{"diffoscope-json-version": 1, "source1": "/srv/reproducible-results/rbuild-debian/r-b-build.4P0qaRbq/b1/jebl2_0.1+git20230701.b3c0f25-1_amd64.changes", "source2": "/srv/reproducible-results/rbuild-debian/r-b-build.4P0qaRbq/b2/jebl2_0.1+git20230701.b3c0f25-1_amd64.changes", "unified_diff": null, "details": [{"source1": "Files", "source2": "Files", "unified_diff": "@@ -1,3 +1,3 @@\n \n- 76ba7e5af5ee9529db8b0d5f7300ecda 308248 doc optional libjebl2-java-doc_0.1+git20230701.b3c0f25-1_all.deb\n+ 00aadd20e11896b7c1b590ddc1fc4a9c 308268 doc optional libjebl2-java-doc_0.1+git20230701.b3c0f25-1_all.deb\n 5a7a03d1c3d5e2eccc0552ab1ba50840 531736 java optional libjebl2-java_0.1+git20230701.b3c0f25-1_all.deb\n"}, {"source1": "libjebl2-java-doc_0.1+git20230701.b3c0f25-1_all.deb", "source2": "libjebl2-java-doc_0.1+git20230701.b3c0f25-1_all.deb", "unified_diff": null, "details": [{"source1": "file list", "source2": "file list", "unified_diff": "@@ -1,3 +1,3 @@\n -rw-r--r-- 0 0 0 4 2023-10-07 20:51:37.000000 debian-binary\n--rw-r--r-- 0 0 0 15104 2023-10-07 20:51:37.000000 control.tar.xz\n--rw-r--r-- 0 0 0 292952 2023-10-07 20:51:37.000000 data.tar.xz\n+-rw-r--r-- 0 0 0 15096 2023-10-07 20:51:37.000000 control.tar.xz\n+-rw-r--r-- 0 0 0 292980 2023-10-07 20:51:37.000000 data.tar.xz\n"}, {"source1": "control.tar.xz", "source2": "control.tar.xz", "unified_diff": null, "details": [{"source1": "control.tar", "source2": "control.tar", "unified_diff": null, "details": [{"source1": "./md5sums", "source2": "./md5sums", "unified_diff": null, "details": [{"source1": "./md5sums", "source2": "./md5sums", "comments": ["Files differ"], "unified_diff": null}]}]}]}, {"source1": "data.tar.xz", "source2": "data.tar.xz", "unified_diff": null, "details": [{"source1": "data.tar", "source2": "data.tar", "unified_diff": null, "details": [{"source1": "file list", "source2": "file list", "unified_diff": "@@ -6,15 +6,15 @@\n drwxr-xr-x 0 root (0) root (0) 0 2023-10-07 20:51:37.000000 ./usr/share/doc/libjebl2-java/api/\n -rw-r--r-- 0 root (0) root (0) 89486 2023-10-07 20:51:37.000000 ./usr/share/doc/libjebl2-java/api/allclasses-index.html\n -rw-r--r-- 0 root (0) root (0) 5808 2023-10-07 20:51:37.000000 ./usr/share/doc/libjebl2-java/api/allpackages-index.html\n -rw-r--r-- 0 root (0) root (0) 13991 2023-10-07 20:51:37.000000 ./usr/share/doc/libjebl2-java/api/constant-values.html\n -rw-r--r-- 0 root (0) root (0) 7240 2023-10-07 20:51:37.000000 ./usr/share/doc/libjebl2-java/api/deprecated-list.html\n -rw-r--r-- 0 root (0) root (0) 410 2023-10-07 20:51:37.000000 ./usr/share/doc/libjebl2-java/api/element-list\n -rw-r--r-- 0 root (0) root (0) 10483 2023-10-07 20:51:37.000000 ./usr/share/doc/libjebl2-java/api/help-doc.html\n--rw-r--r-- 0 root (0) root (0) 739039 2023-10-07 20:51:37.000000 ./usr/share/doc/libjebl2-java/api/index-all.html\n+-rw-r--r-- 0 root (0) root (0) 739060 2023-10-07 20:51:37.000000 ./usr/share/doc/libjebl2-java/api/index-all.html\n -rw-r--r-- 0 root (0) root (0) 7337 2023-10-07 20:51:37.000000 ./usr/share/doc/libjebl2-java/api/index.html\n drwxr-xr-x 0 root (0) root (0) 0 2023-10-07 20:51:37.000000 ./usr/share/doc/libjebl2-java/api/jebl/\n drwxr-xr-x 0 root (0) root (0) 0 2023-10-07 20:51:37.000000 ./usr/share/doc/libjebl2-java/api/jebl/evolution/\n drwxr-xr-x 0 root (0) root (0) 0 2023-10-07 20:51:37.000000 ./usr/share/doc/libjebl2-java/api/jebl/evolution/align/\n -rw-r--r-- 0 root (0) root (0) 26145 2023-10-07 20:51:37.000000 ./usr/share/doc/libjebl2-java/api/jebl/evolution/align/Align.html\n -rw-r--r-- 0 root (0) root (0) 11391 2023-10-07 20:51:37.000000 ./usr/share/doc/libjebl2-java/api/jebl/evolution/align/AlignCommand.html\n -rw-r--r-- 0 root (0) root (0) 8402 2023-10-07 20:51:37.000000 ./usr/share/doc/libjebl2-java/api/jebl/evolution/align/AlignmentTreeBuilderFactory.Result.html\n@@ -613,15 +613,15 @@\n -rw-r--r-- 0 root (0) root (0) 6336 2023-10-07 20:51:37.000000 ./usr/share/doc/libjebl2-java/api/jebl/util/package-tree.html\n -rw-r--r-- 0 root (0) root (0) 12680 2023-10-07 20:51:37.000000 ./usr/share/doc/libjebl2-java/api/jebl/util/package-use.html\n -rw-r--r-- 0 root (0) root (0) 1498 2023-10-07 20:51:37.000000 ./usr/share/doc/libjebl2-java/api/jquery-ui.overrides.css\n drwxr-xr-x 0 root (0) root (0) 0 2023-10-07 20:51:37.000000 ./usr/share/doc/libjebl2-java/api/legal/\n -rw-r--r-- 0 root (0) root (0) 1522 2023-10-07 20:51:37.000000 ./usr/share/doc/libjebl2-java/api/legal/ASSEMBLY_EXCEPTION\n -rw-r--r-- 0 root (0) root (0) 2936 2023-10-07 20:51:37.000000 ./usr/share/doc/libjebl2-java/api/legal/jquery.md\n -rw-r--r-- 0 root (0) root (0) 1870 2023-10-07 20:51:37.000000 ./usr/share/doc/libjebl2-java/api/legal/jqueryUI.md\n--rw-r--r-- 0 root (0) root (0) 203102 2023-10-07 20:51:37.000000 ./usr/share/doc/libjebl2-java/api/member-search-index.js\n+-rw-r--r-- 0 root (0) root (0) 203109 2023-10-07 20:51:37.000000 ./usr/share/doc/libjebl2-java/api/member-search-index.js\n -rw-r--r-- 0 root (0) root (0) 45 2023-10-07 20:51:37.000000 ./usr/share/doc/libjebl2-java/api/module-search-index.js\n -rw-r--r-- 0 root (0) root (0) 823 2023-10-07 20:51:37.000000 ./usr/share/doc/libjebl2-java/api/overview-summary.html\n -rw-r--r-- 0 root (0) root (0) 64815 2023-10-07 20:51:37.000000 ./usr/share/doc/libjebl2-java/api/overview-tree.html\n -rw-r--r-- 0 root (0) root (0) 649 2023-10-07 20:51:37.000000 ./usr/share/doc/libjebl2-java/api/package-search-index.js\n drwxr-xr-x 0 root (0) root (0) 0 2023-10-07 20:51:37.000000 ./usr/share/doc/libjebl2-java/api/resources/\n -rw-r--r-- 0 root (0) root (0) 499 2023-10-07 20:51:37.000000 ./usr/share/doc/libjebl2-java/api/resources/glass.png\n -rw-r--r-- 0 root (0) root (0) 394 2023-10-07 20:51:37.000000 ./usr/share/doc/libjebl2-java/api/resources/x.png\n"}, {"source1": "./usr/share/doc/libjebl2-java/api/index-all.html", "source2": "./usr/share/doc/libjebl2-java/api/index-all.html", "unified_diff": "@@ -4236,15 +4236,15 @@\n
 
\n
next() - Method in class jebl.evolution.io.ImportHelper
\n
 
\n
next(Traceback) - Method in class jebl.evolution.align.Align
\n
\n
Get the next state in the traceback
\n
\n-
next(Traceback) - Method in class jebl.evolution.align.OldNeedlemanWunschAffine
\n+
next(Traceback) - Method in class jebl.evolution.align.NeedlemanWunschLinearSpaceAffine
\n
\n
Get the next state in the traceback
\n
\n
next(Traceback) - Method in class jebl.evolution.align.NonOverlapMultipleLocalAffine
\n
\n
Get the next state in the traceback
\n
\n@@ -4691,41 +4691,41 @@\n
 
\n
prepareAlignment(String, String) - Method in class jebl.evolution.align.SmithWatermanLinearSpace
\n
 
\n
prepareAlignment(String, String) - Method in class jebl.evolution.align.NeedlemanWunschLinearSpaceAffine
\n
 
\n
prepareAlignment(String, String) - Method in class jebl.evolution.align.NonOverlapMultipleLocalAffine
\n
 
\n-
prepareAlignment(String, String) - Method in class jebl.evolution.align.NeedlemanWunsch
\n+
prepareAlignment(String, String) - Method in class jebl.evolution.align.OverlapAlign
\n
 
\n
prepareAlignment(String, String) - Method in class jebl.evolution.align.NeedlemanWunschAffine
\n
 
\n
print() - Method in class jebl.evolution.align.ProfileCharacter
\n
 
\n
print(String) - Method in class jebl.evolution.align.Output
\n
 
\n
print(String) - Method in class jebl.evolution.align.SystemOut
\n
 
\n
printf(Output) - Method in class jebl.evolution.align.Align
\n
\n
Print the matrix (matrices) used to compute the alignment
\n
\n-
printf(Output) - Method in class jebl.evolution.align.OldNeedlemanWunschAffine
\n+
printf(Output) - Method in class jebl.evolution.align.NeedlemanWunschAffine
\n
\n
Print matrix used to calculate this alignment.
\n
\n
printf(Output) - Method in class jebl.evolution.align.SmithWatermanLinearSpace
\n
\n
Print matrix used to calculate this alignment.
\n
\n
printf(Output) - Method in class jebl.evolution.align.NeedlemanWunschLinearSpaceAffine
\n
\n
Print matrix used to calculate this alignment.
\n
\n-
printf(Output) - Method in class jebl.evolution.align.NeedlemanWunsch
\n+
printf(Output) - Method in class jebl.evolution.align.OverlapAlign
\n
\n
Print matrix used to calculate this alignment.
\n
\n
printf(Output) - Method in class jebl.evolution.align.NonOverlapMultipleLocalAffine
\n
\n
Print matrix used to calculate this alignment.
\n
\n@@ -5263,15 +5263,15 @@\n \n
setEdgeLength(Node, Node, double) - Method in class jebl.evolution.trees.SimpleTree
\n
\n
Set edge distance between two adjacent nodes.
\n
\n
setExpectedInputLength(long) - Method in class jebl.evolution.io.ImportHelper
\n
 
\n-
setGapExtend(float) - Method in class jebl.evolution.align.OldNeedlemanWunschAffine
\n+
setGapExtend(float) - Method in class jebl.evolution.align.NeedlemanWunschLinearSpaceAffine
\n
 
\n
setGapExtend(float) - Method in class jebl.evolution.align.NonOverlapMultipleLocalAffine
\n
 
\n
setGapOpen(float) - Method in class jebl.evolution.align.Align
\n
 
\n
setGrowthRate(double) - Method in class jebl.evolution.coalescent.ExponentialGrowth
\n
\n", "details": [{"source1": "html2text {}", "source2": "html2text {}", "unified_diff": "@@ -3846,15 +3846,15 @@\n jebl.evolution.align._\bT_\br_\ba_\bc_\be_\bb_\ba_\bc_\bk_\bP_\bl_\bo_\bt_\bt_\be_\br\n \u00a0\n _\bn_\be_\bx_\bt_\b(_\b) - Method in class jebl.evolution.io._\bI_\bm_\bp_\bo_\br_\bt_\bH_\be_\bl_\bp_\be_\br\n \u00a0\n _\bn_\be_\bx_\bt_\b(_\bT_\br_\ba_\bc_\be_\bb_\ba_\bc_\bk_\b) - Method in class jebl.evolution.align._\bA_\bl_\bi_\bg_\bn\n Get the next state in the traceback\n _\bn_\be_\bx_\bt_\b(_\bT_\br_\ba_\bc_\be_\bb_\ba_\bc_\bk_\b) - Method in class\n- jebl.evolution.align._\bO_\bl_\bd_\bN_\be_\be_\bd_\bl_\be_\bm_\ba_\bn_\bW_\bu_\bn_\bs_\bc_\bh_\bA_\bf_\bf_\bi_\bn_\be\n+ jebl.evolution.align._\bN_\be_\be_\bd_\bl_\be_\bm_\ba_\bn_\bW_\bu_\bn_\bs_\bc_\bh_\bL_\bi_\bn_\be_\ba_\br_\bS_\bp_\ba_\bc_\be_\bA_\bf_\bf_\bi_\bn_\be\n Get the next state in the traceback\n _\bn_\be_\bx_\bt_\b(_\bT_\br_\ba_\bc_\be_\bb_\ba_\bc_\bk_\b) - Method in class\n jebl.evolution.align._\bN_\bo_\bn_\bO_\bv_\be_\br_\bl_\ba_\bp_\bM_\bu_\bl_\bt_\bi_\bp_\bl_\be_\bL_\bo_\bc_\ba_\bl_\bA_\bf_\bf_\bi_\bn_\be\n Get the next state in the traceback\n _\bn_\be_\bx_\bt_\b(_\bT_\br_\ba_\bc_\be_\bb_\ba_\bc_\bk_\b) - Method in class\n jebl.evolution.align._\bS_\bm_\bi_\bt_\bh_\bW_\ba_\bt_\be_\br_\bm_\ba_\bn_\bL_\bi_\bn_\be_\ba_\br_\bS_\bp_\ba_\bc_\be\n Get the next state in the traceback\n@@ -4237,37 +4237,36 @@\n _\bp_\br_\be_\bp_\ba_\br_\be_\bA_\bl_\bi_\bg_\bn_\bm_\be_\bn_\bt_\b(_\bS_\bt_\br_\bi_\bn_\bg_\b,_\b _\bS_\bt_\br_\bi_\bn_\bg_\b) - Method in class\n jebl.evolution.align._\bN_\be_\be_\bd_\bl_\be_\bm_\ba_\bn_\bW_\bu_\bn_\bs_\bc_\bh_\bL_\bi_\bn_\be_\ba_\br_\bS_\bp_\ba_\bc_\be_\bA_\bf_\bf_\bi_\bn_\be\n \u00a0\n _\bp_\br_\be_\bp_\ba_\br_\be_\bA_\bl_\bi_\bg_\bn_\bm_\be_\bn_\bt_\b(_\bS_\bt_\br_\bi_\bn_\bg_\b,_\b _\bS_\bt_\br_\bi_\bn_\bg_\b) - Method in class\n jebl.evolution.align._\bN_\bo_\bn_\bO_\bv_\be_\br_\bl_\ba_\bp_\bM_\bu_\bl_\bt_\bi_\bp_\bl_\be_\bL_\bo_\bc_\ba_\bl_\bA_\bf_\bf_\bi_\bn_\be\n \u00a0\n _\bp_\br_\be_\bp_\ba_\br_\be_\bA_\bl_\bi_\bg_\bn_\bm_\be_\bn_\bt_\b(_\bS_\bt_\br_\bi_\bn_\bg_\b,_\b _\bS_\bt_\br_\bi_\bn_\bg_\b) - Method in class\n- jebl.evolution.align._\bN_\be_\be_\bd_\bl_\be_\bm_\ba_\bn_\bW_\bu_\bn_\bs_\bc_\bh\n+ jebl.evolution.align._\bO_\bv_\be_\br_\bl_\ba_\bp_\bA_\bl_\bi_\bg_\bn\n \u00a0\n _\bp_\br_\be_\bp_\ba_\br_\be_\bA_\bl_\bi_\bg_\bn_\bm_\be_\bn_\bt_\b(_\bS_\bt_\br_\bi_\bn_\bg_\b,_\b _\bS_\bt_\br_\bi_\bn_\bg_\b) - Method in class\n jebl.evolution.align._\bN_\be_\be_\bd_\bl_\be_\bm_\ba_\bn_\bW_\bu_\bn_\bs_\bc_\bh_\bA_\bf_\bf_\bi_\bn_\be\n \u00a0\n _\bp_\br_\bi_\bn_\bt_\b(_\b) - Method in class jebl.evolution.align._\bP_\br_\bo_\bf_\bi_\bl_\be_\bC_\bh_\ba_\br_\ba_\bc_\bt_\be_\br\n \u00a0\n _\bp_\br_\bi_\bn_\bt_\b(_\bS_\bt_\br_\bi_\bn_\bg_\b) - Method in class jebl.evolution.align._\bO_\bu_\bt_\bp_\bu_\bt\n \u00a0\n _\bp_\br_\bi_\bn_\bt_\b(_\bS_\bt_\br_\bi_\bn_\bg_\b) - Method in class jebl.evolution.align._\bS_\by_\bs_\bt_\be_\bm_\bO_\bu_\bt\n \u00a0\n _\bp_\br_\bi_\bn_\bt_\bf_\b(_\bO_\bu_\bt_\bp_\bu_\bt_\b) - Method in class jebl.evolution.align._\bA_\bl_\bi_\bg_\bn\n Print the matrix (matrices) used to compute the alignment\n- _\bp_\br_\bi_\bn_\bt_\bf_\b(_\bO_\bu_\bt_\bp_\bu_\bt_\b) - Method in class\n- jebl.evolution.align._\bO_\bl_\bd_\bN_\be_\be_\bd_\bl_\be_\bm_\ba_\bn_\bW_\bu_\bn_\bs_\bc_\bh_\bA_\bf_\bf_\bi_\bn_\be\n+ _\bp_\br_\bi_\bn_\bt_\bf_\b(_\bO_\bu_\bt_\bp_\bu_\bt_\b) - Method in class jebl.evolution.align._\bN_\be_\be_\bd_\bl_\be_\bm_\ba_\bn_\bW_\bu_\bn_\bs_\bc_\bh_\bA_\bf_\bf_\bi_\bn_\be\n Print matrix used to calculate this alignment.\n _\bp_\br_\bi_\bn_\bt_\bf_\b(_\bO_\bu_\bt_\bp_\bu_\bt_\b) - Method in class\n jebl.evolution.align._\bS_\bm_\bi_\bt_\bh_\bW_\ba_\bt_\be_\br_\bm_\ba_\bn_\bL_\bi_\bn_\be_\ba_\br_\bS_\bp_\ba_\bc_\be\n Print matrix used to calculate this alignment.\n _\bp_\br_\bi_\bn_\bt_\bf_\b(_\bO_\bu_\bt_\bp_\bu_\bt_\b) - Method in class\n jebl.evolution.align._\bN_\be_\be_\bd_\bl_\be_\bm_\ba_\bn_\bW_\bu_\bn_\bs_\bc_\bh_\bL_\bi_\bn_\be_\ba_\br_\bS_\bp_\ba_\bc_\be_\bA_\bf_\bf_\bi_\bn_\be\n Print matrix used to calculate this alignment.\n- _\bp_\br_\bi_\bn_\bt_\bf_\b(_\bO_\bu_\bt_\bp_\bu_\bt_\b) - Method in class jebl.evolution.align._\bN_\be_\be_\bd_\bl_\be_\bm_\ba_\bn_\bW_\bu_\bn_\bs_\bc_\bh\n+ _\bp_\br_\bi_\bn_\bt_\bf_\b(_\bO_\bu_\bt_\bp_\bu_\bt_\b) - Method in class jebl.evolution.align._\bO_\bv_\be_\br_\bl_\ba_\bp_\bA_\bl_\bi_\bg_\bn\n Print matrix used to calculate this alignment.\n _\bp_\br_\bi_\bn_\bt_\bf_\b(_\bO_\bu_\bt_\bp_\bu_\bt_\b) - Method in class\n jebl.evolution.align._\bN_\bo_\bn_\bO_\bv_\be_\br_\bl_\ba_\bp_\bM_\bu_\bl_\bt_\bi_\bp_\bl_\be_\bL_\bo_\bc_\ba_\bl_\bA_\bf_\bf_\bi_\bn_\be\n Print matrix used to calculate this alignment.\n _\bp_\br_\bi_\bn_\bt_\bl_\bn_\b(_\b) - Method in class jebl.evolution.align._\bO_\bu_\bt_\bp_\bu_\bt\n \u00a0\n _\bp_\br_\bi_\bn_\bt_\bl_\bn_\b(_\b) - Method in class jebl.evolution.align._\bS_\by_\bs_\bt_\be_\bm_\bO_\bu_\bt\n@@ -4777,15 +4776,15 @@\n Change length of an existing edge.\n _\bs_\be_\bt_\bE_\bd_\bg_\be_\bL_\be_\bn_\bg_\bt_\bh_\b(_\bN_\bo_\bd_\be_\b,_\b _\bN_\bo_\bd_\be_\b,_\b _\bd_\bo_\bu_\bb_\bl_\be_\b) - Method in class\n jebl.evolution.trees._\bS_\bi_\bm_\bp_\bl_\be_\bT_\br_\be_\be\n Set edge distance between two adjacent nodes.\n _\bs_\be_\bt_\bE_\bx_\bp_\be_\bc_\bt_\be_\bd_\bI_\bn_\bp_\bu_\bt_\bL_\be_\bn_\bg_\bt_\bh_\b(_\bl_\bo_\bn_\bg_\b) - Method in class jebl.evolution.io._\bI_\bm_\bp_\bo_\br_\bt_\bH_\be_\bl_\bp_\be_\br\n \u00a0\n _\bs_\be_\bt_\bG_\ba_\bp_\bE_\bx_\bt_\be_\bn_\bd_\b(_\bf_\bl_\bo_\ba_\bt_\b) - Method in class\n- jebl.evolution.align._\bO_\bl_\bd_\bN_\be_\be_\bd_\bl_\be_\bm_\ba_\bn_\bW_\bu_\bn_\bs_\bc_\bh_\bA_\bf_\bf_\bi_\bn_\be\n+ jebl.evolution.align._\bN_\be_\be_\bd_\bl_\be_\bm_\ba_\bn_\bW_\bu_\bn_\bs_\bc_\bh_\bL_\bi_\bn_\be_\ba_\br_\bS_\bp_\ba_\bc_\be_\bA_\bf_\bf_\bi_\bn_\be\n \u00a0\n _\bs_\be_\bt_\bG_\ba_\bp_\bE_\bx_\bt_\be_\bn_\bd_\b(_\bf_\bl_\bo_\ba_\bt_\b) - Method in class\n jebl.evolution.align._\bN_\bo_\bn_\bO_\bv_\be_\br_\bl_\ba_\bp_\bM_\bu_\bl_\bt_\bi_\bp_\bl_\be_\bL_\bo_\bc_\ba_\bl_\bA_\bf_\bf_\bi_\bn_\be\n \u00a0\n _\bs_\be_\bt_\bG_\ba_\bp_\bO_\bp_\be_\bn_\b(_\bf_\bl_\bo_\ba_\bt_\b) - Method in class jebl.evolution.align._\bA_\bl_\bi_\bg_\bn\n \u00a0\n _\bs_\be_\bt_\bG_\br_\bo_\bw_\bt_\bh_\bR_\ba_\bt_\be_\b(_\bd_\bo_\bu_\bb_\bl_\be_\b) - Method in class\n"}]}, {"source1": "./usr/share/doc/libjebl2-java/api/member-search-index.js", "source2": "./usr/share/doc/libjebl2-java/api/member-search-index.js", "unified_diff": null, "details": [{"source1": "js-beautify {}", "source2": "js-beautify {}", "unified_diff": "@@ -6195,15 +6195,15 @@\n }, {\n \"p\": \"jebl.evolution.align\",\n \"c\": \"Align\",\n \"l\": \"next(Traceback)\",\n \"u\": \"next(jebl.evolution.align.Traceback)\"\n }, {\n \"p\": \"jebl.evolution.align\",\n- \"c\": \"OldNeedlemanWunschAffine\",\n+ \"c\": \"NeedlemanWunschLinearSpaceAffine\",\n \"l\": \"next(Traceback)\",\n \"u\": \"next(jebl.evolution.align.Traceback)\"\n }, {\n \"p\": \"jebl.evolution.align\",\n \"c\": \"NonOverlapMultipleLocalAffine\",\n \"l\": \"next(Traceback)\",\n \"u\": \"next(jebl.evolution.align.Traceback)\"\n@@ -6734,15 +6734,15 @@\n }, {\n \"p\": \"jebl.evolution.align\",\n \"c\": \"NonOverlapMultipleLocalAffine\",\n \"l\": \"prepareAlignment(String, String)\",\n \"u\": \"prepareAlignment(java.lang.String,java.lang.String)\"\n }, {\n \"p\": \"jebl.evolution.align\",\n- \"c\": \"NeedlemanWunsch\",\n+ \"c\": \"OverlapAlign\",\n \"l\": \"prepareAlignment(String, String)\",\n \"u\": \"prepareAlignment(java.lang.String,java.lang.String)\"\n }, {\n \"p\": \"jebl.evolution.align\",\n \"c\": \"NeedlemanWunschAffine\",\n \"l\": \"prepareAlignment(String, String)\",\n \"u\": \"prepareAlignment(java.lang.String,java.lang.String)\"\n@@ -6763,30 +6763,30 @@\n }, {\n \"p\": \"jebl.evolution.align\",\n \"c\": \"Align\",\n \"l\": \"printf(Output)\",\n \"u\": \"printf(jebl.evolution.align.Output)\"\n }, {\n \"p\": \"jebl.evolution.align\",\n- \"c\": \"OldNeedlemanWunschAffine\",\n+ \"c\": \"NeedlemanWunschAffine\",\n \"l\": \"printf(Output)\",\n \"u\": \"printf(jebl.evolution.align.Output)\"\n }, {\n \"p\": \"jebl.evolution.align\",\n \"c\": \"SmithWatermanLinearSpace\",\n \"l\": \"printf(Output)\",\n \"u\": \"printf(jebl.evolution.align.Output)\"\n }, {\n \"p\": \"jebl.evolution.align\",\n \"c\": \"NeedlemanWunschLinearSpaceAffine\",\n \"l\": \"printf(Output)\",\n \"u\": \"printf(jebl.evolution.align.Output)\"\n }, {\n \"p\": \"jebl.evolution.align\",\n- \"c\": \"NeedlemanWunsch\",\n+ \"c\": \"OverlapAlign\",\n \"l\": \"printf(Output)\",\n \"u\": \"printf(jebl.evolution.align.Output)\"\n }, {\n \"p\": \"jebl.evolution.align\",\n \"c\": \"NonOverlapMultipleLocalAffine\",\n \"l\": \"printf(Output)\",\n \"u\": \"printf(jebl.evolution.align.Output)\"\n@@ -7566,15 +7566,15 @@\n \"u\": \"setEdgeLength(jebl.evolution.graphs.Node,jebl.evolution.graphs.Node,double)\"\n }, {\n \"p\": \"jebl.evolution.io\",\n \"c\": \"ImportHelper\",\n \"l\": \"setExpectedInputLength(long)\"\n }, {\n \"p\": \"jebl.evolution.align\",\n- \"c\": \"OldNeedlemanWunschAffine\",\n+ \"c\": \"NeedlemanWunschLinearSpaceAffine\",\n \"l\": \"setGapExtend(float)\"\n }, {\n \"p\": \"jebl.evolution.align\",\n \"c\": \"NonOverlapMultipleLocalAffine\",\n \"l\": \"setGapExtend(float)\"\n }, {\n \"p\": \"jebl.evolution.align\",\n"}]}]}]}]}]}