmol.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/demo/class-use/DemoAlignmentFromFasta.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/demo/class-use/WebStartClientDemo.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/demo/class-use/CookBook.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/demo/class-use/DemoMultipleMC.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/demo/class-use/DemoShowCATHDomain.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/demo/class-use/AlignmentGuiDemo.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/demo/class-use/DemoQuatSymmetryJmol.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/demo/class-use/DemoCE.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/demo/class-use/DemoStructureFromFasta.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/demo/class-use/DemoShowLargeAssembly.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/demo/class-use/DemoCeSymm.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/demo/class-use/DemoShowBiolAssembly.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/demo/class-use/DemoFATCAT.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/demo/class-use/DemoSW3DAligner.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/demo/class-use/DemoRotationAxis.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/demo/class-use/AFPFromFasta.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/demo/class-use/DemoNWALignment.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/class-use/ScaleableMatrixPanel.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/class-use/ScaleableMatrixPanel.GradientRenderer.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/class-use/SelectionImpl.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/class-use/RenderStyle.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/class-use/SequenceDisplay.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/class-use/WrapLayout.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/class-use/JmolViewerImpl.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/class-use/BiojavaJmol.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/class-use/Selection.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/class-use/StructureViewer.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/class-use/JMatrixPanel.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/class-use/CoordManager.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/class-use/StructurePairSelector.html...
+[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/SelectPDBPanel.java:46: warning: invalid input: '&'
+[WARNING] /** A Panel that allows user to specify PDB & chain ID, as well as sub-ranges
+[WARNING] ^
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/class-use/PDBServerPanel.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/class-use/SequenceScalePanel.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/class-use/PDBUploadPanel.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/class-use/ScopSelectPanel.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/class-use/AlignmentCalc.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/class-use/AlignedPosition.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/class-use/SelectMultiplePanel.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/class-use/MenuCreator.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/class-use/SequenceMouseListener.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/class-use/PDBDirPanel.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/class-use/AlternativeAlignmentFrame.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/class-use/ScopInstallationInstance.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/color/class-use/HSVColorSpace.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/color/class-use/ColorInterpolator.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/color/class-use/LogColorMapper.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/color/class-use/LinearColorInterpolator.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/color/class-use/LinearColorInterpolator.InterpolationDirection.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/color/class-use/ContinuousColorMapperTransform.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/color/class-use/GradientPanel.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/color/class-use/SqrtColorMapper.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/color/class-use/GradientMapper.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/color/class-use/ColorUtils.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/color/class-use/ContinuousColorMapper.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/color/class-use/DefaultMatrixMapper.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/events/class-use/AlignmentPositionListener.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/events/class-use/JmolAlignedPositionListener.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/symmetry/gui/class-use/SymmetryListener.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/symmetry/gui/class-use/SymmetryGui.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/symmetry/gui/class-use/SymmetryDisplay.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/symmetry/gui/class-use/SymmetryCalc.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/symmetry/jmolScript/class-use/JmolSymmetryScriptGeneratorPointGroup.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/symmetry/jmolScript/class-use/JmolSymmetryScriptGeneratorDn.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/symmetry/jmolScript/class-use/JmolSymmetryScriptGeneratorC1.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/symmetry/jmolScript/class-use/ColorConverter.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/symmetry/jmolScript/class-use/JmolSymmetryScriptGeneratorI.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/symmetry/jmolScript/class-use/JmolSymmetryScriptGenerator.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/symmetry/jmolScript/class-use/JmolSymmetryScriptGeneratorH.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/symmetry/jmolScript/class-use/JmolSymmetryScriptGeneratorT.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/symmetry/jmolScript/class-use/JmolSymmetryScriptGeneratorO.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/symmetry/jmolScript/class-use/JmolSymmetryScriptGeneratorCn.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/AlignmentCalc.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/DotPlotPanel.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/AboutDialog.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/MultipleAlignmentGUI.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/ChooseDirAction.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/MyTableRowSorter.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/AlignmentCalculationRunnable.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/MyAlignmentLoadListener.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/MyDistMaxListener.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/MultipleAlignmentCalc.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/MyOpenPdbFileListener.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/SelectPDBPanel.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/MyExportListener.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/HelpDialog.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/ChooseDirAction.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/MenuCreator.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/MenuCreator.DotPlotListener.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/JPrintPanel.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/MyOpenPdbFileListener.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/DisplayAFP.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/SystemInfo.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/MyTableRowSorter.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/AboutDialog.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/MultipleAlignmentJmolDisplay.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/ParameterGUI.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/MemoryMonitor.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/MemoryMonitor.Surface.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/MyAlignmentLoadListener.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/AlignmentCalc.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/SelectPDBPanel.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/ShowPDBIDListener.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/StructureLoaderThread.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/MySaveFileListener.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/AlignmentGui.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/DisplayAFP.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/JPrintPanel.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/AlignmentCalculationRunnable.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/AlignmentTextPanel.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/MyDistMaxListener.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/StructureAlignmentDisplay.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/MyExportListener.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/MultipleAlignmentJmolDisplay.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/SystemInfo.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/ConfigPDBInstallPanel.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/ShowPDBIDListener.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/StructureLoaderThread.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/aligpanel/class-use/AligPanelMouseMotionListener.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/aligpanel/class-use/MultipleAlignmentCoordManager.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/aligpanel/class-use/MultipleAligPanelMouseMotionListener.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/MultipleAlignmentGUI.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/MemoryMonitor.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/MemoryMonitor.Surface.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/StructureAlignmentDisplay.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/aligpanel/class-use/MultipleAligPanel.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/aligpanel/class-use/StatusDisplay.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/aligpanel/class-use/AligPanel.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/aligpanel/class-use/MultipleAligPanelMouseMotionListener.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/aligpanel/class-use/MultipleStatusDisplay.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/aligpanel/class-use/AligPanel.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/aligpanel/class-use/MultipleAlignmentCoordManager.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/aligpanel/class-use/StatusDisplay.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/aligpanel/class-use/AFPChainCoordManager.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/aligpanel/class-use/AligPanelMouseMotionListener.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/autosuggest/class-use/JAutoSuggest.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/autosuggest/class-use/SCOPAutoSuggestProvider.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/autosuggest/class-use/AutoSuggestProvider.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/autosuggest/class-use/DefaultAutoSuggestProvider.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/autosuggest/class-use/AutoSuggestProvider.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/jmol/class-use/AtomInfo.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/jmol/class-use/StructureAlignmentJmol.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/jmol/class-use/RasmolCommandListener.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/jmol/class-use/JmolTools.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/jmol/class-use/AtomInfoParser.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/jmol/class-use/MultipleAlignmentJmol.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/jmol/class-use/AtomInfo.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/jmol/class-use/JmolTools.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/jmol/class-use/JmolPanel.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/jmol/class-use/JmolPanel.JmolLoggerAdapter.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/jmol/class-use/StructureAlignmentJmol.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/jmol/class-use/AbstractAlignmentJmol.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/jmol/class-use/MyJmolStatusListener.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/jmol/class-use/AbstractAlignmentJmol.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/webstart/class-use/BrowserOpener.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/webstart/class-use/ConfigXMLHandler.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/webstart/class-use/WebStartMain.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/webstart/class-use/AligUIManager.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/webstart/class-use/JNLPProxy.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/webstart/class-use/ConfigXMLHandler.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/webstart/class-use/BrowserOpener.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/symmetry/jmolScript/class-use/JmolSymmetryScriptGenerator.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/symmetry/jmolScript/class-use/JmolSymmetryScriptGeneratorC1.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/symmetry/jmolScript/class-use/JmolSymmetryScriptGeneratorI.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/symmetry/jmolScript/class-use/JmolSymmetryScriptGeneratorCn.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/symmetry/jmolScript/class-use/JmolSymmetryScriptGeneratorT.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/symmetry/jmolScript/class-use/ColorConverter.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/symmetry/jmolScript/class-use/JmolSymmetryScriptGeneratorPointGroup.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/symmetry/jmolScript/class-use/JmolSymmetryScriptGeneratorH.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/symmetry/jmolScript/class-use/JmolSymmetryScriptGeneratorDn.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/symmetry/jmolScript/class-use/JmolSymmetryScriptGeneratorO.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/symmetry/gui/class-use/SymmetryDisplay.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/symmetry/gui/class-use/SymmetryGui.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/symmetry/gui/class-use/SymmetryListener.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/symmetry/gui/class-use/SymmetryCalc.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/class-use/JmolViewerImpl.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/class-use/SelectionImpl.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/class-use/RenderStyle.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/class-use/WrapLayout.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/class-use/BiojavaJmol.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/class-use/StructureViewer.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/class-use/SequenceDisplay.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/class-use/Selection.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/class-use/JMatrixPanel.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/class-use/ScaleableMatrixPanel.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/class-use/ScaleableMatrixPanel.GradientRenderer.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/events/class-use/JmolAlignedPositionListener.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/events/class-use/AlignmentPositionListener.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/class-use/PDBServerPanel.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/class-use/CoordManager.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/class-use/ScopInstallationInstance.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/class-use/PDBDirPanel.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/class-use/SequenceMouseListener.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/class-use/SelectMultiplePanel.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/class-use/MenuCreator.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/class-use/AlignedPosition.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/class-use/AlternativeAlignmentFrame.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/class-use/ScopSelectPanel.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/class-use/AlignmentCalc.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/class-use/SequenceScalePanel.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/class-use/PDBUploadPanel.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/class-use/StructurePairSelector.html...
-[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/SelectPDBPanel.java:46: warning: invalid input: '&'
-[WARNING] /** A Panel that allows user to specify PDB & chain ID, as well as sub-ranges
-[WARNING] ^
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/color/class-use/LinearColorInterpolator.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/color/class-use/LinearColorInterpolator.InterpolationDirection.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/color/class-use/HSVColorSpace.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/color/class-use/LogColorMapper.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/color/class-use/GradientMapper.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/color/class-use/SqrtColorMapper.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/color/class-use/ContinuousColorMapperTransform.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/color/class-use/DefaultMatrixMapper.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/color/class-use/GradientPanel.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/color/class-use/ColorUtils.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/color/class-use/ColorInterpolator.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/color/class-use/ContinuousColorMapper.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/demo/class-use/AFPFromFasta.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/demo/class-use/DemoShowBiolAssembly.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/demo/class-use/DemoCeSymm.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/demo/class-use/WebStartClientDemo.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/demo/class-use/DemoShowLargeAssembly.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/demo/class-use/DemoStructureFromFasta.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/demo/class-use/DemoRotationAxis.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/demo/class-use/DemoNWALignment.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/demo/class-use/AlignmentGuiDemo.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/demo/class-use/DemoSW3DAligner.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/demo/class-use/DemoCE.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/demo/class-use/DemoFATCAT.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/demo/class-use/DemoQuatSymmetryJmol.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/demo/class-use/CookBook.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/demo/class-use/DemoShowCATHDomain.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/demo/class-use/ShowStructureInJmol.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/demo/class-use/DemoMultipleMC.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/demo/class-use/DemoAlignmentFromFasta.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/webstart/class-use/AligUIManager.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/demo/package-use.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/package-use.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/aligpanel/package-use.html...
@@ -6896,17 +6932,17 @@
 [WARNING] Javadoc Warnings
 [WARNING] warning: The -footer option is no longer supported and will be ignored.
 [WARNING] It may be removed in a future release.
-[WARNING] Loading source files for package org.biojava.nbio.genome.homology...
+[WARNING] Loading source files for package org.biojava.nbio.genome...
 [WARNING] Loading source files for package org.biojava.nbio.genome.io.fastq...
+[WARNING] Loading source files for package org.biojava.nbio.genome.util...
 [WARNING] Loading source files for package org.biojava.nbio.genome.query...
+[WARNING] Loading source files for package org.biojava.nbio.genome.homology...
 [WARNING] Loading source files for package org.biojava.nbio.genome.uniprot...
-[WARNING] Loading source files for package org.biojava.nbio.genome.parsers.cytoband...
 [WARNING] Loading source files for package org.biojava.nbio.genome.parsers.geneid...
-[WARNING] Loading source files for package org.biojava.nbio.genome.parsers.gff...
 [WARNING] Loading source files for package org.biojava.nbio.genome.parsers.twobit...
+[WARNING] Loading source files for package org.biojava.nbio.genome.parsers.gff...
+[WARNING] Loading source files for package org.biojava.nbio.genome.parsers.cytoband...
 [WARNING] Loading source files for package org.biojava.nbio.genome.parsers.genename...
-[WARNING] Loading source files for package org.biojava.nbio.genome.util...
-[WARNING] Loading source files for package org.biojava.nbio.genome...
 [WARNING] Constructing Javadoc information...
 [WARNING] Building index for all the packages and classes...
 [WARNING] Standard Doclet version 17.0.11+9-Debian-1
@@ -6999,52 +7035,52 @@
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/util/package-tree.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/constant-values.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/serialized-form.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/homology/class-use/GFF3FromUniprotBlastHits.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/homology/class-use/BlastHomologyHits.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/class-use/App.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/class-use/GeneFeatureHelper.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/io/fastq/class-use/IlluminaFastqReader.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/io/fastq/class-use/SolexaFastqReader.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/io/fastq/class-use/FastqVariant.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/io/fastq/class-use/FastqBuilder.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/io/fastq/class-use/FastqReader.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/io/fastq/class-use/FastqWriter.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/io/fastq/class-use/SangerFastqReader.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/io/fastq/class-use/IlluminaFastqReader.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/io/fastq/class-use/Fastq.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/io/fastq/class-use/SangerFastqWriter.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/io/fastq/class-use/FastqWriter.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/io/fastq/class-use/FastqTools.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/io/fastq/class-use/ParseListener.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/io/fastq/class-use/SolexaFastqWriter.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/io/fastq/class-use/FastqTools.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/io/fastq/class-use/FastqReader.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/io/fastq/class-use/IlluminaFastqWriter.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/io/fastq/class-use/StreamListener.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/io/fastq/class-use/SangerFastqReader.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/io/fastq/class-use/FastqBuilder.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/util/class-use/SplitFasta.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/util/class-use/ChromosomeMappingTools.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/util/class-use/ProteinMappingTools.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/query/class-use/BlastXMLQuery.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/query/class-use/OutputHitsGFF.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/homology/class-use/GFF3FromUniprotBlastHits.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/homology/class-use/BlastHomologyHits.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/uniprot/class-use/UniprotToFasta.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/cytoband/class-use/StainType.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/cytoband/class-use/CytobandParser.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/cytoband/class-use/Cytoband.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/geneid/class-use/GeneIDXMLReader.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/gff/class-use/GFF3Reader.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/twobit/class-use/TwoBitParser.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/twobit/class-use/TwoBitFacade.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/gff/class-use/GFF3Writer.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/gff/class-use/FeatureI.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/gff/class-use/Feature.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/gff/class-use/GFF3Reader.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/gff/class-use/GeneMarkGTFReader.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/gff/class-use/FeatureList.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/gff/class-use/FeatureI.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/gff/class-use/GFF3Writer.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/gff/class-use/GeneIDGFF2Reader.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/gff/class-use/Location.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/gff/class-use/GCStats.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/gff/class-use/LocIterator.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/gff/class-use/FeatureHelper.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/gff/class-use/Location.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/gff/class-use/GeneMarkGTFReader.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/twobit/class-use/TwoBitParser.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/twobit/class-use/TwoBitFacade.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/cytoband/class-use/StainType.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/cytoband/class-use/CytobandParser.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/cytoband/class-use/Cytoband.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/genename/class-use/GeneName.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/genename/class-use/GeneNamesParser.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/genename/class-use/GeneChromosomePosition.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/genename/class-use/ChromPos.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/genename/class-use/GeneName.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/genename/class-use/GeneChromosomePositionParser.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/util/class-use/SplitFasta.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/util/class-use/ChromosomeMappingTools.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/util/class-use/ProteinMappingTools.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/class-use/App.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/class-use/GeneFeatureHelper.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/package-use.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/homology/package-use.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/io/fastq/package-use.html...
@@ -7104,10 +7140,10 @@
 [WARNING] Javadoc Warnings
 [WARNING] warning: The -footer option is no longer supported and will be ignored.
 [WARNING] It may be removed in a future release.
-[WARNING] Loading source files for package org.biojava.nbio.phosphosite...
-[WARNING] Loading source files for package org.biojava.nbio.protmod.structure...
 [WARNING] Loading source files for package org.biojava.nbio.protmod...
+[WARNING] Loading source files for package org.biojava.nbio.protmod.structure...
 [WARNING] Loading source files for package org.biojava.nbio.protmod.io...
+[WARNING] Loading source files for package org.biojava.nbio.phosphosite...
 [WARNING] Constructing Javadoc information...
 [WARNING] Building index for all the packages and classes...
 [WARNING] Standard Doclet version 17.0.11+9-Debian-1
@@ -7191,30 +7227,30 @@
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/structure/package-tree.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/constant-values.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/serialized-form.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/phosphosite/class-use/Site.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/phosphosite/class-use/Dataset.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/structure/class-use/StructureAtom.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/structure/class-use/StructureGroup.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/structure/class-use/ModifiedCompound.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/structure/class-use/ModifiedCompoundImpl.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/structure/class-use/StructureUtil.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/structure/class-use/ProteinModificationIdentifier.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/structure/class-use/StructureAtomLinkage.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/class-use/Component.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/class-use/ModificationOccurrenceType.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/class-use/ModificationConditionImpl.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/class-use/ProteinModificationImpl.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/class-use/ProteinModificationImpl.Builder.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/class-use/ProteinModification.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/class-use/ModificationCondition.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/class-use/ModificationOccurrenceType.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/class-use/ModificationConditionImpl.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/class-use/Component.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/class-use/ModificationLinkage.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/class-use/ModificationCategory.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/class-use/ProteinModificationRegistry.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/io/class-use/StructureAtomXMLConverter.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/io/class-use/ComponentXMLConverter.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/class-use/ProteinModification.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/class-use/ModificationCategory.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/structure/class-use/ProteinModificationIdentifier.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/structure/class-use/StructureAtomLinkage.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/structure/class-use/ModifiedCompoundImpl.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/structure/class-use/StructureGroup.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/structure/class-use/ModifiedCompound.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/structure/class-use/StructureAtom.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/structure/class-use/StructureUtil.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/io/class-use/ModifiedCompoundXMLConverter.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/io/class-use/StructureGroupXMLConverter.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/io/class-use/StructureAtomXMLConverter.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/io/class-use/ComponentXMLConverter.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/io/class-use/ProteinModificationXmlReader.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/phosphosite/class-use/Site.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/phosphosite/class-use/Dataset.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/phosphosite/package-use.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/package-use.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/io/package-use.html...
@@ -7264,10 +7300,10 @@
 [WARNING] Javadoc Warnings
 [WARNING] warning: The -footer option is no longer supported and will be ignored.
 [WARNING] It may be removed in a future release.
+[WARNING] Loading source files for package demo...
 [WARNING] Loading source files for package org.biojava.nbio.ws.hmmer...
 [WARNING] Loading source files for package org.biojava.nbio.ws.alignment...
 [WARNING] Loading source files for package org.biojava.nbio.ws.alignment.qblast...
-[WARNING] Loading source files for package demo...
 [WARNING] Constructing Javadoc information...
 [WARNING] Building index for all the packages and classes...
 [WARNING] Standard Doclet version 17.0.11+9-Debian-1
@@ -7314,26 +7350,26 @@
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/target/apidocs/org/biojava/nbio/ws/hmmer/package-tree.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/target/apidocs/constant-values.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/target/apidocs/serialized-form.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/target/apidocs/demo/class-use/HmmerDemo.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/target/apidocs/demo/class-use/NCBIQBlastServiceDemo.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/target/apidocs/org/biojava/nbio/ws/hmmer/class-use/RemoteHmmerScan.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/target/apidocs/org/biojava/nbio/ws/hmmer/class-use/HmmerScan.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/target/apidocs/org/biojava/nbio/ws/hmmer/class-use/HmmerDomain.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/target/apidocs/org/biojava/nbio/ws/hmmer/class-use/HmmerResult.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/target/apidocs/org/biojava/nbio/ws/alignment/class-use/RemotePairwiseAlignmentOutputProperties.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/target/apidocs/org/biojava/nbio/ws/alignment/class-use/RemotePairwiseAlignmentProperties.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/target/apidocs/org/biojava/nbio/ws/hmmer/class-use/HmmerDomain.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/target/apidocs/org/biojava/nbio/ws/hmmer/class-use/HmmerScan.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/target/apidocs/org/biojava/nbio/ws/alignment/class-use/RemotePairwiseAlignmentService.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/target/apidocs/org/biojava/nbio/ws/alignment/qblast/class-use/BlastOutputFormatEnum.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/target/apidocs/org/biojava/nbio/ws/alignment/qblast/class-use/BlastMatrixEnum.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/target/apidocs/org/biojava/nbio/ws/alignment/qblast/class-use/NCBIQBlastService.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/target/apidocs/org/biojava/nbio/ws/alignment/qblast/class-use/BlastOutputParameterEnum.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/target/apidocs/org/biojava/nbio/ws/alignment/class-use/RemotePairwiseAlignmentProperties.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/target/apidocs/org/biojava/nbio/ws/alignment/class-use/RemotePairwiseAlignmentOutputProperties.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/target/apidocs/org/biojava/nbio/ws/alignment/qblast/class-use/NCBIQBlastOutputProperties.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/target/apidocs/org/biojava/nbio/ws/alignment/qblast/class-use/BlastOutputAlignmentFormatEnum.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/target/apidocs/org/biojava/nbio/ws/alignment/qblast/class-use/MapToStringTransformer.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/target/apidocs/org/biojava/nbio/ws/alignment/qblast/class-use/BlastAlignmentParameterEnum.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/target/apidocs/org/biojava/nbio/ws/alignment/qblast/class-use/NCBIQBlastAlignmentProperties.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/target/apidocs/org/biojava/nbio/ws/alignment/qblast/class-use/BlastJob.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/target/apidocs/org/biojava/nbio/ws/alignment/qblast/class-use/NCBIQBlastService.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/target/apidocs/org/biojava/nbio/ws/alignment/qblast/class-use/MapToStringTransformer.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/target/apidocs/org/biojava/nbio/ws/alignment/qblast/class-use/BlastOutputParameterEnum.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/target/apidocs/org/biojava/nbio/ws/alignment/qblast/class-use/BlastOutputFormatEnum.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/target/apidocs/org/biojava/nbio/ws/alignment/qblast/class-use/BlastAlignmentParameterEnum.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/target/apidocs/org/biojava/nbio/ws/alignment/qblast/class-use/BlastMatrixEnum.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/target/apidocs/org/biojava/nbio/ws/alignment/qblast/class-use/BlastProgramEnum.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/target/apidocs/demo/class-use/HmmerDemo.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/target/apidocs/demo/class-use/NCBIQBlastServiceDemo.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/target/apidocs/org/biojava/nbio/ws/alignment/qblast/class-use/BlastOutputAlignmentFormatEnum.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/target/apidocs/demo/package-use.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/target/apidocs/org/biojava/nbio/ws/alignment/package-use.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/target/apidocs/org/biojava/nbio/ws/alignment/qblast/package-use.html...
@@ -7383,9 +7419,9 @@
 [WARNING] Javadoc Warnings
 [WARNING] warning: The -footer option is no longer supported and will be ignored.
 [WARNING] It may be removed in a future release.
-[WARNING] Loading source files for package org.biojava.nbio.ronn...
-[WARNING] Loading source files for package org.biojava.nbio.data.sequence...
 [WARNING] Loading source files for package demo...
+[WARNING] Loading source files for package org.biojava.nbio.data.sequence...
+[WARNING] Loading source files for package org.biojava.nbio.ronn...
 [WARNING] Constructing Javadoc information...
 [WARNING] Building index for all the packages and classes...
 [WARNING] Standard Doclet version 17.0.11+9-Debian-1
@@ -7412,20 +7448,20 @@
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-protein-disorder/target/apidocs/org/biojava/nbio/ronn/package-tree.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-protein-disorder/target/apidocs/constant-values.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-protein-disorder/target/apidocs/serialized-form.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-protein-disorder/target/apidocs/org/biojava/nbio/ronn/class-use/RonnConstraint.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-protein-disorder/target/apidocs/org/biojava/nbio/ronn/class-use/RonnConstraint.Threshold.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-protein-disorder/target/apidocs/demo/class-use/PredictDisorder.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-protein-disorder/target/apidocs/org/biojava/nbio/data/sequence/class-use/SequenceUtil.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-protein-disorder/target/apidocs/org/biojava/nbio/data/sequence/class-use/FastaSequence.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-protein-disorder/target/apidocs/org/biojava/nbio/ronn/class-use/ModelLoader.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-protein-disorder/target/apidocs/org/biojava/nbio/ronn/class-use/ModelLoader.Model.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-protein-disorder/target/apidocs/org/biojava/nbio/ronn/class-use/ModelLoader.Threshold.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-protein-disorder/target/apidocs/org/biojava/nbio/ronn/class-use/Timer.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-protein-disorder/target/apidocs/org/biojava/nbio/ronn/class-use/NullOutputStream.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-protein-disorder/target/apidocs/org/biojava/nbio/ronn/class-use/ORonn.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-protein-disorder/target/apidocs/org/biojava/nbio/ronn/class-use/ORonnModel.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-protein-disorder/target/apidocs/org/biojava/nbio/ronn/class-use/RonnConstraint.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-protein-disorder/target/apidocs/org/biojava/nbio/ronn/class-use/RonnConstraint.Threshold.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-protein-disorder/target/apidocs/org/biojava/nbio/ronn/class-use/NullOutputStream.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-protein-disorder/target/apidocs/org/biojava/nbio/ronn/class-use/Timer.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-protein-disorder/target/apidocs/org/biojava/nbio/ronn/class-use/Jronn.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-protein-disorder/target/apidocs/org/biojava/nbio/ronn/class-use/Jronn.Range.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-protein-disorder/target/apidocs/org/biojava/nbio/ronn/class-use/ORonn.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-protein-disorder/target/apidocs/org/biojava/nbio/data/sequence/class-use/SequenceUtil.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-protein-disorder/target/apidocs/org/biojava/nbio/data/sequence/class-use/FastaSequence.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-protein-disorder/target/apidocs/demo/class-use/PredictDisorder.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-protein-disorder/target/apidocs/demo/package-use.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-protein-disorder/target/apidocs/org/biojava/nbio/data/sequence/package-use.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-protein-disorder/target/apidocs/org/biojava/nbio/ronn/package-use.html...
@@ -7476,11 +7512,11 @@
 [WARNING] Javadoc Warnings
 [WARNING] warning: The -footer option is no longer supported and will be ignored.
 [WARNING] It may be removed in a future release.
+[WARNING] Loading source files for package demo...
 [WARNING] Loading source files for package org.biojava.nbio.aaproperties...
 [WARNING] Loading source files for package org.biojava.nbio.aaproperties.xml...
-[WARNING] Loading source files for package org.biojava.nbio.aaproperties.profeat...
 [WARNING] Loading source files for package org.biojava.nbio.aaproperties.profeat.convertor...
-[WARNING] Loading source files for package demo...
+[WARNING] Loading source files for package org.biojava.nbio.aaproperties.profeat...
 [WARNING] Constructing Javadoc information...
 [WARNING] Building index for all the packages and classes...
 [WARNING] Standard Doclet version 17.0.11+9-Debian-1
@@ -7615,25 +7651,35 @@
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/xml/package-summary.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/xml/package-tree.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/constant-values.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/class-use/IPeptideProperties.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/demo/class-use/BioJavaAADemo.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/class-use/Utils.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/class-use/Constraints.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/class-use/AminoAcidProperties.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/class-use/CommandPrompt.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/class-use/CommandPrompt.PropertyName.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/class-use/PeptidePropertiesImpl.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/class-use/AminoAcidProperties.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/class-use/PeptideProperties.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/class-use/PeptideProperties.SingleLetterAACode.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/class-use/Utils.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/class-use/IPeptideProperties.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/class-use/PeptidePropertiesImpl.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/xml/class-use/Isotope.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/xml/class-use/AminoAcidComposition.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/xml/class-use/SchemaGenerator.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/xml/class-use/AminoAcidCompositionTable.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/xml/class-use/MyValidationEventHandler.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/xml/class-use/Element.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/xml/class-use/Isotope.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/xml/class-use/SchemaGenerator.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/xml/class-use/CaseFreeAminoAcidCompoundSet.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/xml/class-use/Name2Count.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/xml/class-use/ModifiedAminoAcidCompoundSet.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/xml/class-use/ElementTable.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/xml/class-use/AminoAcidCompositionTable.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/xml/class-use/Element.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/xml/class-use/ModifiedAminoAcidCompoundSet.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/profeat/convertor/class-use/Convert2Charge.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/profeat/convertor/class-use/Convertor.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/profeat/convertor/class-use/Convert2Polarity.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/profeat/convertor/class-use/Convert2SecondaryStructure.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/profeat/convertor/class-use/Convert2Hydrophobicity.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/profeat/convertor/class-use/Convert2NormalizedVanDerWaalsVolume.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/profeat/convertor/class-use/Convert2SolventAccessibility.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/profeat/convertor/class-use/Convert2Polarizability.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/profeat/class-use/ProfeatPropertiesImpl.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/profeat/class-use/IProfeatProperties.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/profeat/class-use/IProfeatProperties.DISTRIBUTION.html...
 [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/IProfeatProperties.java:106: warning: invalid input: '&'
@@ -7712,16 +7758,6 @@
 [WARNING] * position of the GROUPING.GROUP1 && DISTRIBUTION.ALL = 4/10 (because all occurrences of '1' happens on and before position 4)<br/>
 [WARNING] ^
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/profeat/class-use/ProfeatProperties.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/profeat/class-use/ProfeatPropertiesImpl.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/profeat/convertor/class-use/Convert2Hydrophobicity.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/profeat/convertor/class-use/Convert2SecondaryStructure.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/profeat/convertor/class-use/Convertor.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/profeat/convertor/class-use/Convert2Charge.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/profeat/convertor/class-use/Convert2NormalizedVanDerWaalsVolume.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/profeat/convertor/class-use/Convert2Polarity.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/profeat/convertor/class-use/Convert2SolventAccessibility.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/profeat/convertor/class-use/Convert2Polarizability.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/demo/class-use/BioJavaAADemo.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/demo/package-use.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/package-use.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/profeat/package-use.html...
@@ -7795,13 +7831,13 @@
 [WARNING] Javadoc Warnings
 [WARNING] warning: The -footer option is no longer supported and will be ignored.
 [WARNING] It may be removed in a future release.
-[WARNING] Loading source files for package org.biojava.nbio.survival.data...
 [WARNING] Loading source files for package org.biojava.nbio.survival.cox...
 [WARNING] Loading source files for package org.biojava.nbio.survival.cox.stats...
 [WARNING] Loading source files for package org.biojava.nbio.survival.cox.matrix...
 [WARNING] Loading source files for package org.biojava.nbio.survival.cox.comparators...
-[WARNING] Loading source files for package org.biojava.nbio.survival.kaplanmeier.metadata...
+[WARNING] Loading source files for package org.biojava.nbio.survival.data...
 [WARNING] Loading source files for package org.biojava.nbio.survival.kaplanmeier.figure...
+[WARNING] Loading source files for package org.biojava.nbio.survival.kaplanmeier.metadata...
 [WARNING] Constructing Javadoc information...
 [WARNING] Building index for all the packages and classes...
 [WARNING] Standard Doclet version 17.0.11+9-Debian-1
@@ -7878,57 +7914,57 @@
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/kaplanmeier/metadata/package-summary.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/kaplanmeier/metadata/package-tree.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/serialized-form.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/data/class-use/CompactCharSequence.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/data/class-use/WorkSheet.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/data/class-use/ChangeValue.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/data/class-use/HeaderInfo.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/class-use/SurvivalInfoHelper.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/class-use/StrataInfo.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/class-use/CoxR.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/class-use/SurvivalInfo.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/class-use/CoxCC.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/class-use/SurvivalInfoIndex.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/class-use/CoxCoefficient.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/class-use/SurvivalInfoHelper.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/class-use/ResidualsCoxph.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/class-use/ResidualsCoxph.Type.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/class-use/CoxInfo.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/class-use/SurvFitInfo.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/class-use/CoxHelper.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/class-use/WaldTest.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/class-use/CoxInfo.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/class-use/CoxMethod.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/class-use/CoxScore.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/class-use/SurvivalInfo.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/class-use/CoxVariables.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/class-use/WaldTestInfo.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/class-use/ResidualsCoxph.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/class-use/ResidualsCoxph.Type.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/class-use/CoxCC.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/class-use/CoxMethod.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/class-use/StrataInfo.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/class-use/CoxCoefficient.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/class-use/CoxR.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/class-use/WaldTest.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/class-use/CoxMart.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/class-use/CoxVariables.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/class-use/RiskInfo.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/class-use/CoxScore.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/stats/class-use/Cholesky2.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/stats/class-use/AgScore.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/stats/class-use/Chsolve2.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/stats/class-use/ChiSq.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/stats/class-use/Cholesky2.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/matrix/class-use/Matrix.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/matrix/class-use/StdArrayIO.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/comparators/class-use/SurvivalInfoComparator.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/matrix/class-use/Matrix.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/comparators/class-use/CoxVariablesVariableComparator.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/comparators/class-use/SurvivalInfoComparator.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/comparators/class-use/CoxComparatorInterface.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/comparators/class-use/MeanModelComparator.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/comparators/class-use/CoxVariablesOverallModelFitComparator.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/comparators/class-use/SurvivalInfoValueComparator.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/kaplanmeier/metadata/class-use/DiscreteQuantizerInterface.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/kaplanmeier/metadata/class-use/ClinicalMetaDataOutcome.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/kaplanmeier/metadata/class-use/MeanQuantizer.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/kaplanmeier/metadata/class-use/MetaDataInfo.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/comparators/class-use/CoxVariablesOverallModelFitComparator.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/comparators/class-use/MeanModelComparator.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/data/class-use/WorkSheet.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/data/class-use/ChangeValue.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/data/class-use/CompactCharSequence.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/data/class-use/HeaderInfo.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/kaplanmeier/figure/class-use/CensorStatusSelect.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/kaplanmeier/figure/class-use/GroupResults.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/kaplanmeier/figure/class-use/KMFigureInfo.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/kaplanmeier/figure/class-use/SurvFitKM.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/kaplanmeier/figure/class-use/SurvFitKM.ConfLower.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/kaplanmeier/figure/class-use/SurvFitKM.ConfType.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/kaplanmeier/figure/class-use/SurvFitKM.Error.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/kaplanmeier/figure/class-use/SurvFitKM.Method.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/kaplanmeier/figure/class-use/CensorStatus.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/kaplanmeier/figure/class-use/ExpressionFigure.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/kaplanmeier/figure/class-use/KaplanMeierFigure.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/kaplanmeier/figure/class-use/CensorStatusSelect.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/kaplanmeier/figure/class-use/NumbersAtRiskPanel.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/kaplanmeier/figure/class-use/GroupResults.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/kaplanmeier/figure/class-use/KMFigureInfo.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/kaplanmeier/figure/class-use/CensorStatus.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/kaplanmeier/figure/class-use/KaplanMeierFigure.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/kaplanmeier/metadata/class-use/ClinicalMetaDataOutcome.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/kaplanmeier/metadata/class-use/MetaDataInfo.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/kaplanmeier/metadata/class-use/DiscreteQuantizerInterface.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/kaplanmeier/metadata/class-use/MeanQuantizer.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/package-use.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/comparators/package-use.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/matrix/package-use.html...
@@ -7988,11 +8024,11 @@
 [WARNING] warning: The -footer option is no longer supported and will be ignored.
 [WARNING] It may be removed in a future release.
 [WARNING] Loading source file /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/src/main/java/package-info.java...
+[WARNING] Loading source files for package demo...
 [WARNING] Loading source files for package org.biojava.nbio.ontology...
 [WARNING] Loading source files for package org.biojava.nbio.ontology.io...
 [WARNING] Loading source files for package org.biojava.nbio.ontology.utils...
 [WARNING] Loading source files for package org.biojava.nbio.ontology.obo...
-[WARNING] Loading source files for package demo...
 [WARNING] Constructing Javadoc information...
 [WARNING] Building index for all the packages and classes...
 [WARNING] Standard Doclet version 17.0.11+9-Debian-1
@@ -8089,47 +8125,47 @@
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/utils/package-tree.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/constant-values.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/serialized-form.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/class-use/Variable.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/class-use/Variable.Impl.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/demo/class-use/ParseGO.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/class-use/OntoTools.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/class-use/Ontology.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/class-use/Ontology.Impl.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/class-use/Term.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/class-use/Term.Impl.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/class-use/App.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/class-use/DefaultOps.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/class-use/AbstractTerm.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/class-use/Ontology.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/class-use/Ontology.Impl.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/class-use/AlreadyExistsException.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/class-use/OntologyFactory.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/class-use/RemoteTerm.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/class-use/RemoteTerm.Impl.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/class-use/Triple.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/class-use/Triple.Impl.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/class-use/OntologyTerm.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/class-use/OntologyTerm.Impl.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/class-use/OntologyOps.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/class-use/IntegerOntology.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/class-use/IntegerOntology.IntTerm.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/class-use/App.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/class-use/AbstractTerm.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/class-use/DefaultOps.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/class-use/InvalidTermException.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/class-use/OntologyOps.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/class-use/OntologyTerm.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/class-use/OntologyTerm.Impl.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/class-use/Variable.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/class-use/Variable.Impl.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/class-use/OntologyException.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/class-use/Triple.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/class-use/Triple.Impl.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/class-use/Synonym.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/class-use/AlreadyExistsException.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/class-use/InvalidTermException.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/io/class-use/GOParser.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/class-use/RemoteTerm.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/class-use/RemoteTerm.Impl.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/io/class-use/OboParser.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/io/class-use/GOParser.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/io/class-use/TabDelimParser.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/utils/class-use/SmallMap.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/utils/class-use/AssertionFailure.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/utils/class-use/StaticMemberPlaceHolder.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/utils/class-use/WeakValueHashMap.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/utils/class-use/Annotatable.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/utils/class-use/AbstractAnnotation.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/utils/class-use/SmallAnnotation.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/utils/class-use/KeyedWeakReference.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/utils/class-use/Annotatable.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/utils/class-use/SmallMap.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/utils/class-use/Annotation.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/utils/class-use/WeakValueHashMap.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/utils/class-use/AssertionFailure.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/obo/class-use/OboFileEventListener.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/obo/class-use/OboFileHandler.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/utils/class-use/KeyedWeakReference.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/obo/class-use/OboFileParser.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/obo/class-use/OboFileParser.SOPair.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/demo/class-use/ParseGO.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/obo/class-use/OboFileHandler.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/obo/class-use/OboFileEventListener.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/demo/package-use.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/package-use.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/io/package-use.html...
@@ -8407,171 +8443,171 @@
 [WARNING] warning: The -footer option is no longer supported and will be ignored.
 [WARNING] It may be removed in a future release.
 [WARNING] Loading source file /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/src/main/java/package-info.java...
+[WARNING] Loading source files for package demo...
+[WARNING] Loading source files for package org.biojava.nbio.core.search.io.blast...
+[WARNING] Loading source files for package org.biojava.nbio.core.search.io...
+[WARNING] Loading source files for package org.biojava.nbio.core.util...
+[WARNING] Loading source files for package org.biojava.nbio.core.alignment.template...
+[WARNING] Loading source files for package org.biojava.nbio.core.alignment...
+[WARNING] Loading source files for package org.biojava.nbio.core.alignment.matrices...
 [WARNING] Loading source files for package org.biojava.nbio.core.exceptions...
-[WARNING] Loading source files for package org.biojava.nbio.core.sequence...
 [WARNING] Loading source files for package org.biojava.nbio.core.sequence.template...
-[WARNING] Loading source files for package org.biojava.nbio.core.sequence.features...
-[WARNING] Loading source files for package org.biojava.nbio.core.sequence.reference...
 [WARNING] Loading source files for package org.biojava.nbio.core.sequence.transcription...
-[WARNING] Loading source files for package org.biojava.nbio.core.sequence.io...
+[WARNING] Loading source files for package org.biojava.nbio.core.sequence...
+[WARNING] Loading source files for package org.biojava.nbio.core.sequence.reference...
+[WARNING] Loading source files for package org.biojava.nbio.core.sequence.edits...
 [WARNING] Loading source files for package org.biojava.nbio.core.sequence.io.template...
+[WARNING] Loading source files for package org.biojava.nbio.core.sequence.io...
 [WARNING] Loading source files for package org.biojava.nbio.core.sequence.io.util...
 [WARNING] Loading source files for package org.biojava.nbio.core.sequence.io.embl...
-[WARNING] Loading source files for package org.biojava.nbio.core.sequence.location...
+[WARNING] Loading source files for package org.biojava.nbio.core.sequence.storage...
 [WARNING] Loading source files for package org.biojava.nbio.core.sequence.location.template...
+[WARNING] Loading source files for package org.biojava.nbio.core.sequence.location...
 [WARNING] Loading source files for package org.biojava.nbio.core.sequence.views...
-[WARNING] Loading source files for package org.biojava.nbio.core.sequence.edits...
 [WARNING] Loading source files for package org.biojava.nbio.core.sequence.compound...
+[WARNING] Loading source files for package org.biojava.nbio.core.sequence.features...
 [WARNING] Loading source files for package org.biojava.nbio.core.sequence.loader...
-[WARNING] Loading source files for package org.biojava.nbio.core.sequence.storage...
-[WARNING] Loading source files for package org.biojava.nbio.core.search.io...
-[WARNING] Loading source files for package org.biojava.nbio.core.search.io.blast...
-[WARNING] Loading source files for package org.biojava.nbio.core.util...
-[WARNING] Loading source files for package org.biojava.nbio.core.alignment...
-[WARNING] Loading source files for package org.biojava.nbio.core.alignment.template...
-[WARNING] Loading source files for package org.biojava.nbio.core.alignment.matrices...
-[WARNING] Loading source files for package demo...
-[WARNING] Loading source files for package org.biojava.nbio.phylo...
-[WARNING] Loading source files for package org.biojava.nbio.alignment...
 [WARNING] Loading source files for package org.biojava.nbio.alignment.template...
+[WARNING] Loading source files for package org.biojava.nbio.alignment...
 [WARNING] Loading source files for package org.biojava.nbio.alignment.io...
 [WARNING] Loading source files for package org.biojava.nbio.alignment.routines...
-[WARNING] Loading source files for package org.biojava.nbio.structure.secstruc...
+[WARNING] Loading source files for package org.biojava.nbio.phylo...
 [WARNING] Loading source files for package org.biojava.nbio.structure...
-[WARNING] Loading source files for package org.biojava.nbio.structure.math...
-[WARNING] Loading source files for package org.biojava.nbio.structure.jama...
-[WARNING] Loading source files for package org.biojava.nbio.structure.cluster...
+[WARNING] Loading source files for package org.biojava.nbio.structure.domain...
+[WARNING] Loading source files for package org.biojava.nbio.structure.domain.pdp...
 [WARNING] Loading source files for package org.biojava.nbio.structure.geometry...
+[WARNING] Loading source files for package org.biojava.nbio.structure.cath...
+[WARNING] Loading source files for package org.biojava.nbio.structure.math...
 [WARNING] Loading source files for package org.biojava.nbio.structure.io...
-[WARNING] Loading source files for package org.biojava.nbio.structure.io.cif...
-[WARNING] Loading source files for package org.biojava.nbio.structure.io.util...
 [WARNING] Loading source files for package org.biojava.nbio.structure.io.mmtf...
+[WARNING] Loading source files for package org.biojava.nbio.structure.io.util...
+[WARNING] Loading source files for package org.biojava.nbio.structure.io.cif...
 [WARNING] Loading source files for package org.biojava.nbio.structure.io.sifts...
-[WARNING] Loading source files for package org.biojava.nbio.structure.domain.pdp...
-[WARNING] Loading source files for package org.biojava.nbio.structure.domain...
+[WARNING] Loading source files for package org.biojava.nbio.structure.jama...
+[WARNING] Loading source files for package org.biojava.nbio.structure.xtal.io...
+[WARNING] Loading source files for package org.biojava.nbio.structure.xtal...
+[WARNING] Loading source files for package org.biojava.nbio.structure.chem...
+[WARNING] Loading source files for package org.biojava.nbio.structure.asa...
+[WARNING] Loading source files for package org.biojava.nbio.structure.scop...
+[WARNING] Loading source files for package org.biojava.nbio.structure.contact...
+[WARNING] Loading source files for package org.biojava.nbio.structure.symmetry.geometry...
+[WARNING] Loading source files for package org.biojava.nbio.structure.symmetry.utils...
+[WARNING] Loading source files for package org.biojava.nbio.structure.symmetry.internal...
+[WARNING] Loading source files for package org.biojava.nbio.structure.symmetry.misc...
+[WARNING] Loading source files for package org.biojava.nbio.structure.symmetry.axis...
+[WARNING] Loading source files for package org.biojava.nbio.structure.symmetry.core...
 [WARNING] Loading source files for package org.biojava.nbio.structure.basepairs...
-[WARNING] Loading source files for package org.biojava.nbio.structure.align.client...
+[WARNING] Loading source files for package org.biojava.nbio.structure.quaternary...
+[WARNING] Loading source files for package org.biojava.nbio.structure.secstruc...
+[WARNING] Loading source files for package org.biojava.nbio.structure.ecod...
+[WARNING] Loading source files for package org.biojava.nbio.structure.cluster...
 [WARNING] Loading source files for package org.biojava.nbio.structure.align...
 [WARNING] Loading source files for package org.biojava.nbio.structure.align.fatcat...
 [WARNING] Loading source files for package org.biojava.nbio.structure.align.fatcat.calc...
 [WARNING] Loading source files for package org.biojava.nbio.structure.align.ce...
-[WARNING] Loading source files for package org.biojava.nbio.structure.align.pairwise...
-[WARNING] Loading source files for package org.biojava.nbio.structure.align.model...
-[WARNING] Loading source files for package org.biojava.nbio.structure.align.seq...
+[WARNING] Loading source files for package org.biojava.nbio.structure.align.client...
 [WARNING] Loading source files for package org.biojava.nbio.structure.align.util...
+[WARNING] Loading source files for package org.biojava.nbio.structure.align.model...
+[WARNING] Loading source files for package org.biojava.nbio.structure.align.xml...
 [WARNING] Loading source files for package org.biojava.nbio.structure.align.helper...
+[WARNING] Loading source files for package org.biojava.nbio.structure.align.seq...
 [WARNING] Loading source files for package org.biojava.nbio.structure.align.quaternary...
 [WARNING] Loading source files for package org.biojava.nbio.structure.align.multiple...
 [WARNING] Loading source files for package org.biojava.nbio.structure.align.multiple.util...
 [WARNING] Loading source files for package org.biojava.nbio.structure.align.multiple.mc...
-[WARNING] Loading source files for package org.biojava.nbio.structure.align.xml...
-[WARNING] Loading source files for package org.biojava.nbio.structure.symmetry.axis...
-[WARNING] Loading source files for package org.biojava.nbio.structure.symmetry.geometry...
-[WARNING] Loading source files for package org.biojava.nbio.structure.symmetry.utils...
-[WARNING] Loading source files for package org.biojava.nbio.structure.symmetry.misc...
-[WARNING] Loading source files for package org.biojava.nbio.structure.symmetry.core...
-[WARNING] Loading source files for package org.biojava.nbio.structure.symmetry.internal...
-[WARNING] Loading source files for package org.biojava.nbio.structure.contact...
-[WARNING] Loading source files for package org.biojava.nbio.structure.asa...
-[WARNING] Loading source files for package org.biojava.nbio.structure.cath...
-[WARNING] Loading source files for package org.biojava.nbio.structure.quaternary...
-[WARNING] Loading source files for package org.biojava.nbio.structure.scop...
-[WARNING] Loading source files for package org.biojava.nbio.structure.xtal...
-[WARNING] Loading source files for package org.biojava.nbio.structure.xtal.io...
-[WARNING] Loading source files for package org.biojava.nbio.structure.chem...
-[WARNING] Loading source files for package org.biojava.nbio.structure.ecod...
+[WARNING] Loading source files for package org.biojava.nbio.structure.align.pairwise...
+[WARNING] Loading source files for package org.biojava.nbio.structure.gui...
+[WARNING] Loading source files for package org.biojava.nbio.structure.gui.util...
+[WARNING] Loading source files for package org.biojava.nbio.structure.gui.util.color...
+[WARNING] Loading source files for package org.biojava.nbio.structure.gui.events...
+[WARNING] Loading source files for package org.biojava.nbio.structure.symmetry.gui...
+[WARNING] Loading source files for package org.biojava.nbio.structure.symmetry.jmolScript...
 [WARNING] Loading source files for package org.biojava.nbio.structure.align.gui...
 [WARNING] Loading source files for package org.biojava.nbio.structure.align.gui.aligpanel...
 [WARNING] Loading source files for package org.biojava.nbio.structure.align.gui.autosuggest...
 [WARNING] Loading source files for package org.biojava.nbio.structure.align.gui.jmol...
 [WARNING] Loading source files for package org.biojava.nbio.structure.align.webstart...
-[WARNING] Loading source files for package org.biojava.nbio.structure.symmetry.jmolScript...
-[WARNING] Loading source files for package org.biojava.nbio.structure.symmetry.gui...
-[WARNING] Loading source files for package org.biojava.nbio.structure.gui...
-[WARNING] Loading source files for package org.biojava.nbio.structure.gui.events...
-[WARNING] Loading source files for package org.biojava.nbio.structure.gui.util...
-[WARNING] Loading source files for package org.biojava.nbio.structure.gui.util.color...
-[WARNING] Loading source files for package org.biojava.nbio.genome.homology...
+[WARNING] Loading source files for package org.biojava.nbio.genome...
 [WARNING] Loading source files for package org.biojava.nbio.genome.io.fastq...
+[WARNING] Loading source files for package org.biojava.nbio.genome.util...
 [WARNING] Loading source files for package org.biojava.nbio.genome.query...
+[WARNING] Loading source files for package org.biojava.nbio.genome.homology...
 [WARNING] Loading source files for package org.biojava.nbio.genome.uniprot...
-[WARNING] Loading source files for package org.biojava.nbio.genome.parsers.cytoband...
 [WARNING] Loading source files for package org.biojava.nbio.genome.parsers.geneid...
-[WARNING] Loading source files for package org.biojava.nbio.genome.parsers.gff...
 [WARNING] Loading source files for package org.biojava.nbio.genome.parsers.twobit...
+[WARNING] Loading source files for package org.biojava.nbio.genome.parsers.gff...
+[WARNING] Loading source files for package org.biojava.nbio.genome.parsers.cytoband...
 [WARNING] Loading source files for package org.biojava.nbio.genome.parsers.genename...
-[WARNING] Loading source files for package org.biojava.nbio.genome.util...
-[WARNING] Loading source files for package org.biojava.nbio.genome...
-[WARNING] Loading source files for package org.biojava.nbio.phosphosite...
-[WARNING] Loading source files for package org.biojava.nbio.protmod.structure...
 [WARNING] Loading source files for package org.biojava.nbio.protmod...
+[WARNING] Loading source files for package org.biojava.nbio.protmod.structure...
 [WARNING] Loading source files for package org.biojava.nbio.protmod.io...
+[WARNING] Loading source files for package org.biojava.nbio.phosphosite...
 [WARNING] Loading source files for package org.biojava.nbio.ws.hmmer...
 [WARNING] Loading source files for package org.biojava.nbio.ws.alignment...
 [WARNING] Loading source files for package org.biojava.nbio.ws.alignment.qblast...
-[WARNING] Loading source files for package org.biojava.nbio.ronn...
 [WARNING] Loading source files for package org.biojava.nbio.data.sequence...
+[WARNING] Loading source files for package org.biojava.nbio.ronn...
 [WARNING] Loading source files for package org.biojava.nbio.aaproperties...
 [WARNING] Loading source files for package org.biojava.nbio.aaproperties.xml...
-[WARNING] Loading source files for package org.biojava.nbio.aaproperties.profeat...
 [WARNING] Loading source files for package org.biojava.nbio.aaproperties.profeat.convertor...
-[WARNING] Loading source files for package org.biojava.nbio.survival.data...
+[WARNING] Loading source files for package org.biojava.nbio.aaproperties.profeat...
 [WARNING] Loading source files for package org.biojava.nbio.survival.cox...
 [WARNING] Loading source files for package org.biojava.nbio.survival.cox.stats...
 [WARNING] Loading source files for package org.biojava.nbio.survival.cox.matrix...
 [WARNING] Loading source files for package org.biojava.nbio.survival.cox.comparators...
-[WARNING] Loading source files for package org.biojava.nbio.survival.kaplanmeier.metadata...
+[WARNING] Loading source files for package org.biojava.nbio.survival.data...
 [WARNING] Loading source files for package org.biojava.nbio.survival.kaplanmeier.figure...
+[WARNING] Loading source files for package org.biojava.nbio.survival.kaplanmeier.metadata...
 [WARNING] Loading source files for package org.biojava.nbio.ontology...
 [WARNING] Loading source files for package org.biojava.nbio.ontology.io...
 [WARNING] Loading source files for package org.biojava.nbio.ontology.utils...
 [WARNING] Loading source files for package org.biojava.nbio.ontology.obo...
 [WARNING] Loading source files for package org.biojava.nbio.proteincomparisontool...
-[WARNING] Loading source files for package org.forester.surfacing...
-[WARNING] Loading source files for package org.forester.tools...
-[WARNING] Loading source files for package org.forester.pccx...
-[WARNING] Loading source files for package org.forester.sequence...
-[WARNING] Loading source files for package org.forester.analysis...
-[WARNING] Loading source files for package org.forester.go...
-[WARNING] Loading source files for package org.forester.go.etc...
 [WARNING] Loading source files for package org.forester.archaeopteryx...
+[WARNING] Loading source files for package org.forester.archaeopteryx.phylogeny.data...
 [WARNING] Loading source files for package org.forester.archaeopteryx.tools...
 [WARNING] Loading source files for package org.forester.archaeopteryx.webservices...
-[WARNING] Loading source files for package org.forester.archaeopteryx.phylogeny.data...
-[WARNING] Loading source files for package org.forester.protein...
-[WARNING] Loading source files for package org.forester.io.parsers.tol...
+[WARNING] Loading source files for package org.forester.evoinference.distance...
+[WARNING] Loading source files for package org.forester.evoinference.parsimony...
+[WARNING] Loading source files for package org.forester.evoinference.tools...
+[WARNING] Loading source files for package org.forester.evoinference.matrix.distance...
+[WARNING] Loading source files for package org.forester.evoinference.matrix.character...
+[WARNING] Loading source files for package org.forester.evoinference...
+[WARNING] Loading source files for package org.forester.phylogeny.factories...
+[WARNING] Loading source files for package org.forester.phylogeny...
+[WARNING] Loading source files for package org.forester.phylogeny.data...
+[WARNING] Loading source files for package org.forester.phylogeny.iterators...
+[WARNING] Loading source files for package org.forester.test...
+[WARNING] Loading source files for package org.forester.test.examples...
+[WARNING] Loading source files for package org.forester.tools...
+[WARNING] Loading source files for package org.forester.io.writers...
+[WARNING] Loading source files for package org.forester.io.parsers.nexus...
 [WARNING] Loading source files for package org.forester.io.parsers...
 [WARNING] Loading source files for package org.forester.io.parsers.util...
 [WARNING] Loading source files for package org.forester.io.parsers.phyloxml...
 [WARNING] Loading source files for package org.forester.io.parsers.phyloxml.data...
-[WARNING] Loading source files for package org.forester.io.parsers.nexus...
 [WARNING] Loading source files for package org.forester.io.parsers.nhx...
-[WARNING] Loading source files for package org.forester.io.writers...
-[WARNING] Loading source files for package org.forester.test...
-[WARNING] Loading source files for package org.forester.test.examples...
-[WARNING] Loading source files for package org.forester.evoinference.tools...
-[WARNING] Loading source files for package org.forester.evoinference.parsimony...
-[WARNING] Loading source files for package org.forester.evoinference.distance...
-[WARNING] Loading source files for package org.forester.evoinference.matrix.character...
-[WARNING] Loading source files for package org.forester.evoinference.matrix.distance...
-[WARNING] Loading source files for package org.forester.evoinference...
-[WARNING] Loading source files for package org.forester.msa...
-[WARNING] Loading source files for package org.forester.ws.seqdb...
-[WARNING] Loading source files for package org.forester.ws.hmmer...
+[WARNING] Loading source files for package org.forester.io.parsers.tol...
 [WARNING] Loading source files for package org.forester.ws.wabi...
-[WARNING] Loading source files for package org.forester.msa_compactor...
-[WARNING] Loading source files for package org.forester.rio...
+[WARNING] Loading source files for package org.forester.ws.hmmer...
+[WARNING] Loading source files for package org.forester.ws.seqdb...
 [WARNING] Loading source files for package org.forester.util...
+[WARNING] Loading source files for package org.forester.surfacing...
+[WARNING] Loading source files for package org.forester.datastructures...
+[WARNING] Loading source files for package org.forester.pccx...
+[WARNING] Loading source files for package org.forester.protein...
+[WARNING] Loading source files for package org.forester.analysis...
+[WARNING] Loading source files for package org.forester.go...
+[WARNING] Loading source files for package org.forester.go.etc...
+[WARNING] Loading source files for package org.forester.species...
+[WARNING] Loading source files for package org.forester.msa...
+[WARNING] Loading source files for package org.forester.sdi...
 [WARNING] Loading source files for package org.forester.application...
 [WARNING] Loading source files for package org.forester.development...
-[WARNING] Loading source files for package org.forester.phylogeny...
-[WARNING] Loading source files for package org.forester.phylogeny.data...
-[WARNING] Loading source files for package org.forester.phylogeny.factories...
-[WARNING] Loading source files for package org.forester.phylogeny.iterators...
+[WARNING] Loading source files for package org.forester.sequence...
+[WARNING] Loading source files for package org.forester.msa_compactor...
 [WARNING] Loading source files for package org.forester.applications...
-[WARNING] Loading source files for package org.forester.datastructures...
-[WARNING] Loading source files for package org.forester.sdi...
-[WARNING] Loading source files for package org.forester.species...
+[WARNING] Loading source files for package org.forester.rio...
 [WARNING] Loading source files for package org.jcolorbrewer.ui...
 [WARNING] Loading source files for package org.jcolorbrewer...
 [WARNING] Constructing Javadoc information...
@@ -10696,321 +10732,313 @@
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/jcolorbrewer/ui/package-tree.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/constant-values.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/serialized-form.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/demo/class-use/ParseFastaFileDemo.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/demo/class-use/UncompressFile.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/demo/class-use/DemoSixFrameTranslation.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/demo/class-use/DemoDistanceTree.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/demo/class-use/DemoLoadSubstMax.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/demo/class-use/TestDNANeedlemanWunsch.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/demo/class-use/CookbookMSA.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/demo/class-use/DemoAlignProteins.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/demo/class-use/DemoBioAssemblies.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/demo/class-use/DemoAsa.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/demo/class-use/DemoSCOP.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/demo/class-use/DemoMultipleMC.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/demo/class-use/DemoContacts.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/demo/class-use/DemoMMCIFReader.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/demo/class-use/DemoSecStrucCalc.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/demo/class-use/DemoCrystalInterfaces.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/demo/class-use/DemoDomainsplit.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/demo/class-use/DemoChangeChemCompProvider.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/demo/class-use/DemoLoadSecStruc.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/demo/class-use/DemoMmcifToPdbConverter.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/demo/class-use/DemoCE.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/demo/class-use/DemoMmtfReader.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/demo/class-use/DemoBerkeleyScop.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/demo/class-use/DemoAtomCache.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/demo/class-use/DemoCeSymm.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/demo/class-use/DemoQsAlign.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/demo/class-use/DemoCATH.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/demo/class-use/DemoFATCAT.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/demo/class-use/ChemCompDistribution.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/demo/class-use/DemoCommandLineStartup.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/demo/class-use/DemoSymmetry.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/demo/class-use/DemoLoadStructure.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/demo/class-use/DemoMmtfWriter.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/demo/class-use/ShowStructureInJmol.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/demo/class-use/DemoAlignmentFromFasta.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/demo/class-use/WebStartClientDemo.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/demo/class-use/CookBook.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/demo/class-use/DemoShowCATHDomain.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/demo/class-use/AlignmentGuiDemo.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/demo/class-use/DemoQuatSymmetryJmol.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/demo/class-use/DemoStructureFromFasta.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/demo/class-use/DemoShowLargeAssembly.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/demo/class-use/DemoShowBiolAssembly.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/demo/class-use/DemoSW3DAligner.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/demo/class-use/DemoRotationAxis.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/demo/class-use/AFPFromFasta.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/demo/class-use/DemoNWALignment.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/demo/class-use/HmmerDemo.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/demo/class-use/NCBIQBlastServiceDemo.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/demo/class-use/PredictDisorder.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/demo/class-use/BioJavaAADemo.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/demo/class-use/ParseGO.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/search/io/blast/class-use/BlastTabularParser.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/search/io/blast/class-use/BlastHspBuilder.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/search/io/blast/class-use/BlastHitBuilder.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/search/io/blast/class-use/BlastXMLParser.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/search/io/blast/class-use/BlastResultBuilder.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/search/io/blast/class-use/BlastResult.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/search/io/class-use/Hit.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/search/io/class-use/SearchIO.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/search/io/class-use/ResultFactory.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/search/io/class-use/Result.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/search/io/class-use/Hsp.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/util/class-use/ConcurrencyTools.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/util/class-use/UncompressInputStream.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/util/class-use/StringManipulationHelper.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/util/class-use/SequenceTools.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/util/class-use/Hashcoder.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/util/class-use/FileDownloadUtils.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/util/class-use/SingleLinkageClusterer.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/util/class-use/InputStreamProvider.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/util/class-use/Equals.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/util/class-use/CRC64Checksum.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/util/class-use/FlatFileCache.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/util/class-use/XMLHelper.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/util/class-use/SoftHashMap.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/util/class-use/XMLWriter.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/util/class-use/PrettyXMLWriter.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/alignment/template/class-use/SequencePair.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/alignment/template/class-use/AlignedSequence.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/alignment/template/class-use/AlignedSequence.Step.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/alignment/template/class-use/Profile.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/alignment/template/class-use/Profile.StringFormat.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/alignment/template/class-use/MutableSequencePair.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/alignment/template/class-use/ProfileView.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/alignment/template/class-use/MutableAlignedSequence.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/alignment/template/class-use/SubstitutionMatrix.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/alignment/template/class-use/MutableProfilePair.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/alignment/template/class-use/ProfilePair.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/alignment/template/class-use/MutableProfile.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/alignment/class-use/SimpleAlignedSequence.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/alignment/class-use/SimpleProfilePair.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/alignment/class-use/SimpleProfile.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/alignment/class-use/SimpleSequencePair.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/alignment/matrices/class-use/SubstitutionMatrixHelper.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/alignment/matrices/class-use/AAIndexProvider.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/alignment/matrices/class-use/AAindexFactory.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/alignment/matrices/class-use/AAIndexFileParser.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/alignment/matrices/class-use/ScaledSubstitutionMatrix.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/alignment/matrices/class-use/SimpleSubstitutionMatrix.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/alignment/matrices/class-use/DefaultAAIndexProvider.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/exceptions/class-use/ParserException.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/exceptions/class-use/TranslationException.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/exceptions/class-use/Messages.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/exceptions/class-use/CompoundNotFoundException.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/class-use/AccessionID.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/class-use/Strand.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/class-use/CDSComparator.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/class-use/SequenceComparator.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/class-use/BasicSequence.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/class-use/DNASequence.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/class-use/DNASequence.DNAType.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/class-use/StartCodonSequence.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/class-use/RNASequence.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/class-use/ExonComparator.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/class-use/MultipleSequenceAlignment.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/class-use/ProteinSequence.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/class-use/ExonSequence.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/class-use/GeneSequence.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/class-use/SequenceOptimizationHints.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/class-use/SequenceOptimizationHints.SequenceCollection.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/class-use/SequenceOptimizationHints.SequenceUsage.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/class-use/TranscriptSequence.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/class-use/StopCodonSequence.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/class-use/IntronSequence.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/class-use/CDSSequence.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/class-use/ChromosomeSequence.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/class-use/TaxonomyID.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/class-use/DataSource.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/template/class-use/Compound.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/template/class-use/AbstractCompoundSet.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/exceptions/class-use/Messages.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/exceptions/class-use/TranslationException.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/template/class-use/SequenceMixin.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/template/class-use/SequenceMixin.SequenceIterator.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/template/class-use/AbstractCompound.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/template/class-use/CompoundTranslator.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/template/class-use/AbstractNucleotideCompoundSet.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/template/class-use/ProxySequenceReader.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/template/class-use/SequenceView.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/template/class-use/Accessioned.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/template/class-use/Sequence.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/template/class-use/SequenceReader.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/template/class-use/ComplementCompound.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/template/class-use/SequenceProxyView.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/template/class-use/AbstractSequence.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/template/class-use/AbstractSequence.AnnotationType.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/template/class-use/AbstractNucleotideCompoundSet.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/template/class-use/AbstractCompound.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/template/class-use/Sequence.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/template/class-use/ProxySequenceReader.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/template/class-use/CompoundSet.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/template/class-use/AbstractCompoundSet.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/template/class-use/CompoundTranslator.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/template/class-use/ComplementCompound.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/template/class-use/Compound.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/template/class-use/SequenceReader.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/template/class-use/Accessioned.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/template/class-use/SequenceView.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/template/class-use/AbstractCompoundTranslator.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/template/class-use/LightweightProfile.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/template/class-use/LightweightProfile.StringFormat.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/template/class-use/AbstractCompoundTranslator.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/template/class-use/CompoundSet.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/features/class-use/FeatureInterface.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/features/class-use/TextFeature.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/features/class-use/DatabaseReferenceInterface.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/features/class-use/QuantityFeature.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/features/class-use/QualityFeature.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/features/class-use/FeatureDbReferenceInfo.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/features/class-use/FeaturesKeyWordInterface.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/features/class-use/AbstractFeature.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/features/class-use/DBReferenceInfo.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/features/class-use/FeatureRetriever.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/features/class-use/Qualifier.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/reference/class-use/AbstractReference.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/reference/class-use/ReferenceInterface.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/reference/class-use/GenbankReference.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/transcription/class-use/DNAToRNATranslator.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/transcription/class-use/TranscriptionEngine.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/transcription/class-use/TranscriptionEngine.Builder.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/transcription/class-use/RNAToAminoAcidTranslator.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/transcription/class-use/Table.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/transcription/class-use/Table.CaseInsensitiveTriplet.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/transcription/class-use/Table.Codon.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/transcription/class-use/DNAToRNATranslator.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/transcription/class-use/RNAToAminoAcidTranslator.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/transcription/class-use/CaseInsensitiveCompound.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/transcription/class-use/Frame.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/io/class-use/CasePreservingProteinSequenceCreator.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/io/class-use/GenericInsdcHeaderFormat.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/io/class-use/DNASequenceCreator.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/class-use/ProteinSequence.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/class-use/StopCodonSequence.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/class-use/ExonSequence.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/class-use/CDSSequence.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/class-use/StartCodonSequence.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/class-use/MultipleSequenceAlignment.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/class-use/DataSource.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/class-use/Strand.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/class-use/DNASequence.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/class-use/DNASequence.DNAType.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/class-use/SequenceOptimizationHints.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/class-use/SequenceOptimizationHints.SequenceCollection.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/class-use/SequenceOptimizationHints.SequenceUsage.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/class-use/AccessionID.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/class-use/RNASequence.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/class-use/GeneSequence.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/class-use/TranscriptSequence.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/class-use/IntronSequence.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/class-use/SequenceComparator.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/class-use/TaxonomyID.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/class-use/ExonComparator.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/class-use/CDSComparator.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/class-use/ChromosomeSequence.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/class-use/BasicSequence.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/reference/class-use/AbstractReference.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/reference/class-use/ReferenceInterface.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/reference/class-use/GenbankReference.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/edits/class-use/Edit.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/edits/class-use/Edit.Substitute.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/edits/class-use/Edit.Insert.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/edits/class-use/Edit.Delete.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/edits/class-use/Edit.AbstractEdit.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/io/template/class-use/GenbankHeaderFormatInterface.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/io/template/class-use/SequenceHeaderParserInterface.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/io/template/class-use/FastaHeaderFormatInterface.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/io/template/class-use/SequenceParserInterface.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/io/template/class-use/SequenceCreatorInterface.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/io/class-use/FastaReaderHelper.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/io/class-use/FileProxyProteinSequenceCreator.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/io/class-use/GenbankSequenceParser.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/io/class-use/GenericGenbankHeaderParser.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/io/class-use/FastaWriter.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/io/class-use/FileProxyRNASequenceCreator.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/io/class-use/FastaWriterHelper.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/io/class-use/GenericFastaHeaderParser.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/io/class-use/FastaGeneWriter.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/io/class-use/GenbankWriter.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/io/class-use/FastaSequenceParser.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/io/class-use/GenbankSequenceParser.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/io/class-use/ProteinSequenceCreator.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/io/class-use/FastaReader.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/io/class-use/GenbankWriterHelper.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/io/class-use/FileProxyDNASequenceCreator.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/io/class-use/GenbankReader.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/io/class-use/ABITrace.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/io/class-use/GenericGenbankHeaderFormat.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/io/class-use/GenbankReaderHelper.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/io/class-use/BufferedReaderBytesRead.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/io/class-use/FastaGeneWriter.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/io/class-use/FastaReader.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/io/class-use/FileProxyRNASequenceCreator.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/io/class-use/GenericFastaHeaderFormat.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/io/class-use/BufferedReaderBytesRead.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/io/class-use/PlainFastaHeaderParser.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/io/class-use/RNASequenceCreator.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/io/class-use/GenbankReader.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/io/class-use/IUPACParser.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/io/class-use/IUPACParser.IUPACTable.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/io/template/class-use/SequenceParserInterface.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/io/template/class-use/GenbankHeaderFormatInterface.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/io/template/class-use/SequenceHeaderParserInterface.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/io/template/class-use/SequenceCreatorInterface.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/io/template/class-use/FastaHeaderFormatInterface.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/io/class-use/FileProxyProteinSequenceCreator.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/io/class-use/FastaWriter.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/io/class-use/GenericInsdcHeaderFormat.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/io/class-use/RNASequenceCreator.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/io/class-use/CasePreservingProteinSequenceCreator.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/io/class-use/GenericGenbankHeaderParser.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/io/class-use/ABITrace.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/io/class-use/FastaSequenceParser.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/io/class-use/GenbankWriterHelper.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/io/class-use/DNASequenceCreator.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/io/class-use/GenericFastaHeaderParser.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/io/class-use/FileProxyDNASequenceCreator.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/io/class-use/GenericGenbankHeaderFormat.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/io/util/class-use/ClasspathResource.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/io/util/class-use/IOUtils.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/io/util/class-use/IOUtils.ReaderProcessor.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/io/embl/class-use/EmblReference.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/io/embl/class-use/EmblRecord.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/io/embl/class-use/EmblId.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/io/embl/class-use/EmblReader.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/location/class-use/SimplePoint.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/location/class-use/FuzzyPoint.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/location/class-use/SimpleLocation.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/io/embl/class-use/EmblId.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/io/embl/class-use/EmblRecord.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/storage/class-use/FourBitSequenceReader.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/storage/class-use/FourBitSequenceReader.FourBitArrayWorker.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/storage/class-use/JoiningSequenceReader.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/storage/class-use/SequenceAsStringHelper.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/storage/class-use/TwoBitSequenceReader.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/storage/class-use/TwoBitSequenceReader.TwoBitArrayWorker.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/storage/class-use/BitSequenceReader.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/storage/class-use/BitSequenceReader.BitArrayWorker.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/storage/class-use/ArrayListSequenceReader.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/storage/class-use/SingleCompoundSequenceReader.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/location/template/class-use/Point.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/location/template/class-use/Point.Resolver.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/location/template/class-use/AbstractLocation.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/location/template/class-use/AccesionedLocation.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/location/template/class-use/Location.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/location/template/class-use/Location.Tools.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/location/class-use/SequenceLocation.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/location/class-use/InsdcParser.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/location/class-use/LocationHelper.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/location/class-use/FuzzyPoint.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/location/class-use/InsdcLocations.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/location/class-use/InsdcLocations.OneOfLocation.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/location/class-use/InsdcLocations.GroupLocation.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/location/class-use/InsdcLocations.OrderLocation.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/location/class-use/InsdcLocations.BondLocation.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/location/template/class-use/AccesionedLocation.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/location/template/class-use/Point.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/location/template/class-use/Point.Resolver.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/location/template/class-use/AbstractLocation.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/location/template/class-use/Location.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/location/template/class-use/Location.Tools.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/views/class-use/ComplementSequenceView.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/location/class-use/SimpleLocation.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/location/class-use/LocationHelper.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/location/class-use/SimplePoint.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/views/class-use/RnaSequenceView.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/views/class-use/ReversedSequenceView.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/views/class-use/ComplementSequenceView.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/views/class-use/WindowedSequence.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/edits/class-use/Edit.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/edits/class-use/Edit.Substitute.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/edits/class-use/Edit.Insert.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/edits/class-use/Edit.Delete.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/edits/class-use/Edit.AbstractEdit.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/views/class-use/ReversedSequenceView.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/compound/class-use/CodonCompound.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/compound/class-use/AmbiguityRNACompoundSet.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/compound/class-use/DNACompoundSet.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/compound/class-use/NucleotideCompound.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/compound/class-use/RNACompoundSet.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/compound/class-use/CodonCompound.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/compound/class-use/AmbiguityDNACompoundSet.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/compound/class-use/AminoAcidCompound.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/compound/class-use/AmbiguityDNARNAHybridCompoundSet.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/compound/class-use/AminoAcidCompoundSet.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/compound/class-use/DNACompoundSet.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/compound/class-use/ABITracerCompoundSet.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/loader/class-use/ArrayListProxySequenceReader.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/loader/class-use/SequenceFileProxyLoader.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/loader/class-use/GenbankProxySequenceReader.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/compound/class-use/NucleotideCompound.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/compound/class-use/AmbiguityDNARNAHybridCompoundSet.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/features/class-use/FeatureDbReferenceInfo.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/features/class-use/FeatureInterface.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/features/class-use/AbstractFeature.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/features/class-use/QuantityFeature.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/features/class-use/TextFeature.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/features/class-use/QualityFeature.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/features/class-use/FeatureRetriever.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/features/class-use/DBReferenceInfo.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/features/class-use/Qualifier.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/features/class-use/FeaturesKeyWordInterface.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/features/class-use/DatabaseReferenceInterface.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/loader/class-use/UniprotProxySequenceReader.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/loader/class-use/SequenceFileProxyLoader.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/loader/class-use/StringProxySequenceReader.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/storage/class-use/SingleCompoundSequenceReader.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/storage/class-use/BitSequenceReader.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/storage/class-use/BitSequenceReader.BitArrayWorker.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/storage/class-use/JoiningSequenceReader.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/storage/class-use/ArrayListSequenceReader.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/storage/class-use/TwoBitSequenceReader.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/storage/class-use/TwoBitSequenceReader.TwoBitArrayWorker.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/storage/class-use/SequenceAsStringHelper.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/storage/class-use/FourBitSequenceReader.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/storage/class-use/FourBitSequenceReader.FourBitArrayWorker.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/search/io/class-use/ResultFactory.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/search/io/class-use/Hit.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/search/io/class-use/SearchIO.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/search/io/class-use/Hsp.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/search/io/class-use/Result.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/search/io/blast/class-use/BlastHitBuilder.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/search/io/blast/class-use/BlastXMLParser.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/search/io/blast/class-use/BlastResult.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/search/io/blast/class-use/BlastResultBuilder.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/search/io/blast/class-use/BlastHspBuilder.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/search/io/blast/class-use/BlastTabularParser.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/util/class-use/InputStreamProvider.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/util/class-use/SingleLinkageClusterer.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/util/class-use/FlatFileCache.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/util/class-use/FileDownloadUtils.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/util/class-use/StringManipulationHelper.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/util/class-use/Hashcoder.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/util/class-use/Equals.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/util/class-use/SequenceTools.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/util/class-use/ConcurrencyTools.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/util/class-use/UncompressInputStream.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/util/class-use/XMLHelper.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/util/class-use/PrettyXMLWriter.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/util/class-use/SoftHashMap.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/util/class-use/XMLWriter.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/util/class-use/CRC64Checksum.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/alignment/class-use/SimpleAlignedSequence.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/alignment/class-use/SimpleProfile.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/alignment/class-use/SimpleProfilePair.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/alignment/class-use/SimpleSequencePair.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/alignment/template/class-use/MutableSequencePair.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/alignment/template/class-use/ProfileView.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/alignment/template/class-use/SequencePair.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/alignment/template/class-use/MutableProfilePair.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/alignment/template/class-use/AlignedSequence.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/alignment/template/class-use/AlignedSequence.Step.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/alignment/template/class-use/MutableProfile.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/alignment/template/class-use/ProfilePair.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/alignment/template/class-use/MutableAlignedSequence.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/alignment/template/class-use/SubstitutionMatrix.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/alignment/template/class-use/Profile.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/alignment/template/class-use/Profile.StringFormat.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/alignment/matrices/class-use/SubstitutionMatrixHelper.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/alignment/matrices/class-use/DefaultAAIndexProvider.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/alignment/matrices/class-use/AAIndexFileParser.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/alignment/matrices/class-use/AAindexFactory.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/alignment/matrices/class-use/ScaledSubstitutionMatrix.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/alignment/matrices/class-use/SimpleSubstitutionMatrix.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/alignment/matrices/class-use/AAIndexProvider.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/demo/class-use/UncompressFile.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/demo/class-use/DemoSixFrameTranslation.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/demo/class-use/ParseFastaFileDemo.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/demo/class-use/CookbookMSA.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/demo/class-use/DemoLoadSubstMax.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/demo/class-use/DemoAlignProteins.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/demo/class-use/DemoDistanceTree.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/demo/class-use/TestDNANeedlemanWunsch.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/demo/class-use/DemoCommandLineStartup.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/demo/class-use/ChemCompDistribution.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/demo/class-use/DemoMmtfWriter.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/demo/class-use/DemoCeSymm.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/demo/class-use/DemoAtomCache.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/demo/class-use/DemoSymmetry.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/demo/class-use/DemoLoadSecStruc.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/demo/class-use/DemoBerkeleyScop.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/demo/class-use/DemoLoadStructure.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/demo/class-use/DemoMmcifToPdbConverter.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/demo/class-use/DemoCATH.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/demo/class-use/DemoQsAlign.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/demo/class-use/DemoSecStrucCalc.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/demo/class-use/DemoCE.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/demo/class-use/DemoFATCAT.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/demo/class-use/DemoChangeChemCompProvider.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/demo/class-use/DemoAsa.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/demo/class-use/DemoMMCIFReader.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/demo/class-use/DemoBioAssemblies.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/demo/class-use/DemoSCOP.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/demo/class-use/DemoContacts.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/demo/class-use/DemoCrystalInterfaces.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/demo/class-use/DemoMmtfReader.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/demo/class-use/DemoMultipleMC.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/demo/class-use/DemoDomainsplit.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/demo/class-use/AFPFromFasta.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/demo/class-use/DemoShowBiolAssembly.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/demo/class-use/WebStartClientDemo.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/demo/class-use/DemoShowLargeAssembly.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/demo/class-use/DemoStructureFromFasta.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/demo/class-use/DemoRotationAxis.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/demo/class-use/DemoNWALignment.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/demo/class-use/AlignmentGuiDemo.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/demo/class-use/DemoSW3DAligner.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/demo/class-use/DemoQuatSymmetryJmol.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/demo/class-use/CookBook.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/demo/class-use/DemoShowCATHDomain.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/demo/class-use/ShowStructureInJmol.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/demo/class-use/DemoAlignmentFromFasta.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/demo/class-use/HmmerDemo.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/demo/class-use/NCBIQBlastServiceDemo.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/demo/class-use/PredictDisorder.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/demo/class-use/BioJavaAADemo.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/demo/class-use/ParseGO.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/phylo/class-use/DistanceTreeEvaluator.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/phylo/class-use/ForesterWrapper.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/phylo/class-use/DistanceMatrixCalculator.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/phylo/class-use/TreeConstructor.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/phylo/class-use/TreeType.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/phylo/class-use/TreeConstructorType.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/phylo/class-use/Comparison.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/alignment/class-use/SimpleProfileProfileAligner.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/alignment/class-use/StandardRescoreRefiner.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/alignment/class-use/SimpleGapPenalty.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/loader/class-use/GenbankProxySequenceReader.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/sequence/loader/class-use/ArrayListProxySequenceReader.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/alignment/template/class-use/CallablePairwiseSequenceAligner.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/alignment/template/class-use/HierarchicalClusterer.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/alignment/template/class-use/AbstractProfileProfileAligner.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/alignment/template/class-use/AbstractMatrixAligner.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/alignment/template/class-use/Aligner.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/alignment/template/class-use/PairInProfileScorer.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/alignment/template/class-use/PairwiseSequenceScorer.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/alignment/template/class-use/PairwiseSequenceAligner.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/alignment/template/class-use/RescoreRefiner.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/alignment/template/class-use/GuideTreeNode.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/alignment/template/class-use/MatrixAligner.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/alignment/template/class-use/GapPenalty.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/alignment/template/class-use/GapPenalty.Type.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/alignment/template/class-use/Scorer.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/alignment/template/class-use/CallablePairwiseSequenceScorer.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/alignment/template/class-use/PartitionRefiner.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/alignment/template/class-use/ProfileProfileScorer.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/alignment/template/class-use/ProfileProfileAligner.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/alignment/template/class-use/AbstractScorer.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/alignment/template/class-use/CallableProfileProfileAligner.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/alignment/template/class-use/AbstractPairwiseSequenceAligner.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/alignment/class-use/FractionalSimilarityInProfileScorer.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/alignment/class-use/GuideTree.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/alignment/class-use/GuideTree.Node.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/alignment/class-use/FractionalIdentityInProfileScorer.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/alignment/class-use/SubstitutionMatrixScorer.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/alignment/class-use/FractionalIdentityScorer.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/alignment/class-use/NeedlemanWunsch.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/alignment/class-use/StandardRescoreRefiner.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/alignment/class-use/SimpleGapPenalty.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/alignment/class-use/SmithWaterman.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/alignment/class-use/Alignments.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/alignment/class-use/Alignments.RefinerType.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/alignment/class-use/Alignments.ProfileProfileAlignerType.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/alignment/class-use/Alignments.PairwiseSequenceScorerType.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/alignment/class-use/Alignments.PairwiseSequenceAlignerType.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/alignment/class-use/Alignments.PairInProfileScorerType.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/alignment/class-use/SimpleProfileProfileAligner.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/alignment/class-use/FractionalIdentityScorer.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/alignment/class-use/FractionalSimilarityScorer.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/alignment/class-use/SmithWaterman.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/alignment/class-use/GuideTree.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/alignment/class-use/GuideTree.Node.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/alignment/template/class-use/AbstractMatrixAligner.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/alignment/template/class-use/PairwiseSequenceAligner.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/alignment/template/class-use/GuideTreeNode.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/alignment/template/class-use/ProfileProfileScorer.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/alignment/template/class-use/AbstractPairwiseSequenceAligner.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/alignment/template/class-use/PairwiseSequenceScorer.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/alignment/template/class-use/PairInProfileScorer.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/alignment/template/class-use/CallablePairwiseSequenceScorer.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/alignment/template/class-use/HierarchicalClusterer.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/alignment/template/class-use/PartitionRefiner.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/alignment/template/class-use/AbstractScorer.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/alignment/template/class-use/CallablePairwiseSequenceAligner.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/alignment/template/class-use/MatrixAligner.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/alignment/template/class-use/RescoreRefiner.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/alignment/template/class-use/CallableProfileProfileAligner.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/alignment/template/class-use/GapPenalty.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/alignment/template/class-use/GapPenalty.Type.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/alignment/template/class-use/Scorer.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/alignment/template/class-use/AbstractProfileProfileAligner.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/alignment/template/class-use/ProfileProfileAligner.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/alignment/template/class-use/Aligner.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/alignment/class-use/SubstitutionMatrixScorer.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/alignment/io/class-use/StockholmStructure.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/alignment/io/class-use/StockholmStructure.DatabaseReference.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/alignment/io/class-use/StockholmFileParser.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/alignment/io/class-use/StockholmFileAnnotation.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/alignment/io/class-use/StockholmFileAnnotation.StockholmFileAnnotationReference.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/alignment/io/class-use/StockholmFileParser.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/alignment/routines/class-use/GuanUberbacher.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/alignment/routines/class-use/AnchoredPairwiseSequenceAligner.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/alignment/routines/class-use/AlignerHelper.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/alignment/routines/class-use/AlignerHelper.Subproblem.html...
@@ -11018,652 +11046,668 @@
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/alignment/routines/class-use/AlignerHelper.Anchor.QueryIndexComparator.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/alignment/routines/class-use/AlignerHelper.Cut.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/alignment/routines/class-use/AlignerHelper.Last.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/secstruc/class-use/HBond.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/secstruc/class-use/Ladder.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/secstruc/class-use/SecStrucType.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/secstruc/class-use/SecStrucCalc.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/secstruc/class-use/SecStrucElement.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/secstruc/class-use/BridgeType.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/secstruc/class-use/DSSPParser.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/secstruc/class-use/BetaBridge.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/secstruc/class-use/SecStrucTools.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/secstruc/class-use/SecStrucInfo.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/secstruc/class-use/SecStrucState.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/class-use/Group.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/class-use/ChainImpl.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/class-use/Chain.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/class-use/ExperimentalTechnique.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/alignment/routines/class-use/GuanUberbacher.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/phylo/class-use/TreeConstructorType.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/phylo/class-use/TreeType.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/phylo/class-use/Comparison.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/phylo/class-use/TreeConstructor.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/phylo/class-use/DistanceMatrixCalculator.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/phylo/class-use/ForesterWrapper.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/phylo/class-use/DistanceTreeEvaluator.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/class-use/PdbId.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/class-use/StandardAminoAcid.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/class-use/PDBCrystallographicInfo.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/class-use/DBRef.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/class-use/AugmentedResidueRange.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/class-use/AtomIterator.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/class-use/PDBStatus.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/class-use/PDBStatus.Status.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/class-use/ElementType.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/class-use/SeqMisMatchImpl.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/class-use/PDBHeader.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/class-use/BioAssemblyIdentifier.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/class-use/Atom.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/class-use/EntityInfo.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/class-use/StructureException.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/class-use/URLIdentifier.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/class-use/ResidueRange.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/class-use/AtomImpl.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/class-use/StructureImpl.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/class-use/EntityType.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/class-use/StructureTools.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/class-use/Calc.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/class-use/PDBHeader.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/class-use/Site.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/class-use/AtomPositionMap.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/class-use/AtomPositionMap.GroupMatcher.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/class-use/Atom.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/class-use/Structure.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/class-use/AtomIterator.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/class-use/GroupType.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/class-use/Group.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/class-use/ElementType.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/class-use/ResidueNumber.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/class-use/ChainImpl.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/class-use/BondType.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/class-use/SubstructureIdentifier.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/class-use/SeqMisMatch.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/class-use/ResidueRangeAndLength.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/class-use/StructureIdentifier.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/class-use/EntityInfo.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/class-use/Element.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/class-use/JournalArticle.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/class-use/Mutator.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/class-use/StructureTools.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/class-use/PassthroughIdentifier.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/class-use/PDBStatus.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/class-use/PDBStatus.Status.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/class-use/SeqMisMatch.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/class-use/Bond.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/class-use/URLIdentifier.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/class-use/NucleotideImpl.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/class-use/Site.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/class-use/Element.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/class-use/ResidueRange.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/class-use/PDBRecord.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/class-use/StructureIO.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/class-use/StandardAminoAcid.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/class-use/BondImpl.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/class-use/PDBCrystallographicInfo.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/class-use/PdbId.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/class-use/DatabasePDBRevRecord.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/class-use/StructureIdentifier.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/class-use/GroupIterator.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/class-use/PassthroughIdentifier.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/class-use/AminoAcidImpl.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/class-use/Model.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/class-use/AtomPositionMap.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/class-use/AtomPositionMap.GroupMatcher.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/class-use/HetatomImpl.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/class-use/HetatomImpl.PerformanceBehavior.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/class-use/SubstructureIdentifier.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/class-use/ResidueRangeAndLength.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/class-use/PDBRecord.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/class-use/StructureImpl.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/class-use/AminoAcidImpl.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/class-use/EntityType.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/class-use/StructureIO.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/class-use/Author.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/class-use/Mutator.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/class-use/Calc.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/class-use/Chain.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/class-use/DatabasePDBRevRecord.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/class-use/NucleotideImpl.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/class-use/Model.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/class-use/StructureException.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/class-use/SeqMisMatchImpl.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/class-use/AugmentedResidueRange.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/class-use/BondImpl.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/class-use/AminoAcid.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/class-use/GroupType.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/class-use/Structure.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/math/class-use/SparseSquareMatrix.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/math/class-use/SymbolTable.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/math/class-use/SparseVector.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/jama/class-use/SingularValueDecomposition.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/jama/class-use/Maths.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/jama/class-use/QRDecomposition.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/jama/class-use/EigenvalueDecomposition.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/jama/class-use/LUDecomposition.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/jama/class-use/CholeskyDecomposition.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/jama/class-use/Matrix.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/cluster/class-use/SubunitClustererMethod.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/cluster/class-use/SubunitCluster.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/cluster/class-use/Subunit.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/cluster/class-use/SubunitClustererParameters.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/cluster/class-use/SubunitClusterer.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/cluster/class-use/SubunitExtractor.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/class-use/ExperimentalTechnique.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/domain/class-use/DomainProvider.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/domain/class-use/SerializableCache.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/domain/class-use/LocalProteinDomainParser.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/domain/pdp/class-use/PDPParameters.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/domain/pdp/class-use/SegmentComparator.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/domain/pdp/class-use/Cut.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/domain/pdp/class-use/GetDistanceMatrix.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/domain/pdp/class-use/ShortSegmentRemover.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/domain/pdp/class-use/PDPDistanceMatrix.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/domain/pdp/class-use/CutSites.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/domain/pdp/class-use/ClusterDomains.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/domain/pdp/class-use/Segment.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/domain/pdp/class-use/CutValues.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/domain/pdp/class-use/Domain.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/domain/pdp/class-use/CutDomain.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/geometry/class-use/UnitQuaternions.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/geometry/class-use/Matrices.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/geometry/class-use/SuperPositions.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/geometry/class-use/SuperPositionQuat.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/geometry/class-use/CalcPoint.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/geometry/class-use/SuperPosition.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/geometry/class-use/MomentsOfInertia.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/geometry/class-use/MomentsOfInertia.SymmetryClass.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/geometry/class-use/CalcPoint.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/geometry/class-use/SuperPositionAbstract.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/geometry/class-use/SuperPositionQCP.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/geometry/class-use/SuperPositionSVD.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/geometry/class-use/SuperPosition.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/geometry/class-use/UnitQuaternions.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/geometry/class-use/SuperPositionQuat.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/geometry/class-use/SuperPositions.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/geometry/class-use/SuperPositionAbstract.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/cath/class-use/CathDomain.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/cath/class-use/CathDatabase.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/cath/class-use/CathFactory.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/cath/class-use/CathInstallation.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/cath/class-use/CathNode.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/cath/class-use/CathSegment.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/cath/class-use/CathFragment.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/cath/class-use/CathCategory.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/math/class-use/SparseVector.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/math/class-use/SparseSquareMatrix.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/math/class-use/SymbolTable.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/io/class-use/FastaAFPChainConverter.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/io/class-use/FileConvert.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/io/class-use/CAConverter.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/io/class-use/FastaStructureParser.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/io/class-use/BondMaker.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/io/class-use/PDBFileParser.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/io/class-use/BcifFileReader.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/io/class-use/StructureIOFile.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/io/class-use/EntityFinder.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/io/class-use/CifFileReader.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/io/class-use/PDBFileParser.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/io/class-use/MMTFFileReader.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/io/class-use/FileParsingParameters.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/io/class-use/GroupToSDF.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/io/class-use/StructureSequenceMatcher.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/io/class-use/StructureFiletype.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/io/class-use/LocalPDBDirectory.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/io/class-use/LocalPDBDirectory.FetchBehavior.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/io/class-use/LocalPDBDirectory.ObsoleteBehavior.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/io/class-use/FastaStructureParser.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/io/class-use/PDBParseException.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/io/class-use/EntityFinder.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/io/class-use/ChargeAdder.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/io/class-use/PDBBioAssemblyParser.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/io/class-use/StructureProvider.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/io/class-use/BondMaker.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/io/class-use/StructureSequenceMatcher.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/io/class-use/SSBondImpl.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/io/class-use/StructureFiletype.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/io/class-use/SeqRes2AtomAligner.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/io/class-use/FileParsingParameters.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/io/class-use/GroupToSDF.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/io/class-use/FileConvert.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/io/class-use/PDBFileReader.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/io/class-use/PDBParseException.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/io/cif/class-use/ChemCompConverter.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/io/cif/class-use/CifStructureConverter.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/io/class-use/CAConverter.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/io/class-use/CifFileReader.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/io/class-use/StructureProvider.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/io/class-use/PDBBioAssemblyParser.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/io/class-use/MMTFFileReader.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/io/mmtf/class-use/MmtfSummaryDataBean.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/io/mmtf/class-use/MmtfActions.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/io/mmtf/class-use/MmtfUtils.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/io/mmtf/class-use/MmtfStructureReader.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/io/mmtf/class-use/MmtfStructureWriter.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/io/util/class-use/PDBTemporaryStorageUtils.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/io/util/class-use/PDBTemporaryStorageUtils.LinkRecord.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/io/cif/class-use/CifStructureSupplierImpl.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/io/cif/class-use/ChemCompConsumerImpl.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/io/cif/class-use/MetalBondConverter.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/io/cif/class-use/CifFileConsumer.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/io/cif/class-use/MetalBondConsumerImpl.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/io/cif/class-use/CifStructureConverter.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/io/cif/class-use/ChemCompConverter.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/io/cif/class-use/ChemCompConsumer.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/io/cif/class-use/CifChainSupplierImpl.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/io/cif/class-use/CifFileSupplier.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/io/cif/class-use/ChemCompConsumerImpl.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/io/cif/class-use/CifStructureConsumerImpl.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/io/cif/class-use/ChemCompConsumer.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/io/cif/class-use/CifStructureConsumer.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/io/cif/class-use/CifBean.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/io/cif/class-use/CifStructureSupplierImpl.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/io/cif/class-use/AbstractCifFileSupplier.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/io/cif/class-use/AbstractCifFileSupplier.WrappedAtom.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/io/cif/class-use/CifStructureConsumerImpl.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/io/cif/class-use/CifStructureConsumer.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/io/cif/class-use/MetalBondConsumer.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/io/util/class-use/PDBTemporaryStorageUtils.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/io/util/class-use/PDBTemporaryStorageUtils.LinkRecord.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/io/mmtf/class-use/MmtfStructureReader.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/io/mmtf/class-use/MmtfUtils.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/io/mmtf/class-use/MmtfSummaryDataBean.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/io/mmtf/class-use/MmtfActions.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/io/mmtf/class-use/MmtfStructureWriter.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/io/sifts/class-use/SiftsResidue.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/io/sifts/class-use/SiftsSegment.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/io/cif/class-use/MetalBondConsumerImpl.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/io/cif/class-use/CifBean.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/io/cif/class-use/CifFileConsumer.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/io/sifts/class-use/SiftsXMLParser.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/io/sifts/class-use/SiftsMappingProvider.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/io/sifts/class-use/SiftsSegment.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/io/sifts/class-use/SiftsResidue.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/io/sifts/class-use/SiftsChainToUniprotMapping.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/io/sifts/class-use/SiftsEntity.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/io/sifts/class-use/SiftsChainEntry.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/io/sifts/class-use/SiftsChainToUniprotMapping.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/io/sifts/class-use/SiftsXMLParser.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/domain/pdp/class-use/GetDistanceMatrix.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/domain/pdp/class-use/SegmentComparator.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/domain/pdp/class-use/PDPParameters.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/domain/pdp/class-use/Cut.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/domain/pdp/class-use/CutValues.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/domain/pdp/class-use/PDPDistanceMatrix.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/domain/pdp/class-use/CutDomain.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/domain/pdp/class-use/ClusterDomains.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/domain/pdp/class-use/CutSites.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/domain/pdp/class-use/ShortSegmentRemover.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/domain/pdp/class-use/Segment.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/domain/pdp/class-use/Domain.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/domain/class-use/DomainProvider.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/domain/class-use/SerializableCache.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/domain/class-use/LocalProteinDomainParser.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/jama/class-use/Matrix.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/jama/class-use/LUDecomposition.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/jama/class-use/Maths.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/jama/class-use/CholeskyDecomposition.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/jama/class-use/SingularValueDecomposition.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/jama/class-use/EigenvalueDecomposition.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/jama/class-use/QRDecomposition.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/xtal/io/class-use/SpaceGroupMapRoot.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/xtal/io/class-use/SpaceGroupMapElements.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/xtal/io/class-use/TransfAlgebraicAdapter.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/xtal/io/class-use/TreeMapSpaceGroupWrapper.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/xtal/class-use/SpaceGroup.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/xtal/class-use/BravaisLattice.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/xtal/class-use/CrystalCell.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/xtal/class-use/CrystalBuilder.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/xtal/class-use/SymoplibParser.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/xtal/class-use/CrystalTransform.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/xtal/class-use/UnitCellBoundingBox.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/xtal/class-use/TransformType.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/chem/class-use/ChemicalComponentDictionary.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/chem/class-use/ChemCompAtom.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/chem/class-use/ReducedChemCompProvider.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/chem/class-use/DownloadChemCompProvider.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/chem/class-use/ResidueType.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/chem/class-use/AllChemCompProvider.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/chem/class-use/ChemComp.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/chem/class-use/PolymerType.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/chem/class-use/ChemCompDescriptor.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/chem/class-use/ChemCompBond.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/chem/class-use/ChemCompProvider.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/chem/class-use/ChemCompTools.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/chem/class-use/ZipChemCompProvider.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/chem/class-use/MetalBondDistance.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/chem/class-use/ChemCompGroupFactory.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/asa/class-use/AsaCalculator.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/asa/class-use/GroupAsa.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/scop/class-use/ScopIOException.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/scop/class-use/LocalScopDatabase.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/scop/class-use/ScopDescription.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/scop/class-use/ScopFactory.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/scop/class-use/BerkeleyScopInstallation.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/scop/class-use/ScopCategory.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/scop/class-use/ScopDatabase.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/scop/class-use/ScopNode.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/scop/class-use/ScopMirror.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/scop/class-use/ScopInstallation.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/scop/class-use/ScopDomain.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/scop/class-use/Astral.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/scop/class-use/Astral.AstralSet.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/contact/class-use/AtomIdentifier.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/contact/class-use/Grid.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/contact/class-use/AtomContact.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/contact/class-use/GridCell.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/contact/class-use/GroupContact.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/contact/class-use/AtomContactSet.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/contact/class-use/Contact.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/contact/class-use/StructureInterfaceList.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/contact/class-use/InterfaceFinder.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/contact/class-use/StructureInterface.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/contact/class-use/BoundingBox.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/contact/class-use/StructureInterfaceCluster.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/contact/class-use/GroupContactSet.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/contact/class-use/Pair.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/symmetry/geometry/class-use/SphereSampler.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/symmetry/geometry/class-use/IcosahedralSampler.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/symmetry/geometry/class-use/RectangularPrism.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/symmetry/geometry/class-use/Prism.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/symmetry/geometry/class-use/Polyhedron.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/symmetry/geometry/class-use/Tetrahedron.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/symmetry/geometry/class-use/Octahedron.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/symmetry/geometry/class-use/Icosahedron.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/symmetry/geometry/class-use/DistanceBox.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/symmetry/utils/class-use/PermutationGenerator.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/symmetry/utils/class-use/BlastClustReader.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/symmetry/utils/class-use/SymmetryTools.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/symmetry/utils/class-use/PowerSet.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/symmetry/internal/class-use/ResidueGroup.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/symmetry/internal/class-use/SequenceFunctionOrderDetector.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/symmetry/internal/class-use/SequenceFunctionRefiner.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/symmetry/internal/class-use/SymmetryAxes.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/symmetry/internal/class-use/SymmetryAxes.Axis.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/symmetry/internal/class-use/CESymmParameters.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/symmetry/internal/class-use/CESymmParameters.SymmetryType.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/symmetry/internal/class-use/CESymmParameters.RefineMethod.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/symmetry/internal/class-use/CESymmParameters.OrderDetectorMethod.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/symmetry/internal/class-use/SymmOptimizer.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/symmetry/internal/class-use/CeSymmResult.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/symmetry/internal/class-use/SymmetryRefiner.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/symmetry/internal/class-use/RefinerFailedException.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/symmetry/internal/class-use/OrderDetector.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/symmetry/internal/class-use/CeSymmIterative.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/symmetry/internal/class-use/GraphComponentOrderDetector.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/symmetry/internal/class-use/AngleOrderDetectorPlus.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/symmetry/internal/class-use/CeSymm.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/symmetry/internal/class-use/GraphComponentRefiner.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/symmetry/misc/class-use/ChainSignature.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/symmetry/misc/class-use/ProteinComplexSignature.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/symmetry/axis/class-use/HelixAxisAligner.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/symmetry/axis/class-use/AxisAligner.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/symmetry/axis/class-use/RotationAxisAligner.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/symmetry/core/class-use/Stoichiometry.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/symmetry/core/class-use/Stoichiometry.StringOverflowStrategy.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/symmetry/core/class-use/QuatSymmetryResults.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/symmetry/core/class-use/SymmetryPerceptionMethod.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/symmetry/core/class-use/QuatSymmetrySolver.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/symmetry/core/class-use/RotationGroup.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/symmetry/core/class-use/HelicalRepeatUnit.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/symmetry/core/class-use/HelixLayers.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/symmetry/core/class-use/HelixSolver.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/symmetry/core/class-use/RotationSolver.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/symmetry/core/class-use/QuatSymmetrySubunits.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/symmetry/core/class-use/HelixExtender.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/symmetry/core/class-use/Helix.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/symmetry/core/class-use/Rotation.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/symmetry/core/class-use/SystematicSolver.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/symmetry/core/class-use/PermutationGroup.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/symmetry/core/class-use/QuatSymmetryDetector.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/symmetry/core/class-use/QuatSuperpositionScorer.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/symmetry/core/class-use/QuatSymmetryScores.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/symmetry/core/class-use/C2RotationSolver.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/symmetry/core/class-use/QuatSymmetryParameters.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/basepairs/class-use/MismatchedBasePairParameters.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/basepairs/class-use/TertiaryBasePairParameters.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/basepairs/class-use/BasePairParameters.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/basepairs/class-use/MismatchedBasePairParameters.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/client/class-use/PdbPair.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/client/class-use/StructureName.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/client/class-use/StructureName.Source.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/quaternary/class-use/BioAssemblyInfo.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/quaternary/class-use/BiologicalAssemblyBuilder.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/quaternary/class-use/BioAssemblyTools.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/quaternary/class-use/CartesianProduct.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/quaternary/class-use/BiologicalAssemblyTransformation.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/quaternary/class-use/OrderedPair.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/quaternary/class-use/OperatorResolver.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/secstruc/class-use/BetaBridge.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/secstruc/class-use/HBond.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/secstruc/class-use/DSSPParser.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/secstruc/class-use/Ladder.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/secstruc/class-use/SecStrucTools.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/secstruc/class-use/SecStrucElement.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/secstruc/class-use/SecStrucInfo.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/secstruc/class-use/BridgeType.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/secstruc/class-use/SecStrucType.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/secstruc/class-use/SecStrucState.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/secstruc/class-use/SecStrucCalc.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/ecod/class-use/EcodInstallation.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/ecod/class-use/EcodInstallation.EcodParser.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/ecod/class-use/EcodDomain.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/ecod/class-use/EcodDatabase.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/ecod/class-use/EcodFactory.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/cluster/class-use/SubunitClustererMethod.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/cluster/class-use/Subunit.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/cluster/class-use/SubunitExtractor.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/cluster/class-use/SubunitClusterer.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/cluster/class-use/SubunitClustererParameters.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/cluster/class-use/SubunitCluster.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/class-use/AbstractStructureAlignment.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/class-use/MultipleStructureAligner.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/class-use/StructureAlignment.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/class-use/StructureAlignmentFactory.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/class-use/StrucAligParameters.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/class-use/ClusterAltAligs.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/class-use/CallableStructureAlignment.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/class-use/BioJavaStructureAlignment.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/class-use/AFPTwister.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/class-use/BioJavaStructureAlignment.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/class-use/CallableStructureAlignment.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/class-use/StructurePairAligner.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/class-use/StructureAlignment.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/class-use/StructureAlignmentFactory.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/class-use/MultipleStructureAligner.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/fatcat/class-use/FatCat.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/fatcat/class-use/FatCatFlexible.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/fatcat/class-use/FatCatUserArgumentProcessor.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/fatcat/class-use/FatCatUserArgumentProcessor.FatCatStartupParams.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/fatcat/class-use/FatCatRigid.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/fatcat/class-use/FatCatFlexible.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/fatcat/class-use/FatCat.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/fatcat/calc/class-use/StructureAlignmentOptimizer.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/fatcat/calc/class-use/AFPCalculator.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/fatcat/calc/class-use/FCAlignHelper.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/fatcat/calc/class-use/FatCatParameters.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/fatcat/calc/class-use/AFPPostProcessor.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/fatcat/calc/class-use/FCAlignHelper.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/fatcat/calc/class-use/FatCatAligner.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/fatcat/calc/class-use/AFPOptimizer.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/fatcat/calc/class-use/AFPChainer.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/fatcat/calc/class-use/SigEva.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/fatcat/calc/class-use/AFPOptimizer.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/fatcat/calc/class-use/StructureAlignmentOptimizer.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/fatcat/calc/class-use/FatCatAligner.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/ce/class-use/CeSideChainUserArgumentProcessor.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/ce/class-use/CECPParameters.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/ce/class-use/CECPParameters.DuplicationHint.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/ce/class-use/CeSideChainMain.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/fatcat/calc/class-use/FatCatParameters.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/ce/class-use/CeParameters.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/ce/class-use/CeParameters.ScoringStrategy.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/ce/class-use/CeUserArgumentProcessor.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/ce/class-use/CeUserArgumentProcessor.CeStartupParams.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/ce/class-use/OptimalCECPParameters.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/ce/class-use/OptimalCECPMain.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/ce/class-use/CECPParameters.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/ce/class-use/CECPParameters.DuplicationHint.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/ce/class-use/ConfigStrucAligParams.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/ce/class-use/CeCalculatorEnhanced.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/ce/class-use/MatrixListener.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/ce/class-use/CeMain.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/ce/class-use/UserArgumentProcessor.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/ce/class-use/CeSideChainUserArgumentProcessor.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/ce/class-use/AbstractUserArgumentProcessor.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/ce/class-use/CeSideChainMain.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/ce/class-use/CeCPMain.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/ce/class-use/CeCPMain.CPRange.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/ce/class-use/UserArgumentProcessor.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/ce/class-use/GuiWrapper.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/ce/class-use/OptimalCECPParameters.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/ce/class-use/StartupParameters.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/ce/class-use/MatrixListener.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/ce/class-use/CeMain.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/ce/class-use/CECalculator.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/ce/class-use/CeCPUserArgumentProcessor.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/ce/class-use/CeCPUserArgumentProcessor.CeCPStartupParams.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/ce/class-use/GuiWrapper.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/ce/class-use/CeCalculatorEnhanced.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/ce/class-use/AbstractUserArgumentProcessor.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/ce/class-use/CECalculator.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/pairwise/class-use/FragmentPair.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/pairwise/class-use/Alignable.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/pairwise/class-use/AlignmentProgressListener.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/pairwise/class-use/AltAligComparator.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/pairwise/class-use/Gotoh.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/pairwise/class-use/FragmentJoiner.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/pairwise/class-use/AligNPE.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/pairwise/class-use/StrCompAlignment.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/pairwise/class-use/AlternativeAlignment.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/pairwise/class-use/AlignmentResult.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/model/class-use/AfpChainWriter.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/model/class-use/AFPChain.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/model/class-use/AFP.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/seq/class-use/SmithWaterman3DParameters.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/seq/class-use/SmithWatermanUserArgumentProcessor.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/seq/class-use/SmithWatermanUserArgumentProcessor.SmithWatermanStartupParams.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/seq/class-use/SmithWaterman3Daligner.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/util/class-use/ResourceManager.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/util/class-use/CliTools.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/util/class-use/ConfigurationException.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/util/class-use/AtomCache.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/util/class-use/URLConnectionTools.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/util/class-use/AFPAlignmentDisplay.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/util/class-use/SynchronizedOutFile.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/ce/class-use/CeUserArgumentProcessor.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/ce/class-use/CeUserArgumentProcessor.CeStartupParams.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/client/class-use/StructureName.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/client/class-use/StructureName.Source.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/client/class-use/PdbPair.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/util/class-use/CollectionTools.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/util/class-use/AlignmentTools.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/util/class-use/AlignmentTools.IdentityMap.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/util/class-use/URLConnectionTools.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/util/class-use/ResourceManager.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/util/class-use/RotationAxis.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/util/class-use/UserConfiguration.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/util/class-use/ConfigurationException.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/util/class-use/CliTools.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/util/class-use/AFPAlignmentDisplay.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/util/class-use/AtomCache.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/util/class-use/SynchronizedOutFile.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/util/class-use/AFPChainScorer.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/util/class-use/CollectionTools.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/helper/class-use/JointFragments.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/helper/class-use/AligMatEl.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/helper/class-use/AlignUtils.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/model/class-use/AFP.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/model/class-use/AFPChain.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/model/class-use/AfpChainWriter.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/xml/class-use/AFPChainXMLConverter.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/xml/class-use/MultipleAlignmentXMLParser.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/xml/class-use/PdbPairsMessage.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/xml/class-use/AFPChainXMLParser.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/xml/class-use/AFPChainFlipper.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/xml/class-use/PdbPairXMLConverter.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/xml/class-use/MultipleAlignmentXMLConverter.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/helper/class-use/GapArray.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/helper/class-use/IndexPair.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/helper/class-use/AlignUtils.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/helper/class-use/IdxComparator.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/quaternary/class-use/QsAlignResult.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/helper/class-use/AligMatEl.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/helper/class-use/JointFragments.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/helper/class-use/IndexPair.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/seq/class-use/SmithWaterman3DParameters.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/seq/class-use/SmithWaterman3Daligner.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/seq/class-use/SmithWatermanUserArgumentProcessor.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/seq/class-use/SmithWatermanUserArgumentProcessor.SmithWatermanStartupParams.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/quaternary/class-use/QsRelation.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/quaternary/class-use/QsAlignParameters.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/quaternary/class-use/QsAlignResult.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/quaternary/class-use/QsAlign.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/multiple/class-use/BlockSet.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/multiple/class-use/Block.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/multiple/class-use/MultipleAlignmentEnsemble.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/multiple/class-use/MultipleAlignmentImpl.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/multiple/class-use/MultipleAlignmentEnsembleImpl.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/multiple/class-use/BlockImpl.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/multiple/class-use/BlockSet.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/multiple/class-use/BlockSetImpl.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/multiple/class-use/MultipleAlignment.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/multiple/class-use/ScoresCache.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/multiple/class-use/MultipleAlignmentEnsemble.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/multiple/class-use/BlockImpl.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/multiple/class-use/AbstractScoresCache.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/multiple/class-use/MultipleAlignment.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/multiple/util/class-use/CoreSuperimposer.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/multiple/class-use/BlockSetImpl.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/multiple/util/class-use/MultipleAlignmentTools.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/multiple/util/class-use/MultipleAlignmentScorer.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/multiple/util/class-use/ReferenceSuperimposer.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/multiple/util/class-use/MultipleAlignmentWriter.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/multiple/util/class-use/MultipleAlignmentTools.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/multiple/util/class-use/CoreSuperimposer.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/multiple/util/class-use/MultipleSuperimposer.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/multiple/util/class-use/MultipleAlignmentDisplay.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/multiple/util/class-use/ReferenceSuperimposer.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/multiple/mc/class-use/MultipleMcOptimizer.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/multiple/mc/class-use/MultipleMcParameters.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/multiple/mc/class-use/MultipleMcMain.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/multiple/mc/class-use/MultipleMcOptimizer.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/xml/class-use/AFPChainFlipper.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/xml/class-use/AFPChainXMLConverter.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/xml/class-use/PdbPairsMessage.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/xml/class-use/PdbPairXMLConverter.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/xml/class-use/AFPChainXMLParser.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/xml/class-use/MultipleAlignmentXMLConverter.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/xml/class-use/MultipleAlignmentXMLParser.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/symmetry/axis/class-use/RotationAxisAligner.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/symmetry/axis/class-use/HelixAxisAligner.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/symmetry/axis/class-use/AxisAligner.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/symmetry/geometry/class-use/Octahedron.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/symmetry/geometry/class-use/Tetrahedron.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/symmetry/geometry/class-use/Polyhedron.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/symmetry/geometry/class-use/Prism.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/symmetry/geometry/class-use/RectangularPrism.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/symmetry/geometry/class-use/DistanceBox.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/symmetry/geometry/class-use/Icosahedron.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/symmetry/geometry/class-use/SphereSampler.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/symmetry/geometry/class-use/IcosahedralSampler.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/symmetry/utils/class-use/PermutationGenerator.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/symmetry/utils/class-use/SymmetryTools.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/symmetry/utils/class-use/PowerSet.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/symmetry/utils/class-use/BlastClustReader.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/symmetry/misc/class-use/ChainSignature.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/symmetry/misc/class-use/ProteinComplexSignature.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/symmetry/core/class-use/SystematicSolver.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/symmetry/core/class-use/HelixLayers.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/symmetry/core/class-use/Rotation.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/symmetry/core/class-use/QuatSuperpositionScorer.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/symmetry/core/class-use/RotationSolver.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/symmetry/core/class-use/QuatSymmetryResults.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/symmetry/core/class-use/QuatSymmetryDetector.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/symmetry/core/class-use/RotationGroup.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/symmetry/core/class-use/HelixSolver.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/symmetry/core/class-use/QuatSymmetryScores.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/symmetry/core/class-use/Helix.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/symmetry/core/class-use/QuatSymmetryParameters.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/symmetry/core/class-use/PermutationGroup.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/symmetry/core/class-use/SymmetryPerceptionMethod.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/symmetry/core/class-use/QuatSymmetrySolver.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/symmetry/core/class-use/HelixExtender.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/symmetry/core/class-use/QuatSymmetrySubunits.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/symmetry/core/class-use/HelicalRepeatUnit.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/symmetry/core/class-use/C2RotationSolver.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/symmetry/core/class-use/Stoichiometry.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/symmetry/core/class-use/Stoichiometry.StringOverflowStrategy.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/symmetry/internal/class-use/SequenceFunctionRefiner.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/symmetry/internal/class-use/SymmetryAxes.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/symmetry/internal/class-use/SymmetryAxes.Axis.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/symmetry/internal/class-use/AngleOrderDetectorPlus.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/symmetry/internal/class-use/GraphComponentRefiner.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/symmetry/internal/class-use/CESymmParameters.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/symmetry/internal/class-use/CESymmParameters.SymmetryType.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/symmetry/internal/class-use/CESymmParameters.RefineMethod.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/symmetry/internal/class-use/CESymmParameters.OrderDetectorMethod.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/symmetry/internal/class-use/CeSymmResult.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/symmetry/internal/class-use/GraphComponentOrderDetector.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/symmetry/internal/class-use/OrderDetector.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/symmetry/internal/class-use/SymmOptimizer.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/symmetry/internal/class-use/RefinerFailedException.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/symmetry/internal/class-use/ResidueGroup.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/symmetry/internal/class-use/SequenceFunctionOrderDetector.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/symmetry/internal/class-use/CeSymm.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/symmetry/internal/class-use/SymmetryRefiner.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/symmetry/internal/class-use/CeSymmIterative.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/contact/class-use/GridCell.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/contact/class-use/BoundingBox.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/contact/class-use/GroupContact.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/contact/class-use/Contact.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/contact/class-use/AtomContactSet.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/contact/class-use/StructureInterfaceList.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/contact/class-use/Pair.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/contact/class-use/StructureInterfaceCluster.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/contact/class-use/StructureInterface.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/contact/class-use/AtomContact.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/contact/class-use/Grid.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/contact/class-use/InterfaceFinder.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/contact/class-use/GroupContactSet.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/contact/class-use/AtomIdentifier.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/asa/class-use/GroupAsa.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/asa/class-use/AsaCalculator.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/cath/class-use/CathCategory.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/cath/class-use/CathInstallation.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/cath/class-use/CathSegment.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/cath/class-use/CathDatabase.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/cath/class-use/CathNode.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/cath/class-use/CathFragment.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/cath/class-use/CathDomain.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/cath/class-use/CathFactory.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/quaternary/class-use/CartesianProduct.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/quaternary/class-use/OperatorResolver.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/quaternary/class-use/BioAssemblyInfo.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/quaternary/class-use/BiologicalAssemblyBuilder.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/quaternary/class-use/OrderedPair.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/quaternary/class-use/BiologicalAssemblyTransformation.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/quaternary/class-use/BioAssemblyTools.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/scop/class-use/Astral.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/scop/class-use/Astral.AstralSet.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/scop/class-use/BerkeleyScopInstallation.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/scop/class-use/ScopIOException.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/scop/class-use/ScopDatabase.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/scop/class-use/ScopInstallation.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/scop/class-use/ScopNode.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/scop/class-use/ScopDomain.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/scop/class-use/LocalScopDatabase.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/scop/class-use/ScopDescription.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/scop/class-use/ScopCategory.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/scop/class-use/ScopMirror.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/scop/class-use/ScopFactory.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/xtal/class-use/BravaisLattice.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/xtal/class-use/TransformType.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/xtal/class-use/CrystalBuilder.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/xtal/class-use/SpaceGroup.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/xtal/class-use/SymoplibParser.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/xtal/class-use/CrystalTransform.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/xtal/class-use/CrystalCell.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/xtal/class-use/UnitCellBoundingBox.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/xtal/io/class-use/SpaceGroupMapElements.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/xtal/io/class-use/TreeMapSpaceGroupWrapper.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/xtal/io/class-use/SpaceGroupMapRoot.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/xtal/io/class-use/TransfAlgebraicAdapter.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/chem/class-use/ChemCompTools.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/chem/class-use/AllChemCompProvider.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/chem/class-use/ChemCompProvider.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/chem/class-use/ChemicalComponentDictionary.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/chem/class-use/ChemCompDescriptor.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/chem/class-use/ChemCompBond.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/chem/class-use/ResidueType.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/chem/class-use/PolymerType.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/chem/class-use/ReducedChemCompProvider.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/chem/class-use/ChemCompAtom.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/chem/class-use/DownloadChemCompProvider.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/chem/class-use/MetalBondDistance.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/chem/class-use/ChemCompGroupFactory.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/chem/class-use/ZipChemCompProvider.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/chem/class-use/ChemComp.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/ecod/class-use/EcodDomain.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/ecod/class-use/EcodFactory.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/ecod/class-use/EcodDatabase.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/ecod/class-use/EcodInstallation.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/ecod/class-use/EcodInstallation.EcodParser.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/gui/class-use/MultipleAlignmentCalc.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/gui/class-use/ChooseDirAction.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/gui/class-use/MultipleAlignmentGUI.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/gui/class-use/AlignmentCalculationRunnable.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/gui/class-use/AlignmentCalc.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/gui/class-use/MyTableRowSorter.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/gui/class-use/HelpDialog.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/pairwise/class-use/AligNPE.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/pairwise/class-use/Alignable.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/pairwise/class-use/FragmentJoiner.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/pairwise/class-use/StrCompAlignment.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/pairwise/class-use/FragmentPair.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/pairwise/class-use/AlignmentProgressListener.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/pairwise/class-use/Gotoh.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/pairwise/class-use/AlignmentResult.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/pairwise/class-use/AlternativeAlignment.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/pairwise/class-use/AltAligComparator.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/gui/class-use/StructureViewer.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/gui/class-use/ScaleableMatrixPanel.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/gui/class-use/ScaleableMatrixPanel.GradientRenderer.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/gui/class-use/SelectionImpl.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/gui/class-use/Selection.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/gui/class-use/WrapLayout.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/gui/class-use/SequenceDisplay.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/gui/class-use/JmolViewerImpl.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/gui/class-use/BiojavaJmol.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/gui/class-use/RenderStyle.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/gui/class-use/JMatrixPanel.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/gui/util/class-use/PDBDirPanel.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/gui/util/class-use/PDBServerPanel.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/gui/util/class-use/AlignmentCalc.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/gui/util/class-use/SequenceScalePanel.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/gui/util/class-use/PDBUploadPanel.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/gui/util/class-use/ScopSelectPanel.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/gui/util/class-use/SelectMultiplePanel.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/gui/util/class-use/AlignedPosition.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/gui/util/class-use/SequenceMouseListener.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/gui/util/class-use/CoordManager.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/gui/util/class-use/StructurePairSelector.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/gui/util/class-use/MenuCreator.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/gui/util/class-use/AlternativeAlignmentFrame.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/gui/util/class-use/ScopInstallationInstance.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/gui/util/color/class-use/HSVColorSpace.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/gui/util/color/class-use/ContinuousColorMapper.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/gui/util/color/class-use/ColorInterpolator.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/gui/util/color/class-use/ContinuousColorMapperTransform.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/gui/util/color/class-use/GradientPanel.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/gui/util/color/class-use/SqrtColorMapper.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/gui/util/color/class-use/ColorUtils.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/gui/util/color/class-use/DefaultMatrixMapper.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/gui/util/color/class-use/LinearColorInterpolator.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/gui/util/color/class-use/LinearColorInterpolator.InterpolationDirection.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/gui/util/color/class-use/LogColorMapper.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/gui/util/color/class-use/GradientMapper.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/gui/events/class-use/AlignmentPositionListener.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/gui/events/class-use/JmolAlignedPositionListener.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/symmetry/gui/class-use/SymmetryGui.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/symmetry/gui/class-use/SymmetryCalc.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/symmetry/gui/class-use/SymmetryDisplay.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/symmetry/gui/class-use/SymmetryListener.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/symmetry/jmolScript/class-use/JmolSymmetryScriptGenerator.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/symmetry/jmolScript/class-use/JmolSymmetryScriptGeneratorC1.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/symmetry/jmolScript/class-use/JmolSymmetryScriptGeneratorO.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/symmetry/jmolScript/class-use/ColorConverter.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/symmetry/jmolScript/class-use/JmolSymmetryScriptGeneratorI.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/symmetry/jmolScript/class-use/JmolSymmetryScriptGeneratorDn.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/symmetry/jmolScript/class-use/JmolSymmetryScriptGeneratorT.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/symmetry/jmolScript/class-use/JmolSymmetryScriptGeneratorH.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/symmetry/jmolScript/class-use/JmolSymmetryScriptGeneratorPointGroup.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/symmetry/jmolScript/class-use/JmolSymmetryScriptGeneratorCn.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/gui/class-use/StructureLoaderThread.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/gui/class-use/ShowPDBIDListener.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/gui/class-use/SelectPDBPanel.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/gui/class-use/DisplayAFP.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/gui/class-use/MySaveFileListener.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/gui/class-use/MemoryMonitor.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/gui/class-use/MemoryMonitor.Surface.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/gui/class-use/AboutDialog.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/gui/class-use/MySaveFileListener.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/gui/class-use/MenuCreator.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/gui/class-use/MenuCreator.DotPlotListener.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/gui/class-use/DotPlotPanel.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/gui/class-use/ChooseDirAction.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/gui/class-use/SystemInfo.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/gui/class-use/AlignmentCalc.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/gui/class-use/MyExportListener.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/gui/class-use/AlignmentTextPanel.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/gui/class-use/ParameterGUI.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/gui/class-use/MyOpenPdbFileListener.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/gui/class-use/JPrintPanel.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/gui/class-use/MyAlignmentLoadListener.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/gui/class-use/StructureAlignmentDisplay.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/gui/class-use/MultipleAlignmentJmolDisplay.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/gui/class-use/MyExportListener.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/gui/class-use/MyDistMaxListener.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/gui/class-use/JPrintPanel.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/gui/class-use/ParameterGUI.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/gui/class-use/HelpDialog.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/gui/class-use/DisplayAFP.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/gui/class-use/ShowPDBIDListener.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/gui/class-use/ConfigPDBInstallPanel.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/gui/class-use/MultipleAlignmentGUI.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/gui/class-use/MultipleAlignmentCalc.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/gui/class-use/SelectPDBPanel.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/gui/class-use/MultipleAlignmentJmolDisplay.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/gui/class-use/MyAlignmentLoadListener.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/gui/class-use/MyTableRowSorter.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/gui/class-use/DotPlotPanel.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/gui/class-use/AboutDialog.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/gui/class-use/AlignmentGui.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/gui/class-use/MenuCreator.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/gui/class-use/MenuCreator.DotPlotListener.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/gui/class-use/MyOpenPdbFileListener.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/gui/class-use/AlignmentCalculationRunnable.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/gui/aligpanel/class-use/MultipleAlignmentCoordManager.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/gui/aligpanel/class-use/MultipleAligPanelMouseMotionListener.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/gui/aligpanel/class-use/AligPanel.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/gui/aligpanel/class-use/MultipleAligPanel.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/gui/aligpanel/class-use/AligPanelMouseMotionListener.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/gui/aligpanel/class-use/AFPChainCoordManager.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/gui/aligpanel/class-use/StatusDisplay.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/gui/aligpanel/class-use/AligPanelMouseMotionListener.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/gui/aligpanel/class-use/MultipleStatusDisplay.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/gui/autosuggest/class-use/AutoSuggestProvider.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/gui/aligpanel/class-use/MultipleAligPanel.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/gui/aligpanel/class-use/MultipleAligPanelMouseMotionListener.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/gui/aligpanel/class-use/AFPChainCoordManager.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/gui/autosuggest/class-use/SCOPAutoSuggestProvider.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/gui/autosuggest/class-use/AutoSuggestProvider.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/gui/autosuggest/class-use/JAutoSuggest.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/gui/autosuggest/class-use/DefaultAutoSuggestProvider.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/gui/jmol/class-use/JmolPanel.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/gui/jmol/class-use/JmolPanel.JmolLoggerAdapter.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/gui/jmol/class-use/AtomInfo.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/gui/jmol/class-use/MultipleAlignmentJmol.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/gui/jmol/class-use/RasmolCommandListener.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/gui/jmol/class-use/JmolTools.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/gui/jmol/class-use/AtomInfoParser.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/gui/jmol/class-use/AbstractAlignmentJmol.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/gui/jmol/class-use/MyJmolStatusListener.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/gui/jmol/class-use/StructureAlignmentJmol.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/gui/jmol/class-use/AbstractAlignmentJmol.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/gui/jmol/class-use/RasmolCommandListener.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/gui/jmol/class-use/JmolPanel.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/gui/jmol/class-use/JmolPanel.JmolLoggerAdapter.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/gui/jmol/class-use/AtomInfoParser.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/webstart/class-use/BrowserOpener.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/webstart/class-use/AligUIManager.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/webstart/class-use/WebStartMain.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/webstart/class-use/JNLPProxy.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/webstart/class-use/ConfigXMLHandler.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/webstart/class-use/WebStartMain.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/symmetry/jmolScript/class-use/JmolSymmetryScriptGenerator.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/symmetry/jmolScript/class-use/JmolSymmetryScriptGeneratorDn.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/symmetry/jmolScript/class-use/ColorConverter.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/symmetry/jmolScript/class-use/JmolSymmetryScriptGeneratorCn.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/symmetry/jmolScript/class-use/JmolSymmetryScriptGeneratorI.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/symmetry/jmolScript/class-use/JmolSymmetryScriptGeneratorC1.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/symmetry/jmolScript/class-use/JmolSymmetryScriptGeneratorT.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/symmetry/jmolScript/class-use/JmolSymmetryScriptGeneratorO.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/symmetry/jmolScript/class-use/JmolSymmetryScriptGeneratorH.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/symmetry/jmolScript/class-use/JmolSymmetryScriptGeneratorPointGroup.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/symmetry/gui/class-use/SymmetryGui.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/symmetry/gui/class-use/SymmetryListener.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/symmetry/gui/class-use/SymmetryCalc.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/symmetry/gui/class-use/SymmetryDisplay.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/gui/class-use/JMatrixPanel.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/gui/class-use/JmolViewerImpl.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/gui/class-use/SelectionImpl.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/gui/class-use/BiojavaJmol.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/gui/class-use/WrapLayout.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/gui/class-use/RenderStyle.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/gui/class-use/Selection.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/gui/class-use/ScaleableMatrixPanel.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/gui/class-use/ScaleableMatrixPanel.GradientRenderer.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/gui/class-use/StructureViewer.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/gui/class-use/SequenceDisplay.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/gui/events/class-use/AlignmentPositionListener.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/gui/events/class-use/JmolAlignedPositionListener.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/gui/util/class-use/AlignmentCalc.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/gui/util/class-use/AlignedPosition.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/gui/util/class-use/StructurePairSelector.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/gui/util/class-use/MenuCreator.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/gui/util/class-use/PDBDirPanel.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/gui/util/class-use/ScopInstallationInstance.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/gui/util/class-use/PDBServerPanel.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/gui/util/class-use/SelectMultiplePanel.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/gui/util/class-use/PDBUploadPanel.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/gui/util/class-use/ScopSelectPanel.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/gui/util/class-use/SequenceMouseListener.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/gui/util/class-use/AlternativeAlignmentFrame.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/gui/util/class-use/CoordManager.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/gui/util/class-use/SequenceScalePanel.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/gui/util/color/class-use/LogColorMapper.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/gui/util/color/class-use/ColorInterpolator.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/gui/util/color/class-use/ContinuousColorMapperTransform.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/gui/util/color/class-use/GradientPanel.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/gui/util/color/class-use/LinearColorInterpolator.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/gui/util/color/class-use/LinearColorInterpolator.InterpolationDirection.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/gui/util/color/class-use/ColorUtils.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/gui/util/color/class-use/ContinuousColorMapper.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/gui/util/color/class-use/SqrtColorMapper.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/gui/util/color/class-use/DefaultMatrixMapper.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/gui/util/color/class-use/GradientMapper.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/gui/util/color/class-use/HSVColorSpace.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/genome/homology/class-use/GFF3FromUniprotBlastHits.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/genome/homology/class-use/BlastHomologyHits.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/genome/class-use/App.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/genome/class-use/GeneFeatureHelper.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/genome/io/fastq/class-use/SolexaFastqReader.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/genome/io/fastq/class-use/FastqVariant.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/genome/io/fastq/class-use/FastqWriter.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/genome/io/fastq/class-use/SangerFastqReader.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/genome/io/fastq/class-use/SolexaFastqWriter.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/genome/io/fastq/class-use/FastqTools.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/genome/io/fastq/class-use/SolexaFastqReader.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/genome/io/fastq/class-use/IlluminaFastqReader.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/genome/io/fastq/class-use/StreamListener.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/genome/io/fastq/class-use/ParseListener.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/genome/io/fastq/class-use/IlluminaFastqReader.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/genome/io/fastq/class-use/IlluminaFastqWriter.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/genome/io/fastq/class-use/FastqBuilder.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/genome/io/fastq/class-use/Fastq.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/genome/io/fastq/class-use/SolexaFastqWriter.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/genome/io/fastq/class-use/FastqReader.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/genome/io/fastq/class-use/SangerFastqWriter.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/genome/query/class-use/OutputHitsGFF.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/genome/io/fastq/class-use/StreamListener.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/genome/io/fastq/class-use/Fastq.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/genome/io/fastq/class-use/FastqBuilder.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/genome/io/fastq/class-use/FastqWriter.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/genome/util/class-use/SplitFasta.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/genome/util/class-use/ProteinMappingTools.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/genome/util/class-use/ChromosomeMappingTools.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/genome/query/class-use/BlastXMLQuery.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/genome/query/class-use/OutputHitsGFF.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/genome/homology/class-use/GFF3FromUniprotBlastHits.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/genome/homology/class-use/BlastHomologyHits.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/genome/uniprot/class-use/UniprotToFasta.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/genome/parsers/cytoband/class-use/StainType.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/genome/parsers/cytoband/class-use/CytobandParser.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/genome/parsers/cytoband/class-use/Cytoband.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/genome/parsers/geneid/class-use/GeneIDXMLReader.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/genome/parsers/gff/class-use/LocIterator.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/genome/parsers/twobit/class-use/TwoBitParser.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/genome/parsers/twobit/class-use/TwoBitFacade.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/genome/parsers/gff/class-use/GCStats.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/genome/parsers/gff/class-use/GeneIDGFF2Reader.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/genome/parsers/gff/class-use/Feature.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/genome/parsers/gff/class-use/GeneMarkGTFReader.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/genome/parsers/gff/class-use/FeatureI.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/genome/parsers/gff/class-use/FeatureHelper.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/genome/parsers/gff/class-use/FeatureList.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/genome/parsers/gff/class-use/GFF3Writer.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/genome/parsers/gff/class-use/FeatureI.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/genome/parsers/gff/class-use/GFF3Reader.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/genome/parsers/gff/class-use/FeatureList.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/genome/parsers/gff/class-use/FeatureHelper.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/genome/parsers/gff/class-use/GCStats.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/genome/parsers/gff/class-use/LocIterator.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/genome/parsers/gff/class-use/GeneMarkGTFReader.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/genome/parsers/gff/class-use/Feature.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/genome/parsers/gff/class-use/Location.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/genome/parsers/twobit/class-use/TwoBitFacade.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/genome/parsers/twobit/class-use/TwoBitParser.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/genome/parsers/cytoband/class-use/StainType.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/genome/parsers/cytoband/class-use/Cytoband.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/genome/parsers/cytoband/class-use/CytobandParser.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/genome/parsers/genename/class-use/ChromPos.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/genome/parsers/genename/class-use/GeneChromosomePosition.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/genome/parsers/genename/class-use/GeneNamesParser.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/genome/parsers/genename/class-use/GeneChromosomePositionParser.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/genome/parsers/genename/class-use/ChromPos.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/genome/parsers/genename/class-use/GeneNamesParser.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/genome/parsers/genename/class-use/GeneName.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/genome/util/class-use/ChromosomeMappingTools.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/genome/util/class-use/ProteinMappingTools.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/genome/util/class-use/SplitFasta.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/genome/class-use/App.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/genome/class-use/GeneFeatureHelper.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/phosphosite/class-use/Dataset.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/phosphosite/class-use/Site.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/protmod/structure/class-use/StructureAtomLinkage.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/protmod/structure/class-use/ModifiedCompoundImpl.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/protmod/structure/class-use/StructureUtil.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/protmod/structure/class-use/ModifiedCompound.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/protmod/structure/class-use/StructureAtom.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/protmod/structure/class-use/ProteinModificationIdentifier.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/protmod/structure/class-use/StructureGroup.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/protmod/class-use/ModificationLinkage.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/protmod/class-use/ModificationCondition.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/protmod/class-use/ProteinModificationRegistry.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/protmod/class-use/ProteinModification.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/protmod/class-use/ModificationConditionImpl.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/protmod/class-use/ModificationCategory.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/protmod/class-use/ModificationConditionImpl.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/protmod/class-use/Component.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/protmod/class-use/ProteinModification.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/protmod/class-use/ModificationOccurrenceType.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/protmod/class-use/ModificationLinkage.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/protmod/class-use/ModificationCondition.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/protmod/class-use/ProteinModificationImpl.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/protmod/class-use/ProteinModificationImpl.Builder.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/protmod/class-use/Component.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/protmod/io/class-use/ModifiedCompoundXMLConverter.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/protmod/io/class-use/ProteinModificationXmlReader.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/protmod/io/class-use/StructureAtomXMLConverter.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/protmod/io/class-use/StructureGroupXMLConverter.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/protmod/structure/class-use/StructureGroup.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/protmod/structure/class-use/ModifiedCompound.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/protmod/structure/class-use/StructureAtom.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/protmod/structure/class-use/StructureUtil.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/protmod/structure/class-use/StructureAtomLinkage.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/protmod/structure/class-use/ModifiedCompoundImpl.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/protmod/structure/class-use/ProteinModificationIdentifier.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/protmod/io/class-use/ComponentXMLConverter.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/protmod/io/class-use/StructureGroupXMLConverter.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/protmod/io/class-use/StructureAtomXMLConverter.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/protmod/io/class-use/ProteinModificationXmlReader.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/protmod/io/class-use/ModifiedCompoundXMLConverter.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/phosphosite/class-use/Site.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/phosphosite/class-use/Dataset.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/ws/hmmer/class-use/RemoteHmmerScan.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/ws/hmmer/class-use/HmmerResult.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/ws/hmmer/class-use/HmmerDomain.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/ws/hmmer/class-use/HmmerScan.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/ws/hmmer/class-use/HmmerDomain.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/ws/hmmer/class-use/HmmerResult.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/ws/alignment/class-use/RemotePairwiseAlignmentProperties.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/ws/alignment/class-use/RemotePairwiseAlignmentService.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/ws/alignment/class-use/RemotePairwiseAlignmentOutputProperties.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/ws/alignment/qblast/class-use/NCBIQBlastAlignmentProperties.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/ws/alignment/qblast/class-use/BlastAlignmentParameterEnum.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/ws/alignment/qblast/class-use/BlastJob.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/ws/alignment/qblast/class-use/BlastMatrixEnum.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/ws/alignment/qblast/class-use/MapToStringTransformer.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/ws/alignment/qblast/class-use/NCBIQBlastService.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/ws/alignment/qblast/class-use/BlastProgramEnum.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/ws/alignment/qblast/class-use/NCBIQBlastOutputProperties.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/ws/alignment/qblast/class-use/NCBIQBlastAlignmentProperties.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/ws/alignment/qblast/class-use/BlastOutputFormatEnum.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/ws/alignment/qblast/class-use/BlastOutputAlignmentFormatEnum.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/ws/alignment/qblast/class-use/NCBIQBlastService.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/ws/alignment/qblast/class-use/BlastMatrixEnum.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/ws/alignment/qblast/class-use/NCBIQBlastOutputProperties.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/ws/alignment/qblast/class-use/BlastOutputParameterEnum.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/ws/alignment/qblast/class-use/BlastJob.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/ws/alignment/qblast/class-use/BlastAlignmentParameterEnum.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/ws/alignment/qblast/class-use/BlastOutputFormatEnum.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/ronn/class-use/ModelLoader.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/ronn/class-use/ModelLoader.Model.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/ronn/class-use/ModelLoader.Threshold.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/ronn/class-use/ORonn.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/data/sequence/class-use/SequenceUtil.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/data/sequence/class-use/FastaSequence.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/ronn/class-use/Jronn.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/ronn/class-use/Jronn.Range.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/ronn/class-use/NullOutputStream.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/ronn/class-use/RonnConstraint.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/ronn/class-use/RonnConstraint.Threshold.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/ronn/class-use/ORonnModel.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/ronn/class-use/ORonn.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/ronn/class-use/Timer.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/ronn/class-use/NullOutputStream.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/data/sequence/class-use/FastaSequence.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/data/sequence/class-use/SequenceUtil.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/ronn/class-use/ORonnModel.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/ronn/class-use/ModelLoader.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/ronn/class-use/ModelLoader.Model.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/ronn/class-use/ModelLoader.Threshold.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/aaproperties/class-use/AminoAcidProperties.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/aaproperties/class-use/PeptideProperties.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/aaproperties/class-use/PeptideProperties.SingleLetterAACode.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/aaproperties/class-use/Constraints.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/aaproperties/class-use/IPeptideProperties.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/aaproperties/class-use/PeptidePropertiesImpl.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/aaproperties/class-use/Utils.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/aaproperties/class-use/IPeptideProperties.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/aaproperties/class-use/CommandPrompt.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/aaproperties/class-use/CommandPrompt.PropertyName.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/aaproperties/xml/class-use/AminoAcidCompositionTable.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/aaproperties/xml/class-use/Name2Count.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/aaproperties/xml/class-use/SchemaGenerator.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/aaproperties/xml/class-use/ElementTable.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/aaproperties/xml/class-use/CaseFreeAminoAcidCompoundSet.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/aaproperties/class-use/PeptideProperties.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/aaproperties/class-use/PeptideProperties.SingleLetterAACode.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/aaproperties/class-use/PeptidePropertiesImpl.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/aaproperties/class-use/Constraints.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/aaproperties/xml/class-use/ModifiedAminoAcidCompoundSet.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/aaproperties/xml/class-use/Isotope.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/aaproperties/xml/class-use/AminoAcidComposition.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/aaproperties/xml/class-use/ElementTable.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/aaproperties/xml/class-use/AminoAcidCompositionTable.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/aaproperties/xml/class-use/Name2Count.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/aaproperties/xml/class-use/Element.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/aaproperties/xml/class-use/AminoAcidComposition.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/aaproperties/xml/class-use/MyValidationEventHandler.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/aaproperties/xml/class-use/CaseFreeAminoAcidCompoundSet.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/aaproperties/xml/class-use/SchemaGenerator.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/aaproperties/profeat/convertor/class-use/Convert2Hydrophobicity.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/aaproperties/profeat/convertor/class-use/Convert2Polarizability.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/aaproperties/profeat/convertor/class-use/Convert2SolventAccessibility.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/aaproperties/profeat/convertor/class-use/Convertor.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/aaproperties/profeat/convertor/class-use/Convert2Polarity.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/aaproperties/profeat/convertor/class-use/Convert2Charge.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/aaproperties/profeat/convertor/class-use/Convert2NormalizedVanDerWaalsVolume.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/aaproperties/profeat/convertor/class-use/Convert2SecondaryStructure.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/aaproperties/profeat/class-use/IProfeatProperties.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/aaproperties/profeat/class-use/IProfeatProperties.DISTRIBUTION.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/aaproperties/profeat/class-use/IProfeatProperties.TRANSITION.html...
@@ -11671,515 +11715,507 @@
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/aaproperties/profeat/class-use/IProfeatProperties.ATTRIBUTE.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/aaproperties/profeat/class-use/ProfeatProperties.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/aaproperties/profeat/class-use/ProfeatPropertiesImpl.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/aaproperties/profeat/convertor/class-use/Convert2Polarity.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/aaproperties/profeat/convertor/class-use/Convertor.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/aaproperties/profeat/convertor/class-use/Convert2SolventAccessibility.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/aaproperties/profeat/convertor/class-use/Convert2SecondaryStructure.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/aaproperties/profeat/convertor/class-use/Convert2NormalizedVanDerWaalsVolume.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/aaproperties/profeat/convertor/class-use/Convert2Polarizability.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/aaproperties/profeat/convertor/class-use/Convert2Hydrophobicity.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/aaproperties/profeat/convertor/class-use/Convert2Charge.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/survival/data/class-use/CompactCharSequence.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/survival/data/class-use/ChangeValue.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/survival/data/class-use/WorkSheet.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/survival/data/class-use/HeaderInfo.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/survival/cox/class-use/CoxVariables.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/survival/cox/class-use/CoxMart.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/survival/cox/class-use/CoxCoefficient.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/survival/cox/class-use/SurvivalInfoIndex.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/survival/cox/class-use/RiskInfo.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/survival/cox/class-use/CoxCC.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/survival/cox/class-use/WaldTestInfo.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/survival/cox/class-use/CoxR.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/survival/cox/class-use/CoxMethod.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/survival/cox/class-use/WaldTest.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/survival/cox/class-use/CoxHelper.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/survival/cox/class-use/CoxScore.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/survival/cox/class-use/WaldTestInfo.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/survival/cox/class-use/SurvivalInfoHelper.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/survival/cox/class-use/SurvFitInfo.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/survival/cox/class-use/CoxScore.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/survival/cox/class-use/CoxMart.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/survival/cox/class-use/CoxHelper.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/survival/cox/class-use/ResidualsCoxph.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/survival/cox/class-use/ResidualsCoxph.Type.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/survival/cox/class-use/CoxInfo.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/survival/cox/class-use/CoxR.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/survival/cox/class-use/StrataInfo.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/survival/cox/class-use/SurvFitInfo.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/survival/cox/class-use/CoxVariables.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/survival/cox/class-use/CoxCC.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/survival/cox/class-use/RiskInfo.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/survival/cox/class-use/SurvivalInfoIndex.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/survival/cox/class-use/CoxCoefficient.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/survival/cox/class-use/SurvivalInfo.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/survival/cox/stats/class-use/Cholesky2.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/survival/cox/stats/class-use/AgScore.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/survival/cox/class-use/WaldTest.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/survival/cox/class-use/StrataInfo.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/survival/cox/class-use/CoxInfo.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/survival/cox/stats/class-use/Chsolve2.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/survival/cox/stats/class-use/Cholesky2.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/survival/cox/stats/class-use/ChiSq.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/survival/cox/matrix/class-use/StdArrayIO.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/survival/cox/stats/class-use/AgScore.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/survival/cox/matrix/class-use/Matrix.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/survival/cox/comparators/class-use/CoxVariablesVariableComparator.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/survival/cox/comparators/class-use/SurvivalInfoComparator.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/survival/cox/comparators/class-use/CoxVariablesOverallModelFitComparator.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/survival/cox/matrix/class-use/StdArrayIO.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/survival/cox/comparators/class-use/MeanModelComparator.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/survival/cox/comparators/class-use/SurvivalInfoValueComparator.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/survival/cox/comparators/class-use/CoxComparatorInterface.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/survival/kaplanmeier/metadata/class-use/DiscreteQuantizerInterface.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/survival/kaplanmeier/metadata/class-use/MeanQuantizer.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/survival/kaplanmeier/metadata/class-use/MetaDataInfo.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/survival/kaplanmeier/metadata/class-use/ClinicalMetaDataOutcome.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/survival/kaplanmeier/figure/class-use/GroupResults.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/survival/kaplanmeier/figure/class-use/KMFigureInfo.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/survival/cox/comparators/class-use/SurvivalInfoComparator.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/survival/cox/comparators/class-use/CoxVariablesOverallModelFitComparator.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/survival/cox/comparators/class-use/CoxVariablesVariableComparator.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/survival/data/class-use/CompactCharSequence.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/survival/data/class-use/ChangeValue.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/survival/data/class-use/WorkSheet.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/survival/data/class-use/HeaderInfo.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/survival/kaplanmeier/figure/class-use/ExpressionFigure.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/survival/kaplanmeier/figure/class-use/CensorStatus.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/survival/kaplanmeier/figure/class-use/CensorStatusSelect.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/survival/kaplanmeier/figure/class-use/KMFigureInfo.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/survival/kaplanmeier/figure/class-use/KaplanMeierFigure.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/survival/kaplanmeier/figure/class-use/GroupResults.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/survival/kaplanmeier/figure/class-use/NumbersAtRiskPanel.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/survival/kaplanmeier/figure/class-use/CensorStatusSelect.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/survival/kaplanmeier/figure/class-use/SurvFitKM.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/survival/kaplanmeier/figure/class-use/SurvFitKM.ConfLower.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/survival/kaplanmeier/figure/class-use/SurvFitKM.ConfType.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/survival/kaplanmeier/figure/class-use/SurvFitKM.Error.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/survival/kaplanmeier/figure/class-use/SurvFitKM.Method.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/survival/kaplanmeier/figure/class-use/CensorStatus.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/ontology/class-use/Variable.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/ontology/class-use/Variable.Impl.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/ontology/class-use/Synonym.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/ontology/class-use/AlreadyExistsException.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/ontology/class-use/Ontology.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/ontology/class-use/Ontology.Impl.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/ontology/class-use/OntologyOps.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/survival/kaplanmeier/metadata/class-use/MeanQuantizer.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/survival/kaplanmeier/metadata/class-use/DiscreteQuantizerInterface.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/survival/kaplanmeier/metadata/class-use/MetaDataInfo.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/survival/kaplanmeier/metadata/class-use/ClinicalMetaDataOutcome.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/ontology/class-use/OntologyTerm.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/ontology/class-use/OntologyTerm.Impl.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/ontology/class-use/AbstractTerm.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/ontology/class-use/InvalidTermException.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/ontology/class-use/Variable.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/ontology/class-use/Variable.Impl.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/ontology/class-use/RemoteTerm.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/ontology/class-use/RemoteTerm.Impl.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/ontology/class-use/OntoTools.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/ontology/class-use/App.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/ontology/class-use/IntegerOntology.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/ontology/class-use/IntegerOntology.IntTerm.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/ontology/class-use/OntologyOps.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/ontology/class-use/DefaultOps.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/ontology/class-use/Term.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/ontology/class-use/Term.Impl.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/ontology/class-use/OntoTools.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/ontology/class-use/OntologyFactory.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/ontology/class-use/DefaultOps.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/ontology/class-use/RemoteTerm.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/ontology/class-use/RemoteTerm.Impl.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/ontology/class-use/Triple.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/ontology/class-use/Triple.Impl.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/ontology/class-use/AbstractTerm.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/ontology/class-use/OntologyFactory.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/ontology/class-use/Synonym.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/ontology/class-use/AlreadyExistsException.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/ontology/class-use/OntologyException.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/ontology/io/class-use/OboParser.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/ontology/class-use/InvalidTermException.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/ontology/class-use/IntegerOntology.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/ontology/class-use/IntegerOntology.IntTerm.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/ontology/class-use/Ontology.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/ontology/class-use/Ontology.Impl.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/ontology/io/class-use/GOParser.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/ontology/io/class-use/TabDelimParser.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/ontology/utils/class-use/AbstractAnnotation.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/ontology/utils/class-use/AssertionFailure.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/ontology/io/class-use/OboParser.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/ontology/utils/class-use/Annotation.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/ontology/utils/class-use/StaticMemberPlaceHolder.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/ontology/utils/class-use/Annotatable.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/ontology/utils/class-use/WeakValueHashMap.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/ontology/utils/class-use/AssertionFailure.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/ontology/utils/class-use/SmallMap.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/ontology/utils/class-use/Annotation.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/ontology/utils/class-use/KeyedWeakReference.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/ontology/utils/class-use/SmallAnnotation.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/ontology/utils/class-use/KeyedWeakReference.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/ontology/utils/class-use/Annotatable.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/ontology/utils/class-use/AbstractAnnotation.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/ontology/obo/class-use/OboFileEventListener.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/ontology/obo/class-use/OboFileParser.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/ontology/obo/class-use/OboFileParser.SOPair.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/ontology/obo/class-use/OboFileHandler.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/proteincomparisontool/class-use/HelloWorld.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/surfacing/class-use/DomainParsimonyCalculator.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/surfacing/class-use/BasicDomainSimilarityCalculator.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/surfacing/class-use/CombinationsBasedPairwiseDomainSimilarityCalculator.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/surfacing/class-use/PairwiseDomainSimilarityCalculator.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/surfacing/class-use/ProteinCountsBasedPairwiseDomainSimilarityCalculator.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/surfacing/class-use/SurfacingConstants.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/surfacing/class-use/DomainSimilarityCalculator.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/surfacing/class-use/DomainSimilarityCalculator.GoAnnotationOutput.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/surfacing/class-use/DomainSimilarityCalculator.Detailedness.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/surfacing/class-use/PairwiseGenomeComparator.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/surfacing/class-use/DomainSimilarity.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/surfacing/class-use/DomainSimilarity.PRINT_OPTION.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/surfacing/class-use/DomainSimilarity.DomainSimilaritySortField.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/surfacing/class-use/DomainSimilarity.DomainSimilarityScoring.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/surfacing/class-use/DirectedCombinableDomains.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/surfacing/class-use/CombinationsBasedPairwiseDomainSimilarity.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/surfacing/class-use/SimpleDomain.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/surfacing/class-use/DomainLengths.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/surfacing/class-use/DomainArchitectureBasedGenomeSimilarityCalculator.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/surfacing/class-use/BasicCombinableDomains.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/surfacing/class-use/BasicBinaryDomainCombination.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/surfacing/class-use/AdjactantDirectedCombinableDomains.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/surfacing/class-use/AdjactantDirectedBinaryDomainCombination.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/surfacing/class-use/SurfacingUtil.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/surfacing/class-use/DomainCountsBasedPairwiseSimilarityCalculator.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/surfacing/class-use/DomainCountsDifferenceUtil.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/surfacing/class-use/DomainCountsDifferenceUtil.COPY_CALCULATION_MODE.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/surfacing/class-use/PairwiseDomainSimilarity.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/surfacing/class-use/CountsBasedPairwiseDomainSimilarity.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/surfacing/class-use/DomainLengthsTable.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/surfacing/class-use/TestSurfacing.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/surfacing/class-use/DirectedBinaryDomainCombination.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/surfacing/class-use/BasicGenomeWideCombinableDomains.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/surfacing/class-use/MappingResults.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/surfacing/class-use/CombinableDomains.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/surfacing/class-use/GenomeWideCombinableDomains.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/surfacing/class-use/GenomeWideCombinableDomains.GenomeWideCombinableDomainsSortOrder.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/tools/class-use/SupportCount.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/tools/class-use/PhylogenyDecorator.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/tools/class-use/PhylogenyDecorator.FIELD.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/tools/class-use/ConfidenceAssessor.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/tools/class-use/TreeSplitMatrix.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/pccx/class-use/Coverage.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/pccx/class-use/BranchCountingBasedScoringMethod.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/pccx/class-use/BranchLengthBasedScoringMethod.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/pccx/class-use/ScoringMethodForExternalNode.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/pccx/class-use/CoverageExtender.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/pccx/class-use/ModelingUtils.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/pccx/class-use/BasicExternalNodeBasedCoverageExtender.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/pccx/class-use/CoverageCalculator.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/pccx/class-use/CoverageCalculationOptions.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/pccx/class-use/ExternalNodeBasedCoverageMethodOptions.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/pccx/class-use/ExternalNodeBasedCoverageMethod.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/pccx/class-use/ExternalNodeBasedCoverage.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/pccx/class-use/LogBranchLengthBasedScoringMethod.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/pccx/class-use/CoverageCalculationMethod.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/pccx/class-use/TestPccx.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/sequence/class-use/BasicSequence.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/sequence/class-use/MolecularSequence.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/sequence/class-use/MolecularSequence.TYPE.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/analysis/class-use/TaxonomyDataManager.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/analysis/class-use/AncestralTaxonomyInferenceException.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/analysis/class-use/AncestralTaxonomyInference.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/go/class-use/GoXRef.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/go/class-use/GoXRef.Type.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/go/class-use/BasicGoRelationship.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/go/class-use/GoTerm.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/go/class-use/GoId.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/go/class-use/GoRelationship.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/go/class-use/GoRelationship.Type.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/go/class-use/PfamToGoParser.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/go/class-use/PfamToGoMapping.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/go/class-use/Mapping.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/go/class-use/GoNameSpace.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/go/class-use/GoNameSpace.GoNamespaceType.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/go/class-use/GoUtils.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/go/class-use/TestGo.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/go/class-use/OBOparser.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/go/class-use/OBOparser.ReturnType.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/go/class-use/BasicGoXRef.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/go/class-use/BasicGoTerm.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/go/class-use/BasicGoSubset.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/go/class-use/GoSubset.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/go/class-use/GoSubset.Type.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/go/etc/class-use/MetaOntologizer.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/go/etc/class-use/OntologizerResult.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/go/etc/class-use/OntologizerResult.TYPE.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/archaeopteryx/class-use/TreeFontSet.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/archaeopteryx/class-use/ArchaeopteryxE.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/archaeopteryx/class-use/TreePanel.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/archaeopteryx/class-use/MainFrameApplet.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/archaeopteryx/class-use/TreePanelUtil.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/archaeopteryx/class-use/MainPanel.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/archaeopteryx/class-use/TreeColorSet.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/archaeopteryx/class-use/ArchaeopteryxA.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/archaeopteryx/class-use/AptxUtil.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/archaeopteryx/class-use/AptxUtil.GraphicsExportType.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/archaeopteryx/class-use/UrlTreeReader.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/archaeopteryx/class-use/Configuration.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/archaeopteryx/class-use/Configuration.UI.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/archaeopteryx/class-use/Configuration.EXT_NODE_DATA_RETURN_ON.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/archaeopteryx/class-use/FontChooser.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/archaeopteryx/class-use/MainFrameApplication.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/archaeopteryx/class-use/Options.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/archaeopteryx/class-use/Options.PHYLOGENY_GRAPHICS_TYPE.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/archaeopteryx/class-use/Options.NODE_LABEL_DIRECTION.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/archaeopteryx/class-use/Options.CLADOGRAM_TYPE.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/archaeopteryx/class-use/Archaeopteryx.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/archaeopteryx/class-use/Constants.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/archaeopteryx/class-use/Configuration.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/archaeopteryx/class-use/Configuration.UI.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/archaeopteryx/class-use/Configuration.EXT_NODE_DATA_RETURN_ON.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/archaeopteryx/class-use/MainFrame.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/archaeopteryx/class-use/ArchaeopteryxE.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/archaeopteryx/class-use/TreeFontSet.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/archaeopteryx/tools/class-use/PhylogeneticInferrer.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/archaeopteryx/tools/class-use/PhylogeneticInferrer.MSA_PRG.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/archaeopteryx/tools/class-use/AncestralTaxonomyInferrer.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/archaeopteryx/class-use/Constants.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/archaeopteryx/class-use/UrlTreeReader.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/archaeopteryx/class-use/TreePanelUtil.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/archaeopteryx/class-use/Archaeopteryx.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/archaeopteryx/class-use/AptxUtil.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/archaeopteryx/class-use/AptxUtil.GraphicsExportType.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/archaeopteryx/class-use/MainFrameApplet.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/archaeopteryx/class-use/MainPanel.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/archaeopteryx/phylogeny/data/class-use/RenderableVector.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/archaeopteryx/phylogeny/data/class-use/RenderableDomainArchitecture.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/archaeopteryx/phylogeny/data/class-use/RenderableMsaSequence.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/archaeopteryx/phylogeny/data/class-use/RenderablePhylogenyData.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/archaeopteryx/tools/class-use/RunnableProcess.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/archaeopteryx/tools/class-use/ProcessPool.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/archaeopteryx/tools/class-use/ImageLoader.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/archaeopteryx/tools/class-use/ProcessRunning.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/archaeopteryx/tools/class-use/PhyloInferenceDialog.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/archaeopteryx/tools/class-use/ProcessPool.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/archaeopteryx/tools/class-use/InferenceManager.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/archaeopteryx/tools/class-use/PhyloInferenceDialog.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/archaeopteryx/tools/class-use/Blast.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/archaeopteryx/tools/class-use/PhylogeneticInferrer.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/archaeopteryx/tools/class-use/PhylogeneticInferrer.MSA_PRG.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/archaeopteryx/tools/class-use/SequenceDataRetriver.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/archaeopteryx/tools/class-use/AncestralTaxonomyInferrer.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/archaeopteryx/tools/class-use/PhylogeneticInferenceOptions.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/archaeopteryx/tools/class-use/Blast.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/archaeopteryx/webservices/class-use/WebserviceUtil.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/archaeopteryx/webservices/class-use/PhylogeniesWebserviceClient.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/archaeopteryx/webservices/class-use/BasicPhylogeniesWebserviceClient.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/archaeopteryx/webservices/class-use/WebservicesManager.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/archaeopteryx/webservices/class-use/WebservicesManager.WsPhylogenyFormat.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/archaeopteryx/webservices/class-use/PhylogeniesWebserviceClient.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/archaeopteryx/phylogeny/data/class-use/RenderableDomainArchitecture.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/archaeopteryx/phylogeny/data/class-use/RenderableMsaSequence.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/archaeopteryx/phylogeny/data/class-use/RenderablePhylogenyData.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/archaeopteryx/phylogeny/data/class-use/RenderableVector.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/protein/class-use/Protein.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/protein/class-use/ProteinId.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/protein/class-use/BasicDomain.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/protein/class-use/BinaryDomainCombination.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/protein/class-use/BinaryDomainCombination.OutputFormat.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/protein/class-use/BinaryDomainCombination.DomainCombinationType.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/protein/class-use/Domain.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/protein/class-use/BasicProtein.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/io/parsers/tol/class-use/TolParser.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/io/parsers/tol/class-use/TolXmlMapping.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/io/parsers/tol/class-use/TolXmlHandler.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/archaeopteryx/webservices/class-use/WebserviceUtil.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/evoinference/distance/class-use/NeighborJoining.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/evoinference/distance/class-use/Sset.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/evoinference/distance/class-use/NeighborJoiningR.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/evoinference/distance/class-use/PairwiseDistanceCalculator.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/evoinference/distance/class-use/PairwiseDistanceCalculator.PWD_DISTANCE_METHOD.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/evoinference/distance/class-use/Sarray.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/evoinference/distance/class-use/NeighborJoiningF.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/evoinference/parsimony/class-use/FitchParsimony.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/evoinference/parsimony/class-use/DolloParsimony.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/evoinference/parsimony/class-use/SankoffParsimony.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/evoinference/tools/class-use/BootstrapResampler.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/evoinference/matrix/distance/class-use/DistanceMatrix.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/evoinference/matrix/distance/class-use/DistanceMatrix.Format.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/evoinference/matrix/distance/class-use/BasicSymmetricalDistanceMatrix.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/evoinference/matrix/character/class-use/BasicCharacterStateMatrix.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/evoinference/matrix/character/class-use/CharacterStateMatrix.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/evoinference/matrix/character/class-use/CharacterStateMatrix.NucleotideStates.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/evoinference/matrix/character/class-use/CharacterStateMatrix.GainLossStates.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/evoinference/matrix/character/class-use/CharacterStateMatrix.Format.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/evoinference/matrix/character/class-use/CharacterStateMatrix.BinaryStates.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/evoinference/class-use/TestPhylogenyReconstruction.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/phylogeny/factories/class-use/ParserBasedPhylogenyFactory.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/phylogeny/factories/class-use/PhylogenyFactory.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/phylogeny/class-use/PhylogenyNode.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/phylogeny/class-use/PhylogenyNode.NH_CONVERSION_SUPPORT_VALUE_STYLE.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/phylogeny/class-use/Phylogeny.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/phylogeny/class-use/PhylogenyBranch.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/phylogeny/class-use/PhylogenyMethods.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/phylogeny/class-use/PhylogenyMethods.PhylogenyNodeField.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/phylogeny/class-use/PhylogenyMethods.DESCENDANT_SORT_PRIORITY.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/phylogeny/data/class-use/Point.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/phylogeny/data/class-use/Confidence.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/phylogeny/data/class-use/Annotation.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/phylogeny/data/class-use/DomainArchitecture.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/phylogeny/data/class-use/MultipleUris.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/phylogeny/data/class-use/SequenceRelation.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/phylogeny/data/class-use/SequenceRelation.SEQUENCE_RELATION_TYPE.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/phylogeny/data/class-use/PhylogenyData.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/phylogeny/data/class-use/Sequence.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/phylogeny/data/class-use/Taxonomy.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/phylogeny/data/class-use/Distribution.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/phylogeny/data/class-use/PhylogenyDataUtil.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/phylogeny/data/class-use/ProteinDomain.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/phylogeny/data/class-use/Identifier.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/phylogeny/data/class-use/Event.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/phylogeny/data/class-use/Event.EventType.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/phylogeny/data/class-use/Date.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/phylogeny/data/class-use/Uri.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/phylogeny/data/class-use/Accession.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/phylogeny/data/class-use/Accession.Source.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/phylogeny/data/class-use/NodeVisualData.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/phylogeny/data/class-use/NodeVisualData.NodeShape.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/phylogeny/data/class-use/NodeVisualData.NodeFill.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/phylogeny/data/class-use/NodeVisualData.FontType.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/phylogeny/data/class-use/Reference.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/phylogeny/data/class-use/BranchColor.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/phylogeny/data/class-use/PropertiesMap.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/phylogeny/data/class-use/BranchData.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/phylogeny/data/class-use/Property.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/phylogeny/data/class-use/Property.AppliesTo.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/phylogeny/data/class-use/BranchWidth.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/phylogeny/data/class-use/Polygon.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/phylogeny/data/class-use/BinaryCharacters.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/phylogeny/data/class-use/NodeDataField.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/phylogeny/data/class-use/NodeData.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/phylogeny/iterators/class-use/LevelOrderTreeIterator.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/phylogeny/iterators/class-use/PostorderTreeIterator.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/phylogeny/iterators/class-use/PhylogenyNodeIterator.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/phylogeny/iterators/class-use/PostOrderStackObject.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/phylogeny/iterators/class-use/PreorderTreeIterator.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/phylogeny/iterators/class-use/ExternalForwardIterator.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/test/class-use/Test.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/test/examples/class-use/Example3.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/test/examples/class-use/Example1.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/test/examples/class-use/Example2.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/test/examples/class-use/Example5.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/test/examples/class-use/Example4.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/tools/class-use/TreeSplitMatrix.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/tools/class-use/SupportCount.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/tools/class-use/ConfidenceAssessor.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/tools/class-use/PhylogenyDecorator.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/tools/class-use/PhylogenyDecorator.FIELD.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/io/writers/class-use/PhyloXmlNodeWriter.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/io/writers/class-use/PhylogenyWriter.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/io/writers/class-use/PhylogenyWriter.FORMAT.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/io/writers/class-use/SequenceWriter.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/io/writers/class-use/SequenceWriter.SEQ_FORMAT.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/io/parsers/nexus/class-use/NexusPhylogeniesParser.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/io/parsers/nexus/class-use/NexusBinaryStatesMatrixParser.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/io/parsers/nexus/class-use/NexusCharactersParser.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/io/parsers/nexus/class-use/PaupLogParser.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/io/parsers/nexus/class-use/NexusFormatException.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/io/parsers/nexus/class-use/NexusConstants.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/io/parsers/class-use/IteratingPhylogenyParser.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/io/parsers/class-use/GeneralMsaParser.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/io/parsers/class-use/SymmetricalDistanceMatrixParser.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/io/parsers/class-use/SymmetricalDistanceMatrixParser.InputMatrixType.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/io/parsers/class-use/HmmPfamOutputParser.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/io/parsers/class-use/HmmPfamOutputParser.ReturnType.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/io/parsers/class-use/HmmPfamOutputParser.FilterType.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/io/parsers/class-use/PhylogenyParser.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/io/parsers/class-use/HmmscanPerDomainTableParser.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/io/parsers/class-use/HmmscanPerDomainTableParser.ReturnType.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/io/parsers/class-use/HmmscanPerDomainTableParser.INDIVIDUAL_SCORE_CUTOFF.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/io/parsers/class-use/HmmscanPerDomainTableParser.FilterType.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/io/parsers/class-use/HmmPfamOutputParser.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/io/parsers/class-use/HmmPfamOutputParser.ReturnType.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/io/parsers/class-use/HmmPfamOutputParser.FilterType.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/io/parsers/class-use/FastaParser.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/io/parsers/class-use/PhylogenyParser.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/io/parsers/class-use/GeneralMsaParser.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/io/parsers/util/class-use/PhylogenyParserException.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/io/parsers/util/class-use/ParserUtils.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/io/parsers/util/class-use/PhylogenyParserException.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/io/parsers/phyloxml/class-use/PhyloXmlUtil.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/io/parsers/phyloxml/class-use/PhyloXmlMapping.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/io/parsers/phyloxml/class-use/PhyloXmlException.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/io/parsers/phyloxml/class-use/PhyloXmlParser.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/io/parsers/phyloxml/class-use/PhyloXmlMapping.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/io/parsers/phyloxml/class-use/XmlElement.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/io/parsers/phyloxml/class-use/PhyloXmlParser.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/io/parsers/phyloxml/class-use/PhyloXmlDataFormatException.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/io/parsers/phyloxml/class-use/PhyloXmlHandler.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/io/parsers/phyloxml/data/class-use/AnnotationParser.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/io/parsers/phyloxml/data/class-use/UriParser.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/io/parsers/phyloxml/data/class-use/DistributionParser.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/io/parsers/phyloxml/data/class-use/PointParser.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/io/parsers/phyloxml/data/class-use/EventParser.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/io/parsers/phyloxml/data/class-use/SequenceRelationParser.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/io/parsers/phyloxml/data/class-use/DistributionParser.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/io/parsers/phyloxml/data/class-use/TaxonomyParser.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/io/parsers/phyloxml/data/class-use/ColorParser.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/io/parsers/phyloxml/data/class-use/DomainArchitectureParser.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/io/parsers/phyloxml/data/class-use/BranchWidthParser.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/io/parsers/phyloxml/data/class-use/DateParser.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/io/parsers/phyloxml/data/class-use/SequenceParser.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/io/parsers/phyloxml/data/class-use/DomainArchitectureParser.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/io/parsers/phyloxml/data/class-use/AccessionParser.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/io/parsers/phyloxml/data/class-use/ColorParser.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/io/parsers/phyloxml/data/class-use/UriParser.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/io/parsers/phyloxml/data/class-use/ProteinDomainParser.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/io/parsers/phyloxml/data/class-use/PolygonParser.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/io/parsers/phyloxml/data/class-use/AnnotationParser.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/io/parsers/phyloxml/data/class-use/BinaryCharactersParser.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/io/parsers/phyloxml/data/class-use/ConfidenceParser.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/io/parsers/phyloxml/data/class-use/PhylogenyDataPhyloXmlParser.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/io/parsers/phyloxml/data/class-use/IdentifierParser.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/io/parsers/phyloxml/data/class-use/ReferenceParser.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/io/parsers/phyloxml/data/class-use/ConfidenceParser.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/io/parsers/phyloxml/data/class-use/PropertyParser.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/io/parsers/phyloxml/data/class-use/SequenceRelationParser.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/io/parsers/nexus/class-use/NexusCharactersParser.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/io/parsers/nexus/class-use/NexusPhylogeniesParser.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/io/parsers/nexus/class-use/PaupLogParser.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/io/parsers/nexus/class-use/NexusFormatException.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/io/parsers/nexus/class-use/NexusBinaryStatesMatrixParser.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/io/parsers/nexus/class-use/NexusConstants.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/io/parsers/phyloxml/data/class-use/PolygonParser.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/io/parsers/phyloxml/data/class-use/DateParser.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/io/parsers/phyloxml/data/class-use/PointParser.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/io/parsers/phyloxml/data/class-use/AccessionParser.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/io/parsers/phyloxml/data/class-use/ReferenceParser.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/io/parsers/nhx/class-use/NHXParser.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/io/parsers/nhx/class-use/NHXParser.TAXONOMY_EXTRACTION.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/io/parsers/nhx/class-use/NHXtags.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/io/parsers/nhx/class-use/NHXFormatException.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/io/writers/class-use/PhylogenyWriter.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/io/writers/class-use/PhylogenyWriter.FORMAT.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/io/writers/class-use/PhyloXmlNodeWriter.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/io/writers/class-use/SequenceWriter.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/io/writers/class-use/SequenceWriter.SEQ_FORMAT.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/test/class-use/Test.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/test/examples/class-use/Example4.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/test/examples/class-use/Example1.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/test/examples/class-use/Example3.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/test/examples/class-use/Example2.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/test/examples/class-use/Example5.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/evoinference/tools/class-use/BootstrapResampler.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/evoinference/parsimony/class-use/DolloParsimony.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/evoinference/parsimony/class-use/SankoffParsimony.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/evoinference/parsimony/class-use/FitchParsimony.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/evoinference/distance/class-use/NeighborJoiningR.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/evoinference/distance/class-use/NeighborJoiningF.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/evoinference/distance/class-use/NeighborJoining.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/evoinference/distance/class-use/Sset.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/evoinference/distance/class-use/PairwiseDistanceCalculator.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/evoinference/distance/class-use/PairwiseDistanceCalculator.PWD_DISTANCE_METHOD.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/evoinference/distance/class-use/Sarray.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/evoinference/matrix/character/class-use/CharacterStateMatrix.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/evoinference/matrix/character/class-use/CharacterStateMatrix.NucleotideStates.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/evoinference/matrix/character/class-use/CharacterStateMatrix.GainLossStates.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/evoinference/matrix/character/class-use/CharacterStateMatrix.Format.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/evoinference/matrix/character/class-use/CharacterStateMatrix.BinaryStates.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/evoinference/matrix/character/class-use/BasicCharacterStateMatrix.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/evoinference/matrix/distance/class-use/DistanceMatrix.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/evoinference/matrix/distance/class-use/DistanceMatrix.Format.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/evoinference/matrix/distance/class-use/BasicSymmetricalDistanceMatrix.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/evoinference/class-use/TestPhylogenyReconstruction.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/msa/class-use/Mafft.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/msa/class-use/MsaInferrer.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/msa/class-use/MsaFormatException.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/msa/class-use/Msa.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/msa/class-use/Msa.MSA_FORMAT.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/msa/class-use/ResampleableMsa.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/msa/class-use/MsaMethods.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/msa/class-use/DeleteableMsa.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/msa/class-use/BasicMsa.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/msa/class-use/ClustalOmega.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/ws/seqdb/class-use/SequenceDatabaseEntry.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/ws/seqdb/class-use/UniProtEntry.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/ws/seqdb/class-use/SequenceDbWsTools.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/ws/seqdb/class-use/EbiDbEntry.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/ws/seqdb/class-use/UniProtTaxonomy.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/ws/hmmer/class-use/Test.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/ws/wabi/class-use/RestUtil.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/io/parsers/nhx/class-use/NHXtags.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/io/parsers/tol/class-use/TolXmlMapping.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/io/parsers/tol/class-use/TolXmlHandler.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/io/parsers/tol/class-use/TolParser.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/ws/wabi/class-use/WabiTools.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/ws/wabi/class-use/TxSearch.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/ws/wabi/class-use/TxSearch.TAX_RANK.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/ws/wabi/class-use/TxSearch.TAX_NAME_CLASS.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/ws/wabi/class-use/TxSearch.RANKS.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/ws/wabi/class-use/WabiTools.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/msa_compactor/class-use/MsaProperties.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/msa_compactor/class-use/Chart.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/msa_compactor/class-use/GapContribution.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/msa_compactor/class-use/MsaCompactor.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/rio/class-use/RIO.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/rio/class-use/RIO.REROOTING.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/rio/class-use/RIOException.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/rio/class-use/TestRIO.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/util/class-use/SequenceAccessionTools.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/util/class-use/SystemCommandExecutor.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/util/class-use/CommandLineArguments.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/util/class-use/GeneralTable.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/util/class-use/BasicDescriptiveStatistics.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/util/class-use/ExternalProgram.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/util/class-use/AsciiHistogram.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/util/class-use/ForesterUtil.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/util/class-use/BasicTable.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/ws/wabi/class-use/RestUtil.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/ws/hmmer/class-use/Test.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/ws/seqdb/class-use/UniProtTaxonomy.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/ws/seqdb/class-use/EbiDbEntry.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/ws/seqdb/class-use/UniProtEntry.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/ws/seqdb/class-use/SequenceDatabaseEntry.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/ws/seqdb/class-use/SequenceDbWsTools.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/util/class-use/IllegalFormatUseException.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/util/class-use/StringInt.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/util/class-use/StringInt.DescendingIntComparator.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/util/class-use/TaxonomyColors.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/util/class-use/IllegalFormatUseException.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/util/class-use/TaxonomyUtil.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/util/class-use/ForesterConstants.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/util/class-use/ForesterConstants.PhylogeneticTreeFormats.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/util/class-use/CommandProcessBuilder.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/util/class-use/TaxonomyUtil.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/util/class-use/FailedConditionCheckException.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/util/class-use/BasicTableParser.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/util/class-use/BasicDescriptiveStatistics.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/util/class-use/BasicTable.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/util/class-use/CommandLineArguments.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/util/class-use/DescriptiveStatistics.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/util/class-use/ExternalProgram.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/util/class-use/BasicTableParser.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/util/class-use/AsciiHistogram.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/util/class-use/SequenceAccessionTools.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/util/class-use/ForesterUtil.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/util/class-use/TaxonomyColors.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/util/class-use/EasyWriter.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/util/class-use/GeneralTable.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/util/class-use/CommandProcessBuilder.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/util/class-use/SystemCommandExecutor.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/util/class-use/WindowsUtils.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/application/class-use/support_transfer.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/application/class-use/gsdi.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/application/class-use/pfam2go_extractor.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/application/class-use/fasta_split.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/util/class-use/FailedConditionCheckException.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/surfacing/class-use/SurfacingConstants.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/surfacing/class-use/TestSurfacing.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/surfacing/class-use/AdjactantDirectedBinaryDomainCombination.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/surfacing/class-use/CombinationsBasedPairwiseDomainSimilarityCalculator.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/surfacing/class-use/DomainCountsBasedPairwiseSimilarityCalculator.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/surfacing/class-use/BasicBinaryDomainCombination.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/surfacing/class-use/BasicDomainSimilarityCalculator.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/surfacing/class-use/SimpleDomain.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/surfacing/class-use/PairwiseDomainSimilarityCalculator.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/surfacing/class-use/CombinationsBasedPairwiseDomainSimilarity.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/surfacing/class-use/DomainSimilarity.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/surfacing/class-use/DomainSimilarity.PRINT_OPTION.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/surfacing/class-use/DomainSimilarity.DomainSimilaritySortField.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/surfacing/class-use/DomainSimilarity.DomainSimilarityScoring.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/surfacing/class-use/ProteinCountsBasedPairwiseDomainSimilarityCalculator.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/surfacing/class-use/DomainSimilarityCalculator.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/surfacing/class-use/DomainSimilarityCalculator.GoAnnotationOutput.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/surfacing/class-use/DomainSimilarityCalculator.Detailedness.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/surfacing/class-use/CombinableDomains.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/surfacing/class-use/DirectedBinaryDomainCombination.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/surfacing/class-use/SurfacingUtil.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/surfacing/class-use/AdjactantDirectedCombinableDomains.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/surfacing/class-use/DirectedCombinableDomains.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/surfacing/class-use/CountsBasedPairwiseDomainSimilarity.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/surfacing/class-use/MappingResults.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/surfacing/class-use/DomainParsimonyCalculator.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/surfacing/class-use/PairwiseGenomeComparator.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/surfacing/class-use/DomainArchitectureBasedGenomeSimilarityCalculator.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/surfacing/class-use/PairwiseDomainSimilarity.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/surfacing/class-use/GenomeWideCombinableDomains.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/surfacing/class-use/GenomeWideCombinableDomains.GenomeWideCombinableDomainsSortOrder.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/surfacing/class-use/DomainLengthsTable.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/surfacing/class-use/DomainCountsDifferenceUtil.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/surfacing/class-use/DomainCountsDifferenceUtil.COPY_CALCULATION_MODE.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/surfacing/class-use/BasicGenomeWideCombinableDomains.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/surfacing/class-use/DomainLengths.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/surfacing/class-use/BasicCombinableDomains.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/datastructures/class-use/Queue.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/datastructures/class-use/IntMatrix.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/pccx/class-use/ScoringMethodForExternalNode.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/pccx/class-use/CoverageExtender.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/pccx/class-use/ModelingUtils.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/pccx/class-use/CoverageCalculationMethod.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/pccx/class-use/Coverage.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/pccx/class-use/TestPccx.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/pccx/class-use/BranchLengthBasedScoringMethod.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/pccx/class-use/LogBranchLengthBasedScoringMethod.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/pccx/class-use/CoverageCalculationOptions.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/pccx/class-use/BranchCountingBasedScoringMethod.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/pccx/class-use/ExternalNodeBasedCoverage.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/pccx/class-use/CoverageCalculator.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/pccx/class-use/ExternalNodeBasedCoverageMethod.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/pccx/class-use/BasicExternalNodeBasedCoverageExtender.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/pccx/class-use/ExternalNodeBasedCoverageMethodOptions.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/protein/class-use/BinaryDomainCombination.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/protein/class-use/BinaryDomainCombination.OutputFormat.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/protein/class-use/BinaryDomainCombination.DomainCombinationType.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/protein/class-use/BasicProtein.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/protein/class-use/Protein.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/protein/class-use/BasicDomain.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/protein/class-use/ProteinId.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/protein/class-use/Domain.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/analysis/class-use/AncestralTaxonomyInferenceException.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/analysis/class-use/TaxonomyDataManager.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/analysis/class-use/AncestralTaxonomyInference.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/go/class-use/PfamToGoMapping.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/go/class-use/GoSubset.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/go/class-use/GoSubset.Type.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/go/class-use/OBOparser.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/go/class-use/OBOparser.ReturnType.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/go/class-use/GoRelationship.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/go/class-use/GoRelationship.Type.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/go/class-use/GoId.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/go/class-use/GoTerm.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/go/class-use/BasicGoSubset.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/go/class-use/BasicGoXRef.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/go/class-use/GoXRef.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/go/class-use/GoXRef.Type.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/go/class-use/GoUtils.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/go/class-use/GoNameSpace.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/go/class-use/GoNameSpace.GoNamespaceType.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/go/class-use/TestGo.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/go/class-use/PfamToGoParser.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/go/class-use/BasicGoTerm.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/go/class-use/BasicGoRelationship.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/go/class-use/Mapping.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/go/etc/class-use/MetaOntologizer.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/go/etc/class-use/OntologizerResult.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/go/etc/class-use/OntologizerResult.TYPE.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/species/class-use/Species.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/species/class-use/BasicSpecies.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/msa/class-use/MsaMethods.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/msa/class-use/DeleteableMsa.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/msa/class-use/MsaInferrer.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/msa/class-use/MsaFormatException.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/msa/class-use/ClustalOmega.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/msa/class-use/Mafft.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/msa/class-use/Msa.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/msa/class-use/Msa.MSA_FORMAT.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/msa/class-use/BasicMsa.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/msa/class-use/ResampleableMsa.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/sdi/class-use/SDIR.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/sdi/class-use/GSDII.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/sdi/class-use/TestGSDI.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/sdi/class-use/SDI.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/sdi/class-use/SDIutil.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/sdi/class-use/SDIutil.TaxonomyComparisonBase.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/sdi/class-use/SDIutil.ALGORITHM.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/sdi/class-use/GSDI.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/sdi/class-use/GSDIR.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/sdi/class-use/SDIException.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/application/class-use/obo_tool.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/application/class-use/nj.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/application/class-use/phylostrip.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/application/class-use/phyloxml_converter.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/application/class-use/gene_tree_preprocess.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/application/class-use/pfam_go.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/application/class-use/mcc.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/application/class-use/check_fasta.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/application/class-use/msa_compactor.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/application/class-use/support_statistics.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/application/class-use/decoratorX.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/application/class-use/pfamacc2pfamid.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/application/class-use/surfacing.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/application/class-use/annotator.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/application/class-use/rio.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/application/class-use/count_support.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/application/class-use/pccx.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/application/class-use/confadd.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/application/class-use/check_fasta.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/application/class-use/nj.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/application/class-use/fasta_split.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/application/class-use/table2fasta.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/application/class-use/gsdi.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/application/class-use/meta_ontologizer.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/application/class-use/pccx.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/application/class-use/pfamacc2go.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/application/class-use/table2fasta.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/application/class-use/support_statistics.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/application/class-use/annotator.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/application/class-use/pfam2go_extractor.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/application/class-use/dom_dup.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/application/class-use/pfam_go.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/application/class-use/gene_tree_preprocess.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/application/class-use/confadd.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/application/class-use/phylostrip.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/application/class-use/goac.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/application/class-use/mcc.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/application/class-use/pfamacc2pfamid.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/application/class-use/count_support.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/application/class-use/support_transfer.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/application/class-use/phyloxml_converter.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/application/class-use/decorator.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/application/class-use/dom_dup.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/application/class-use/surfacing.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/application/class-use/decoratorX.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/development/class-use/ResidueRenderer.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/development/class-use/MsaRenderer.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/development/class-use/DevelopmentTools.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/development/class-use/neTest.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/development/class-use/neTest.DoublePointer.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/development/class-use/Test.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/development/class-use/AbstractRenderer.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/development/class-use/RandomThing.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/development/class-use/Time.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/development/class-use/DevelopmentTools.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/development/class-use/ResidueRenderer.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/development/class-use/Hello3d.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/development/class-use/RandomThing.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/development/class-use/AbstractRenderer.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/development/class-use/MsaRenderer.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/development/class-use/Test.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/development/class-use/HmmerRest.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/phylogeny/class-use/PhylogenyNode.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/phylogeny/class-use/PhylogenyNode.NH_CONVERSION_SUPPORT_VALUE_STYLE.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/phylogeny/class-use/PhylogenyBranch.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/phylogeny/class-use/PhylogenyMethods.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/phylogeny/class-use/PhylogenyMethods.PhylogenyNodeField.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/phylogeny/class-use/PhylogenyMethods.DESCENDANT_SORT_PRIORITY.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/phylogeny/class-use/Phylogeny.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/phylogeny/data/class-use/Distribution.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/phylogeny/data/class-use/Uri.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/phylogeny/data/class-use/NodeData.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/phylogeny/data/class-use/DomainArchitecture.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/phylogeny/data/class-use/Polygon.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/phylogeny/data/class-use/Date.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/phylogeny/data/class-use/PhylogenyData.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/phylogeny/data/class-use/Property.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/phylogeny/data/class-use/Property.AppliesTo.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/phylogeny/data/class-use/NodeVisualData.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/phylogeny/data/class-use/NodeVisualData.NodeShape.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/phylogeny/data/class-use/NodeVisualData.NodeFill.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/phylogeny/data/class-use/NodeVisualData.FontType.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/phylogeny/data/class-use/BinaryCharacters.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/phylogeny/data/class-use/Annotation.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/phylogeny/data/class-use/Event.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/phylogeny/data/class-use/Event.EventType.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/phylogeny/data/class-use/BranchData.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/phylogeny/data/class-use/Sequence.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/phylogeny/data/class-use/Identifier.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/phylogeny/data/class-use/Confidence.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/phylogeny/data/class-use/MultipleUris.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/phylogeny/data/class-use/Point.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/phylogeny/data/class-use/BranchWidth.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/phylogeny/data/class-use/Taxonomy.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/phylogeny/data/class-use/SequenceRelation.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/phylogeny/data/class-use/SequenceRelation.SEQUENCE_RELATION_TYPE.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/phylogeny/data/class-use/Reference.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/phylogeny/data/class-use/PropertiesMap.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/phylogeny/data/class-use/Accession.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/phylogeny/data/class-use/Accession.Source.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/phylogeny/data/class-use/NodeDataField.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/phylogeny/data/class-use/BranchColor.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/phylogeny/data/class-use/PhylogenyDataUtil.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/phylogeny/data/class-use/ProteinDomain.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/phylogeny/factories/class-use/ParserBasedPhylogenyFactory.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/phylogeny/factories/class-use/PhylogenyFactory.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/phylogeny/iterators/class-use/PostOrderStackObject.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/phylogeny/iterators/class-use/PreorderTreeIterator.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/phylogeny/iterators/class-use/PostorderTreeIterator.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/phylogeny/iterators/class-use/ExternalForwardIterator.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/phylogeny/iterators/class-use/LevelOrderTreeIterator.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/phylogeny/iterators/class-use/PhylogenyNodeIterator.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/applications/class-use/get_genome_counts_per_char.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/applications/class-use/get_distances.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/applications/class-use/get_loss_nodes.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/applications/class-use/phylo2coloredgraphics.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/sequence/class-use/MolecularSequence.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/sequence/class-use/MolecularSequence.TYPE.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/sequence/class-use/BasicSequence.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/msa_compactor/class-use/MsaProperties.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/msa_compactor/class-use/GapContribution.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/msa_compactor/class-use/MsaCompactor.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/msa_compactor/class-use/Chart.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/applications/class-use/map_lengths.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/applications/class-use/aa.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/applications/class-use/get_shared_chars.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/applications/class-use/domainloss_replacement.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/applications/class-use/reinv_count.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/applications/class-use/genome_counts_for_once_appearing_dcs.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/applications/class-use/shared_chars_in_ext_nodes.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/applications/class-use/set_comparator.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/applications/class-use/phylo2coloredgraphics.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/applications/class-use/get_distances.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/applications/class-use/reinv_count.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/applications/class-use/get_genome_counts_per_char.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/applications/class-use/core_chars.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/applications/class-use/get_subtree_specific_chars.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/applications/class-use/subtree_feature_count.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/applications/class-use/wiki_examples.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/applications/class-use/simple_node_processor.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/applications/class-use/tax_code_cleaner.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/applications/class-use/inverted_dcs.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/applications/class-use/get_loss_nodes.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/applications/class-use/aa.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/applications/class-use/genome_counts_for_once_appearing_dcs.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/applications/class-use/phylo2graphics.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/applications/class-use/wiki_examples.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/applications/class-use/set_comparator.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/applications/class-use/aaa.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/applications/class-use/core_chars.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/applications/class-use/simple_node_processor.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/datastructures/class-use/IntMatrix.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/datastructures/class-use/Queue.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/sdi/class-use/SDI.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/sdi/class-use/TestGSDI.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/sdi/class-use/GSDI.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/sdi/class-use/GSDII.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/sdi/class-use/SDIR.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/sdi/class-use/SDIException.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/sdi/class-use/SDIutil.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/sdi/class-use/SDIutil.TaxonomyComparisonBase.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/sdi/class-use/SDIutil.ALGORITHM.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/sdi/class-use/GSDIR.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/species/class-use/BasicSpecies.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/species/class-use/Species.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/applications/class-use/get_shared_chars.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/applications/class-use/inverted_dcs.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/applications/class-use/domainloss_replacement.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/rio/class-use/RIO.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/rio/class-use/RIO.REROOTING.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/rio/class-use/TestRIO.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/rio/class-use/RIOException.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/jcolorbrewer/ui/class-use/QualitativeColorPalettePanel.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/jcolorbrewer/ui/class-use/ColorPaletteChooserDialog.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/jcolorbrewer/ui/class-use/DivergingColorPalettePanel.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/jcolorbrewer/ui/class-use/SequentialColorPalettePanel.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/jcolorbrewer/ui/class-use/PaletteIcon.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/jcolorbrewer/ui/class-use/QualitativeColorPalettePanel.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/jcolorbrewer/ui/class-use/ColorPanelSelectionModel.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/jcolorbrewer/ui/class-use/ColorPaletteChooserDialog.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/jcolorbrewer/class-use/ColorBrewer.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/demo/package-use.html...
 [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/aaproperties/package-use.html...
@@ -12361,26 +12397,26 @@
 [INFO] ------------------------------------------------------------------------
 [INFO] Reactor Summary for biojava 6.1.0:
 [INFO] 
-[INFO] biojava ............................................ SUCCESS [ 20.599 s]
-[INFO] biojava-core ....................................... SUCCESS [  9.166 s]
-[INFO] biojava-forester ................................... SUCCESS [ 10.019 s]
-[INFO] biojava-alignment .................................. SUCCESS [  3.242 s]
-[INFO] biojava-structure .................................. SUCCESS [ 10.995 s]
-[INFO] biojava-jcolorbrewer ............................... SUCCESS [  1.798 s]
-[INFO] biojava-structure-gui .............................. SUCCESS [  4.700 s]
-[INFO] biojava-genome ..................................... SUCCESS [  3.205 s]
-[INFO] biojava-modfinder .................................. SUCCESS [  2.471 s]
-[INFO] biojava-ws ......................................... SUCCESS [  1.922 s]
-[INFO] biojava-protein-disorder ........................... SUCCESS [  1.860 s]
-[INFO] biojava-aa-prop .................................... SUCCESS [  2.683 s]
-[INFO] biojava-survival ................................... SUCCESS [  2.731 s]
-[INFO] biojava-ontology ................................... SUCCESS [  2.481 s]
-[INFO] biojava-protein-comparison-tool .................... SUCCESS [  1.306 s]
+[INFO] biojava ............................................ SUCCESS [ 20.491 s]
+[INFO] biojava-core ....................................... SUCCESS [ 10.034 s]
+[INFO] biojava-forester ................................... SUCCESS [ 11.026 s]
+[INFO] biojava-alignment .................................. SUCCESS [  3.577 s]
+[INFO] biojava-structure .................................. SUCCESS [ 10.939 s]
+[INFO] biojava-jcolorbrewer ............................... SUCCESS [  1.741 s]
+[INFO] biojava-structure-gui .............................. SUCCESS [  4.560 s]
+[INFO] biojava-genome ..................................... SUCCESS [  3.193 s]
+[INFO] biojava-modfinder .................................. SUCCESS [  2.295 s]
+[INFO] biojava-ws ......................................... SUCCESS [  2.108 s]
+[INFO] biojava-protein-disorder ........................... SUCCESS [  1.816 s]
+[INFO] biojava-aa-prop .................................... SUCCESS [  2.266 s]
+[INFO] biojava-survival ................................... SUCCESS [  2.703 s]
+[INFO] biojava-ontology ................................... SUCCESS [  2.348 s]
+[INFO] biojava-protein-comparison-tool .................... SUCCESS [  1.295 s]
 [INFO] ------------------------------------------------------------------------
 [INFO] BUILD SUCCESS
 [INFO] ------------------------------------------------------------------------
-[INFO] Total time:  01:19 min
-[INFO] Finished at: 2025-06-18T12:41:13-12:00
+[INFO] Total time:  01:21 min
+[INFO] Finished at: 2024-05-17T09:04:21+14:00
 [INFO] ------------------------------------------------------------------------
 make[1]: Leaving directory '/build/reproducible-path/biojava6-live-6.1.0+dfsg'
    dh_auto_test
@@ -12442,295 +12478,295 @@
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
 SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Running org.biojava.nbio.core.sequence.EditSequenceTest
+[INFO] Running org.biojava.nbio.core.search.io.blast.BlastTabularParserTest
+createObjects
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
 SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.014 s - in org.biojava.nbio.core.sequence.EditSequenceTest
-[INFO] Running org.biojava.nbio.core.sequence.MultipleSequenceAlignmentTest
+getFileExtensions
+setFile
+[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.735 s - in org.biojava.nbio.core.search.io.blast.BlastTabularParserTest
+[INFO] Running org.biojava.nbio.core.search.io.blast.BlastXMLParserTest
+getFileExtensions
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
 SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 11, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.148 s - in org.biojava.nbio.core.sequence.MultipleSequenceAlignmentTest
-[INFO] Running org.biojava.nbio.core.sequence.TranslationTest
+setFile
+[WARNING] Tests run: 6, Failures: 0, Errors: 0, Skipped: 3, Time elapsed: 0.017 s - in org.biojava.nbio.core.search.io.blast.BlastXMLParserTest
+[INFO] Running org.biojava.nbio.core.search.io.SearchIOTest
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
 SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 12, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.257 s - in org.biojava.nbio.core.sequence.TranslationTest
-[INFO] Running org.biojava.nbio.core.sequence.ExonComparatorTest
+[WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.045 s - in org.biojava.nbio.core.search.io.SearchIOTest
+[INFO] Running org.biojava.nbio.core.search.io.HspTest
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
 SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.06 s - in org.biojava.nbio.core.sequence.ExonComparatorTest
-[INFO] Running org.biojava.nbio.core.sequence.SequenceViewTest
+getAlignment
+hashCode
+equals
+[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.042 s - in org.biojava.nbio.core.search.io.HspTest
+[INFO] Running org.biojava.nbio.core.util.StringManipulationHelperTest
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
 SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.024 s - in org.biojava.nbio.core.sequence.SequenceViewTest
-[INFO] Running org.biojava.nbio.core.sequence.io.GenericFastaHeaderParserTest
+[INFO] Tests run: 20, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.287 s - in org.biojava.nbio.core.util.StringManipulationHelperTest
+[INFO] Running org.biojava.nbio.core.util.EqualsTest
+[INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.09 s - in org.biojava.nbio.core.util.EqualsTest
+[INFO] Running org.biojava.nbio.core.util.XMLHelperTest
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
 SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.018 s - in org.biojava.nbio.core.sequence.io.GenericFastaHeaderParserTest
-[INFO] Running org.biojava.nbio.core.sequence.io.FastaReaderTest
+[INFO] Tests run: 12, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.367 s - in org.biojava.nbio.core.util.XMLHelperTest
+[INFO] Running org.biojava.nbio.core.util.PrettyXMLWriterTest
+<to>
+  <a>22</a>
+  <b>43.22</b>
+  <text>some text</text>
+  <dt tz="UTC">2021-08-15</dt>
+</to>
+
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
 SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.099 s - in org.biojava.nbio.core.sequence.io.FastaReaderTest
-[INFO] Running org.biojava.nbio.core.sequence.io.FastaWriterTest
+[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.05 s - in org.biojava.nbio.core.util.PrettyXMLWriterTest
+[INFO] Running org.biojava.nbio.core.util.FileDownloadUtilsTest
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
 SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.022 s - in org.biojava.nbio.core.sequence.io.FastaWriterTest
-[INFO] Running org.biojava.nbio.core.sequence.io.ABITracerTest
+[WARNING] Tests run: 18, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.633 s - in org.biojava.nbio.core.util.FileDownloadUtilsTest
+[INFO] Running org.biojava.nbio.core.util.SoftHashMapTest
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
 SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.373 s - in org.biojava.nbio.core.sequence.io.ABITracerTest
-[INFO] Running org.biojava.nbio.core.sequence.io.GenbankCookbookTest
+[WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.057 s - in org.biojava.nbio.core.util.SoftHashMapTest
+[INFO] Running org.biojava.nbio.core.util.HashcoderTest
+[INFO] Tests run: 21, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.125 s - in org.biojava.nbio.core.util.HashcoderTest
+[INFO] Running org.biojava.nbio.core.util.CRC64ChecksumTest
+[INFO] Tests run: 17, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.095 s - in org.biojava.nbio.core.util.CRC64ChecksumTest
+[INFO] Running org.biojava.nbio.core.util.FlatFileCacheTest
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
 SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.08 s - in org.biojava.nbio.core.sequence.io.GenbankCookbookTest
-[INFO] Running org.biojava.nbio.core.sequence.io.CasePreservingProteinSequenceCreatorTest
+[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.085 s - in org.biojava.nbio.core.util.FlatFileCacheTest
+[INFO] Running org.biojava.nbio.core.util.SingleLinkageClustererTest
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
 SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.048 s - in org.biojava.nbio.core.sequence.io.CasePreservingProteinSequenceCreatorTest
-[INFO] Running org.biojava.nbio.core.sequence.io.GenbankWriterTest
+[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.051 s - in org.biojava.nbio.core.util.SingleLinkageClustererTest
+[INFO] Running org.biojava.nbio.core.util.SequenceToolsTest
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
 SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.123 s - in org.biojava.nbio.core.sequence.io.GenbankWriterTest
-[INFO] Running org.biojava.nbio.core.sequence.io.embl.EmblReaderTest
-[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.02 s - in org.biojava.nbio.core.sequence.io.embl.EmblReaderTest
-[INFO] Running org.biojava.nbio.core.sequence.io.FastaGeneWriterTest
+[WARNING] Tests run: 21, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.289 s - in org.biojava.nbio.core.util.SequenceToolsTest
+[INFO] Running org.biojava.nbio.core.util.TestUncompressInputStream
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
 SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.056 s - in org.biojava.nbio.core.sequence.io.FastaGeneWriterTest
-[INFO] Running org.biojava.nbio.core.sequence.io.GenbankReaderTest
+[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.031 s - in org.biojava.nbio.core.util.TestUncompressInputStream
+[INFO] Running org.biojava.nbio.core.alignment.SimpleProfileTest
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
 SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.111 s - in org.biojava.nbio.core.sequence.io.GenbankReaderTest
-[INFO] Running org.biojava.nbio.core.sequence.location.LocationParserTest
-[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.007 s - in org.biojava.nbio.core.sequence.location.LocationParserTest
-[INFO] Running org.biojava.nbio.core.sequence.location.InsdcParserTest
+[WARNING] Tests run: 54, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.092 s - in org.biojava.nbio.core.alignment.SimpleProfileTest
+[INFO] Running org.biojava.nbio.core.alignment.matrices.SubstitutionMatrixTest
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
 SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.147 s - in org.biojava.nbio.core.sequence.location.InsdcParserTest
-[INFO] Running org.biojava.nbio.core.sequence.location.LocationTest
+[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.076 s - in org.biojava.nbio.core.alignment.matrices.SubstitutionMatrixTest
+[INFO] Running org.biojava.nbio.core.alignment.matrices.DefaultAAIndexProviderTest
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
 SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.032 s - in org.biojava.nbio.core.sequence.location.LocationTest
+[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.165 s - in org.biojava.nbio.core.alignment.matrices.DefaultAAIndexProviderTest
+[INFO] Running org.biojava.nbio.core.alignment.matrices.AAindexFactoryTest
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
 SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Running org.biojava.nbio.core.sequence.location.TargetedLocationParserTest
-[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.02 s - in org.biojava.nbio.core.sequence.location.TargetedLocationParserTest
-[INFO] Running org.biojava.nbio.core.sequence.TaxonomyIDTest
-[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.041 s - in org.biojava.nbio.core.sequence.TaxonomyIDTest
-[INFO] Running org.biojava.nbio.core.sequence.StrandTest
-[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.04 s - in org.biojava.nbio.core.sequence.StrandTest
-[INFO] Running org.biojava.nbio.core.sequence.views.WindowViewTests
+[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.19 s - in org.biojava.nbio.core.alignment.matrices.AAindexFactoryTest
+[INFO] Running org.biojava.nbio.core.alignment.matrices.SubstitutionMatrixHelperTest
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
 SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.021 s - in org.biojava.nbio.core.sequence.views.WindowViewTests
-[INFO] Running org.biojava.nbio.core.sequence.RNASequenceTest
+[INFO] Tests run: 23, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.212 s - in org.biojava.nbio.core.alignment.matrices.SubstitutionMatrixHelperTest
+[INFO] Running org.biojava.nbio.core.alignment.SimpleSequencePairTest
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
 SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.089 s - in org.biojava.nbio.core.sequence.RNASequenceTest
-[INFO] Running org.biojava.nbio.core.sequence.JoiningSequenceReaderTest
+[INFO] Tests run: 35, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.039 s - in org.biojava.nbio.core.alignment.SimpleSequencePairTest
+[INFO] Running org.biojava.nbio.core.alignment.SimpleAlignedSequenceTest
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
 SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.023 s - in org.biojava.nbio.core.sequence.JoiningSequenceReaderTest
-[INFO] Running org.biojava.nbio.core.sequence.compound.AmbiguityDNACompoundTest
+[WARNING] Tests run: 35, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.034 s - in org.biojava.nbio.core.alignment.SimpleAlignedSequenceTest
+[INFO] Running org.biojava.nbio.core.fasta.TestFASTAReader
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
 SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.023 s - in org.biojava.nbio.core.sequence.compound.AmbiguityDNACompoundTest
-[INFO] Running org.biojava.nbio.core.sequence.ChromosomeSequenceTest
+[INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.068 s - in org.biojava.nbio.core.fasta.TestFASTAReader
+[INFO] Running org.biojava.nbio.core.sequence.EditSequenceTest
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
 SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 26, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.141 s - in org.biojava.nbio.core.sequence.ChromosomeSequenceTest
-[INFO] Running org.biojava.nbio.core.sequence.ExonSequenceTest
+[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.032 s - in org.biojava.nbio.core.sequence.EditSequenceTest
+[INFO] Running org.biojava.nbio.core.sequence.ProteinSequenceTest
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
 SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.059 s - in org.biojava.nbio.core.sequence.ExonSequenceTest
-[INFO] Running org.biojava.nbio.core.sequence.TestSequenceEquals
+[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.056 s - in org.biojava.nbio.core.sequence.ProteinSequenceTest
+[INFO] Running org.biojava.nbio.core.sequence.MultipleSequenceAlignmentTest
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
 SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.024 s - in org.biojava.nbio.core.sequence.TestSequenceEquals
-[INFO] Running org.biojava.nbio.core.sequence.GeneSequenceTest
+[INFO] Tests run: 11, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.159 s - in org.biojava.nbio.core.sequence.MultipleSequenceAlignmentTest
+[INFO] Running org.biojava.nbio.core.sequence.io.FastaReaderTest
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
 SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[WARNING] Tests run: 11, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.079 s - in org.biojava.nbio.core.sequence.GeneSequenceTest
+[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.093 s - in org.biojava.nbio.core.sequence.io.FastaReaderTest
+[INFO] Running org.biojava.nbio.core.sequence.io.GenbankWriterTest
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
 SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Running org.biojava.nbio.core.sequence.loader.GenbankProxySequenceReaderTest
-[INFO] Tests run: 16, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.067 s - in org.biojava.nbio.core.sequence.loader.GenbankProxySequenceReaderTest
-[INFO] Running org.biojava.nbio.core.sequence.loader.SimpleGenbankProxySequenceReaderTest
+[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.158 s - in org.biojava.nbio.core.sequence.io.GenbankWriterTest
+[INFO] Running org.biojava.nbio.core.sequence.io.GenbankReaderTest
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
 SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.228 s - in org.biojava.nbio.core.sequence.loader.SimpleGenbankProxySequenceReaderTest
-[INFO] Running org.biojava.nbio.core.sequence.DNATest
+[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.113 s - in org.biojava.nbio.core.sequence.io.GenbankReaderTest
+[INFO] Running org.biojava.nbio.core.sequence.io.GenbankCookbookTest
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
 SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 20, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.091 s - in org.biojava.nbio.core.sequence.DNATest
-[INFO] Running org.biojava.nbio.core.sequence.ProteinSequenceTest
+[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.072 s - in org.biojava.nbio.core.sequence.io.GenbankCookbookTest
+[INFO] Running org.biojava.nbio.core.sequence.io.embl.EmblReaderTest
+[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.025 s - in org.biojava.nbio.core.sequence.io.embl.EmblReaderTest
+[INFO] Running org.biojava.nbio.core.sequence.io.FastaGeneWriterTest
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
 SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.053 s - in org.biojava.nbio.core.sequence.ProteinSequenceTest
-[INFO] Running org.biojava.nbio.core.sequence.TranscriptSequenceTest
+[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.058 s - in org.biojava.nbio.core.sequence.io.FastaGeneWriterTest
+[INFO] Running org.biojava.nbio.core.sequence.io.GenericFastaHeaderParserTest
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
 SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[WARNING] Tests run: 11, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.087 s - in org.biojava.nbio.core.sequence.TranscriptSequenceTest
-[INFO] Running org.biojava.nbio.core.search.io.HspTest
+[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.019 s - in org.biojava.nbio.core.sequence.io.GenericFastaHeaderParserTest
+[INFO] Running org.biojava.nbio.core.sequence.io.FastaWriterTest
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
 SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-getAlignment
-hashCode
-equals
-[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.041 s - in org.biojava.nbio.core.search.io.HspTest
-[INFO] Running org.biojava.nbio.core.search.io.blast.BlastTabularParserTest
-createObjects
+[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.024 s - in org.biojava.nbio.core.sequence.io.FastaWriterTest
+[INFO] Running org.biojava.nbio.core.sequence.io.ABITracerTest
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
 SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-getFileExtensions
-setFile
-[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.591 s - in org.biojava.nbio.core.search.io.blast.BlastTabularParserTest
-[INFO] Running org.biojava.nbio.core.search.io.blast.BlastXMLParserTest
-getFileExtensions
+[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.582 s - in org.biojava.nbio.core.sequence.io.ABITracerTest
+[INFO] Running org.biojava.nbio.core.sequence.io.CasePreservingProteinSequenceCreatorTest
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
 SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-setFile
-[WARNING] Tests run: 6, Failures: 0, Errors: 0, Skipped: 3, Time elapsed: 0.017 s - in org.biojava.nbio.core.search.io.blast.BlastXMLParserTest
-[INFO] Running org.biojava.nbio.core.search.io.SearchIOTest
+[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.047 s - in org.biojava.nbio.core.sequence.io.CasePreservingProteinSequenceCreatorTest
+[INFO] Running org.biojava.nbio.core.sequence.StrandTest
+[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.038 s - in org.biojava.nbio.core.sequence.StrandTest
+[INFO] Running org.biojava.nbio.core.sequence.ExonSequenceTest
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
 SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.04 s - in org.biojava.nbio.core.search.io.SearchIOTest
-[INFO] Running org.biojava.nbio.core.TestAmbiguityCompoundSet
+[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.046 s - in org.biojava.nbio.core.sequence.ExonSequenceTest
+[INFO] Running org.biojava.nbio.core.sequence.ExonComparatorTest
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
 SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.066 s - in org.biojava.nbio.core.TestAmbiguityCompoundSet
-[INFO] Running org.biojava.nbio.core.util.EqualsTest
-[INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.085 s - in org.biojava.nbio.core.util.EqualsTest
-[INFO] Running org.biojava.nbio.core.util.StringManipulationHelperTest
+[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.054 s - in org.biojava.nbio.core.sequence.ExonComparatorTest
+[INFO] Running org.biojava.nbio.core.sequence.location.LocationParserTest
+[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.006 s - in org.biojava.nbio.core.sequence.location.LocationParserTest
+[INFO] Running org.biojava.nbio.core.sequence.location.LocationTest
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
 SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 20, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.193 s - in org.biojava.nbio.core.util.StringManipulationHelperTest
-[INFO] Running org.biojava.nbio.core.util.CRC64ChecksumTest
-[INFO] Tests run: 17, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.087 s - in org.biojava.nbio.core.util.CRC64ChecksumTest
-[INFO] Running org.biojava.nbio.core.util.SequenceToolsTest
+[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.019 s - in org.biojava.nbio.core.sequence.location.LocationTest
+[INFO] Running org.biojava.nbio.core.sequence.location.InsdcParserTest
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
 SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[WARNING] Tests run: 21, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.213 s - in org.biojava.nbio.core.util.SequenceToolsTest
-[INFO] Running org.biojava.nbio.core.util.PrettyXMLWriterTest
-<to>
-  <a>22</a>
-  <b>43.22</b>
-  <text>some text</text>
-  <dt tz="UTC">2021-08-15</dt>
-</to>
-
+[INFO] Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.528 s - in org.biojava.nbio.core.sequence.location.InsdcParserTest
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
 SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.055 s - in org.biojava.nbio.core.util.PrettyXMLWriterTest
-[INFO] Running org.biojava.nbio.core.util.FlatFileCacheTest
+[INFO] Running org.biojava.nbio.core.sequence.location.TargetedLocationParserTest
+[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.035 s - in org.biojava.nbio.core.sequence.location.TargetedLocationParserTest
+[INFO] Running org.biojava.nbio.core.sequence.DNATest
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
 SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.458 s - in org.biojava.nbio.core.util.FlatFileCacheTest
-[INFO] Running org.biojava.nbio.core.util.TestUncompressInputStream
+[INFO] Tests run: 20, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.288 s - in org.biojava.nbio.core.sequence.DNATest
+[INFO] Running org.biojava.nbio.core.sequence.views.WindowViewTests
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
 SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.017 s - in org.biojava.nbio.core.util.TestUncompressInputStream
-[INFO] Running org.biojava.nbio.core.util.SingleLinkageClustererTest
+[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.015 s - in org.biojava.nbio.core.sequence.views.WindowViewTests
+[INFO] Running org.biojava.nbio.core.sequence.TaxonomyIDTest
+[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.06 s - in org.biojava.nbio.core.sequence.TaxonomyIDTest
+[INFO] Running org.biojava.nbio.core.sequence.GeneSequenceTest
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
 SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.052 s - in org.biojava.nbio.core.util.SingleLinkageClustererTest
-[INFO] Running org.biojava.nbio.core.util.HashcoderTest
-[INFO] Tests run: 21, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.12 s - in org.biojava.nbio.core.util.HashcoderTest
-[INFO] Running org.biojava.nbio.core.util.FileDownloadUtilsTest
+[WARNING] Tests run: 11, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.08 s - in org.biojava.nbio.core.sequence.GeneSequenceTest
+[INFO] Running org.biojava.nbio.core.sequence.TestSequenceEquals
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
 SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[WARNING] Tests run: 18, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.292 s - in org.biojava.nbio.core.util.FileDownloadUtilsTest
-[INFO] Running org.biojava.nbio.core.util.XMLHelperTest
+[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.017 s - in org.biojava.nbio.core.sequence.TestSequenceEquals
+[INFO] Running org.biojava.nbio.core.sequence.SequenceViewTest
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
 SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 12, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.206 s - in org.biojava.nbio.core.util.XMLHelperTest
-[INFO] Running org.biojava.nbio.core.util.SoftHashMapTest
+[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.026 s - in org.biojava.nbio.core.sequence.SequenceViewTest
+[INFO] Running org.biojava.nbio.core.sequence.TranslationTest
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
 SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.047 s - in org.biojava.nbio.core.util.SoftHashMapTest
-[INFO] Running org.biojava.nbio.core.fasta.TestFASTAReader
+[INFO] Tests run: 12, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.3 s - in org.biojava.nbio.core.sequence.TranslationTest
+[INFO] Running org.biojava.nbio.core.sequence.JoiningSequenceReaderTest
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
 SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.035 s - in org.biojava.nbio.core.fasta.TestFASTAReader
-[INFO] Running org.biojava.nbio.core.alignment.SimpleSequencePairTest
+[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.023 s - in org.biojava.nbio.core.sequence.JoiningSequenceReaderTest
+[INFO] Running org.biojava.nbio.core.sequence.RNASequenceTest
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
 SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 35, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.046 s - in org.biojava.nbio.core.alignment.SimpleSequencePairTest
-[INFO] Running org.biojava.nbio.core.alignment.SimpleProfileTest
+[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.095 s - in org.biojava.nbio.core.sequence.RNASequenceTest
+[INFO] Running org.biojava.nbio.core.sequence.compound.AmbiguityDNACompoundTest
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
 SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[WARNING] Tests run: 54, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.084 s - in org.biojava.nbio.core.alignment.SimpleProfileTest
-[INFO] Running org.biojava.nbio.core.alignment.SimpleAlignedSequenceTest
+[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.023 s - in org.biojava.nbio.core.sequence.compound.AmbiguityDNACompoundTest
+[INFO] Running org.biojava.nbio.core.sequence.TranscriptSequenceTest
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
 SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[WARNING] Tests run: 35, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.046 s - in org.biojava.nbio.core.alignment.SimpleAlignedSequenceTest
-[INFO] Running org.biojava.nbio.core.alignment.matrices.SubstitutionMatrixTest
+[WARNING] Tests run: 11, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.092 s - in org.biojava.nbio.core.sequence.TranscriptSequenceTest
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
 SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.079 s - in org.biojava.nbio.core.alignment.matrices.SubstitutionMatrixTest
-[INFO] Running org.biojava.nbio.core.alignment.matrices.AAindexFactoryTest
+[INFO] Running org.biojava.nbio.core.sequence.loader.GenbankProxySequenceReaderTest
+[INFO] Tests run: 16, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.06 s - in org.biojava.nbio.core.sequence.loader.GenbankProxySequenceReaderTest
+[INFO] Running org.biojava.nbio.core.sequence.loader.SimpleGenbankProxySequenceReaderTest
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
 SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.14 s - in org.biojava.nbio.core.alignment.matrices.AAindexFactoryTest
-[INFO] Running org.biojava.nbio.core.alignment.matrices.DefaultAAIndexProviderTest
+[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.205 s - in org.biojava.nbio.core.sequence.loader.SimpleGenbankProxySequenceReaderTest
+[INFO] Running org.biojava.nbio.core.sequence.ChromosomeSequenceTest
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
 SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.154 s - in org.biojava.nbio.core.alignment.matrices.DefaultAAIndexProviderTest
-[INFO] Running org.biojava.nbio.core.alignment.matrices.SubstitutionMatrixHelperTest
+[INFO] Tests run: 26, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.145 s - in org.biojava.nbio.core.sequence.ChromosomeSequenceTest
+[INFO] Running org.biojava.nbio.core.TestAmbiguityCompoundSet
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
 SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 23, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.16 s - in org.biojava.nbio.core.alignment.matrices.SubstitutionMatrixHelperTest
+[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.073 s - in org.biojava.nbio.core.TestAmbiguityCompoundSet
 [INFO] 
 [INFO] Results:
 [INFO] 
@@ -12777,90 +12813,90 @@
 [INFO] -------------------------------------------------------
 [INFO]  T E S T S
 [INFO] -------------------------------------------------------
-[INFO] Running org.biojava.nbio.phylo.TestDistanceTreeEvaluator
+[INFO] Running org.biojava.nbio.alignment.SimpleSubstitutionMatrixTest
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
 SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.085 s - in org.biojava.nbio.phylo.TestDistanceTreeEvaluator
-[INFO] Running org.biojava.nbio.phylo.TestForesterWrapper
+[INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.089 s - in org.biojava.nbio.alignment.SimpleSubstitutionMatrixTest
+[INFO] Running org.biojava.nbio.alignment.SimpleProfilePairTest
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
 SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.086 s - in org.biojava.nbio.phylo.TestForesterWrapper
-[INFO] Running org.biojava.nbio.alignment.FractionalIdentityScorerTest
+[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.101 s - in org.biojava.nbio.alignment.SimpleProfilePairTest
+[INFO] Running org.biojava.nbio.alignment.SmithWatermanTest
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
 SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.088 s - in org.biojava.nbio.alignment.FractionalIdentityScorerTest
-[INFO] Running org.biojava.nbio.alignment.LocalAlignmentTest
+[INFO] Tests run: 15, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.119 s - in org.biojava.nbio.alignment.SmithWatermanTest
+[INFO] Running org.biojava.nbio.alignment.FractionalIdentityScorerTest
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
 SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.083 s - in org.biojava.nbio.alignment.LocalAlignmentTest
-[INFO] Running org.biojava.nbio.alignment.FractionalSimilarityScorerTest
+[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.106 s - in org.biojava.nbio.alignment.FractionalIdentityScorerTest
+[INFO] Running org.biojava.nbio.alignment.io.TestStockholmParser
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
 SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.097 s - in org.biojava.nbio.alignment.FractionalSimilarityScorerTest
-[INFO] Running org.biojava.nbio.alignment.SimpleProfileProfileAlignerTest
+[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.087 s - in org.biojava.nbio.alignment.io.TestStockholmParser
+[INFO] Running org.biojava.nbio.alignment.SimpleGapPenaltyTest
+[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.053 s - in org.biojava.nbio.alignment.SimpleGapPenaltyTest
+[INFO] Running org.biojava.nbio.alignment.GuideTreeTest
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
 SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 15, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.131 s - in org.biojava.nbio.alignment.SimpleProfileProfileAlignerTest
-[INFO] Running org.biojava.nbio.alignment.io.TestStockholmParser
+[INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.139 s - in org.biojava.nbio.alignment.GuideTreeTest
+[INFO] Running org.biojava.nbio.alignment.SimpleProfileProfileAlignerTest
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
 SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.089 s - in org.biojava.nbio.alignment.io.TestStockholmParser
-[INFO] Running org.biojava.nbio.alignment.NeedlemanWunschTest
+[INFO] Tests run: 15, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.107 s - in org.biojava.nbio.alignment.SimpleProfileProfileAlignerTest
+[INFO] Running org.biojava.nbio.alignment.LocalAlignmentTest
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
 SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 23, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.221 s - in org.biojava.nbio.alignment.NeedlemanWunschTest
-[INFO] Running org.biojava.nbio.alignment.SmithWatermanTest
+[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.087 s - in org.biojava.nbio.alignment.LocalAlignmentTest
+[INFO] Running org.biojava.nbio.alignment.FractionalSimilarityScorerTest
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
 SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 15, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.127 s - in org.biojava.nbio.alignment.SmithWatermanTest
-[INFO] Running org.biojava.nbio.alignment.TestDNAAlignment
+[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.082 s - in org.biojava.nbio.alignment.FractionalSimilarityScorerTest
+[INFO] Running org.biojava.nbio.alignment.NeedlemanWunschTest
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
 SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.383 s - in org.biojava.nbio.alignment.TestDNAAlignment
-[INFO] Running org.biojava.nbio.alignment.SimpleSubstitutionMatrixTest
+[INFO] Tests run: 23, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.207 s - in org.biojava.nbio.alignment.NeedlemanWunschTest
+[INFO] Running org.biojava.nbio.alignment.aaindex.TestAAINDEXLoading
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
 SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.102 s - in org.biojava.nbio.alignment.SimpleSubstitutionMatrixTest
-[INFO] Running org.biojava.nbio.alignment.SimpleProfilePairTest
+[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.14 s - in org.biojava.nbio.alignment.aaindex.TestAAINDEXLoading
+[INFO] Running org.biojava.nbio.alignment.TestSubOptimalMSA
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
 SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.088 s - in org.biojava.nbio.alignment.SimpleProfilePairTest
-[INFO] Running org.biojava.nbio.alignment.aaindex.TestAAINDEXLoading
+[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.125 s - in org.biojava.nbio.alignment.TestSubOptimalMSA
+[INFO] Running org.biojava.nbio.alignment.routines.GuanUberbacherTest
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
 SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.142 s - in org.biojava.nbio.alignment.aaindex.TestAAINDEXLoading
+[INFO] Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.095 s - in org.biojava.nbio.alignment.routines.GuanUberbacherTest
 [INFO] Running org.biojava.nbio.alignment.routines.AlignerHelperTest
-[INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.058 s - in org.biojava.nbio.alignment.routines.AlignerHelperTest
-[INFO] Running org.biojava.nbio.alignment.routines.GuanUberbacherTest
+[INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.064 s - in org.biojava.nbio.alignment.routines.AlignerHelperTest
+[INFO] Running org.biojava.nbio.alignment.TestDNAAlignment
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
 SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.116 s - in org.biojava.nbio.alignment.routines.GuanUberbacherTest
-[INFO] Running org.biojava.nbio.alignment.SimpleGapPenaltyTest
-[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.061 s - in org.biojava.nbio.alignment.SimpleGapPenaltyTest
-[INFO] Running org.biojava.nbio.alignment.GuideTreeTest
+[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.29 s - in org.biojava.nbio.alignment.TestDNAAlignment
+[INFO] Running org.biojava.nbio.phylo.TestForesterWrapper
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
 SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.146 s - in org.biojava.nbio.alignment.GuideTreeTest
-[INFO] Running org.biojava.nbio.alignment.TestSubOptimalMSA
+[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.08 s - in org.biojava.nbio.phylo.TestForesterWrapper
+[INFO] Running org.biojava.nbio.phylo.TestDistanceTreeEvaluator
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
 SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.13 s - in org.biojava.nbio.alignment.TestSubOptimalMSA
+[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.058 s - in org.biojava.nbio.phylo.TestDistanceTreeEvaluator
 [INFO] 
 [INFO] Results:
 [INFO] 
@@ -12891,259 +12927,223 @@
 [INFO] -------------------------------------------------------
 [INFO]  T E S T S
 [INFO] -------------------------------------------------------
-[INFO] Running org.biojava.nbio.structure.TestCloning
-[WARNING] Tests run: 7, Failures: 0, Errors: 0, Skipped: 7, Time elapsed: 0.004 s - in org.biojava.nbio.structure.TestCloning
-[INFO] Running org.biojava.nbio.structure.secstruc.TestDSSPParser
-[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.008 s - in org.biojava.nbio.structure.secstruc.TestDSSPParser
-[INFO] Running org.biojava.nbio.structure.secstruc.TestSecStrucCalc
-[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.006 s - in org.biojava.nbio.structure.secstruc.TestSecStrucCalc
-[INFO] Running org.biojava.nbio.structure.TestLoadStructureFromURL
-[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.006 s - in org.biojava.nbio.structure.TestLoadStructureFromURL
-[INFO] Running org.biojava.nbio.structure.Test4hhb
+[INFO] Running org.biojava.nbio.structure.TestCalc
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
 SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.359 s - in org.biojava.nbio.structure.Test4hhb
-[INFO] Running org.biojava.nbio.structure.TestURLIdentifier
+[INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.111 s - in org.biojava.nbio.structure.TestCalc
+[INFO] Running org.biojava.nbio.structure.HetatomImplTest
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
 SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.19 s - in org.biojava.nbio.structure.TestURLIdentifier
-[INFO] Running org.biojava.nbio.structure.ResidueNumberTest
-[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.011 s - in org.biojava.nbio.structure.ResidueNumberTest
-[INFO] Running org.biojava.nbio.structure.TestStructureSerialization
+[INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.061 s - in org.biojava.nbio.structure.HetatomImplTest
+[INFO] Running org.biojava.nbio.structure.ResidueRangeTest
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
 SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.259 s - in org.biojava.nbio.structure.TestStructureSerialization
-[INFO] Running org.biojava.nbio.structure.TestParsingCalcium
-[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.006 s - in org.biojava.nbio.structure.TestParsingCalcium
-[INFO] Running org.biojava.nbio.structure.TestCalc
+[WARNING] Tests run: 14, Failures: 0, Errors: 0, Skipped: 7, Time elapsed: 0.067 s - in org.biojava.nbio.structure.ResidueRangeTest
+[INFO] Running org.biojava.nbio.structure.TestChargeAdder
+[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.006 s - in org.biojava.nbio.structure.TestChargeAdder
+[INFO] Running org.biojava.nbio.structure.geometry.TestSuperPositionQCP
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
 SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.06 s - in org.biojava.nbio.structure.TestCalc
-[INFO] Running org.biojava.nbio.structure.TestChargeAdder
-[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.007 s - in org.biojava.nbio.structure.TestChargeAdder
-[INFO] Running org.biojava.nbio.structure.ElementTest
-[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.012 s - in org.biojava.nbio.structure.ElementTest
-[INFO] Running org.biojava.nbio.structure.TestEntityHeuristics
+[WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.028 s - in org.biojava.nbio.structure.geometry.TestSuperPositionQCP
+[INFO] Running org.biojava.nbio.structure.geometry.TestSuperPosition
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
 SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.78 s - in org.biojava.nbio.structure.TestEntityHeuristics
-[INFO] Running org.biojava.nbio.structure.cluster.TestSubunitCluster
+[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.834 s - in org.biojava.nbio.structure.geometry.TestSuperPosition
+[INFO] Running org.biojava.nbio.structure.geometry.TestUnitQuaternions
+[WARNING] Tests run: 4, Failures: 0, Errors: 0, Skipped: 3, Time elapsed: 0.015 s - in org.biojava.nbio.structure.geometry.TestUnitQuaternions
+[INFO] Running org.biojava.nbio.structure.TestStructureSerialization
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
 SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[WARNING] Tests run: 5, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.116 s - in org.biojava.nbio.structure.cluster.TestSubunitCluster
-[INFO] Running org.biojava.nbio.structure.cluster.TestSubunitExtractor
-[WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 3, Time elapsed: 0.008 s - in org.biojava.nbio.structure.cluster.TestSubunitExtractor
-[INFO] Running org.biojava.nbio.structure.AtomPositionMapTest
-[WARNING] Tests run: 5, Failures: 0, Errors: 0, Skipped: 5, Time elapsed: 0.006 s - in org.biojava.nbio.structure.AtomPositionMapTest
-[INFO] Running org.biojava.nbio.structure.geometry.TestSuperPosition
+[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.117 s - in org.biojava.nbio.structure.TestStructureSerialization
+[INFO] Running org.biojava.nbio.structure.PdbFileFormat30Test
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
 SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.814 s - in org.biojava.nbio.structure.geometry.TestSuperPosition
-[INFO] Running org.biojava.nbio.structure.geometry.TestUnitQuaternions
-[WARNING] Tests run: 4, Failures: 0, Errors: 0, Skipped: 3, Time elapsed: 0.015 s - in org.biojava.nbio.structure.geometry.TestUnitQuaternions
-[INFO] Running org.biojava.nbio.structure.geometry.TestSuperPositionQCP
+[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.839 s - in org.biojava.nbio.structure.PdbFileFormat30Test
+[INFO] Running org.biojava.nbio.structure.TestNucleotides
+[WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 3, Time elapsed: 0.006 s - in org.biojava.nbio.structure.TestNucleotides
+[INFO] Running org.biojava.nbio.structure.io.TestDifficultMmCIFFiles
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
 SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.03 s - in org.biojava.nbio.structure.geometry.TestSuperPositionQCP
-[INFO] Running org.biojava.nbio.structure.TestAtomIterator
-[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.006 s - in org.biojava.nbio.structure.TestAtomIterator
-[INFO] Running org.biojava.nbio.structure.io.FastaAFPChainConverterTest
-[WARNING] Tests run: 5, Failures: 0, Errors: 0, Skipped: 5, Time elapsed: 0.009 s - in org.biojava.nbio.structure.io.FastaAFPChainConverterTest
-[INFO] Running org.biojava.nbio.structure.io.TestDifficultMmCIFFiles
+[WARNING] Tests run: 7, Failures: 0, Errors: 0, Skipped: 5, Time elapsed: 0.849 s - in org.biojava.nbio.structure.io.TestDifficultMmCIFFiles
+[INFO] Running org.biojava.nbio.structure.io.TestParseMmCIFLigands
+[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.008 s - in org.biojava.nbio.structure.io.TestParseMmCIFLigands
+[INFO] Running org.biojava.nbio.structure.io.TestWriteLargeCoordinatePDB
+[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.009 s - in org.biojava.nbio.structure.io.TestWriteLargeCoordinatePDB
+[INFO] Running org.biojava.nbio.structure.io.StructureSequenceMatcherTest
+[WARNING] Tests run: 4, Failures: 0, Errors: 0, Skipped: 4, Time elapsed: 0.01 s - in org.biojava.nbio.structure.io.StructureSequenceMatcherTest
+[INFO] Running org.biojava.nbio.structure.io.mmtf.TestMmtfStructureReader
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
 SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[WARNING] Tests run: 7, Failures: 0, Errors: 0, Skipped: 5, Time elapsed: 0.8 s - in org.biojava.nbio.structure.io.TestDifficultMmCIFFiles
-[INFO] Running org.biojava.nbio.structure.io.TestSiftsParsing
-[WARNING] Tests run: 4, Failures: 0, Errors: 0, Skipped: 4, Time elapsed: 0.007 s - in org.biojava.nbio.structure.io.TestSiftsParsing
-[INFO] Running org.biojava.nbio.structure.io.TestNonDepositedFiles
+[WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 1.032 s - in org.biojava.nbio.structure.io.mmtf.TestMmtfStructureReader
+[INFO] Running org.biojava.nbio.structure.io.mmtf.TestMmtfRoundTrip
+[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.006 s - in org.biojava.nbio.structure.io.mmtf.TestMmtfRoundTrip
+[INFO] Running org.biojava.nbio.structure.io.mmtf.TestMmtfUtils
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
 SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[WARNING] Tests run: 14, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 1.397 s - in org.biojava.nbio.structure.io.TestNonDepositedFiles
-[INFO] Running org.biojava.nbio.structure.io.TestParseMmCIFLigands
-[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.007 s - in org.biojava.nbio.structure.io.TestParseMmCIFLigands
-[INFO] Running org.biojava.nbio.structure.io.TestHeaderOnly
+[WARNING] Tests run: 16, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.073 s - in org.biojava.nbio.structure.io.mmtf.TestMmtfUtils
+[INFO] Running org.biojava.nbio.structure.io.mmtf.TestMmtfPerformance
+[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.006 s - in org.biojava.nbio.structure.io.mmtf.TestMmtfPerformance
+[INFO] Running org.biojava.nbio.structure.io.mmtf.TestMmtfStructureWriter
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
 SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.958 s - in org.biojava.nbio.structure.io.TestHeaderOnly
-[INFO] Running org.biojava.nbio.structure.io.cif.CifFileConsumerImplTest
+[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.76 s - in org.biojava.nbio.structure.io.mmtf.TestMmtfStructureWriter
+[INFO] Running org.biojava.nbio.structure.io.mmtf.TestBondFinding
+[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.007 s - in org.biojava.nbio.structure.io.mmtf.TestBondFinding
+[INFO] Running org.biojava.nbio.structure.io.TestNonDepositedFiles
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
 SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.094 s - in org.biojava.nbio.structure.io.cif.CifFileConsumerImplTest
-[INFO] Running org.biojava.nbio.structure.io.TestDBRefParsing
+[WARNING] Tests run: 14, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 1.36 s - in org.biojava.nbio.structure.io.TestNonDepositedFiles
+[INFO] Running org.biojava.nbio.structure.io.cif.CifFileConsumerImplTest
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
 SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.071 s - in org.biojava.nbio.structure.io.TestDBRefParsing
+[INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.978 s - in org.biojava.nbio.structure.io.cif.CifFileConsumerImplTest
+[INFO] Running org.biojava.nbio.structure.io.TestURLBasedFileParsing
+[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.008 s - in org.biojava.nbio.structure.io.TestURLBasedFileParsing
+[INFO] Running org.biojava.nbio.structure.io.TestParseMmCIFFeatures
+[WARNING] Tests run: 4, Failures: 0, Errors: 0, Skipped: 4, Time elapsed: 0.007 s - in org.biojava.nbio.structure.io.TestParseMmCIFFeatures
 [INFO] Running org.biojava.nbio.structure.io.TestQuaternaryStructureProviders
 [WARNING] Tests run: 7, Failures: 0, Errors: 0, Skipped: 7, Time elapsed: 0.007 s - in org.biojava.nbio.structure.io.TestQuaternaryStructureProviders
-[INFO] Running org.biojava.nbio.structure.io.TestMMcifOrganismParsing
-[WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 3, Time elapsed: 0.007 s - in org.biojava.nbio.structure.io.TestMMcifOrganismParsing
-[INFO] Running org.biojava.nbio.structure.io.StructureSequenceMatcherTest
-[WARNING] Tests run: 4, Failures: 0, Errors: 0, Skipped: 4, Time elapsed: 0.007 s - in org.biojava.nbio.structure.io.StructureSequenceMatcherTest
 [INFO] Running org.biojava.nbio.structure.io.TestParseOnAsymId
-[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.007 s - in org.biojava.nbio.structure.io.TestParseOnAsymId
-[INFO] Running org.biojava.nbio.structure.io.mmcif.TestChemCompProvider
+[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.008 s - in org.biojava.nbio.structure.io.TestParseOnAsymId
+[INFO] Running org.biojava.nbio.structure.io.TestMMcifOrganismParsing
+[WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 3, Time elapsed: 0.008 s - in org.biojava.nbio.structure.io.TestMMcifOrganismParsing
+[INFO] Running org.biojava.nbio.structure.io.TestHeaderOnly
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
 SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-Using PDB_DIR=/tmp as temporary file directory
-[WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.382 s - in org.biojava.nbio.structure.io.mmcif.TestChemCompProvider
-[INFO] Running org.biojava.nbio.structure.io.mmcif.TestParseMmcifHeader
+[WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.883 s - in org.biojava.nbio.structure.io.TestHeaderOnly
+[INFO] Running org.biojava.nbio.structure.io.sifts.SiftsChainToUniprotMappingTest
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
 SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.849 s - in org.biojava.nbio.structure.io.mmcif.TestParseMmcifHeader
-[INFO] Running org.biojava.nbio.structure.io.mmcif.TestMmcifV5Changes
+[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.033 s - in org.biojava.nbio.structure.io.sifts.SiftsChainToUniprotMappingTest
+[INFO] Running org.biojava.nbio.structure.io.TestDBRefParsing
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
 SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.884 s - in org.biojava.nbio.structure.io.mmcif.TestMmcifV5Changes
-[INFO] Running org.biojava.nbio.structure.io.mmcif.TestEntityNameAndType
-[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.006 s - in org.biojava.nbio.structure.io.mmcif.TestEntityNameAndType
-[INFO] Running org.biojava.nbio.structure.io.mmcif.TestParseInternalChainId
-[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.007 s - in org.biojava.nbio.structure.io.mmcif.TestParseInternalChainId
+[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.064 s - in org.biojava.nbio.structure.io.TestDBRefParsing
 [INFO] Running org.biojava.nbio.structure.io.TestHardBioUnits
 [WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.007 s - in org.biojava.nbio.structure.io.TestHardBioUnits
-[INFO] Running org.biojava.nbio.structure.io.TestWriteLargeCoordinatePDB
-[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.006 s - in org.biojava.nbio.structure.io.TestWriteLargeCoordinatePDB
-[INFO] Running org.biojava.nbio.structure.io.mmtf.TestMmtfStructureReader
-SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
-SLF4J: Defaulting to no-operation (NOP) logger implementation
-SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 2.237 s - in org.biojava.nbio.structure.io.mmtf.TestMmtfStructureReader
-[INFO] Running org.biojava.nbio.structure.io.mmtf.TestBondFinding
-[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.007 s - in org.biojava.nbio.structure.io.mmtf.TestBondFinding
-[INFO] Running org.biojava.nbio.structure.io.mmtf.TestMmtfUtils
+[INFO] Running org.biojava.nbio.structure.io.FastaAFPChainConverterTest
+[WARNING] Tests run: 5, Failures: 0, Errors: 0, Skipped: 5, Time elapsed: 0.007 s - in org.biojava.nbio.structure.io.FastaAFPChainConverterTest
+[INFO] Running org.biojava.nbio.structure.io.mmcif.TestParseInternalChainId
+[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.006 s - in org.biojava.nbio.structure.io.mmcif.TestParseInternalChainId
+[INFO] Running org.biojava.nbio.structure.io.mmcif.TestMmcifV5Changes
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
 SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[WARNING] Tests run: 16, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.085 s - in org.biojava.nbio.structure.io.mmtf.TestMmtfUtils
-[INFO] Running org.biojava.nbio.structure.io.mmtf.TestMmtfRoundTrip
-[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.008 s - in org.biojava.nbio.structure.io.mmtf.TestMmtfRoundTrip
-[INFO] Running org.biojava.nbio.structure.io.mmtf.TestMmtfStructureWriter
+[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.852 s - in org.biojava.nbio.structure.io.mmcif.TestMmcifV5Changes
+[INFO] Running org.biojava.nbio.structure.io.mmcif.TestEntityNameAndType
+[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.005 s - in org.biojava.nbio.structure.io.mmcif.TestEntityNameAndType
+[INFO] Running org.biojava.nbio.structure.io.mmcif.TestParseMmcifHeader
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
 SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.917 s - in org.biojava.nbio.structure.io.mmtf.TestMmtfStructureWriter
-[INFO] Running org.biojava.nbio.structure.io.mmtf.TestMmtfPerformance
-[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.006 s - in org.biojava.nbio.structure.io.mmtf.TestMmtfPerformance
-[INFO] Running org.biojava.nbio.structure.io.TestMMCIFWriting
+[WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.829 s - in org.biojava.nbio.structure.io.mmcif.TestParseMmcifHeader
+[INFO] Running org.biojava.nbio.structure.io.mmcif.TestChemCompProvider
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
 SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[WARNING] Tests run: 4, Failures: 0, Errors: 0, Skipped: 3, Time elapsed: 0.129 s - in org.biojava.nbio.structure.io.TestMMCIFWriting
-[INFO] Running org.biojava.nbio.structure.io.sifts.SiftsChainToUniprotMappingTest
+Using PDB_DIR=/tmp as temporary file directory
+[WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.4 s - in org.biojava.nbio.structure.io.mmcif.TestChemCompProvider
+[INFO] Running org.biojava.nbio.structure.io.TestTitleParsing
+[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.007 s - in org.biojava.nbio.structure.io.TestTitleParsing
+[INFO] Running org.biojava.nbio.structure.io.TestShortLines
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
 SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.04 s - in org.biojava.nbio.structure.io.sifts.SiftsChainToUniprotMappingTest
-[INFO] Running org.biojava.nbio.structure.io.TestURLBasedFileParsing
-[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.007 s - in org.biojava.nbio.structure.io.TestURLBasedFileParsing
-[INFO] Running org.biojava.nbio.structure.io.TestParseMmCIFFeatures
-[WARNING] Tests run: 4, Failures: 0, Errors: 0, Skipped: 4, Time elapsed: 0.008 s - in org.biojava.nbio.structure.io.TestParseMmCIFFeatures
-[INFO] Running org.biojava.nbio.structure.io.TestShortLines
+[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.274 s - in org.biojava.nbio.structure.io.TestShortLines
+[INFO] Running org.biojava.nbio.structure.io.TestMMCIFWriting
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
 SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.332 s - in org.biojava.nbio.structure.io.TestShortLines
-[INFO] Running org.biojava.nbio.structure.io.TestTitleParsing
-[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.007 s - in org.biojava.nbio.structure.io.TestTitleParsing
-[INFO] Running org.biojava.nbio.structure.TestPdbId
-[1ABC, PDB_00011ABC, 2ABC, 1ABA, 1100]
-[1100, 1ABA, 1ABC, 2ABC, PDB_00011ABC]
-[1100, 1ABA, 1ABC, 2ABC, PDB_00011ABC]
-[INFO] Tests run: 12, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.066 s - in org.biojava.nbio.structure.TestPdbId
-[INFO] Running org.biojava.nbio.structure.ResidueRangeTest
+[WARNING] Tests run: 4, Failures: 0, Errors: 0, Skipped: 3, Time elapsed: 0.12 s - in org.biojava.nbio.structure.io.TestMMCIFWriting
+[INFO] Running org.biojava.nbio.structure.io.TestSiftsParsing
+[WARNING] Tests run: 4, Failures: 0, Errors: 0, Skipped: 4, Time elapsed: 0.007 s - in org.biojava.nbio.structure.io.TestSiftsParsing
+[INFO] Running org.biojava.nbio.structure.TestStructureCrossReferences
+[WARNING] Tests run: 4, Failures: 0, Errors: 0, Skipped: 4, Time elapsed: 0.008 s - in org.biojava.nbio.structure.TestStructureCrossReferences
+[INFO] Running org.biojava.nbio.structure.SiteTest
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
 SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[WARNING] Tests run: 14, Failures: 0, Errors: 0, Skipped: 7, Time elapsed: 0.065 s - in org.biojava.nbio.structure.ResidueRangeTest
-[INFO] Running org.biojava.nbio.structure.TestBond
-[WARNING] Tests run: 15, Failures: 0, Errors: 0, Skipped: 15, Time elapsed: 0.01 s - in org.biojava.nbio.structure.TestBond
-[INFO] Running org.biojava.nbio.structure.redmine.Test1DARSeqAlign
-[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.007 s - in org.biojava.nbio.structure.redmine.Test1DARSeqAlign
-[INFO] Running org.biojava.nbio.structure.SiteTest
+[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.032 s - in org.biojava.nbio.structure.SiteTest
+[INFO] Running org.biojava.nbio.structure.ChemCompTest
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
 SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.028 s - in org.biojava.nbio.structure.SiteTest
-[INFO] Running org.biojava.nbio.structure.PdbFileFormat30Test
+[WARNING] Tests run: 4, Failures: 0, Errors: 0, Skipped: 3, Time elapsed: 0.239 s - in org.biojava.nbio.structure.ChemCompTest
+[INFO] Running org.biojava.nbio.structure.xtal.TestSpaceGroup
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
 SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.835 s - in org.biojava.nbio.structure.PdbFileFormat30Test
-[INFO] Running org.biojava.nbio.structure.basepairs.TestBasePairParameters
-[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.006 s - in org.biojava.nbio.structure.basepairs.TestBasePairParameters
-[INFO] Running org.biojava.nbio.structure.align.client.TestStructureName
+[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.461 s - in org.biojava.nbio.structure.xtal.TestSpaceGroup
+[INFO] Running org.biojava.nbio.structure.xtal.TestInterfaceClustering
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
 SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[WARNING] Tests run: 6, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.027 s - in org.biojava.nbio.structure.align.client.TestStructureName
-[INFO] Running org.biojava.nbio.structure.align.TestAlignmentConsistency
-[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.007 s - in org.biojava.nbio.structure.align.TestAlignmentConsistency
-[INFO] Running org.biojava.nbio.structure.align.ce.CeCPMainTest
+[WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 2.822 s - in org.biojava.nbio.structure.xtal.TestInterfaceClustering
+[INFO] Running org.biojava.nbio.structure.xtal.TestCrystalInfo
+[WARNING] Tests run: 4, Failures: 0, Errors: 0, Skipped: 4, Time elapsed: 0.007 s - in org.biojava.nbio.structure.xtal.TestCrystalInfo
+[INFO] Running org.biojava.nbio.structure.xtal.TestCrystalCell
+[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.015 s - in org.biojava.nbio.structure.xtal.TestCrystalCell
+[INFO] Running org.biojava.nbio.structure.TestAtomCache
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
 SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[WARNING] Tests run: 5, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.057 s - in org.biojava.nbio.structure.align.ce.CeCPMainTest
-[INFO] Running org.biojava.nbio.structure.align.ce.TestSmallAlignment
-[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.006 s - in org.biojava.nbio.structure.align.ce.TestSmallAlignment
-[INFO] Running org.biojava.nbio.structure.align.util.RotationAxisTest
+[WARNING] Tests run: 7, Failures: 0, Errors: 0, Skipped: 4, Time elapsed: 0.452 s - in org.biojava.nbio.structure.TestAtomCache
+[INFO] Running org.biojava.nbio.structure.TestExperimentalTechniques
+[WARNING] Tests run: 4, Failures: 0, Errors: 0, Skipped: 4, Time elapsed: 0.006 s - in org.biojava.nbio.structure.TestExperimentalTechniques
+[INFO] Running org.biojava.nbio.structure.TestVeryLongFileName
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
 SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.021 s - in org.biojava.nbio.structure.align.util.RotationAxisTest
-[INFO] Running org.biojava.nbio.structure.align.util.AtomCacheTest
+[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.051 s - in org.biojava.nbio.structure.TestVeryLongFileName
+[INFO] Running org.biojava.nbio.structure.TestAtomIterator
+[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.008 s - in org.biojava.nbio.structure.TestAtomIterator
+[INFO] Running org.biojava.nbio.structure.TestEntityResIndexMapping
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
 SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[WARNING] Tests run: 10, Failures: 0, Errors: 0, Skipped: 8, Time elapsed: 0.06 s - in org.biojava.nbio.structure.align.util.AtomCacheTest
-[INFO] Running org.biojava.nbio.structure.align.multiple.TestAFPChainConversion
+[WARNING] Tests run: 4, Failures: 0, Errors: 0, Skipped: 3, Time elapsed: 0.48 s - in org.biojava.nbio.structure.TestEntityResIndexMapping
+[INFO] Running org.biojava.nbio.structure.TestKeywords
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
 SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.03 s - in org.biojava.nbio.structure.align.multiple.TestAFPChainConversion
-[INFO] Running org.biojava.nbio.structure.align.multiple.util.TestMultipleAlignmentScorer
+[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.873 s - in org.biojava.nbio.structure.TestKeywords
+[INFO] Running org.biojava.nbio.structure.redmine.Test1DARSeqAlign
+[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.006 s - in org.biojava.nbio.structure.redmine.Test1DARSeqAlign
+[INFO] Running org.biojava.nbio.structure.Test2JA5
+[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.007 s - in org.biojava.nbio.structure.Test2JA5
+[INFO] Running org.biojava.nbio.structure.TestURLIdentifier
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
 SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.055 s - in org.biojava.nbio.structure.align.multiple.util.TestMultipleAlignmentScorer
-[INFO] Running org.biojava.nbio.structure.align.multiple.util.TestMultipleAlignmentXMLParser
-[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.006 s - in org.biojava.nbio.structure.align.multiple.util.TestMultipleAlignmentXMLParser
-[INFO] Running org.biojava.nbio.structure.align.multiple.util.TestMultipleAlignmentWriter
-[WARNING] Tests run: 6, Failures: 0, Errors: 0, Skipped: 6, Time elapsed: 0.007 s - in org.biojava.nbio.structure.align.multiple.util.TestMultipleAlignmentWriter
-[INFO] Running org.biojava.nbio.structure.align.multiple.util.TestMultipleAlignmentTools
-[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.013 s - in org.biojava.nbio.structure.align.multiple.util.TestMultipleAlignmentTools
-[INFO] Running org.biojava.nbio.structure.symmetry.utils.TestSymmetryTools
+[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.22 s - in org.biojava.nbio.structure.TestURLIdentifier
+[INFO] Running org.biojava.nbio.structure.chem.TestDownloadChemCompProvider
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
 SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.016 s - in org.biojava.nbio.structure.symmetry.utils.TestSymmetryTools
-[INFO] Running org.biojava.nbio.structure.symmetry.internal.TestSequenceFunctionOrderDetector
-[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.007 s - in org.biojava.nbio.structure.symmetry.internal.TestSequenceFunctionOrderDetector
-[INFO] Running org.biojava.nbio.structure.symmetry.internal.TestSingleRefiner
+[WARNING] Tests run: 5, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.231 s - in org.biojava.nbio.structure.chem.TestDownloadChemCompProvider
+[INFO] Running org.biojava.nbio.structure.asa.TestAsaCalc
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
 SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.024 s - in org.biojava.nbio.structure.symmetry.internal.TestSingleRefiner
-[INFO] Running org.biojava.nbio.structure.symmetry.internal.TestCeSymm
-[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.006 s - in org.biojava.nbio.structure.symmetry.internal.TestCeSymm
-[INFO] Running org.biojava.nbio.structure.symmetry.internal.TestSymmetryAxes
-[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.021 s - in org.biojava.nbio.structure.symmetry.internal.TestSymmetryAxes
-[INFO] Running org.biojava.nbio.structure.TestExperimentalTechniques
-[WARNING] Tests run: 4, Failures: 0, Errors: 0, Skipped: 4, Time elapsed: 0.015 s - in org.biojava.nbio.structure.TestExperimentalTechniques
+[WARNING] Tests run: 6, Failures: 0, Errors: 0, Skipped: 4, Time elapsed: 0.025 s - in org.biojava.nbio.structure.asa.TestAsaCalc
+[INFO] Running org.biojava.nbio.structure.TestCloning
+[WARNING] Tests run: 7, Failures: 0, Errors: 0, Skipped: 7, Time elapsed: 0.006 s - in org.biojava.nbio.structure.TestCloning
 [INFO] Running org.biojava.nbio.structure.contact.TestInterfaceFinder
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
@@ -13154,90 +13154,126 @@
 <CA R 0 3.0 3.0 3.0, CA R 0 5.0 8.0 4.0> - 5.477225575051661
 Interface <B, C>
 <CA R 0 7.0 3.0 3.0, CA R 0 5.0 8.0 4.0> - 5.477225575051661
-[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.074 s - in org.biojava.nbio.structure.contact.TestInterfaceFinder
+[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.075 s - in org.biojava.nbio.structure.contact.TestInterfaceFinder
 [INFO] Running org.biojava.nbio.structure.contact.TestContactCalc
 [WARNING] Tests run: 6, Failures: 0, Errors: 0, Skipped: 6, Time elapsed: 0.008 s - in org.biojava.nbio.structure.contact.TestContactCalc
-[INFO] Running org.biojava.nbio.structure.TestAltLocs
+[INFO] Running org.biojava.nbio.structure.symmetry.utils.TestSymmetryTools
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
 SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[WARNING] Tests run: 15, Failures: 0, Errors: 0, Skipped: 11, Time elapsed: 0.411 s - in org.biojava.nbio.structure.TestAltLocs
-[INFO] Running org.biojava.nbio.structure.asa.TestAsaCalc
+[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.015 s - in org.biojava.nbio.structure.symmetry.utils.TestSymmetryTools
+[INFO] Running org.biojava.nbio.structure.symmetry.internal.TestSequenceFunctionOrderDetector
+[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.006 s - in org.biojava.nbio.structure.symmetry.internal.TestSequenceFunctionOrderDetector
+[INFO] Running org.biojava.nbio.structure.symmetry.internal.TestCeSymm
+[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.006 s - in org.biojava.nbio.structure.symmetry.internal.TestCeSymm
+[INFO] Running org.biojava.nbio.structure.symmetry.internal.TestSymmetryAxes
+[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.018 s - in org.biojava.nbio.structure.symmetry.internal.TestSymmetryAxes
+[INFO] Running org.biojava.nbio.structure.symmetry.internal.TestSingleRefiner
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
 SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[WARNING] Tests run: 6, Failures: 0, Errors: 0, Skipped: 4, Time elapsed: 0.032 s - in org.biojava.nbio.structure.asa.TestAsaCalc
-[INFO] Running org.biojava.nbio.structure.TestVeryLongFileName
+[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.028 s - in org.biojava.nbio.structure.symmetry.internal.TestSingleRefiner
+[INFO] Running org.biojava.nbio.structure.basepairs.TestBasePairParameters
+[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.006 s - in org.biojava.nbio.structure.basepairs.TestBasePairParameters
+[INFO] Running org.biojava.nbio.structure.TestBond
+[WARNING] Tests run: 15, Failures: 0, Errors: 0, Skipped: 15, Time elapsed: 0.008 s - in org.biojava.nbio.structure.TestBond
+[INFO] Running org.biojava.nbio.structure.TestBioAssemblyIdentifier
+[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.008 s - in org.biojava.nbio.structure.TestBioAssemblyIdentifier
+[INFO] Running org.biojava.nbio.structure.secstruc.TestDSSPParser
+[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.008 s - in org.biojava.nbio.structure.secstruc.TestDSSPParser
+[INFO] Running org.biojava.nbio.structure.secstruc.TestSecStrucCalc
+[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.006 s - in org.biojava.nbio.structure.secstruc.TestSecStrucCalc
+[INFO] Running org.biojava.nbio.structure.SourceCompoundTest
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
 SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.052 s - in org.biojava.nbio.structure.TestVeryLongFileName
-[INFO] Running org.biojava.nbio.structure.TestDNAAlignment
-[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.007 s - in org.biojava.nbio.structure.TestDNAAlignment
-[INFO] Running org.biojava.nbio.structure.ChemCompTest
+[INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.147 s - in org.biojava.nbio.structure.SourceCompoundTest
+[INFO] Running org.biojava.nbio.structure.TestStructureImpl
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
 SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[WARNING] Tests run: 4, Failures: 0, Errors: 0, Skipped: 3, Time elapsed: 0.278 s - in org.biojava.nbio.structure.ChemCompTest
-[INFO] Running org.biojava.nbio.structure.TestStructureImpl
+[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.056 s - in org.biojava.nbio.structure.TestStructureImpl
+[INFO] Running org.biojava.nbio.structure.Test4hhb
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
 SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.063 s - in org.biojava.nbio.structure.TestStructureImpl
-[INFO] Running org.biojava.nbio.structure.TestStructureCrossReferences
-[WARNING] Tests run: 4, Failures: 0, Errors: 0, Skipped: 4, Time elapsed: 0.009 s - in org.biojava.nbio.structure.TestStructureCrossReferences
-[INFO] Running org.biojava.nbio.structure.TestAtomCache
+[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.906 s - in org.biojava.nbio.structure.Test4hhb
+[INFO] Running org.biojava.nbio.structure.PDBStatusTest
+[WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 3, Time elapsed: 0.006 s - in org.biojava.nbio.structure.PDBStatusTest
+[INFO] Running org.biojava.nbio.structure.TestAltLocs
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
 SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[WARNING] Tests run: 7, Failures: 0, Errors: 0, Skipped: 4, Time elapsed: 0.401 s - in org.biojava.nbio.structure.TestAtomCache
-[INFO] Running org.biojava.nbio.structure.PDBStatusTest
-[WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 3, Time elapsed: 0.007 s - in org.biojava.nbio.structure.PDBStatusTest
-[INFO] Running org.biojava.nbio.structure.SourceCompoundTest
+[WARNING] Tests run: 15, Failures: 0, Errors: 0, Skipped: 11, Time elapsed: 0.449 s - in org.biojava.nbio.structure.TestAltLocs
+[INFO] Running org.biojava.nbio.structure.ElementTest
+[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.011 s - in org.biojava.nbio.structure.ElementTest
+[INFO] Running org.biojava.nbio.structure.TestParsingCalcium
+[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.007 s - in org.biojava.nbio.structure.TestParsingCalcium
+[INFO] Running org.biojava.nbio.structure.TestPdbId
+[1ABC, PDB_00011ABC, 2ABC, 1ABA, 1100]
+[1100, 1ABA, 1ABC, 2ABC, PDB_00011ABC]
+[1100, 1ABA, 1ABC, 2ABC, PDB_00011ABC]
+[INFO] Tests run: 12, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.082 s - in org.biojava.nbio.structure.TestPdbId
+[INFO] Running org.biojava.nbio.structure.TestEntityHeuristics
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
 SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.236 s - in org.biojava.nbio.structure.SourceCompoundTest
-[INFO] Running org.biojava.nbio.structure.TestBioAssemblyIdentifier
-[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.007 s - in org.biojava.nbio.structure.TestBioAssemblyIdentifier
-[INFO] Running org.biojava.nbio.structure.HetatomImplTest
+[INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.822 s - in org.biojava.nbio.structure.TestEntityHeuristics
+[INFO] Running org.biojava.nbio.structure.ResidueNumberTest
+[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.012 s - in org.biojava.nbio.structure.ResidueNumberTest
+[INFO] Running org.biojava.nbio.structure.cluster.TestSubunitExtractor
+[WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 3, Time elapsed: 0.008 s - in org.biojava.nbio.structure.cluster.TestSubunitExtractor
+[INFO] Running org.biojava.nbio.structure.cluster.TestSubunitCluster
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
 SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.059 s - in org.biojava.nbio.structure.HetatomImplTest
-[INFO] Running org.biojava.nbio.structure.TestNucleotides
-[WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 3, Time elapsed: 0.006 s - in org.biojava.nbio.structure.TestNucleotides
-[INFO] Running org.biojava.nbio.structure.TestKeywords
+[WARNING] Tests run: 5, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.112 s - in org.biojava.nbio.structure.cluster.TestSubunitCluster
+[INFO] Running org.biojava.nbio.structure.align.TestAlignmentConsistency
+[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.007 s - in org.biojava.nbio.structure.align.TestAlignmentConsistency
+[INFO] Running org.biojava.nbio.structure.align.ce.CeCPMainTest
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
 SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.328 s - in org.biojava.nbio.structure.TestKeywords
-[INFO] Running org.biojava.nbio.structure.xtal.TestCrystalInfo
-[WARNING] Tests run: 4, Failures: 0, Errors: 0, Skipped: 4, Time elapsed: 0.009 s - in org.biojava.nbio.structure.xtal.TestCrystalInfo
-[INFO] Running org.biojava.nbio.structure.xtal.TestInterfaceClustering
+[WARNING] Tests run: 5, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.068 s - in org.biojava.nbio.structure.align.ce.CeCPMainTest
+[INFO] Running org.biojava.nbio.structure.align.ce.TestSmallAlignment
+[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.007 s - in org.biojava.nbio.structure.align.ce.TestSmallAlignment
+[INFO] Running org.biojava.nbio.structure.align.client.TestStructureName
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
 SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 3.702 s - in org.biojava.nbio.structure.xtal.TestInterfaceClustering
-[INFO] Running org.biojava.nbio.structure.xtal.TestSpaceGroup
+[WARNING] Tests run: 6, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.031 s - in org.biojava.nbio.structure.align.client.TestStructureName
+[INFO] Running org.biojava.nbio.structure.align.util.AtomCacheTest
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
 SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.395 s - in org.biojava.nbio.structure.xtal.TestSpaceGroup
-[INFO] Running org.biojava.nbio.structure.xtal.TestCrystalCell
-[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.016 s - in org.biojava.nbio.structure.xtal.TestCrystalCell
-[INFO] Running org.biojava.nbio.structure.Test2JA5
-[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.006 s - in org.biojava.nbio.structure.Test2JA5
-[INFO] Running org.biojava.nbio.structure.chem.TestDownloadChemCompProvider
+[WARNING] Tests run: 10, Failures: 0, Errors: 0, Skipped: 8, Time elapsed: 0.075 s - in org.biojava.nbio.structure.align.util.AtomCacheTest
+[INFO] Running org.biojava.nbio.structure.align.util.RotationAxisTest
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
 SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[WARNING] Tests run: 5, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.265 s - in org.biojava.nbio.structure.chem.TestDownloadChemCompProvider
-[INFO] Running org.biojava.nbio.structure.TestEntityResIndexMapping
+[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.023 s - in org.biojava.nbio.structure.align.util.RotationAxisTest
+[INFO] Running org.biojava.nbio.structure.align.multiple.TestAFPChainConversion
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
 SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[WARNING] Tests run: 4, Failures: 0, Errors: 0, Skipped: 3, Time elapsed: 0.488 s - in org.biojava.nbio.structure.TestEntityResIndexMapping
+[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.037 s - in org.biojava.nbio.structure.align.multiple.TestAFPChainConversion
+[INFO] Running org.biojava.nbio.structure.align.multiple.util.TestMultipleAlignmentXMLParser
+[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.008 s - in org.biojava.nbio.structure.align.multiple.util.TestMultipleAlignmentXMLParser
+[INFO] Running org.biojava.nbio.structure.align.multiple.util.TestMultipleAlignmentScorer
+SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
+SLF4J: Defaulting to no-operation (NOP) logger implementation
+SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
+[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.061 s - in org.biojava.nbio.structure.align.multiple.util.TestMultipleAlignmentScorer
+[INFO] Running org.biojava.nbio.structure.align.multiple.util.TestMultipleAlignmentTools
+[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.012 s - in org.biojava.nbio.structure.align.multiple.util.TestMultipleAlignmentTools
+[INFO] Running org.biojava.nbio.structure.align.multiple.util.TestMultipleAlignmentWriter
+[WARNING] Tests run: 6, Failures: 0, Errors: 0, Skipped: 6, Time elapsed: 0.009 s - in org.biojava.nbio.structure.align.multiple.util.TestMultipleAlignmentWriter
+[INFO] Running org.biojava.nbio.structure.TestLoadStructureFromURL
+[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.006 s - in org.biojava.nbio.structure.TestLoadStructureFromURL
+[INFO] Running org.biojava.nbio.structure.AtomPositionMapTest
+[WARNING] Tests run: 5, Failures: 0, Errors: 0, Skipped: 5, Time elapsed: 0.006 s - in org.biojava.nbio.structure.AtomPositionMapTest
+[INFO] Running org.biojava.nbio.structure.TestDNAAlignment
+[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.007 s - in org.biojava.nbio.structure.TestDNAAlignment
 [INFO] 
 [INFO] Results:
 [INFO] 
@@ -13284,21 +13320,21 @@
 [INFO] -------------------------------------------------------
 [INFO]  T E S T S
 [INFO] -------------------------------------------------------
-[INFO] Running org.biojava.nbio.structure.symmetry.TestJmolSymmetryScriptGenerator
-[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.061 s - in org.biojava.nbio.structure.symmetry.TestJmolSymmetryScriptGenerator
-[INFO] Running org.biojava.nbio.structure.gui.JmolViewerImplTest
-[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.05 s - in org.biojava.nbio.structure.gui.JmolViewerImplTest
 [INFO] Running org.biojava.nbio.structure.gui.TestAtomInfo
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
 SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.055 s - in org.biojava.nbio.structure.gui.TestAtomInfo
+[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.064 s - in org.biojava.nbio.structure.gui.TestAtomInfo
 [INFO] Running org.biojava.nbio.structure.gui.ViewerTest
-[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.053 s - in org.biojava.nbio.structure.gui.ViewerTest
-[INFO] Running org.biojava.nbio.structure.gui.StructureViewerTest
-[INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.064 s - in org.biojava.nbio.structure.gui.StructureViewerTest
+[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.062 s - in org.biojava.nbio.structure.gui.ViewerTest
 [INFO] Running org.biojava.nbio.structure.gui.RenderStyleTest
-[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.055 s - in org.biojava.nbio.structure.gui.RenderStyleTest
+[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.066 s - in org.biojava.nbio.structure.gui.RenderStyleTest
+[INFO] Running org.biojava.nbio.structure.gui.StructureViewerTest
+[INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.056 s - in org.biojava.nbio.structure.gui.StructureViewerTest
+[INFO] Running org.biojava.nbio.structure.gui.JmolViewerImplTest
+[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.058 s - in org.biojava.nbio.structure.gui.JmolViewerImplTest
+[INFO] Running org.biojava.nbio.structure.symmetry.TestJmolSymmetryScriptGenerator
+[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.052 s - in org.biojava.nbio.structure.symmetry.TestJmolSymmetryScriptGenerator
 [INFO] 
 [INFO] Results:
 [INFO] 
@@ -13330,47 +13366,47 @@
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
 SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.062 s - in org.biojava.nbio.genome.TestChromosomeMappingTools
+[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.086 s - in org.biojava.nbio.genome.TestChromosomeMappingTools
+[INFO] Running org.biojava.nbio.genome.TestIssue355
+[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.049 s - in org.biojava.nbio.genome.TestIssue355
+[INFO] Running org.biojava.nbio.genome.io.fastq.SolexaFastqReaderTest
+[INFO] Tests run: 25, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.208 s - in org.biojava.nbio.genome.io.fastq.SolexaFastqReaderTest
+[INFO] Running org.biojava.nbio.genome.io.fastq.StreamingFastqParserTest
+[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.053 s - in org.biojava.nbio.genome.io.fastq.StreamingFastqParserTest
+[INFO] Running org.biojava.nbio.genome.io.fastq.FastqBuilderTest
+[INFO] Tests run: 23, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.064 s - in org.biojava.nbio.genome.io.fastq.FastqBuilderTest
 [INFO] Running org.biojava.nbio.genome.io.fastq.IlluminaFastqReaderTest
-[INFO] Tests run: 25, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.146 s - in org.biojava.nbio.genome.io.fastq.IlluminaFastqReaderTest
+[INFO] Tests run: 25, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.145 s - in org.biojava.nbio.genome.io.fastq.IlluminaFastqReaderTest
+[INFO] Running org.biojava.nbio.genome.io.fastq.SolexaFastqWriterTest
+[INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.092 s - in org.biojava.nbio.genome.io.fastq.SolexaFastqWriterTest
+[INFO] Running org.biojava.nbio.genome.io.fastq.SangerFastqReaderTest
+[INFO] Tests run: 29, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.154 s - in org.biojava.nbio.genome.io.fastq.SangerFastqReaderTest
+[INFO] Running org.biojava.nbio.genome.io.fastq.SangerFastqWriterTest
+[INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.075 s - in org.biojava.nbio.genome.io.fastq.SangerFastqWriterTest
 [INFO] Running org.biojava.nbio.genome.io.fastq.FastqToolsTest
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
 SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 40, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.119 s - in org.biojava.nbio.genome.io.fastq.FastqToolsTest
-[INFO] Running org.biojava.nbio.genome.io.fastq.SolexaFastqReaderTest
-[INFO] Tests run: 25, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.124 s - in org.biojava.nbio.genome.io.fastq.SolexaFastqReaderTest
-[INFO] Running org.biojava.nbio.genome.io.fastq.FastqBuilderTest
-[INFO] Tests run: 23, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.063 s - in org.biojava.nbio.genome.io.fastq.FastqBuilderTest
-[INFO] Running org.biojava.nbio.genome.io.fastq.SolexaFastqWriterTest
-[INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.081 s - in org.biojava.nbio.genome.io.fastq.SolexaFastqWriterTest
+[INFO] Tests run: 40, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.101 s - in org.biojava.nbio.genome.io.fastq.FastqToolsTest
 [INFO] Running org.biojava.nbio.genome.io.fastq.ConvertTest
-[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.138 s - in org.biojava.nbio.genome.io.fastq.ConvertTest
-[INFO] Running org.biojava.nbio.genome.io.fastq.SangerFastqReaderTest
-[INFO] Tests run: 29, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.139 s - in org.biojava.nbio.genome.io.fastq.SangerFastqReaderTest
+[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.109 s - in org.biojava.nbio.genome.io.fastq.ConvertTest
+[INFO] Running org.biojava.nbio.genome.io.fastq.FastqVariantTest
+[INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.049 s - in org.biojava.nbio.genome.io.fastq.FastqVariantTest
 [INFO] Running org.biojava.nbio.genome.io.fastq.IlluminaFastqWriterTest
-[INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.079 s - in org.biojava.nbio.genome.io.fastq.IlluminaFastqWriterTest
-[INFO] Running org.biojava.nbio.genome.io.fastq.StreamingFastqParserTest
-[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.054 s - in org.biojava.nbio.genome.io.fastq.StreamingFastqParserTest
+[INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.071 s - in org.biojava.nbio.genome.io.fastq.IlluminaFastqWriterTest
 [INFO] Running org.biojava.nbio.genome.io.fastq.FastqTest
-[INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.056 s - in org.biojava.nbio.genome.io.fastq.FastqTest
-[INFO] Running org.biojava.nbio.genome.io.fastq.SangerFastqWriterTest
-[INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.077 s - in org.biojava.nbio.genome.io.fastq.SangerFastqWriterTest
-[INFO] Running org.biojava.nbio.genome.io.fastq.FastqVariantTest
-[INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.065 s - in org.biojava.nbio.genome.io.fastq.FastqVariantTest
-[INFO] Running org.biojava.nbio.genome.TestGenomeMapping
-[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.051 s - in org.biojava.nbio.genome.TestGenomeMapping
+[INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.064 s - in org.biojava.nbio.genome.io.fastq.FastqTest
 [INFO] Running org.biojava.nbio.genome.FeatureListTest
-[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.052 s - in org.biojava.nbio.genome.FeatureListTest
+[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.051 s - in org.biojava.nbio.genome.FeatureListTest
+[INFO] Running org.biojava.nbio.genome.TestGenomeMapping
+[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.048 s - in org.biojava.nbio.genome.TestGenomeMapping
 [INFO] Running org.biojava.nbio.genome.GeneFeatureHelperTest
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
 SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.481 s - in org.biojava.nbio.genome.GeneFeatureHelperTest
-[INFO] Running org.biojava.nbio.genome.TestIssue355
-[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.049 s - in org.biojava.nbio.genome.TestIssue355
+[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.488 s - in org.biojava.nbio.genome.GeneFeatureHelperTest
 [INFO] Running org.biojava.nbio.genome.TestLocation
-[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.053 s - in org.biojava.nbio.genome.TestLocation
+[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.046 s - in org.biojava.nbio.genome.TestLocation
 [INFO] 
 [INFO] Results:
 [INFO] 
@@ -13398,20 +13434,20 @@
 [INFO] -------------------------------------------------------
 [INFO]  T E S T S
 [INFO] -------------------------------------------------------
-[INFO] Running org.biojava.nbio.protmod.structure.ProteinModificationRegistryTest
+[INFO] Running org.biojava.nbio.protmod.structure.ProteinModificationParserTest
+[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.054 s - in org.biojava.nbio.protmod.structure.ProteinModificationParserTest
+[INFO] Running org.biojava.nbio.protmod.structure.ModifiedCompoundSerializationTest
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
 SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.244 s - in org.biojava.nbio.protmod.structure.ProteinModificationRegistryTest
-[INFO] Running org.biojava.nbio.protmod.structure.ModifiedCompoundSerializationTest
+[WARNING] Tests run: 6, Failures: 0, Errors: 0, Skipped: 5, Time elapsed: 0.226 s - in org.biojava.nbio.protmod.structure.ModifiedCompoundSerializationTest
+[INFO] Running org.biojava.nbio.protmod.structure.ProteinModificationRegistryTest
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
 SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[WARNING] Tests run: 6, Failures: 0, Errors: 0, Skipped: 5, Time elapsed: 0.245 s - in org.biojava.nbio.protmod.structure.ModifiedCompoundSerializationTest
-[INFO] Running org.biojava.nbio.protmod.structure.ProteinModificationParserTest
-[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.066 s - in org.biojava.nbio.protmod.structure.ProteinModificationParserTest
+[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.266 s - in org.biojava.nbio.protmod.structure.ProteinModificationRegistryTest
 [INFO] Running org.biojava.nbio.protmod.phosphosite.TestAcetylation
-[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.048 s - in org.biojava.nbio.protmod.phosphosite.TestAcetylation
+[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.047 s - in org.biojava.nbio.protmod.phosphosite.TestAcetylation
 [INFO] 
 [INFO] Results:
 [INFO] 
@@ -13440,7 +13476,7 @@
 [INFO]  T E S T S
 [INFO] -------------------------------------------------------
 [INFO] Running org.biojava.nbio.ws.hmmer.TestRemoteHmmerScan
-[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.078 s - in org.biojava.nbio.ws.hmmer.TestRemoteHmmerScan
+[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.047 s - in org.biojava.nbio.ws.hmmer.TestRemoteHmmerScan
 [INFO] 
 [INFO] Results:
 [INFO] 
@@ -13469,12 +13505,12 @@
 [INFO]  T E S T S
 [INFO] -------------------------------------------------------
 [INFO] Running org.biojava.nbio.ronn.NonstandardProteinCompoundTest
-[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 6.056 s - in org.biojava.nbio.ronn.NonstandardProteinCompoundTest
+[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 6.051 s - in org.biojava.nbio.ronn.NonstandardProteinCompoundTest
 [INFO] Running org.biojava.nbio.ronn.JronnTest
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
 SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.839 s - in org.biojava.nbio.ronn.JronnTest
+[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 3.758 s - in org.biojava.nbio.ronn.JronnTest
 [INFO] 
 [INFO] Results:
 [INFO] 
@@ -13502,27 +13538,6 @@
 [INFO] -------------------------------------------------------
 [INFO]  T E S T S
 [INFO] -------------------------------------------------------
-[INFO] Running org.biojava.nbio.aaproperties.PeptidePropertiesImplTest
-SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
-SLF4J: Defaulting to no-operation (NOP) logger implementation
-SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 24, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.566 s - in org.biojava.nbio.aaproperties.PeptidePropertiesImplTest
-[INFO] Running org.biojava.nbio.aaproperties.CookBookTest
-SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
-SLF4J: Defaulting to no-operation (NOP) logger implementation
-SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.372 s - in org.biojava.nbio.aaproperties.CookBookTest
-[INFO] Running org.biojava.nbio.aaproperties.GenbankCommandPromptTest
-SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
-SLF4J: Defaulting to no-operation (NOP) logger implementation
-SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-SequenceName,MolecularWeight,ExtinctionCoefficient_True,ExtinctionCoefficient_False,IsoelectricPoint
-NP_000257                133 aa            linear   PRI 27-MAR-2008,15043.5262,5960.0,6585.0,9.1715
-SequenceName,A,N,MolecularWeight
-NP_000257                133 aa            linear   PRI 27-MAR-2008,0.0451,0.0075,15043.5262
-SequenceName,A,N,MolecularWeight
-NP_000257                133 aa            linear   PRI 27-MAR-2008,0.0451,0.0075,15043.5262
-[INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.414 s - in org.biojava.nbio.aaproperties.GenbankCommandPromptTest
 [INFO] Running org.biojava.nbio.aaproperties.CommandPromptTest
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
@@ -13539,27 +13554,48 @@
 SAOV_0114,0.101,0.0525,53660.5723
 SAOV_0094,0.0537,0.0767,45884.0164
 SAA6008_00126,0.0955,0.0414,95002.026
-[INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.454 s - in org.biojava.nbio.aaproperties.CommandPromptTest
-[INFO] Running org.biojava.nbio.aaproperties.xml.AminoAcidTest
+[INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.458 s - in org.biojava.nbio.aaproperties.CommandPromptTest
+[INFO] Running org.biojava.nbio.aaproperties.GenbankCommandPromptTest
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
 SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.458 s - in org.biojava.nbio.aaproperties.xml.AminoAcidTest
-[INFO] Running org.biojava.nbio.aaproperties.xml.ElementTest
+SequenceName,MolecularWeight,ExtinctionCoefficient_True,ExtinctionCoefficient_False,IsoelectricPoint
+NP_000257                133 aa            linear   PRI 27-MAR-2008,15043.5262,5960.0,6585.0,9.1715
+SequenceName,A,N,MolecularWeight
+NP_000257                133 aa            linear   PRI 27-MAR-2008,0.0451,0.0075,15043.5262
+SequenceName,A,N,MolecularWeight
+NP_000257                133 aa            linear   PRI 27-MAR-2008,0.0451,0.0075,15043.5262
+[INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.387 s - in org.biojava.nbio.aaproperties.GenbankCommandPromptTest
+[INFO] Running org.biojava.nbio.aaproperties.CookBookTest
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
 SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.394 s - in org.biojava.nbio.aaproperties.xml.ElementTest
+[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.367 s - in org.biojava.nbio.aaproperties.CookBookTest
 [INFO] Running org.biojava.nbio.aaproperties.xml.GenerateJavaCodesFromTextTest
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
 SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.08 s - in org.biojava.nbio.aaproperties.xml.GenerateJavaCodesFromTextTest
+[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.072 s - in org.biojava.nbio.aaproperties.xml.GenerateJavaCodesFromTextTest
+[INFO] Running org.biojava.nbio.aaproperties.xml.ElementTest
+SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
+SLF4J: Defaulting to no-operation (NOP) logger implementation
+SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
+[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.515 s - in org.biojava.nbio.aaproperties.xml.ElementTest
+[INFO] Running org.biojava.nbio.aaproperties.xml.AminoAcidTest
+SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
+SLF4J: Defaulting to no-operation (NOP) logger implementation
+SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
+[INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.559 s - in org.biojava.nbio.aaproperties.xml.AminoAcidTest
 [INFO] Running org.biojava.nbio.aaproperties.profeat.CookBookTest
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
 SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.056 s - in org.biojava.nbio.aaproperties.profeat.CookBookTest
+[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.059 s - in org.biojava.nbio.aaproperties.profeat.CookBookTest
+[INFO] Running org.biojava.nbio.aaproperties.PeptidePropertiesImplTest
+SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
+SLF4J: Defaulting to no-operation (NOP) logger implementation
+SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
+[INFO] Tests run: 24, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.551 s - in org.biojava.nbio.aaproperties.PeptidePropertiesImplTest
 [INFO] 
 [INFO] Results:
 [INFO] 
@@ -13610,17 +13646,17 @@
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
 SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.15 s - in org.biojava.nbio.ontology.TestParseSBO
+[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.144 s - in org.biojava.nbio.ontology.TestParseSBO
 [INFO] Running org.biojava.nbio.ontology.TestParseOBO
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
 SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.13 s - in org.biojava.nbio.ontology.TestParseOBO
+[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.113 s - in org.biojava.nbio.ontology.TestParseOBO
 [INFO] Running org.biojava.nbio.ontology.TestOboFileParsing
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
 SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.193 s - in org.biojava.nbio.ontology.TestOboFileParsing
+[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.183 s - in org.biojava.nbio.ontology.TestOboFileParsing
 [INFO] 
 [INFO] Results:
 [INFO] 
@@ -13648,26 +13684,26 @@
 [INFO] ------------------------------------------------------------------------
 [INFO] Reactor Summary for biojava 6.1.0:
 [INFO] 
-[INFO] biojava ............................................ SUCCESS [  0.003 s]
+[INFO] biojava ............................................ SUCCESS [  0.002 s]
 [INFO] biojava-core ....................................... SUCCESS [09:50 min]
-[INFO] biojava-forester ................................... SUCCESS [  0.081 s]
+[INFO] biojava-forester ................................... SUCCESS [  0.104 s]
 [INFO] biojava-alignment .................................. SUCCESS [03:00 min]
 [INFO] biojava-structure .................................. SUCCESS [16:20 min]
-[INFO] biojava-jcolorbrewer ............................... SUCCESS [  0.014 s]
+[INFO] biojava-jcolorbrewer ............................... SUCCESS [  0.018 s]
 [INFO] biojava-structure-gui .............................. SUCCESS [01:00 min]
 [INFO] biojava-genome ..................................... SUCCESS [03:00 min]
-[INFO] biojava-modfinder .................................. SUCCESS [ 40.084 s]
-[INFO] biojava-ws ......................................... SUCCESS [ 10.047 s]
-[INFO] biojava-protein-disorder ........................... SUCCESS [ 20.181 s]
+[INFO] biojava-modfinder .................................. SUCCESS [ 40.045 s]
+[INFO] biojava-ws ......................................... SUCCESS [ 10.027 s]
+[INFO] biojava-protein-disorder ........................... SUCCESS [ 20.023 s]
 [INFO] biojava-aa-prop .................................... SUCCESS [01:20 min]
-[INFO] biojava-survival ................................... SUCCESS [  0.032 s]
-[INFO] biojava-ontology ................................... SUCCESS [ 30.112 s]
-[INFO] biojava-protein-comparison-tool .................... SUCCESS [  0.042 s]
+[INFO] biojava-survival ................................... SUCCESS [  0.011 s]
+[INFO] biojava-ontology ................................... SUCCESS [ 30.024 s]
+[INFO] biojava-protein-comparison-tool .................... SUCCESS [  0.032 s]
 [INFO] ------------------------------------------------------------------------
 [INFO] BUILD SUCCESS
 [INFO] ------------------------------------------------------------------------
 [INFO] Total time:  36:12 min
-[INFO] Finished at: 2025-06-18T13:17:27-12:00
+[INFO] Finished at: 2024-05-17T09:40:34+14:00
 [INFO] ------------------------------------------------------------------------
    create-stamp debian/debhelper-build-stamp
    dh_prep
@@ -13884,26 +13920,26 @@
 [INFO] ------------------------------------------------------------------------
 [INFO] Reactor Summary for biojava 6.1.0:
 [INFO] 
-[INFO] biojava ............................................ SUCCESS [  0.423 s]
-[INFO] biojava-core ....................................... SUCCESS [  0.076 s]
-[INFO] biojava-forester ................................... SUCCESS [  0.048 s]
-[INFO] biojava-alignment .................................. SUCCESS [  0.041 s]
+[INFO] biojava ............................................ SUCCESS [  0.351 s]
+[INFO] biojava-core ....................................... SUCCESS [  0.053 s]
+[INFO] biojava-forester ................................... SUCCESS [  0.040 s]
+[INFO] biojava-alignment .................................. SUCCESS [  0.026 s]
 [INFO] biojava-structure .................................. SUCCESS [  0.039 s]
-[INFO] biojava-jcolorbrewer ............................... SUCCESS [  0.041 s]
-[INFO] biojava-structure-gui .............................. SUCCESS [  0.035 s]
-[INFO] biojava-genome ..................................... SUCCESS [  0.046 s]
-[INFO] biojava-modfinder .................................. SUCCESS [  0.034 s]
-[INFO] biojava-ws ......................................... SUCCESS [  0.030 s]
-[INFO] biojava-protein-disorder ........................... SUCCESS [  0.029 s]
-[INFO] biojava-aa-prop .................................... SUCCESS [  0.032 s]
-[INFO] biojava-survival ................................... SUCCESS [  0.033 s]
-[INFO] biojava-ontology ................................... SUCCESS [  0.039 s]
-[INFO] biojava-protein-comparison-tool .................... SUCCESS [  0.032 s]
+[INFO] biojava-jcolorbrewer ............................... SUCCESS [  0.023 s]
+[INFO] biojava-structure-gui .............................. SUCCESS [  0.038 s]
+[INFO] biojava-genome ..................................... SUCCESS [  0.026 s]
+[INFO] biojava-modfinder .................................. SUCCESS [  0.029 s]
+[INFO] biojava-ws ......................................... SUCCESS [  0.028 s]
+[INFO] biojava-protein-disorder ........................... SUCCESS [  0.023 s]
+[INFO] biojava-aa-prop .................................... SUCCESS [  0.023 s]
+[INFO] biojava-survival ................................... SUCCESS [  0.022 s]
+[INFO] biojava-ontology ................................... SUCCESS [  0.024 s]
+[INFO] biojava-protein-comparison-tool .................... SUCCESS [  0.022 s]
 [INFO] ------------------------------------------------------------------------
 [INFO] BUILD SUCCESS
 [INFO] ------------------------------------------------------------------------
-[INFO] Total time:  1.196 s
-[INFO] Finished at: 2025-06-18T13:17:29-12:00
+[INFO] Total time:  0.939 s
+[INFO] Finished at: 2024-05-17T09:40:36+14:00
 [INFO] ------------------------------------------------------------------------
 	mh_resolve_dependencies --non-interactive --offline --build -plibbiojava6-java --javadoc --base-directory=/build/reproducible-path/biojava6-live-6.1.0\+dfsg --non-explore
 Analysing pom.xml...
@@ -14139,8 +14175,8 @@
 dpkg-gencontrol: warning: package libbiojava6-java-doc: substitution variable ${maven:DocDepends} unused, but is defined
    dh_md5sums
    dh_builddeb
-dpkg-deb: building package 'libbiojava6-java' in '../libbiojava6-java_6.1.0+dfsg-4_all.deb'.
 dpkg-deb: building package 'libbiojava6-java-doc' in '../libbiojava6-java-doc_6.1.0+dfsg-4_all.deb'.
+dpkg-deb: building package 'libbiojava6-java' in '../libbiojava6-java_6.1.0+dfsg-4_all.deb'.
  dpkg-genbuildinfo --build=binary -O../biojava6-live_6.1.0+dfsg-4_amd64.buildinfo
  dpkg-genchanges --build=binary -O../biojava6-live_6.1.0+dfsg-4_amd64.changes
 dpkg-genchanges: info: binary-only upload (no source code included)
@@ -14148,12 +14184,14 @@
 dpkg-buildpackage: info: binary-only upload (no source included)
 dpkg-genchanges: info: not including original source code in upload
 I: copying local configuration
+I: user script /srv/workspace/pbuilder/1102110/tmp/hooks/B01_cleanup starting
+I: user script /srv/workspace/pbuilder/1102110/tmp/hooks/B01_cleanup finished
 I: unmounting dev/ptmx filesystem
 I: unmounting dev/pts filesystem
 I: unmounting dev/shm filesystem
 I: unmounting proc filesystem
 I: unmounting sys filesystem
 I: cleaning the build env 
-I: removing directory /srv/workspace/pbuilder/395956 and its subdirectories
-I: Current time: Wed Jun 18 13:23:14 -12 2025
-I: pbuilder-time-stamp: 1750296194
+I: removing directory /srv/workspace/pbuilder/1102110 and its subdirectories
+I: Current time: Fri May 17 09:46:53 +14 2024
+I: pbuilder-time-stamp: 1715888813