/usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.o0eJwLEG/biojava-live_1.9.5+dfsg-3.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.o0eJwLEG/biojava-live_1.9.5+dfsg-3.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.o0eJwLEG/biojava-live_1.9.5+dfsg-3.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.o0eJwLEG/b1/biojava-live_1.9.5+dfsg-3_i386.changes /srv/reproducible-results/rbuild-debian/r-b-build.o0eJwLEG/b2/biojava-live_1.9.5+dfsg-3

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/srv/reproducible-results/rbuild-debian/r-b-build.o0eJwLEG/b1/biojava-live_1.9.5+dfsg-3_i386.changes vs.

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libbiojava-java-doc_1.9.5+dfsg-3_all.deb ¶

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1	·50ef7~~b2842cfc~~e~~8aa86~~9db~~0e79e4f124~~·4132~~460~~·doc·optional·libbiojava-java-doc_1.9.5+dfsg-3_all.deb	1	·eb7377f183fe7ddb79beb234c63a95f9·4132512·doc·optional·libbiojava-java-doc_1.9.5+dfsg-3_all.deb
2	·6ec0c1383500d11b6b00a5311b9fae01·5428·java·optional·libbiojava-java_1.9.5+dfsg-3_all.deb	2	·6ec0c1383500d11b6b00a5311b9fae01·5428·java·optional·libbiojava-java_1.9.5+dfsg-3_all.deb
3	·ae088cf95f45e829fc10791a8ee09699·3154200·java·optional·libbiojava1.9-java_1.9.5+dfsg-3_all.deb	3	·ae088cf95f45e829fc10791a8ee09699·3154200·java·optional·libbiojava1.9-java_1.9.5+dfsg-3_all.deb


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1	-rw-r--r--···0········0········0········4·2023-05-12·09:09:08.000000·debian-binary	1	-rw-r--r--···0········0········0········4·2023-05-12·09:09:08.000000·debian-binary
2	-rw-r--r--···0········0········0···118584·2023-05-12·09:09:08.000000·control.tar.xz	2	-rw-r--r--···0········0········0···118588·2023-05-12·09:09:08.000000·control.tar.xz
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Offset 1559, 15 lines modified		Offset 1559, 15 lines modified
1559	<div·class="block">add·a·search·pattern·to·the·searches·to·be·conducted	1559	<div·class="block">add·a·search·pattern·to·the·searches·to·be·conducted
1560	·by·this·object.</div>	1560	·by·this·object.</div>
1561	</dd>	1561	</dd>
1562	<dt><a·href="org/biojava/stats/svm/DiagonalAddKernel.html#addPos(java.lang.Object)"·class="member-name-link">addPos(Object)</a>·-·Method·in·class·org.biojava.stats.svm.<a·href="org/biojava/stats/svm/DiagonalAddKernel.html"·title="class·in·org.biojava.stats.svm">DiagonalAddKernel</a></dt>	1562	<dt><a·href="org/biojava/stats/svm/DiagonalAddKernel.html#addPos(java.lang.Object)"·class="member-name-link">addPos(Object)</a>·-·Method·in·class·org.biojava.stats.svm.<a·href="org/biojava/stats/svm/DiagonalAddKernel.html"·title="class·in·org.biojava.stats.svm">DiagonalAddKernel</a></dt>
1563	<dd> </dd>	1563	<dd> </dd>
1564	<dt><a·href="org/biojava/bio/seq/io/agave/AGAVEMapLocation.html#addPosition(org.biojava.bio.seq.io.agave.AGAVEMapPosition)"·class="member-name-link">addPosition(AGAVEMapPosition)</a>·-·Method·in·class·org.biojava.bio.seq.io.agave.<a·href="org/biojava/bio/seq/io/agave/AGAVEMapLocation.html"·title="class·in·org.biojava.bio.seq.io.agave">AGAVEMapLocation</a></dt>	1564	<dt><a·href="org/biojava/bio/seq/io/agave/AGAVEMapLocation.html#addPosition(org.biojava.bio.seq.io.agave.AGAVEMapPosition)"·class="member-name-link">addPosition(AGAVEMapPosition)</a>·-·Method·in·class·org.biojava.bio.seq.io.agave.<a·href="org/biojava/bio/seq/io/agave/AGAVEMapLocation.html"·title="class·in·org.biojava.bio.seq.io.agave">AGAVEMapLocation</a></dt>
1565	<dd> </dd>	1565	<dd> </dd>
1566	<dt><a·href="org/biojava/bio/program/sax/~~ClustalW~~AlignmentSAXParser.html#addPrefixMapping(java.lang.String,java.lang.String)"·class="member-name-link">addPrefixMapping(String,·String)</a>·-·Method·in·class·org.biojava.bio.program.sax.<a·href="org/biojava/bio/program/sax/~~ClustalW~~AlignmentSAXParser[·...·truncated·by·diffoscope;·len:·60,·SHA:·~~193~~f60c~~c3ea169~~9a9~~34f~~ae83~~824920d83~~b~~31ec9a~~2e5f46~~b7b2~~2681~~1d9~~c~~1a8~~394·...·]AlignmentSAXParser</a></dt>	1566	<dt><a·href="org/biojava/bio/program/sax/SequenceAlignmentSAXParser.html#addPrefixMapping(java.lang.String,java.lang.String)"·class="member-name-link">addPrefixMapping(String,·String)</a>·-·Method·in·class·org.biojava.bio.program.sax.<a·href="org/biojava/bio/program/sax/SequenceAlignmentSAXParser[·...·truncated·by·diffoscope;·len:·60,·SHA:·f5ec141522c9598ada624d3aec771be9b98808d257c6fcd092618b3cf0636cf9·...·]AlignmentSAXParser</a></dt>
1567	<dd>	1567	<dd>
1568	<div·class="block">Adds·a·namespace·prefix·to·URI·mapping·as·(key,value)·pairs.</div>	1568	<div·class="block">Adds·a·namespace·prefix·to·URI·mapping·as·(key,value)·pairs.</div>
1569	</dd>	1569	</dd>
1570	<dt><a·href="org/biojava/bio/seq/io/agave/AGAVERelatedAnnot.html#addProp(org.biojava.bio.seq.io.agave.AGAVEProperty)"·class="member-name-link">addProp(AGAVEProperty)</a>·-·Method·in·class·org.biojava.bio.seq.io.agave.<a·href="org/biojava/bio/seq/io/agave/AGAVERelatedAnnot.html"·title="class·in·org.biojava.bio.seq.io.agave">AGAVERelatedAnnot</a></dt>	1570	<dt><a·href="org/biojava/bio/seq/io/agave/AGAVERelatedAnnot.html#addProp(org.biojava.bio.seq.io.agave.AGAVEProperty)"·class="member-name-link">addProp(AGAVEProperty)</a>·-·Method·in·class·org.biojava.bio.seq.io.agave.<a·href="org/biojava/bio/seq/io/agave/AGAVERelatedAnnot.html"·title="class·in·org.biojava.bio.seq.io.agave">AGAVERelatedAnnot</a></dt>
1571	<dd> </dd>	1571	<dd> </dd>
1572	<dt><a·href="org/biojava/bio/seq/io/agave/AGAVEXref.html#addProp(org.biojava.bio.seq.io.agave.AGAVEProperty)"·class="member-name-link">addProp(AGAVEProperty)</a>·-·Method·in·class·org.biojava.bio.seq.io.agave.<a·href="org/biojava/bio/seq/io/agave/AGAVEXref.html"·title="class·in·org.biojava.bio.seq.io.agave">AGAVEXref</a></dt>	1572	<dt><a·href="org/biojava/bio/seq/io/agave/AGAVEXref.html#addProp(org.biojava.bio.seq.io.agave.AGAVEProperty)"·class="member-name-link">addProp(AGAVEProperty)</a>·-·Method·in·class·org.biojava.bio.seq.io.agave.<a·href="org/biojava/bio/seq/io/agave/AGAVEXref.html"·title="class·in·org.biojava.bio.seq.io.agave">AGAVEXref</a></dt>
1573	<dd> </dd>	1573	<dd> </dd>
Offset 5096, 15 lines modified		Offset 5096, 15 lines modified
5096	<dd>	5096	<dd>
5097	<div·class="block">A·listener·that·remembers·the·ChangeEvent·of·the·last·change.</div>	5097	<div·class="block">A·listener·that·remembers·the·ChangeEvent·of·the·last·change.</div>
5098	</dd>	5098	</dd>
5099	<dt><a·href="org/biojava/utils/ChangeListener.LoggingListener.html"·class="type-name-link"·title="class·in·org.biojava.utils">ChangeListener.LoggingListener</a>·-·Class·in·<a·href="org/biojava/utils/package-summary.html">org.biojava.utils</a></dt>	5099	<dt><a·href="org/biojava/utils/ChangeListener.LoggingListener.html"·class="type-name-link"·title="class·in·org.biojava.utils">ChangeListener.LoggingListener</a>·-·Class·in·<a·href="org/biojava/utils/package-summary.html">org.biojava.utils</a></dt>
5100	<dd>	5100	<dd>
5101	<div·class="block">A·listener·that·writes·information·about·the·event·stream·to·a·PrintStream.</div>	5101	<div·class="block">A·listener·that·writes·information·about·the·event·stream·to·a·PrintStream.</div>
5102	</dd>	5102	</dd>
5103	<dt><a·href="org/biojava/bio/program/sax/~~ClustalW~~AlignmentSAXParser.html#changeState(int)"·class="member-name-link">changeState(int)</a>·-·Method·in·class·org.biojava.bio.program.sax.<a·href="org/biojava/bio/program/sax/~~ClustalW~~AlignmentSAXParser.html"·title="class·in·org.biojava.bio.program.sax"[·...·truncated·by·diffoscope;·len:·9,·SHA:·~~75f2c52~~6~~571570a~~8~~422c1e30011d84~~e~~c9f1~~2~~5d6~~540c69f5e7511583262d~~ddfc3~~·...·]AlignmentSAXParser</a></dt>	5103	<dt><a·href="org/biojava/bio/program/sax/SequenceAlignmentSAXParser.html#changeState(int)"·class="member-name-link">changeState(int)</a>·-·Method·in·class·org.biojava.bio.program.sax.<a·href="org/biojava/bio/program/sax/SequenceAlignmentSAXParser.html"·title="class·in·org.biojava.bio.program.sax"[·...·truncated·by·diffoscope;·len:·9,·SHA:·6db49dd4611038ff318756465c28286a6e36a227785cff8ea545a06bd63116ad·...·]AlignmentSAXParser</a></dt>
5104	<dd>	5104	<dd>
5105	<div·class="block">Centralise·chaining·of·iState·field·to·help	5105	<div·class="block">Centralise·chaining·of·iState·field·to·help
5106	·with·debugging.</div>	5106	·with·debugging.</div>
5107	</dd>	5107	</dd>
5108	<dt><a·href="org/biojava/utils/ChangeForwarder.html#changeSupport()"·class="member-name-link">changeSupport()</a>·-·Method·in·class·org.biojava.utils.<a·href="org/biojava/utils/ChangeForwarder.html"·title="class·in·org.biojava.utils">ChangeForwarder</a></dt>	5108	<dt><a·href="org/biojava/utils/ChangeForwarder.html#changeSupport()"·class="member-name-link">changeSupport()</a>·-·Method·in·class·org.biojava.utils.<a·href="org/biojava/utils/ChangeForwarder.html"·title="class·in·org.biojava.utils">ChangeForwarder</a></dt>
5109	<dd>	5109	<dd>
5110	<div·class="block">Return·the·underlying·<code>ChangeSupport</code>·instance·that·can·be·used·to	5110	<div·class="block">Return·the·underlying·<code>ChangeSupport</code>·instance·that·can·be·used·to
Offset 5221, 15 lines modified		Offset 5221, 15 lines modified
5221	</dd>	5221	</dd>
5222	<dt><a·href="org/biojava/bio/seq/io/SymbolTokenization.html#CHARACTER"·class="member-name-link">CHARACTER</a>·-·Static·variable·in·interface·org.biojava.bio.seq.io.<a·href="org/biojava/bio/seq/io/SymbolTokenization.html"·title="interface·in·org.biojava.bio.seq.io">SymbolTokenization</a></dt>	5222	<dt><a·href="org/biojava/bio/seq/io/SymbolTokenization.html#CHARACTER"·class="member-name-link">CHARACTER</a>·-·Static·variable·in·interface·org.biojava.bio.seq.io.<a·href="org/biojava/bio/seq/io/SymbolTokenization.html"·title="interface·in·org.biojava.bio.seq.io">SymbolTokenization</a></dt>
5223	<dd> </dd>	5223	<dd> </dd>
5224	<dt><a·href="org/biojava/bio/program/blast2html/Blast2HTMLHandler.html#characters(char%5B%5D,int,int)"·class="member-name-link">characters(char[],·int,·int)</a>·-·Method·in·class·org.biojava.bio.program.blast2html.<a·href="org/biojava/bio/program/blast2html/Blast2HTMLHandler.html"·title="class·in·org.biojava.bio.program.blast2html">Blast2HTMLHandler</a></dt>	5224	<dt><a·href="org/biojava/bio/program/blast2html/Blast2HTMLHandler.html#characters(char%5B%5D,int,int)"·class="member-name-link">characters(char[],·int,·int)</a>·-·Method·in·class·org.biojava.bio.program.blast2html.<a·href="org/biojava/bio/program/blast2html/Blast2HTMLHandler.html"·title="class·in·org.biojava.bio.program.blast2html">Blast2HTMLHandler</a></dt>
5225	<dd>	5225	<dd>
5226	<div·class="block">Describe·<code>characters</code>·method·here.</div>	5226	<div·class="block">Describe·<code>characters</code>·method·here.</div>
5227	</dd>	5227	</dd>
5228	<dt><a·href="org/biojava/bio/program/sax/~~ClustalW~~AlignmentSAXParser.html#characters(char%5B%5D,int,int)"·class="member-name-link">characters(char[],·int,·int)</a>·-·Method·in·class·org.biojava.bio.program.sax.<a·href="org/biojava/bio/program/sax/~~ClustalW~~AlignmentSAXParser.html"·title="class·in·or[·...·truncated·by·diffoscope;·len:·35,·SHA:·~~4415481b~~f~~f73c~~0c~~3c7afdece50~~9~~4ef~~3~~765797b727~~5e~~d65c~~e~~45af80b1bd~~442~~81e~~·...·]AlignmentSAXParser</a></dt>	5228	<dt><a·href="org/biojava/bio/program/sax/SequenceAlignmentSAXParser.html#characters(char%5B%5D,int,int)"·class="member-name-link">characters(char[],·int,·int)</a>·-·Method·in·class·org.biojava.bio.program.sax.<a·href="org/biojava/bio/program/sax/SequenceAlignmentSAXParser.html"·title="class·in·or[·...·truncated·by·diffoscope;·len:·35,·SHA:·cfe3dfa4d508cf228061218f9a5c31a1881f0c0450e6fdbe0d09fe3aa74d2e8b·...·]AlignmentSAXParser</a></dt>
5229	<dd>	5229	<dd>
5230	<div·class="block">Utility·method·to·centralize·the·sending·of·a·SAX·characters	5230	<div·class="block">Utility·method·to·centralize·the·sending·of·a·SAX·characters
5231	·message·a·document·handler.</div>	5231	·message·a·document·handler.</div>
5232	</dd>	5232	</dd>
5233	<dt><a·href="org/biojava/bio/program/ssbind/SeqSimilarityAdapter.html#characters(char%5B%5D,int,int)"·class="member-name-link">characters(char[],·int,·int)</a>·-·Method·in·class·org.biojava.bio.program.ssbind.<a·href="org/biojava/bio/program/ssbind/SeqSimilarityAdapter.html"·title="class·in·org.biojava.bio.program.ssbind">SeqSimilarityAdapter</a></dt>	5233	<dt><a·href="org/biojava/bio/program/ssbind/SeqSimilarityAdapter.html#characters(char%5B%5D,int,int)"·class="member-name-link">characters(char[],·int,·int)</a>·-·Method·in·class·org.biojava.bio.program.ssbind.<a·href="org/biojava/bio/program/ssbind/SeqSimilarityAdapter.html"·title="class·in·org.biojava.bio.program.ssbind">SeqSimilarityAdapter</a></dt>
5234	<dd> </dd>	5234	<dd> </dd>
5235	<dt><a·href="org/biojava/bio/program/xml/SimpleXMLEmitter.html#characters(char%5B%5D,int,int)"·class="member-name-link">characters(char[],·int,·int)</a>·-·Method·in·class·org.biojava.bio.program.xml.<a·href="org/biojava/bio/program/xml/SimpleXMLEmitter.html"·title="class·in·org.biojava.bio.program.xml">SimpleXMLEmitter</a></dt>	5235	<dt><a·href="org/biojava/bio/program/xml/SimpleXMLEmitter.html#characters(char%5B%5D,int,int)"·class="member-name-link">characters(char[],·int,·int)</a>·-·Method·in·class·org.biojava.bio.program.xml.<a·href="org/biojava/bio/program/xml/SimpleXMLEmitter.html"·title="class·in·org.biojava.bio.program.xml">SimpleXMLEmitter</a></dt>
Offset 8350, 15 lines modified		Offset 8350, 15 lines modified
8350	<dd> </dd>	8350	<dd> </dd>
8351	<dt><a·href="org/biojava/bio/program/tagvalue/TagDropper.html#doRetain()"·class="member-name-link">doRetain()</a>·-·Method·in·class·org.biojava.bio.program.tagvalue.<a·href="org/biojava/bio/program/tagvalue/TagDropper.html"·title="class·in·org.biojava.bio.program.tagvalue">TagDropper</a></dt>	8351	<dt><a·href="org/biojava/bio/program/tagvalue/TagDropper.html#doRetain()"·class="member-name-link">doRetain()</a>·-·Method·in·class·org.biojava.bio.program.tagvalue.<a·href="org/biojava/bio/program/tagvalue/TagDropper.html"·title="class·in·org.biojava.bio.program.tagvalue">TagDropper</a></dt>
8352	<dd>	8352	<dd>
8353	<div·class="block">Find·out·if·known·tags·are·retained·or·dropped.</div>	8353	<div·class="block">Find·out·if·known·tags·are·retained·or·dropped.</div>
8354	</dd>	8354	</dd>
8355	<dt><a·href="org/biojava/bio/gui/sequence/AbstractPeptideDigestRenderer.html#doSortPeptides()"·class="member-name-link">doSortPeptides()</a>·-·Method·in·class·org.biojava.bio.gui.sequence.<a·href="org/biojava/bio/gui/sequence/AbstractPeptideDigestRenderer.html"·title="class·in·org.biojava.bio.gui.sequence">AbstractPeptideDigestRenderer</a></dt>	8355	<dt><a·href="org/biojava/bio/gui/sequence/AbstractPeptideDigestRenderer.html#doSortPeptides()"·class="member-name-link">doSortPeptides()</a>·-·Method·in·class·org.biojava.bio.gui.sequence.<a·href="org/biojava/bio/gui/sequence/AbstractPeptideDigestRenderer.html"·title="class·in·org.biojava.bio.gui.sequence">AbstractPeptideDigestRenderer</a></dt>
8356	<dd> </dd>	8356	<dd> </dd>
8357	<dt><a·href="org/biojava/bio/symbol/Abstract~~ManyToOn~~eTranslationTable.html#doTranslate(org.biojava.bio.symbol.Symbol)"·class="member-name-link">doTranslate(Symbol)</a>·-·Method·in·class·org.biojava.bio.symbol.<a·href="org/biojava/bio/symbol/Abstract~~ManyToOn~~eTranslationTable.html"·title="class·in·org[·...·truncated·by·diffoscope;·len:·37,·SHA:·befc3b5f12cc4~~0d0e~~8bc5dbae6f~~572~~0ea1~~b1174~~9a0db0~~90d4fd~~3634a7~~5e1~~f118·...·]eTranslationTable</a></dt>	8357	<dt><a·href="org/biojava/bio/symbol/AbstractReversibleTranslationTable.html#doTranslate(org.biojava.bio.symbol.Symbol)"·class="member-name-link">doTranslate(Symbol)</a>·-·Method·in·class·org.biojava.bio.symbol.<a·href="org/biojava/bio/symbol/AbstractReversibleTranslationTable.html"·title="class·in·o[·...·truncated·by·diffoscope;·len:·40,·SHA:·da676fb3ab65a72e275c4e5e5830295db92aef0e994cb9fed8e77b5384b48fe0·...·]eTranslationTable</a></dt>
8358	<dd>	8358	<dd>
8359	<div·class="block">this·method·is·expected·to·translate·any·symbol	8359	<div·class="block">this·method·is·expected·to·translate·any·symbol
8360	·in·the·source·alphabet.</div>	8360	·in·the·source·alphabet.</div>
8361	</dd>	8361	</dd>
8362	<dt><a·href="org/biojava/bio/symbol/SimpleManyToOneTranslationTable.html#doTranslate(org.biojava.bio.symbol.Symbol)"·class="member-name-link">doTranslate(Symbol)</a>·-·Method·in·class·org.biojava.bio.symbol.<a·href="org/biojava/bio/symbol/SimpleManyToOneTranslationTable.html"·title="class·in·org.biojava.bio.symbol">SimpleManyToOneTranslationTable</a></dt>	8362	<dt><a·href="org/biojava/bio/symbol/SimpleManyToOneTranslationTable.html#doTranslate(org.biojava.bio.symbol.Symbol)"·class="member-name-link">doTranslate(Symbol)</a>·-·Method·in·class·org.biojava.bio.symbol.<a·href="org/biojava/bio/symbol/SimpleManyToOneTranslationTable.html"·title="class·in·org.biojava.bio.symbol">SimpleManyToOneTranslationTable</a></dt>
8363	<dd> </dd>	8363	<dd> </dd>
8364	<dt><a·href="org/biojava/bio/symbol/SimpleReversibleTranslationTable.html#doTranslate(org.biojava.bio.symbol.Symbol)"·class="member-name-link">doTranslate(Symbol)</a>·-·Method·in·class·org.biojava.bio.symbol.<a·href="org/biojava/bio/symbol/SimpleReversibleTranslationTable.html"·title="class·in·org.biojava.bio.symbol">SimpleReversibleTranslationTable</a></dt>	8364	<dt><a·href="org/biojava/bio/symbol/SimpleReversibleTranslationTable.html#doTranslate(org.biojava.bio.symbol.Symbol)"·class="member-name-link">doTranslate(Symbol)</a>·-·Method·in·class·org.biojava.bio.symbol.<a·href="org/biojava/bio/symbol/SimpleReversibleTranslationTable.html"·title="class·in·org.biojava.bio.symbol">SimpleReversibleTranslationTable</a></dt>
Offset 9283, 15 lines modified		Offset 9283, 15 lines modified
9283	<dd> </dd>	9283	<dd> </dd>
9284	<dt><a·href="org/biojava/utils/stax/StAXContentHandler.html#endElement(java.lang.String,java.lang.String,java.lang.String,org.biojava.utils.stax.StAXContentHandler)"·class="member-name-link">endElement(String,·String,·String,·StAXContentHandler)</a>·-·Method·in·interface·org.biojava.utils.stax.<a·href="org/biojava/utils/stax/StAXContentHandler.html"·title="interface·in·org.biojava.utils.stax">StAXContentHandler</a></dt>	9284	<dt><a·href="org/biojava/utils/stax/StAXContentHandler.html#endElement(java.lang.String,java.lang.String,java.lang.String,org.biojava.utils.stax.StAXContentHandler)"·class="member-name-link">endElement(String,·String,·String,·StAXContentHandler)</a>·-·Method·in·interface·org.biojava.utils.stax.<a·href="org/biojava/utils/stax/StAXContentHandler.html"·title="interface·in·org.biojava.utils.stax">StAXContentHandler</a></dt>
9285	<dd> </dd>	9285	<dd> </dd>
9286	<dt><a·href="org/biojava/utils/stax/StAXContentHandlerBase.html#endElement(java.lang.String,java.lang.String,java.lang.String,org.biojava.utils.stax.StAXContentHandler)"·class="member-name-link">endElement(String,·String,·String,·StAXContentHandler)</a>·-·Method·in·class·org.biojava.utils.stax.<a·href="org/biojava/utils/stax/StAXContentHandlerBase.html"·title="class·in·org.biojava.utils.stax">StAXContentHandlerBase</a></dt>	9286	<dt><a·href="org/biojava/utils/stax/StAXContentHandlerBase.html#endElement(java.lang.String,java.lang.String,java.lang.String,org.biojava.utils.stax.StAXContentHandler)"·class="member-name-link">endElement(String,·String,·String,·StAXContentHandler)</a>·-·Method·in·class·org.biojava.utils.stax.<a·href="org/biojava/utils/stax/StAXContentHandlerBase.html"·title="class·in·org.biojava.utils.stax">StAXContentHandlerBase</a></dt>
9287	<dd> </dd>	9287	<dd> </dd>
9288	<dt><a·href="org/biojava/utils/stax/StringElementHandlerBase.html#endElement(java.lang.String,java.lang.String,java.lang.String,org.biojava.utils.stax.StAXContentHandler)"·class="member-name-link">endElement(String,·String,·String,·StAXContentHandler)</a>·-·Method·in·class·org.biojava.utils.stax.<a·href="org/biojava/utils/stax/StringElementHandlerBase.html"·title="class·in·org.biojava.utils.stax">StringElementHandlerBase</a></dt>	9288	<dt><a·href="org/biojava/utils/stax/StringElementHandlerBase.html#endElement(java.lang.String,java.lang.String,java.lang.String,org.biojava.utils.stax.StAXContentHandler)"·class="member-name-link">endElement(String,·String,·String,·StAXContentHandler)</a>·-·Method·in·class·org.biojava.utils.stax.<a·href="org/biojava/utils/stax/StringElementHandlerBase.html"·title="class·in·org.biojava.utils.stax">StringElementHandlerBase</a></dt>
9289	<dd> </dd>	9289	<dd> </dd>
9290	<dt><a·href="org/biojava/bio/program/sax/~~ClustalW~~AlignmentSAXParser.html#endElement(org.biojava.bio.program.sax.QName)"·class="member-name-link">endElement(QName)</a>·-·Method·in·class·org.biojava.bio.program.sax.<a·href="org/biojava/bio/program/sax/~~ClustalW~~AlignmentSAXParser.html"·title="class·i[·...·truncated·by·diffoscope;·len:·39,·SHA:·~~7666b60~~5~~43d6~~0~~eb8335bb~~ebfd5~~c970d3ec199~~2~~d1fbb502a6~~845~~a559f~~6832~~1d8e~~·...·]AlignmentSAXParser</a></dt>	9290	<dt><a·href="org/biojava/bio/program/sax/SequenceAlignmentSAXParser.html#endElement(org.biojava.bio.program.sax.QName)"·class="member-name-link">endElement(QName)</a>·-·Method·in·class·org.biojava.bio.program.sax.<a·href="org/biojava/bio/program/sax/SequenceAlignmentSAXParser.html"·title="class·i[·...·truncated·by·diffoscope;·len:·39,·SHA:·b00bcfa59f0940acec4152e16d156a6c05f422f268c71133f98608a3632c7bdf·...·]AlignmentSAXParser</a></dt>
9291	<dd>	9291	<dd>
9292	<div·class="block">Utility·method·to·centralize·the·sending·of·a·SAX·endElement	9292	<div·class="block">Utility·method·to·centralize·the·sending·of·a·SAX·endElement
9293	·message·a·document·handler.</div>	9293	·message·a·document·handler.</div>
9294	</dd>	9294	</dd>
9295	<dt><a·href="org/biojava/bio/seq/io/agave/AGAVEBioSeqHandler.html#endElementHandler(java.lang.String,java.lang.String,java.lang.String,org.biojava.bio.seq.io.agave.StAXContentHandler)"·class="member-name-link">endElementHandler(String,·String,·String,·StAXContentHandler)</a>·-·Method·in·class·org.biojava.bio.seq.io.agave.<a·href="org/biojava/bio/seq/io/agave/AGAVEBioSeqHandler.html"·title="class·in·org.biojava.bio.seq.io.agave">AGAVEBioSeqHandler</a></dt>	9295	<dt><a·href="org/biojava/bio/seq/io/agave/AGAVEBioSeqHandler.html#endElementHandler(java.lang.String,java.lang.String,java.lang.String,org.biojava.bio.seq.io.agave.StAXContentHandler)"·class="member-name-link">endElementHandler(String,·String,·String,·StAXContentHandler)</a>·-·Method·in·class·org.biojava.bio.seq.io.agave.<a·href="org/biojava/bio/seq/io/agave/AGAVEBioSeqHandler.html"·title="class·in·org.biojava.bio.seq.io.agave">AGAVEBioSeqHandler</a></dt>
9296	<dd> </dd>	9296	<dd> </dd>
9297	<dt><a·href="org/biojava/bio/seq/io/agave/AGAVEChromosomeHandler.html#endElementHandler(java.lang.String,java.lang.String,java.lang.String,org.biojava.bio.seq.io.agave.StAXContentHandler)"·class="member-name-link">endElementHandler(String,·String,·String,·StAXContentHandler)</a>·-·Method·in·class·org.biojava.bio.seq.io.agave.<a·href="org/biojava/bio/seq/io/agave/AGAVEChromosomeHandler.html"·title="class·in·org.biojava.bio.seq.io.agave">AGAVEChromosomeHandler</a></dt>	9297	<dt><a·href="org/biojava/bio/seq/io/agave/AGAVEChromosomeHandler.html#endElementHandler(java.lang.String,java.lang.String,java.lang.String,org.biojava.bio.seq.io.agave.StAXContentHandler)"·class="member-name-link">endElementHandler(String,·String,·String,·StAXContentHandler)</a>·-·Method·in·class·org.biojava.bio.seq.io.agave.<a·href="org/biojava/bio/seq/io/agave/AGAVEChromosomeHandler.html"·title="class·in·org.biojava.bio.seq.io.agave">AGAVEChromosomeHandler</a></dt>
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14395	</dd>	14395	</dd>
14396	<dt><a·href="org/biojava/utils/bytecode/GeneratedCodeMethod.html#getContainingClass()"·class="member-name-link">getContainingClass()</a>·-·Method·in·class·org.biojava.utils.bytecode.<a·href="org/biojava/utils/bytecode/GeneratedCodeMethod.html"·title="class·in·org.biojava.utils.bytecode">GeneratedCodeMethod</a></dt>	14396	<dt><a·href="org/biojava/utils/bytecode/GeneratedCodeMethod.html#getContainingClass()"·class="member-name-link">getContainingClass()</a>·-·Method·in·class·org.biojava.utils.bytecode.<a·href="org/biojava/utils/bytecode/GeneratedCodeMethod.html"·title="class·in·org.biojava.utils.bytecode">GeneratedCodeMethod</a></dt>
14397	<dd> </dd>	14397	<dd> </dd>
14398	<dt><a·href="org/biojavax/bio/seq/SimpleRichFeatureRelationship.html#getContainsTerm()"·class="member-name-link">getContainsTerm()</a>·-·Static·method·in·class·org.biojavax.bio.seq.<a·href="org/biojavax/bio/seq/SimpleRichFeatureRelationship.html"·title="class·in·org.biojavax.bio.seq">SimpleRichFeatureRelationship</a></dt>	14398	<dt><a·href="org/biojavax/bio/seq/SimpleRichFeatureRelationship.html#getContainsTerm()"·class="member-name-link">getContainsTerm()</a>·-·Static·method·in·class·org.biojavax.bio.seq.<a·href="org/biojavax/bio/seq/SimpleRichFeatureRelationship.html"·title="class·in·org.biojavax.bio.seq">SimpleRichFeatureRelationship</a></dt>
14399	<dd>	14399	<dd>
14400	<div·class="block">Gets·the·default·CONTAINS·term·used·for·defining·the·relationship·between·features.</div>	14400	<div·class="block">Gets·the·default·CONTAINS·term·used·for·defining·the·relationship·between·features.</div>
14401	</dd>	14401	</dd>
14402	<dt><a·href="org/biojava/bio/program/sax/~~ClustalW~~AlignmentSAXParser.html#getContentHandler()"·class="member-name-link">getContentHandler()</a>·-·Method·in·class·org.biojava.bio.program.sax.<a·href="org/biojava/bio/program/sax/~~ClustalW~~AlignmentSAXParser.html"·title="class·in·org.biojava.bio.progra[·...·truncated·by·diffoscope;·len:·15,·SHA:·b5a71~~34f9~~f4~~8e90~~b~~5c21~~d18~~fc2f~~7~~e17a6~~3dd9~~175278~~f8ab~~61b7~~1a0~~03dc9056d9~~·...·]AlignmentSAXParser</a></dt>	14402	<dt><a·href="org/biojava/bio/program/sax/SequenceAlignmentSAXParser.html#getContentHandler()"·class="member-name-link">getContentHandler()</a>·-·Method·in·class·org.biojava.bio.program.sax.<a·href="org/biojava/bio/program/sax/SequenceAlignmentSAXParser.html"·title="class·in·org.biojava.bio.progra[·...·truncated·by·diffoscope;·len:·15,·SHA:·40da911ac0f0476bda30dc180e1037f468f379d9b81fd1f8f2fe10c60409720f·...·]AlignmentSAXParser</a></dt>
14403	<dd>	14403	<dd>
14404	<div·class="block">Return·the·content·handler.</div>	14404	<div·class="block">Return·the·content·handler.</div>
14405	</dd>	14405	</dd>
14406	<dt><a·href="org/biojava/bio/program/sax/blastxml/BlastXMLParserFacade.html#getContentHandler()"·class="member-name-link">getContentHandler()</a>·-·Method·in·class·org.biojava.bio.program.sax.blastxml.<a·href="org/biojava/bio/program/sax/blastxml/BlastXMLParserFacade.html"·title="class·in·org.biojava.bio.program.sax.blastxml">BlastXMLParserFacade</a></dt>	14406	<dt><a·href="org/biojava/bio/program/sax/blastxml/BlastXMLParserFacade.html#getContentHandler()"·class="member-name-link">getContentHandler()</a>·-·Method·in·class·org.biojava.bio.program.sax.blastxml.<a·href="org/biojava/bio/program/sax/blastxml/BlastXMLParserFacade.html"·title="class·in·org.biojava.bio.program.sax.blastxml">BlastXMLParserFacade</a></dt>
14407	<dd>	14407	<dd>
14408	<div·class="block">correct·this·later</div>	14408	<div·class="block">correct·this·later</div>
14409	</dd>	14409	</dd>
14410	<dt><a·href="org/biojava/bio/program/sax/~~ClustalW~~AlignmentSAXParser.html#getContentStream(org.xml.sax.InputSource)"·class="member-name-link">getContentStream(InputSource)</a>·-·Method·in·class·org.biojava.bio.program.sax.<a·href="org/biojava/bio/program/sax/~~ClustalW~~AlignmentSAXParser.html"·title=[·...·truncated·by·diffoscope;·len:·47,·SHA:·c~~f090031c2cf~~a~~6c70~~c7962d7ee8~~23ec46~~408d5~~ab57~~f47c1b9~~a9865~~d125b22e26·...·]AlignmentSAXParser</a></dt>	14410	<dt><a·href="org/biojava/bio/program/sax/SequenceAlignmentSAXParser.html#getContentStream(org.xml.sax.InputSource)"·class="member-name-link">getContentStream(InputSource)</a>·-·Method·in·class·org.biojava.bio.program.sax.<a·href="org/biojava/bio/program/sax/SequenceAlignmentSAXParser.html"·title=[·...·truncated·by·diffoscope;·len:·47,·SHA:·87761e6db1aabb2eccd6282147cda89917f9458c242f4a91f0342d92027eabe4·...·]AlignmentSAXParser</a></dt>
14411	<dd>	14411	<dd>
14412	<div·class="block">Create·a·stream·from·an·an·InputSource,·picking·the	14412	<div·class="block">Create·a·stream·from·an·an·InputSource,·picking·the
14413	·correct·stream·according·to·order·of·precedance.</div>	14413	·correct·stream·according·to·order·of·precedance.</div>
14414	</dd>	14414	</dd>
14415	<dt><a·href="org/biojava/bio/seq/projection/ProjectedFeatureHolder.html#getContext()"·class="member-name-link">getContext()</a>·-·Method·in·class·org.biojava.bio.seq.projection.<a·href="org/biojava/bio/seq/projection/ProjectedFeatureHolder.html"·title="class·in·org.biojava.bio.seq.projection">ProjectedFeatureHolder</a></dt>	14415	<dt><a·href="org/biojava/bio/seq/projection/ProjectedFeatureHolder.html#getContext()"·class="member-name-link">getContext()</a>·-·Method·in·class·org.biojava.bio.seq.projection.<a·href="org/biojava/bio/seq/projection/ProjectedFeatureHolder.html"·title="class·in·org.biojava.bio.seq.projection">ProjectedFeatureHolder</a></dt>
14416	<dd> </dd>	14416	<dd> </dd>
14417	<dt><a·href="org/biojava/stats/svm/TrainingEvent.html#getContext()"·class="member-name-link">getContext()</a>·-·Method·in·class·org.biojava.stats.svm.<a·href="org/biojava/stats/svm/TrainingEvent.html"·title="class·in·org.biojava.stats.svm">TrainingEvent</a></dt>	14417	<dt><a·href="org/biojava/stats/svm/TrainingEvent.html#getContext()"·class="member-name-link">getContext()</a>·-·Method·in·class·org.biojava.stats.svm.<a·href="org/biojava/stats/svm/TrainingEvent.html"·title="class·in·org.biojava.stats.svm">TrainingEvent</a></dt>
Offset 15333, 15 lines modified		Offset 15333, 15 lines modified
15333	·end·type·produced·by·the·primary·(intra-site·or·downstream)	15333	·end·type·produced·by·the·primary·(intra-site·or·downstream)
15334	·cut.</div>	15334	·cut.</div>
15335	</dd>	15335	</dd>
15336	<dt><a·href="org/biojava/bio/dp/AbstractTrainer.html#getDP()"·class="member-name-link">getDP()</a>·-·Method·in·class·org.biojava.bio.dp.<a·href="org/biojava/bio/dp/AbstractTrainer.html"·title="class·in·org.biojava.bio.dp">AbstractTrainer</a></dt>	15336	<dt><a·href="org/biojava/bio/dp/AbstractTrainer.html#getDP()"·class="member-name-link">getDP()</a>·-·Method·in·class·org.biojava.bio.dp.<a·href="org/biojava/bio/dp/AbstractTrainer.html"·title="class·in·org.biojava.bio.dp">AbstractTrainer</a></dt>
15337	<dd> </dd>	15337	<dd> </dd>
15338	<dt><a·href="org/biojava/bio/dp/TrainingAlgorithm.html#getDP()"·class="member-name-link">getDP()</a>·-·Method·in·interface·org.biojava.bio.dp.<a·href="org/biojava/bio/dp/TrainingAlgorithm.html"·title="interface·in·org.biojava.bio.dp">TrainingAlgorithm</a></dt>	15338	<dt><a·href="org/biojava/bio/dp/TrainingAlgorithm.html#getDP()"·class="member-name-link">getDP()</a>·-·Method·in·interface·org.biojava.bio.dp.<a·href="org/biojava/bio/dp/TrainingAlgorithm.html"·title="interface·in·org.biojava.bio.dp">TrainingAlgorithm</a></dt>
15339	<dd> </dd>	15339	<dd> </dd>
15340	<dt><a·href="org/biojava/bio/program/sax/~~ClustalW~~AlignmentSAXParser.html#getDTDHandler()"·class="member-name-link">getDTDHandler()</a>·-·Method·in·class·org.biojava.bio.program.sax.<a·href="org/biojava/bio/program/sax/~~ClustalW~~AlignmentSAXParser.html"·title="class·in·org.biojava.bio.program.sax">C[·...·truncated·by·diffoscope;·len:·7,·SHA:·~~1349~~29f1728ca~~d86e~~2~~5f4bcf~~a92~~96d57b~~82bc2~~483~~c~~ff527ccb~~4b991df~~8d1fe16~~·...·]AlignmentSAXParser</a></dt>	15340	<dt><a·href="org/biojava/bio/program/sax/SequenceAlignmentSAXParser.html#getDTDHandler()"·class="member-name-link">getDTDHandler()</a>·-·Method·in·class·org.biojava.bio.program.sax.<a·href="org/biojava/bio/program/sax/SequenceAlignmentSAXParser.html"·title="class·in·org.biojava.bio.program.sax">S[·...·truncated·by·diffoscope;·len:·7,·SHA:·2e726ca09cd21a16530a423322ea38464cf23367bc69361ad4874869daa5b595·...·]AlignmentSAXParser</a></dt>
15341	<dd>	15341	<dd>
15342	<div·class="block">Do-nothing·implementation·of·interface·method</div>	15342	<div·class="block">Do-nothing·implementation·of·interface·method</div>
15343	</dd>	15343	</dd>
15344	<dt><a·href="org/biojava/bio/program/sax/blastxml/BlastXMLParserFacade.html#getDTDHandler()"·class="member-name-link">getDTDHandler()</a>·-·Method·in·class·org.biojava.bio.program.sax.blastxml.<a·href="org/biojava/bio/program/sax/blastxml/BlastXMLParserFacade.html"·title="class·in·org.biojava.bio.program.sax.blastxml">BlastXMLParserFacade</a></dt>	15344	<dt><a·href="org/biojava/bio/program/sax/blastxml/BlastXMLParserFacade.html#getDTDHandler()"·class="member-name-link">getDTDHandler()</a>·-·Method·in·class·org.biojava.bio.program.sax.blastxml.<a·href="org/biojava/bio/program/sax/blastxml/BlastXMLParserFacade.html"·title="class·in·org.biojava.bio.program.sax.blastxml">BlastXMLParserFacade</a></dt>
15345	<dd> </dd>	15345	<dd> </dd>
15346	<dt><a·href="org/biojava/bio/proteomics/StructureTools.html#getE()"·class="member-name-link">getE()</a>·-·Method·in·class·org.biojava.bio.proteomics.<a·href="org/biojava/bio/proteomics/StructureTools.html"·title="class·in·org.biojava.bio.proteomics">StructureTools</a></dt>	15346	<dt><a·href="org/biojava/bio/proteomics/StructureTools.html#getE()"·class="member-name-link">getE()</a>·-·Method·in·class·org.biojava.bio.proteomics.<a·href="org/biojava/bio/proteomics/StructureTools.html"·title="class·in·org.biojava.bio.proteomics">StructureTools</a></dt>
15347	<dd> </dd>	15347	<dd> </dd>
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15505	<dd>	15505	<dd>
15506	<div·class="block">Get·the·current·string·indicating·that·a·record·has·ended.</div>	15506	<div·class="block">Get·the·current·string·indicating·that·a·record·has·ended.</div>
15507	</dd>	15507	</dd>
15508	<dt><a·href="org/biojava/bio/program/tagvalue/RegexParser.html#getEndOfRecord()"·class="member-name-link">getEndOfRecord()</a>·-·Method·in·class·org.biojava.bio.program.tagvalue.<a·href="org/biojava/bio/program/tagvalue/RegexParser.html"·title="class·in·org.biojava.bio.program.tagvalue">RegexParser</a></dt>	15508	<dt><a·href="org/biojava/bio/program/tagvalue/RegexParser.html#getEndOfRecord()"·class="member-name-link">getEndOfRecord()</a>·-·Method·in·class·org.biojava.bio.program.tagvalue.<a·href="org/biojava/bio/program/tagvalue/RegexParser.html"·title="class·in·org.biojava.bio.program.tagvalue">RegexParser</a></dt>
15509	<dd>	15509	<dd>
15510	<div·class="block">Get·the·explicit·end-of-record·string.</div>	15510	<div·class="block">Get·the·explicit·end-of-record·string.</div>
15511	</dd>	15511	</dd>
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18	-rw-r--r--···0·root·········(0)·root·········(0)·····2936·2023-05-12·09:09:08.000000·./usr/share/doc/libbiojava-java/apidocs/legal/jquery.md	18	-rw-r--r--···0·root·········(0)·root·········(0)·····2936·2023-05-12·09:09:08.000000·./usr/share/doc/libbiojava-java/apidocs/legal/jquery.md
19	-rw-r--r--···0·root·········(0)·root·········(0)·····1870·2023-05-12·09:09:08.000000·./usr/share/doc/libbiojava-java/apidocs/legal/jqueryUI.md	19	-rw-r--r--···0·root·········(0)·root·········(0)·····1870·2023-05-12·09:09:08.000000·./usr/share/doc/libbiojava-java/apidocs/legal/jqueryUI.md
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22	drwxr-xr-x···0·root·········(0)·root·········(0)········0·2023-05-12·09:09:08.000000·./usr/share/doc/libbiojava-java/apidocs/org/	22	drwxr-xr-x···0·root·········(0)·root·········(0)········0·2023-05-12·09:09:08.000000·./usr/share/doc/libbiojava-java/apidocs/org/
23	drwxr-xr-x···0·root·········(0)·root·········(0)········0·2023-05-12·09:09:08.000000·./usr/share/doc/libbiojava-java/apidocs/org/biojava/	23	drwxr-xr-x···0·root·········(0)·root·········(0)········0·2023-05-12·09:09:08.000000·./usr/share/doc/libbiojava-java/apidocs/org/biojava/
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25	drwxr-xr-x···0·root·········(0)·root·········(0)········0·2023-05-12·09:09:08.000000·./usr/share/doc/libbiojava-java/apidocs/org/biojava/bibliography/	25	drwxr-xr-x···0·root·········(0)·root·········(0)········0·2023-05-12·09:09:08.000000·./usr/share/doc/libbiojava-java/apidocs/org/biojava/bibliography/
26	-rw-r--r--···0·root·········(0)·root·········(0)····34030·2023-05-12·09:09:08.000000·./usr/share/doc/libbiojava-java/apidocs/org/biojava/bibliography/BibRef.html	26	-rw-r--r--···0·root·········(0)·root·········(0)····34030·2023-05-12·09:09:08.000000·./usr/share/doc/libbiojava-java/apidocs/org/biojava/bibliography/BibRef.html
27	-rw-r--r--···0·root·········(0)·root·········(0)····14355·2023-05-12·09:09:08.000000·./usr/share/doc/libbiojava-java/apidocs/org/biojava/bibliography/BibRefException.html	27	-rw-r--r--···0·root·········(0)·root·········(0)····14355·2023-05-12·09:09:08.000000·./usr/share/doc/libbiojava-java/apidocs/org/biojava/bibliography/BibRefException.html


Offset 1463, 15 lines modified		Offset 1463, 15 lines modified
1463	······add·a·search·pattern·to·the·searches·to·be·conducted·by·this·object.	1463	······add·a·search·pattern·to·the·searches·to·be·conducted·by·this·object.
1464	··addPos(Object)·-·Method·in·class·org.biojava.stats.svm.DiagonalAddKernel	1464	··addPos(Object)·-·Method·in·class·org.biojava.stats.svm.DiagonalAddKernel
1465	······	1465	······
1466	··addPosition(AGAVEMapPosition)·-·Method·in·class	1466	··addPosition(AGAVEMapPosition)·-·Method·in·class
1467	··org.biojava.bio.seq.io.agave.AGAVEMapLocation	1467	··org.biojava.bio.seq.io.agave.AGAVEMapLocation
1468	······	1468	······
1469	··addPrefixMapping(String,_String)·-·Method·in·class	1469	··addPrefixMapping(String,_String)·-·Method·in·class
1470	··org.biojava.bio.program.sax.~~ClustalW~~AlignmentSAXParser	1470	··org.biojava.bio.program.sax.SequenceAlignmentSAXParser
1471	······Adds·a·namespace·prefix·to·URI·mapping·as·(key,value)·pairs.	1471	······Adds·a·namespace·prefix·to·URI·mapping·as·(key,value)·pairs.
1472	··addProp(AGAVEProperty)·-·Method·in·class	1472	··addProp(AGAVEProperty)·-·Method·in·class
1473	··org.biojava.bio.seq.io.agave.AGAVERelatedAnnot	1473	··org.biojava.bio.seq.io.agave.AGAVERelatedAnnot
1474	······	1474	······
1475	··addProp(AGAVEProperty)·-·Method·in·class	1475	··addProp(AGAVEProperty)·-·Method·in·class
1476	··org.biojava.bio.seq.io.agave.AGAVEXref	1476	··org.biojava.bio.seq.io.agave.AGAVEXref
1477	······	1477	······
Offset 4480, 15 lines modified		Offset 4480, 15 lines modified
4480	······An·implementation·that·always·vetoes·everything.	4480	······An·implementation·that·always·vetoes·everything.
4481	··ChangeListener.ChangeEventRecorder·-·Class·in·org.biojava.utils	4481	··ChangeListener.ChangeEventRecorder·-·Class·in·org.biojava.utils
4482	······A·listener·that·remembers·the·ChangeEvent·of·the·last·change.	4482	······A·listener·that·remembers·the·ChangeEvent·of·the·last·change.
4483	··ChangeListener.LoggingListener·-·Class·in·org.biojava.utils	4483	··ChangeListener.LoggingListener·-·Class·in·org.biojava.utils
4484	······A·listener·that·writes·information·about·the·event·stream·to·a	4484	······A·listener·that·writes·information·about·the·event·stream·to·a
4485	······PrintStream.	4485	······PrintStream.
4486	··changeState(int)·-·Method·in·class	4486	··changeState(int)·-·Method·in·class
4487	··org.biojava.bio.program.sax.~~ClustalW~~AlignmentSAXParser	4487	··org.biojava.bio.program.sax.SequenceAlignmentSAXParser
4488	······Centralise·chaining·of·iState·field·to·help·with·debugging.	4488	······Centralise·chaining·of·iState·field·to·help·with·debugging.
4489	··changeSupport()·-·Method·in·class·org.biojava.utils.ChangeForwarder	4489	··changeSupport()·-·Method·in·class·org.biojava.utils.ChangeForwarder
4490	······Return·the·underlying·ChangeSupport·instance·that·can·be·used·to·fire	4490	······Return·the·underlying·ChangeSupport·instance·that·can·be·used·to·fire
4491	······ChangeEvents·and·mannage·listeners.	4491	······ChangeEvents·and·mannage·listeners.
4492	··ChangeSupport·-·Class·in·org.biojava.utils	4492	··ChangeSupport·-·Class·in·org.biojava.utils
4493	······A·utility·class·to·provide·management·for·informing·ChangeListeners·of	4493	······A·utility·class·to·provide·management·for·informing·ChangeListeners·of
4494	······ChangeEvents.	4494	······ChangeEvents.
Offset 4572, 15 lines modified		Offset 4572, 15 lines modified
4572	··CHARACTER·-·Static·variable·in·interface	4572	··CHARACTER·-·Static·variable·in·interface
4573	··org.biojava.bio.seq.io.SymbolTokenization	4573	··org.biojava.bio.seq.io.SymbolTokenization
4574	······	4574	······
4575	··characters(char[],_int,_int)·-·Method·in·class	4575	··characters(char[],_int,_int)·-·Method·in·class
4576	··org.biojava.bio.program.blast2html.Blast2HTMLHandler	4576	··org.biojava.bio.program.blast2html.Blast2HTMLHandler
4577	······Describe·characters·method·here.	4577	······Describe·characters·method·here.
4578	··characters(char[],_int,_int)·-·Method·in·class	4578	··characters(char[],_int,_int)·-·Method·in·class
4579	··org.biojava.bio.program.sax.~~ClustalW~~AlignmentSAXParser	4579	··org.biojava.bio.program.sax.SequenceAlignmentSAXParser
4580	······Utility·method·to·centralize·the·sending·of·a·SAX·characters·message·a	4580	······Utility·method·to·centralize·the·sending·of·a·SAX·characters·message·a
4581	······document·handler.	4581	······document·handler.
4582	··characters(char[],_int,_int)·-·Method·in·class	4582	··characters(char[],_int,_int)·-·Method·in·class
4583	··org.biojava.bio.program.ssbind.SeqSimilarityAdapter	4583	··org.biojava.bio.program.ssbind.SeqSimilarityAdapter
4584	······	4584	······
4585	··characters(char[],_int,_int)·-·Method·in·class	4585	··characters(char[],_int,_int)·-·Method·in·class
4586	··org.biojava.bio.program.xml.SimpleXMLEmitter	4586	··org.biojava.bio.program.xml.SimpleXMLEmitter
Offset 7271, 15 lines modified		Offset 7271, 15 lines modified
7271	······	7271	······
7272	··doRetain()·-·Method·in·class·org.biojava.bio.program.tagvalue.TagDropper	7272	··doRetain()·-·Method·in·class·org.biojava.bio.program.tagvalue.TagDropper
7273	······Find·out·if·known·tags·are·retained·or·dropped.	7273	······Find·out·if·known·tags·are·retained·or·dropped.
7274	··doSortPeptides()·-·Method·in·class	7274	··doSortPeptides()·-·Method·in·class
7275	··org.biojava.bio.gui.sequence.AbstractPeptideDigestRenderer	7275	··org.biojava.bio.gui.sequence.AbstractPeptideDigestRenderer
7276	······	7276	······
7277	··doTranslate(Symbol)·-·Method·in·class	7277	··doTranslate(Symbol)·-·Method·in·class
7278	··org.biojava.bio.symbol.Abstract~~ManyToOn~~eTranslationTable	7278	··org.biojava.bio.symbol.AbstractReversibleTranslationTable
7279	······this·method·is·expected·to·translate·any·symbol·in·the·source·alphabet.	7279	······this·method·is·expected·to·translate·any·symbol·in·the·source·alphabet.
7280	··doTranslate(Symbol)·-·Method·in·class	7280	··doTranslate(Symbol)·-·Method·in·class
7281	··org.biojava.bio.symbol.SimpleManyToOneTranslationTable	7281	··org.biojava.bio.symbol.SimpleManyToOneTranslationTable
7282	······	7282	······
7283	··doTranslate(Symbol)·-·Method·in·class	7283	··doTranslate(Symbol)·-·Method·in·class
7284	··org.biojava.bio.symbol.SimpleReversibleTranslationTable	7284	··org.biojava.bio.symbol.SimpleReversibleTranslationTable
7285	······	7285	······
Offset 8033, 15 lines modified		Offset 8033, 15 lines modified
8033	··endElement(String,_String,_String,_StAXContentHandler)·-·Method·in·class	8033	··endElement(String,_String,_String,_StAXContentHandler)·-·Method·in·class
8034	··org.biojava.utils.stax.StAXContentHandlerBase	8034	··org.biojava.utils.stax.StAXContentHandlerBase
8035	······	8035	······
8036	··endElement(String,_String,_String,_StAXContentHandler)·-·Method·in·class	8036	··endElement(String,_String,_String,_StAXContentHandler)·-·Method·in·class
8037	··org.biojava.utils.stax.StringElementHandlerBase	8037	··org.biojava.utils.stax.StringElementHandlerBase
8038	······	8038	······
8039	··endElement(QName)·-·Method·in·class	8039	··endElement(QName)·-·Method·in·class
8040	··org.biojava.bio.program.sax.~~ClustalW~~AlignmentSAXParser	8040	··org.biojava.bio.program.sax.SequenceAlignmentSAXParser
8041	······Utility·method·to·centralize·the·sending·of·a·SAX·endElement·message·a	8041	······Utility·method·to·centralize·the·sending·of·a·SAX·endElement·message·a
8042	······document·handler.	8042	······document·handler.
8043	··endElementHandler(String,_String,_String,_StAXContentHandler)·-·Method·in	8043	··endElementHandler(String,_String,_String,_StAXContentHandler)·-·Method·in
8044	··class·org.biojava.bio.seq.io.agave.AGAVEBioSeqHandler	8044	··class·org.biojava.bio.seq.io.agave.AGAVEBioSeqHandler
8045	······	8045	······
8046	··endElementHandler(String,_String,_String,_StAXContentHandler)·-·Method·in	8046	··endElementHandler(String,_String,_String,_StAXContentHandler)·-·Method·in
8047	··class·org.biojava.bio.seq.io.agave.AGAVEChromosomeHandler	8047	··class·org.biojava.bio.seq.io.agave.AGAVEChromosomeHandler
Offset 12491, 21 lines modified		Offset 12491, 21 lines modified
12491	··org.biojava.utils.bytecode.GeneratedCodeMethod	12491	··org.biojava.utils.bytecode.GeneratedCodeMethod
12492	······	12492	······
12493	··getContainsTerm()·-·Static·method·in·class	12493	··getContainsTerm()·-·Static·method·in·class
12494	··org.biojavax.bio.seq.SimpleRichFeatureRelationship	12494	··org.biojavax.bio.seq.SimpleRichFeatureRelationship
12495	······Gets·the·default·CONTAINS·term·used·for·defining·the·relationship·between	12495	······Gets·the·default·CONTAINS·term·used·for·defining·the·relationship·between
12496	······features.	12496	······features.
12497	··getContentHandler()·-·Method·in·class	12497	··getContentHandler()·-·Method·in·class
12498	··org.biojava.bio.program.sax.~~ClustalW~~AlignmentSAXParser	12498	··org.biojava.bio.program.sax.SequenceAlignmentSAXParser
12499	······Return·the·content·handler.	12499	······Return·the·content·handler.
12500	··getContentHandler()·-·Method·in·class	12500	··getContentHandler()·-·Method·in·class
12501	··org.biojava.bio.program.sax.blastxml.BlastXMLParserFacade	12501	··org.biojava.bio.program.sax.blastxml.BlastXMLParserFacade
12502	······correct·this·later	12502	······correct·this·later
12503	··getContentStream(InputSource)·-·Method·in·class	12503	··getContentStream(InputSource)·-·Method·in·class
12504	··org.biojava.bio.program.sax.~~ClustalW~~AlignmentSAXParser	12504	··org.biojava.bio.program.sax.SequenceAlignmentSAXParser
12505	······Create·a·stream·from·an·an·InputSource,·picking·the·correct·stream	12505	······Create·a·stream·from·an·an·InputSource,·picking·the·correct·stream
12506	······according·to·order·of·precedance.	12506	······according·to·order·of·precedance.
12507	··getContext()·-·Method·in·class	12507	··getContext()·-·Method·in·class
12508	··org.biojava.bio.seq.projection.ProjectedFeatureHolder	12508	··org.biojava.bio.seq.projection.ProjectedFeatureHolder
12509	······	12509	······
12510	··getContext()·-·Method·in·class·org.biojava.stats.svm.TrainingEvent	12510	··getContext()·-·Method·in·class·org.biojava.stats.svm.TrainingEvent
12511	······	12511	······
Offset 13274, 15 lines modified		Offset 13274, 15 lines modified
13274	······getDownstreamEndType·returns·the·double-stranded·end·type·produced·by·the	13274	······getDownstreamEndType·returns·the·double-stranded·end·type·produced·by·the
13275	······primary·(intra-site·or·downstream)·cut.	13275	······primary·(intra-site·or·downstream)·cut.
13276	··getDP()·-·Method·in·class·org.biojava.bio.dp.AbstractTrainer	13276	··getDP()·-·Method·in·class·org.biojava.bio.dp.AbstractTrainer
13277	······	13277	······
13278	··getDP()·-·Method·in·interface·org.biojava.bio.dp.TrainingAlgorithm	13278	··getDP()·-·Method·in·interface·org.biojava.bio.dp.TrainingAlgorithm
13279	······	13279	······
13280	··getDTDHandler()·-·Method·in·class	13280	··getDTDHandler()·-·Method·in·class
13281	··org.biojava.bio.program.sax.~~ClustalW~~AlignmentSAXParser	13281	··org.biojava.bio.program.sax.SequenceAlignmentSAXParser
13282	······Do-nothing·implementation·of·interface·method	13282	······Do-nothing·implementation·of·interface·method
13283	··getDTDHandler()·-·Method·in·class	13283	··getDTDHandler()·-·Method·in·class
13284	··org.biojava.bio.program.sax.blastxml.BlastXMLParserFacade	13284	··org.biojava.bio.program.sax.blastxml.BlastXMLParserFacade
13285	······	13285	······
13286	··getE()·-·Method·in·class·org.biojava.bio.proteomics.StructureTools	13286	··getE()·-·Method·in·class·org.biojava.bio.proteomics.StructureTools
13287	······	13287	······
13288	··getEcNumber(Annotation)·-·Method·in·class	13288	··getEcNumber(Annotation)·-·Method·in·class
Offset 13426, 15 lines modified		Offset 13426, 15 lines modified
13426	··getEndOfRecord()·-·Method·in·class	13426	··getEndOfRecord()·-·Method·in·class
13427	··org.biojava.bio.program.tagvalue.LineSplitParser	13427	··org.biojava.bio.program.tagvalue.LineSplitParser
13428	······Get·the·current·string·indicating·that·a·record·has·ended.	13428	······Get·the·current·string·indicating·that·a·record·has·ended.
13429	··getEndOfRecord()·-·Method·in·class	13429	··getEndOfRecord()·-·Method·in·class
13430	··org.biojava.bio.program.tagvalue.RegexParser	13430	··org.biojava.bio.program.tagvalue.RegexParser
13431	······Get·the·explicit·end-of-record·string.	13431	······Get·the·explicit·end-of-record·string.
13432	··getEntityResolver()·-·Method·in·class	13432	··getEntityResolver()·-·Method·in·class
13433	··org.biojava.bio.program.sax.~~ClustalW~~AlignmentSAXParser	13433	··org.biojava.bio.program.sax.SequenceAlignmentSAXParser
13434	······Do-nothing·implementation·of·interface·method	13434	······Do-nothing·implementation·of·interface·method
Max diff block lines reached; 19329/25670 bytes (75.30%) of diff not shown.


Offset 2253, 15 lines modified		Offset 2253, 15 lines modified
2253	},·{	2253	},·{
2254	····"p":·"org.biojava.bio.seq.io.agave",	2254	····"p":·"org.biojava.bio.seq.io.agave",
2255	····"c":·"AGAVEMapLocation",	2255	····"c":·"AGAVEMapLocation",
2256	····"l":·"addPosition(AGAVEMapPosition)",	2256	····"l":·"addPosition(AGAVEMapPosition)",
2257	····"u":·"addPosition(org.biojava.bio.seq.io.agave.AGAVEMapPosition)"	2257	····"u":·"addPosition(org.biojava.bio.seq.io.agave.AGAVEMapPosition)"
2258	},·{	2258	},·{
2259	····"p":·"org.biojava.bio.program.sax",	2259	····"p":·"org.biojava.bio.program.sax",
2260	····"c":·"~~ClustalW~~AlignmentSAXParser",	2260	····"c":·"SequenceAlignmentSAXParser",
2261	····"l":·"addPrefixMapping(String,·String)",	2261	····"l":·"addPrefixMapping(String,·String)",
2262	····"u":·"addPrefixMapping(java.lang.String,java.lang.String)"	2262	····"u":·"addPrefixMapping(java.lang.String,java.lang.String)"
2263	},·{	2263	},·{
2264	····"p":·"org.biojava.bio.seq.io.agave",	2264	····"p":·"org.biojava.bio.seq.io.agave",
2265	····"c":·"AGAVERelatedAnnot",	2265	····"c":·"AGAVERelatedAnnot",
2266	····"l":·"addProp(AGAVEProperty)",	2266	····"l":·"addProp(AGAVEProperty)",
2267	····"u":·"addProp(org.biojava.bio.seq.io.agave.AGAVEProperty)"	2267	····"u":·"addProp(org.biojava.bio.seq.io.agave.AGAVEProperty)"
Offset 6168, 15 lines modified		Offset 6168, 15 lines modified
6168	},·{	6168	},·{
6169	····"p":·"org.biojava.utils",	6169	····"p":·"org.biojava.utils",
6170	····"c":·"ChangeForwarder",	6170	····"c":·"ChangeForwarder",
6171	····"l":·"ChangeForwarder(Object,·ChangeSupport)",	6171	····"l":·"ChangeForwarder(Object,·ChangeSupport)",
6172	····"u":·"%3Cinit%3E(java.lang.Object,org.biojava.utils.ChangeSupport)"	6172	····"u":·"%3Cinit%3E(java.lang.Object,org.biojava.utils.ChangeSupport)"
6173	},·{	6173	},·{
6174	····"p":·"org.biojava.bio.program.sax",	6174	····"p":·"org.biojava.bio.program.sax",
6175	····"c":·"~~ClustalW~~AlignmentSAXParser",	6175	····"c":·"SequenceAlignmentSAXParser",
6176	····"l":·"changeState(int)"	6176	····"l":·"changeState(int)"
6177	},·{	6177	},·{
6178	····"p":·"org.biojava.utils",	6178	····"p":·"org.biojava.utils",
6179	····"c":·"ChangeForwarder",	6179	····"c":·"ChangeForwarder",
6180	····"l":·"changeSupport()"	6180	····"l":·"changeSupport()"
6181	},·{	6181	},·{
6182	····"p":·"org.biojava.utils",	6182	····"p":·"org.biojava.utils",
Offset 6289, 15 lines modified		Offset 6289, 15 lines modified
6289	},·{	6289	},·{
6290	····"p":·"org.biojava.bio.program.blast2html",	6290	····"p":·"org.biojava.bio.program.blast2html",
6291	····"c":·"Blast2HTMLHandler",	6291	····"c":·"Blast2HTMLHandler",
6292	····"l":·"characters(char[],·int,·int)",	6292	····"l":·"characters(char[],·int,·int)",
6293	····"u":·"characters(char[],int,int)"	6293	····"u":·"characters(char[],int,int)"
6294	},·{	6294	},·{
6295	····"p":·"org.biojava.bio.program.sax",	6295	····"p":·"org.biojava.bio.program.sax",
6296	····"c":·"~~ClustalW~~AlignmentSAXParser",	6296	····"c":·"SequenceAlignmentSAXParser",
6297	····"l":·"characters(char[],·int,·int)",	6297	····"l":·"characters(char[],·int,·int)",
6298	····"u":·"characters(char[],int,int)"	6298	····"u":·"characters(char[],int,int)"
6299	},·{	6299	},·{
6300	····"p":·"org.biojava.bio.program.ssbind",	6300	····"p":·"org.biojava.bio.program.ssbind",
6301	····"c":·"SeqSimilarityAdapter",	6301	····"c":·"SeqSimilarityAdapter",
6302	····"l":·"characters(char[],·int,·int)",	6302	····"l":·"characters(char[],·int,·int)",
6303	····"u":·"characters(char[],int,int)"	6303	····"u":·"characters(char[],int,int)"
Offset 10199, 15 lines modified		Offset 10199, 15 lines modified
10199	····"l":·"doRetain()"	10199	····"l":·"doRetain()"
10200	},·{	10200	},·{
10201	····"p":·"org.biojava.bio.gui.sequence",	10201	····"p":·"org.biojava.bio.gui.sequence",
10202	····"c":·"AbstractPeptideDigestRenderer",	10202	····"c":·"AbstractPeptideDigestRenderer",
10203	····"l":·"doSortPeptides()"	10203	····"l":·"doSortPeptides()"
10204	},·{	10204	},·{
10205	····"p":·"org.biojava.bio.symbol",	10205	····"p":·"org.biojava.bio.symbol",
10206	····"c":·"Abstract~~ManyToOn~~eTranslationTable",	10206	····"c":·"AbstractReversibleTranslationTable",
10207	····"l":·"doTranslate(Symbol)",	10207	····"l":·"doTranslate(Symbol)",
10208	····"u":·"doTranslate(org.biojava.bio.symbol.Symbol)"	10208	····"u":·"doTranslate(org.biojava.bio.symbol.Symbol)"
10209	},·{	10209	},·{
10210	····"p":·"org.biojava.bio.symbol",	10210	····"p":·"org.biojava.bio.symbol",
10211	····"c":·"SimpleManyToOneTranslationTable",	10211	····"c":·"SimpleManyToOneTranslationTable",
10212	····"l":·"doTranslate(Symbol)",	10212	····"l":·"doTranslate(Symbol)",
10213	····"u":·"doTranslate(org.biojava.bio.symbol.Symbol)"	10213	····"u":·"doTranslate(org.biojava.bio.symbol.Symbol)"
Offset 11030, 15 lines modified		Offset 11030, 15 lines modified
11030	····"l":·"endDocument()"	11030	····"l":·"endDocument()"
11031	},·{	11031	},·{
11032	····"p":·"org.biojava.bio.program.xml",	11032	····"p":·"org.biojava.bio.program.xml",
11033	····"c":·"BaseXMLWriter",	11033	····"c":·"BaseXMLWriter",
11034	····"l":·"endElement()"	11034	····"l":·"endElement()"
11035	},·{	11035	},·{
11036	····"p":·"org.biojava.bio.program.sax",	11036	····"p":·"org.biojava.bio.program.sax",
11037	····"c":·"~~ClustalW~~AlignmentSAXParser",	11037	····"c":·"SequenceAlignmentSAXParser",
11038	····"l":·"endElement(QName)",	11038	····"l":·"endElement(QName)",
11039	····"u":·"endElement(org.biojava.bio.program.sax.QName)"	11039	····"u":·"endElement(org.biojava.bio.program.sax.QName)"
11040	},·{	11040	},·{
11041	····"p":·"org.biojava.bio.program.blast2html",	11041	····"p":·"org.biojava.bio.program.blast2html",
11042	····"c":·"Blast2HTMLHandler",	11042	····"c":·"Blast2HTMLHandler",
11043	····"l":·"endElement(String,·String,·String)",	11043	····"l":·"endElement(String,·String,·String)",
11044	····"u":·"endElement(java.lang.String,java.lang.String,java.lang.String)"	11044	····"u":·"endElement(java.lang.String,java.lang.String,java.lang.String)"
Offset 17692, 23 lines modified		Offset 17692, 23 lines modified
17692	····"l":·"getContainingClass()"	17692	····"l":·"getContainingClass()"
17693	},·{	17693	},·{
17694	····"p":·"org.biojavax.bio.seq",	17694	····"p":·"org.biojavax.bio.seq",
17695	····"c":·"SimpleRichFeatureRelationship",	17695	····"c":·"SimpleRichFeatureRelationship",
17696	····"l":·"getContainsTerm()"	17696	····"l":·"getContainsTerm()"
17697	},·{	17697	},·{
17698	····"p":·"org.biojava.bio.program.sax",	17698	····"p":·"org.biojava.bio.program.sax",
17699	····"c":·"~~ClustalW~~AlignmentSAXParser",	17699	····"c":·"SequenceAlignmentSAXParser",
17700	····"l":·"getContentHandler()"	17700	····"l":·"getContentHandler()"
17701	},·{	17701	},·{
17702	····"p":·"org.biojava.bio.program.sax.blastxml",	17702	····"p":·"org.biojava.bio.program.sax.blastxml",
17703	····"c":·"BlastXMLParserFacade",	17703	····"c":·"BlastXMLParserFacade",
17704	····"l":·"getContentHandler()"	17704	····"l":·"getContentHandler()"
17705	},·{	17705	},·{
17706	····"p":·"org.biojava.bio.program.sax",	17706	····"p":·"org.biojava.bio.program.sax",
17707	····"c":·"~~ClustalW~~AlignmentSAXParser",	17707	····"c":·"SequenceAlignmentSAXParser",
17708	····"l":·"getContentStream(InputSource)",	17708	····"l":·"getContentStream(InputSource)",
17709	····"u":·"getContentStream(org.xml.sax.InputSource)"	17709	····"u":·"getContentStream(org.xml.sax.InputSource)"
17710	},·{	17710	},·{
17711	····"p":·"org.biojava.bio.seq.projection",	17711	····"p":·"org.biojava.bio.seq.projection",
17712	····"c":·"ProjectedFeatureHolder",	17712	····"c":·"ProjectedFeatureHolder",
17713	····"l":·"getContext()"	17713	····"l":·"getContext()"
17714	},·{	17714	},·{
Offset 18898, 15 lines modified		Offset 18898, 15 lines modified
18898	····"l":·"getDP()"	18898	····"l":·"getDP()"
18899	},·{	18899	},·{
18900	····"p":·"org.biojava.bio.dp",	18900	····"p":·"org.biojava.bio.dp",
18901	····"c":·"TrainingAlgorithm",	18901	····"c":·"TrainingAlgorithm",
18902	····"l":·"getDP()"	18902	····"l":·"getDP()"
18903	},·{	18903	},·{
18904	····"p":·"org.biojava.bio.program.sax",	18904	····"p":·"org.biojava.bio.program.sax",
18905	····"c":·"~~ClustalW~~AlignmentSAXParser",	18905	····"c":·"SequenceAlignmentSAXParser",
18906	····"l":·"getDTDHandler()"	18906	····"l":·"getDTDHandler()"
18907	},·{	18907	},·{
18908	····"p":·"org.biojava.bio.program.sax.blastxml",	18908	····"p":·"org.biojava.bio.program.sax.blastxml",
18909	····"c":·"BlastXMLParserFacade",	18909	····"c":·"BlastXMLParserFacade",
18910	····"l":·"getDTDHandler()"	18910	····"l":·"getDTDHandler()"
18911	},·{	18911	},·{
18912	····"p":·"org.biojava.bio.proteomics",	18912	····"p":·"org.biojava.bio.proteomics",
Offset 19128, 15 lines modified		Offset 19128, 15 lines modified
19128	····"l":·"getEndOfRecord()"	19128	····"l":·"getEndOfRecord()"
19129	},·{	19129	},·{
19130	····"p":·"org.biojava.bio.program.tagvalue",	19130	····"p":·"org.biojava.bio.program.tagvalue",
19131	····"c":·"RegexParser",	19131	····"c":·"RegexParser",
19132	····"l":·"getEndOfRecord()"	19132	····"l":·"getEndOfRecord()"
19133	},·{	19133	},·{
19134	····"p":·"org.biojava.bio.program.sax",	19134	····"p":·"org.biojava.bio.program.sax",
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