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| 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 | 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 11725, 15 lines modified | Offset 11725, 15 lines modified | ||
| 11725 | </dd> | 11725 | </dd> |
| 11726 | <dt><a·href="org/biojava/bio/seq/io/SwissprotFileFormer.html#formatLocation(java.lang.StringBuffer,org.biojava.bio.symbol.Location)"·class="member-name-link">formatLocation(StringBuffer,·Location)</a>·-·Method·in·class·org.biojava.bio.seq.io.<a·href="org/biojava/bio/seq/io/SwissprotFileFormer.html"·title="class·in·org.biojava.bio.seq.io">SwissprotFileFormer</a></dt> | 11726 | <dt><a·href="org/biojava/bio/seq/io/SwissprotFileFormer.html#formatLocation(java.lang.StringBuffer,org.biojava.bio.symbol.Location)"·class="member-name-link">formatLocation(StringBuffer,·Location)</a>·-·Method·in·class·org.biojava.bio.seq.io.<a·href="org/biojava/bio/seq/io/SwissprotFileFormer.html"·title="class·in·org.biojava.bio.seq.io">SwissprotFileFormer</a></dt> |
| 11727 | <dd> | 11727 | <dd> |
| 11728 | <div·class="deprecation-block"><span·class="deprecated-label">Deprecated.</span></div> | 11728 | <div·class="deprecation-block"><span·class="deprecated-label">Deprecated.</span></div> |
| 11729 | <div·class="block"><code>formatLocation</code>·creates·a·String·representation·of | 11729 | <div·class="block"><code>formatLocation</code>·creates·a·String·representation·of |
| 11730 | ·a·<code>Location</code>.</div> | 11730 | ·a·<code>Location</code>.</div> |
| 11731 | </dd> | 11731 | </dd> |
| 11732 | <dt><a·href="org/biojava/bio/seq/io/ | 11732 | <dt><a·href="org/biojava/bio/seq/io/GenbankFileFormer.html#formatLocation(java.lang.StringBuffer,org.biojava.bio.symbol.Location,org.biojava.bio.seq.StrandedFeature.Strand)"·class="member-name-link">formatLocation(StringBuffer,·Location,·StrandedFeature.Strand)</a>·-·Method·in·class·org.bioj[·...·truncated·by·diffoscope;·len:·118,·SHA:·d484fc8cd1ab96621842b899dab2e921cea1e764039dd595c4e3cd1d109db859·...·]FileFormer</a></dt> |
| 11733 | <dd> | 11733 | <dd> |
| 11734 | <div·class="block"><code>formatLocation</code>·creates·an·EMBL/Genbank·style | 11734 | <div·class="block"><code>formatLocation</code>·creates·an·EMBL/Genbank·style |
| 11735 | ·representation·of·a·<code>Location</code>.</div> | 11735 | ·representation·of·a·<code>Location</code>.</div> |
| 11736 | </dd> | 11736 | </dd> |
| 11737 | <dt><a·href="org/biojava/bio/seq/io/SeqFileFormer.html#formatLocation(java.lang.StringBuffer,org.biojava.bio.symbol.Location,org.biojava.bio.seq.StrandedFeature.Strand)"·class="member-name-link">formatLocation(StringBuffer,·Location,·StrandedFeature.Strand)</a>·-·Method·in·interface·org.biojava.bio.seq.io.<a·href="org/biojava/bio/seq/io/SeqFileFormer.html"·title="interface·in·org.biojava.bio.seq.io">SeqFileFormer</a></dt> | 11737 | <dt><a·href="org/biojava/bio/seq/io/SeqFileFormer.html#formatLocation(java.lang.StringBuffer,org.biojava.bio.symbol.Location,org.biojava.bio.seq.StrandedFeature.Strand)"·class="member-name-link">formatLocation(StringBuffer,·Location,·StrandedFeature.Strand)</a>·-·Method·in·interface·org.biojava.bio.seq.io.<a·href="org/biojava/bio/seq/io/SeqFileFormer.html"·title="interface·in·org.biojava.bio.seq.io">SeqFileFormer</a></dt> |
| 11738 | <dd> | 11738 | <dd> |
| 11739 | <div·class="deprecation-block"><span·class="deprecated-label">Deprecated.</span></div> | 11739 | <div·class="deprecation-block"><span·class="deprecated-label">Deprecated.</span></div> |
| Offset 11742, 29 lines modified | Offset 11742, 29 lines modified | ||
| 11742 | </dd> | 11742 | </dd> |
| 11743 | <dt><a·href="org/biojava/bio/seq/io/SwissprotFileFormer.html#formatLocation(java.lang.StringBuffer,org.biojava.bio.symbol.Location,org.biojava.bio.seq.StrandedFeature.Strand)"·class="member-name-link">formatLocation(StringBuffer,·Location,·StrandedFeature.Strand)</a>·-·Method·in·class·org.biojava.bio.seq.io.<a·href="org/biojava/bio/seq/io/SwissprotFileFormer.html"·title="class·in·org.biojava.bio.seq.io">SwissprotFileFormer</a></dt> | 11743 | <dt><a·href="org/biojava/bio/seq/io/SwissprotFileFormer.html#formatLocation(java.lang.StringBuffer,org.biojava.bio.symbol.Location,org.biojava.bio.seq.StrandedFeature.Strand)"·class="member-name-link">formatLocation(StringBuffer,·Location,·StrandedFeature.Strand)</a>·-·Method·in·class·org.biojava.bio.seq.io.<a·href="org/biojava/bio/seq/io/SwissprotFileFormer.html"·title="class·in·org.biojava.bio.seq.io">SwissprotFileFormer</a></dt> |
| 11744 | <dd> | 11744 | <dd> |
| 11745 | <div·class="deprecation-block"><span·class="deprecated-label">Deprecated.</span></div> | 11745 | <div·class="deprecation-block"><span·class="deprecated-label">Deprecated.</span></div> |
| 11746 | <div·class="block"><code>formatLocation</code>·creates·a·String·representation·of | 11746 | <div·class="block"><code>formatLocation</code>·creates·a·String·representation·of |
| 11747 | ·a·<code>Location</code>.</div> | 11747 | ·a·<code>Location</code>.</div> |
| 11748 | </dd> | 11748 | </dd> |
| 11749 | <dt><a·href="org/biojava/bio/seq/io/ | 11749 | <dt><a·href="org/biojava/bio/seq/io/GenbankFileFormer.html#formatLocation(org.biojava.bio.seq.Feature)"·class="member-name-link">formatLocation(Feature)</a>·-·Method·in·class·org.biojava.bio.seq.io.<a·href="org/biojava/bio/seq/io/GenbankFileFormer.html"·title="class·in·org.biojava.bio.seq.io[·...·truncated·by·diffoscope;·len:·9,·SHA:·cc33bd8bf5e685e2fb9c733a2487417621d34796b46414447766667d8dde93df·...·]FileFormer</a></dt> |
| 11750 | <dd> | 11750 | <dd> |
| 11751 | <div·class="block">Formats·the·location·of·a·feature.</div> | 11751 | <div·class="block">Formats·the·location·of·a·feature.</div> |
| 11752 | </dd> | 11752 | </dd> |
| 11753 | <dt><a·href="org/biojava/bio/seq/io/SeqFileFormer.html#formatLocation(org.biojava.bio.seq.Feature)"·class="member-name-link">formatLocation(Feature)</a>·-·Method·in·interface·org.biojava.bio.seq.io.<a·href="org/biojava/bio/seq/io/SeqFileFormer.html"·title="interface·in·org.biojava.bio.seq.io">SeqFileFormer</a></dt> | 11753 | <dt><a·href="org/biojava/bio/seq/io/SeqFileFormer.html#formatLocation(org.biojava.bio.seq.Feature)"·class="member-name-link">formatLocation(Feature)</a>·-·Method·in·interface·org.biojava.bio.seq.io.<a·href="org/biojava/bio/seq/io/SeqFileFormer.html"·title="interface·in·org.biojava.bio.seq.io">SeqFileFormer</a></dt> |
| 11754 | <dd> | 11754 | <dd> |
| 11755 | <div·class="deprecation-block"><span·class="deprecated-label">Deprecated.</span></div> | 11755 | <div·class="deprecation-block"><span·class="deprecated-label">Deprecated.</span></div> |
| 11756 | <div·class="block">Formats·the·location·of·a·feature.</div> | 11756 | <div·class="block">Formats·the·location·of·a·feature.</div> |
| 11757 | </dd> | 11757 | </dd> |
| 11758 | <dt><a·href="org/biojava/bio/seq/io/SwissprotFileFormer.html#formatLocation(org.biojava.bio.seq.Feature)"·class="member-name-link">formatLocation(Feature)</a>·-·Method·in·class·org.biojava.bio.seq.io.<a·href="org/biojava/bio/seq/io/SwissprotFileFormer.html"·title="class·in·org.biojava.bio.seq.io">SwissprotFileFormer</a></dt> | 11758 | <dt><a·href="org/biojava/bio/seq/io/SwissprotFileFormer.html#formatLocation(org.biojava.bio.seq.Feature)"·class="member-name-link">formatLocation(Feature)</a>·-·Method·in·class·org.biojava.bio.seq.io.<a·href="org/biojava/bio/seq/io/SwissprotFileFormer.html"·title="class·in·org.biojava.bio.seq.io">SwissprotFileFormer</a></dt> |
| 11759 | <dd> | 11759 | <dd> |
| 11760 | <div·class="deprecation-block"><span·class="deprecated-label">Deprecated.</span></div> | 11760 | <div·class="deprecation-block"><span·class="deprecated-label">Deprecated.</span></div> |
| 11761 | <div·class="block">Creates·a·string·representation·of·the·location·of·a·feature</div> | 11761 | <div·class="block">Creates·a·string·representation·of·the·location·of·a·feature</div> |
| 11762 | </dd> | 11762 | </dd> |
| 11763 | <dt><a·href="org/biojava/bio/seq/io/ | 11763 | <dt><a·href="org/biojava/bio/seq/io/GenbankFileFormer.html#formatLocation(org.biojava.bio.symbol.Location,org.biojava.bio.seq.StrandedFeature.Strand)"·class="member-name-link">formatLocation(Location,·StrandedFeature.Strand)</a>·-·Method·in·class·org.biojava.bio.seq.io.<a·href="org/biojava/b[·...·truncated·by·diffoscope;·len:·81,·SHA:·cc87f04a6457cd87ed5d2f22ceb03b526ad33ad8f3fe1e1dd8a449830a9e54ee·...·]FileFormer</a></dt> |
| 11764 | <dd> | 11764 | <dd> |
| 11765 | <div·class="block"><code>formatLocation</code>·creates·an·EMBL/Genbank·style | 11765 | <div·class="block"><code>formatLocation</code>·creates·an·EMBL/Genbank·style |
| 11766 | ·representation·of·a·<code>Location</code>.</div> | 11766 | ·representation·of·a·<code>Location</code>.</div> |
| 11767 | </dd> | 11767 | </dd> |
| 11768 | <dt><a·href="org/biojava/bio/alignment/AlignmentPair.html#formatOutput()"·class="member-name-link">formatOutput()</a>·-·Method·in·class·org.biojava.bio.alignment.<a·href="org/biojava/bio/alignment/AlignmentPair.html"·title="class·in·org.biojava.bio.alignment">AlignmentPair</a></dt> | 11768 | <dt><a·href="org/biojava/bio/alignment/AlignmentPair.html#formatOutput()"·class="member-name-link">formatOutput()</a>·-·Method·in·class·org.biojava.bio.alignment.<a·href="org/biojava/bio/alignment/AlignmentPair.html"·title="class·in·org.biojava.bio.alignment">AlignmentPair</a></dt> |
| 11769 | <dd> </dd> | 11769 | <dd> </dd> |
| 11770 | <dt><a·href="org/biojava/bio/alignment/AlignmentPair.html#formatOutput(int)"·class="member-name-link">formatOutput(int)</a>·-·Method·in·class·org.biojava.bio.alignment.<a·href="org/biojava/bio/alignment/AlignmentPair.html"·title="class·in·org.biojava.bio.alignment">AlignmentPair</a></dt> | 11770 | <dt><a·href="org/biojava/bio/alignment/AlignmentPair.html#formatOutput(int)"·class="member-name-link">formatOutput(int)</a>·-·Method·in·class·org.biojava.bio.alignment.<a·href="org/biojava/bio/alignment/AlignmentPair.html"·title="class·in·org.biojava.bio.alignment">AlignmentPair</a></dt> |
| Offset 29486, 15 lines modified | Offset 29486, 15 lines modified | ||
| 29486 | </dd> | 29486 | </dd> |
| 29487 | <dt><a·href="org/biojava/bio/program/tagvalue/LineSplitParser.html#parse(java.lang.Object)"·class="member-name-link">parse(Object)</a>·-·Method·in·class·org.biojava.bio.program.tagvalue.<a·href="org/biojava/bio/program/tagvalue/LineSplitParser.html"·title="class·in·org.biojava.bio.program.tagvalue">LineSplitParser</a></dt> | 29487 | <dt><a·href="org/biojava/bio/program/tagvalue/LineSplitParser.html#parse(java.lang.Object)"·class="member-name-link">parse(Object)</a>·-·Method·in·class·org.biojava.bio.program.tagvalue.<a·href="org/biojava/bio/program/tagvalue/LineSplitParser.html"·title="class·in·org.biojava.bio.program.tagvalue">LineSplitParser</a></dt> |
| 29488 | <dd> </dd> | 29488 | <dd> </dd> |
| 29489 | <dt><a·href="org/biojava/bio/program/tagvalue/RegexParser.html#parse(java.lang.Object)"·class="member-name-link">parse(Object)</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> | 29489 | <dt><a·href="org/biojava/bio/program/tagvalue/RegexParser.html#parse(java.lang.Object)"·class="member-name-link">parse(Object)</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> |
| 29490 | <dd> </dd> | 29490 | <dd> </dd> |
| 29491 | <dt><a·href="org/biojava/bio/program/tagvalue/TagValueParser.html#parse(java.lang.Object)"·class="member-name-link">parse(Object)</a>·-·Method·in·interface·org.biojava.bio.program.tagvalue.<a·href="org/biojava/bio/program/tagvalue/TagValueParser.html"·title="interface·in·org.biojava.bio.program.tagvalue">TagValueParser</a></dt> | 29491 | <dt><a·href="org/biojava/bio/program/tagvalue/TagValueParser.html#parse(java.lang.Object)"·class="member-name-link">parse(Object)</a>·-·Method·in·interface·org.biojava.bio.program.tagvalue.<a·href="org/biojava/bio/program/tagvalue/TagValueParser.html"·title="interface·in·org.biojava.bio.program.tagvalue">TagValueParser</a></dt> |
| 29492 | <dd> </dd> | 29492 | <dd> </dd> |
| 29493 | <dt><a·href="org/biojava/bio/program/fastq/ | 29493 | <dt><a·href="org/biojava/bio/program/fastq/SolexaFastqReader.html#parse(java.lang.Readable,org.biojava.bio.program.fastq.ParseListener)"·class="member-name-link">parse(Readable,·ParseListener)</a>·-·Method·in·class·org.biojava.bio.program.fastq.<a·href="org/biojava/bio/program/fastq/SolexaFastqRead[·...·truncated·by·diffoscope;·len:·61,·SHA:·4497622aef5a8ae4764dba10ac20a6d571371e89d80a092e2e260d79ac095bd7·...·]aFastqReader</a></dt> |
| 29494 | <dd> </dd> | 29494 | <dd> </dd> |
| 29495 | <dt><a·href="org/biojava/bio/program/fastq/FastqReader.html#parse(java.lang.Readable,org.biojava.bio.program.fastq.ParseListener)"·class="member-name-link">parse(Readable,·ParseListener)</a>·-·Method·in·interface·org.biojava.bio.program.fastq.<a·href="org/biojava/bio/program/fastq/FastqReader.html"·title="interface·in·org.biojava.bio.program.fastq">FastqReader</a></dt> | 29495 | <dt><a·href="org/biojava/bio/program/fastq/FastqReader.html#parse(java.lang.Readable,org.biojava.bio.program.fastq.ParseListener)"·class="member-name-link">parse(Readable,·ParseListener)</a>·-·Method·in·interface·org.biojava.bio.program.fastq.<a·href="org/biojava/bio/program/fastq/FastqReader.html"·title="interface·in·org.biojava.bio.program.fastq">FastqReader</a></dt> |
| 29496 | <dd> | 29496 | <dd> |
| 29497 | <div·class="block">Parse·the·specified·readable.</div> | 29497 | <div·class="block">Parse·the·specified·readable.</div> |
| 29498 | </dd> | 29498 | </dd> |
| 29499 | <dt><a·href="org/biojava/bio/program/sax/SequenceAlignmentSAXParser.html#parse(java.lang.String)"·class="member-name-link">parse(String)</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">SequenceAlignmentSAXParser</a></dt> | 29499 | <dt><a·href="org/biojava/bio/program/sax/SequenceAlignmentSAXParser.html#parse(java.lang.String)"·class="member-name-link">parse(String)</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">SequenceAlignmentSAXParser</a></dt> |
| 29500 | <dd> | 29500 | <dd> |
| Offset 31237, 27 lines modified | Offset 31237, 27 lines modified | ||
| 31237 | </dd> | 31237 | </dd> |
| 31238 | <dt><a·href="org/biojava/bio/seq/io/MSFAlignmentFormat.html#read(java.io.BufferedReader)"·class="member-name-link">read(BufferedReader)</a>·-·Method·in·class·org.biojava.bio.seq.io.<a·href="org/biojava/bio/seq/io/MSFAlignmentFormat.html"·title="class·in·org.biojava.bio.seq.io">MSFAlignmentFormat</a></dt> | 31238 | <dt><a·href="org/biojava/bio/seq/io/MSFAlignmentFormat.html#read(java.io.BufferedReader)"·class="member-name-link">read(BufferedReader)</a>·-·Method·in·class·org.biojava.bio.seq.io.<a·href="org/biojava/bio/seq/io/MSFAlignmentFormat.html"·title="class·in·org.biojava.bio.seq.io">MSFAlignmentFormat</a></dt> |
| 31239 | <dd> | 31239 | <dd> |
| 31240 | <div·class="block">Reads·an·MSF·Alignment·File</div> | 31240 | <div·class="block">Reads·an·MSF·Alignment·File</div> |
| 31241 | </dd> | 31241 | </dd> |
| 31242 | <dt><a·href="org/biojava/bio/program/tagvalue/Parser.html#read(java.io.BufferedReader,org.biojava.bio.program.tagvalue.TagValueParser,org.biojava.bio.program.tagvalue.TagValueListener)"·class="member-name-link">read(BufferedReader,·TagValueParser,·TagValueListener)</a>·-·Method·in·class·org.biojava.bio.program.tagvalue.<a·href="org/biojava/bio/program/tagvalue/Parser.html"·title="class·in·org.biojava.bio.program.tagvalue">Parser</a></dt> | 31242 | <dt><a·href="org/biojava/bio/program/tagvalue/Parser.html#read(java.io.BufferedReader,org.biojava.bio.program.tagvalue.TagValueParser,org.biojava.bio.program.tagvalue.TagValueListener)"·class="member-name-link">read(BufferedReader,·TagValueParser,·TagValueListener)</a>·-·Method·in·class·org.biojava.bio.program.tagvalue.<a·href="org/biojava/bio/program/tagvalue/Parser.html"·title="class·in·org.biojava.bio.program.tagvalue">Parser</a></dt> |
| 31243 | <dd> </dd> | 31243 | <dd> </dd> |
| 31244 | <dt><a·href="org/biojava/bio/program/fastq/ | 31244 | <dt><a·href="org/biojava/bio/program/fastq/SolexaFastqReader.html#read(java.io.File)"·class="member-name-link">read(File)</a>·-·Method·in·class·org.biojava.bio.program.fastq.<a·href="org/biojava/bio/program/fastq/SolexaFastqReader.html"·title="class·in·org.biojava.bio.program.fastq">SolexaFastqReader</a></dt> |
| 31245 | <dd> </dd> | 31245 | <dd> </dd> |
| 31246 | <dt><a·href="org/biojava/bio/program/fastq/FastqReader.html#read(java.io.File)"·class="member-name-link">read(File)</a>·-·Method·in·interface·org.biojava.bio.program.fastq.<a·href="org/biojava/bio/program/fastq/FastqReader.html"·title="interface·in·org.biojava.bio.program.fastq">FastqReader</a></dt> | 31246 | <dt><a·href="org/biojava/bio/program/fastq/FastqReader.html#read(java.io.File)"·class="member-name-link">read(File)</a>·-·Method·in·interface·org.biojava.bio.program.fastq.<a·href="org/biojava/bio/program/fastq/FastqReader.html"·title="interface·in·org.biojava.bio.program.fastq">FastqReader</a></dt> |
| 31247 | <dd> | 31247 | <dd> |
| 31248 | <div·class="block">Read·zero·or·more·FASTQ·formatted·sequences·from·the·specified·file.</div> | 31248 | <div·class="block">Read·zero·or·more·FASTQ·formatted·sequences·from·the·specified·file.</div> |
| 31249 | </dd> | 31249 | </dd> |
| 31250 | <dt><a·href="org/biojava/bio/program/fastq/ | 31250 | <dt><a·href="org/biojava/bio/program/fastq/SolexaFastqReader.html#read(java.io.InputStream)"·class="member-name-link">read(InputStream)</a>·-·Method·in·class·org.biojava.bio.program.fastq.<a·href="org/biojava/bio/program/fastq/SolexaFastqReader.html"·title="class·in·org.biojava.bio.program.fastq">S[·...·truncated·by·diffoscope;·len:·4,·SHA:·9d1ef9d117cff52eb3b6f29bcdd584b16059b28078ceb90ad0f4084cba816e3b·...·]aFastqReader</a></dt> |
| 31251 | <dd> </dd> | 31251 | <dd> </dd> |
| 31252 | <dt><a·href="org/biojava/bio/program/fastq/FastqReader.html#read(java.io.InputStream)"·class="member-name-link">read(InputStream)</a>·-·Method·in·interface·org.biojava.bio.program.fastq.<a·href="org/biojava/bio/program/fastq/FastqReader.html"·title="interface·in·org.biojava.bio.program.fastq">FastqReader</a></dt> | 31252 | <dt><a·href="org/biojava/bio/program/fastq/FastqReader.html#read(java.io.InputStream)"·class="member-name-link">read(InputStream)</a>·-·Method·in·interface·org.biojava.bio.program.fastq.<a·href="org/biojava/bio/program/fastq/FastqReader.html"·title="interface·in·org.biojava.bio.program.fastq">FastqReader</a></dt> |
| 31253 | <dd> | 31253 | <dd> |
| 31254 | <div·class="block">Read·zero·or·more·FASTQ·formatted·sequences·from·the·specified·input·stream.</div> | 31254 | <div·class="block">Read·zero·or·more·FASTQ·formatted·sequences·from·the·specified·input·stream.</div> |
| 31255 | </dd> | 31255 | </dd> |
| 31256 | <dt><a·href="org/biojava/bio/program/fastq/ | 31256 | <dt><a·href="org/biojava/bio/program/fastq/SolexaFastqReader.html#read(java.net.URL)"·class="member-name-link">read(URL)</a>·-·Method·in·class·org.biojava.bio.program.fastq.<a·href="org/biojava/bio/program/fastq/SolexaFastqReader.html"·title="class·in·org.biojava.bio.program.fastq">SolexaFastqReader</a></dt> |
| 31257 | <dd> </dd> | 31257 | <dd> </dd> |
| 31258 | <dt><a·href="org/biojava/bio/program/fastq/FastqReader.html#read(java.net.URL)"·class="member-name-link">read(URL)</a>·-·Method·in·interface·org.biojava.bio.program.fastq.<a·href="org/biojava/bio/program/fastq/FastqReader.html"·title="interface·in·org.biojava.bio.program.fastq">FastqReader</a></dt> | 31258 | <dt><a·href="org/biojava/bio/program/fastq/FastqReader.html#read(java.net.URL)"·class="member-name-link">read(URL)</a>·-·Method·in·interface·org.biojava.bio.program.fastq.<a·href="org/biojava/bio/program/fastq/FastqReader.html"·title="interface·in·org.biojava.bio.program.fastq">FastqReader</a></dt> |
| 31259 | <dd> | 31259 | <dd> |
| 31260 | <div·class="block">Read·zero·or·more·FASTQ·formatted·sequences·from·the·specified·url.</div> | 31260 | <div·class="block">Read·zero·or·more·FASTQ·formatted·sequences·from·the·specified·url.</div> |
| 31261 | </dd> | 31261 | </dd> |
| 31262 | <dt><a·href="org/biojavax/bio/seq/io/EMBLFormat.html#readableFileNames"·class="member-name-link">readableFileNames</a>·-·Static·variable·in·class·org.biojavax.bio.seq.io.<a·href="org/biojavax/bio/seq/io/EMBLFormat.html"·title="class·in·org.biojavax.bio.seq.io">EMBLFormat</a></dt> | 31262 | <dt><a·href="org/biojavax/bio/seq/io/EMBLFormat.html#readableFileNames"·class="member-name-link">readableFileNames</a>·-·Static·variable·in·class·org.biojavax.bio.seq.io.<a·href="org/biojavax/bio/seq/io/EMBLFormat.html"·title="class·in·org.biojavax.bio.seq.io">EMBLFormat</a></dt> |
| 31263 | <dd> </dd> | 31263 | <dd> </dd> |
| Offset 41034, 15 lines modified | Offset 41034, 15 lines modified | ||
| 41034 | </dd> | 41034 | </dd> |
| 41035 | <dt><a·href="org/biojava/bio/seq/StrandParser.html"·class="type-name-link"·title="class·in·org.biojava.bio.seq">StrandParser</a>·-·Class·in·<a·href="org/biojava/bio/seq/package-summary.html">org.biojava.bio.seq</a></dt> | 41035 | <dt><a·href="org/biojava/bio/seq/StrandParser.html"·class="type-name-link"·title="class·in·org.biojava.bio.seq">StrandParser</a>·-·Class·in·<a·href="org/biojava/bio/seq/package-summary.html">org.biojava.bio.seq</a></dt> |
| 41036 | <dd> | 41036 | <dd> |
| 41037 | <div·class="block">Process·strings·and·return·strand·objects.</div> | 41037 | <div·class="block">Process·strings·and·return·strand·objects.</div> |
| 41038 | </dd> | 41038 | </dd> |
| 41039 | <dt><a·href="org/biojava/bio/seq/StrandParser.html#%3Cinit%3E()"·class="member-name-link">StrandParser()</a>·-·Constructor·for·class·org.biojava.bio.seq.<a·href="org/biojava/bio/seq/StrandParser.html"·title="class·in·org.biojava.bio.seq">StrandParser</a></dt> | 41039 | <dt><a·href="org/biojava/bio/seq/StrandParser.html#%3Cinit%3E()"·class="member-name-link">StrandParser()</a>·-·Constructor·for·class·org.biojava.bio.seq.<a·href="org/biojava/bio/seq/StrandParser.html"·title="class·in·org.biojava.bio.seq">StrandParser</a></dt> |
| 41040 | <dd> </dd> | 41040 | <dd> </dd> |
| 41041 | <dt><a·href="org/biojava/bio/program/fastq/ | 41041 | <dt><a·href="org/biojava/bio/program/fastq/SolexaFastqReader.html#stream(java.lang.Readable,org.biojava.bio.program.fastq.StreamListener)"·class="member-name-link">stream(Readable,·StreamListener)</a>·-·Method·in·class·org.biojava.bio.program.fastq.<a·href="org/biojava/bio/program/fastq/SolexaFastq[·...·truncated·by·diffoscope;·len:·65,·SHA:·6a2df33d3987a474ee54f0f2830339b0dbd27841f0491cd60c820a3e652b9d76·...·]aFastqReader</a></dt> |
| 41042 | <dd> </dd> | 41042 | <dd> </dd> |
| 41043 | <dt><a·href="org/biojava/bio/program/fastq/FastqReader.html#stream(java.lang.Readable,org.biojava.bio.program.fastq.StreamListener)"·class="member-name-link">stream(Readable,·StreamListener)</a>·-·Method·in·interface·org.biojava.bio.program.fastq.<a·href="org/biojava/bio/program/fastq/FastqReader.html"·title="interface·in·org.biojava.bio.program.fastq">FastqReader</a></dt> | 41043 | <dt><a·href="org/biojava/bio/program/fastq/FastqReader.html#stream(java.lang.Readable,org.biojava.bio.program.fastq.StreamListener)"·class="member-name-link">stream(Readable,·StreamListener)</a>·-·Method·in·interface·org.biojava.bio.program.fastq.<a·href="org/biojava/bio/program/fastq/FastqReader.html"·title="interface·in·org.biojava.bio.program.fastq">FastqReader</a></dt> |
| 41044 | <dd> | 41044 | <dd> |
| 41045 | <div·class="block">Stream·the·specified·readable.</div> | 41045 | <div·class="block">Stream·the·specified·readable.</div> |
| 41046 | </dd> | 41046 | </dd> |
| 41047 | <dt><a·href="org/biojava/bio/program/fastq/StreamListener.html"·class="type-name-link"·title="interface·in·org.biojava.bio.program.fastq">StreamListener</a>·-·Interface·in·<a·href="org/biojava/bio/program/fastq/package-summary.html">org.biojava.bio.program.fastq</a></dt> | 41047 | <dt><a·href="org/biojava/bio/program/fastq/StreamListener.html"·class="type-name-link"·title="interface·in·org.biojava.bio.program.fastq">StreamListener</a>·-·Interface·in·<a·href="org/biojava/bio/program/fastq/package-summary.html">org.biojava.bio.program.fastq</a></dt> |
| 41048 | <dd> | 41048 | <dd> |
| 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 | 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 10256, 38 lines modified | Offset 10256, 38 lines modified | ||
| 10256 | ··Format·-·Interface·in·org.biojava.bio.program.formats | 10256 | ··Format·-·Interface·in·org.biojava.bio.program.formats |
| 10257 | ······A·file·format·supported·by·the·tag-value·event-based·parsing·system. | 10257 | ······A·file·format·supported·by·the·tag-value·event-based·parsing·system. |
| 10258 | ··formatLocation(StringBuffer,_Location)·-·Method·in·class | 10258 | ··formatLocation(StringBuffer,_Location)·-·Method·in·class |
| 10259 | ··org.biojava.bio.seq.io.SwissprotFileFormer | 10259 | ··org.biojava.bio.seq.io.SwissprotFileFormer |
| 10260 | ······Deprecated. | 10260 | ······Deprecated. |
| 10261 | ······formatLocation·creates·a·String·representation·of·a·Location. | 10261 | ······formatLocation·creates·a·String·representation·of·a·Location. |
| 10262 | ··formatLocation(StringBuffer,_Location,_StrandedFeature.Strand)·-·Method·in | 10262 | ··formatLocation(StringBuffer,_Location,_StrandedFeature.Strand)·-·Method·in |
| 10263 | ··class·org.biojava.bio.seq.io. | 10263 | ··class·org.biojava.bio.seq.io.GenbankFileFormer |
| 10264 | ······formatLocation·creates·an·EMBL/Genbank·style·representation·of·a | 10264 | ······formatLocation·creates·an·EMBL/Genbank·style·representation·of·a |
| 10265 | ······Location. | 10265 | ······Location. |
| 10266 | ··formatLocation(StringBuffer,_Location,_StrandedFeature.Strand)·-·Method·in | 10266 | ··formatLocation(StringBuffer,_Location,_StrandedFeature.Strand)·-·Method·in |
| 10267 | ··interface·org.biojava.bio.seq.io.SeqFileFormer | 10267 | ··interface·org.biojava.bio.seq.io.SeqFileFormer |
| 10268 | ······Deprecated. | 10268 | ······Deprecated. |
| 10269 | ······formatLocation·creates·a·String·representation·of·a·Location. | 10269 | ······formatLocation·creates·a·String·representation·of·a·Location. |
| 10270 | ··formatLocation(StringBuffer,_Location,_StrandedFeature.Strand)·-·Method·in | 10270 | ··formatLocation(StringBuffer,_Location,_StrandedFeature.Strand)·-·Method·in |
| 10271 | ··class·org.biojava.bio.seq.io.SwissprotFileFormer | 10271 | ··class·org.biojava.bio.seq.io.SwissprotFileFormer |
| 10272 | ······Deprecated. | 10272 | ······Deprecated. |
| 10273 | ······formatLocation·creates·a·String·representation·of·a·Location. | 10273 | ······formatLocation·creates·a·String·representation·of·a·Location. |
| 10274 | ··formatLocation(Feature)·-·Method·in·class | 10274 | ··formatLocation(Feature)·-·Method·in·class |
| 10275 | ··org.biojava.bio.seq.io. | 10275 | ··org.biojava.bio.seq.io.GenbankFileFormer |
| 10276 | ······Formats·the·location·of·a·feature. | 10276 | ······Formats·the·location·of·a·feature. |
| 10277 | ··formatLocation(Feature)·-·Method·in·interface | 10277 | ··formatLocation(Feature)·-·Method·in·interface |
| 10278 | ··org.biojava.bio.seq.io.SeqFileFormer | 10278 | ··org.biojava.bio.seq.io.SeqFileFormer |
| 10279 | ······Deprecated. | 10279 | ······Deprecated. |
| 10280 | ······Formats·the·location·of·a·feature. | 10280 | ······Formats·the·location·of·a·feature. |
| 10281 | ··formatLocation(Feature)·-·Method·in·class | 10281 | ··formatLocation(Feature)·-·Method·in·class |
| 10282 | ··org.biojava.bio.seq.io.SwissprotFileFormer | 10282 | ··org.biojava.bio.seq.io.SwissprotFileFormer |
| 10283 | ······Deprecated. | 10283 | ······Deprecated. |
| 10284 | ······Creates·a·string·representation·of·the·location·of·a·feature | 10284 | ······Creates·a·string·representation·of·the·location·of·a·feature |
| 10285 | ··formatLocation(Location,_StrandedFeature.Strand)·-·Method·in·class | 10285 | ··formatLocation(Location,_StrandedFeature.Strand)·-·Method·in·class |
| 10286 | ··org.biojava.bio.seq.io. | 10286 | ··org.biojava.bio.seq.io.GenbankFileFormer |
| 10287 | ······formatLocation·creates·an·EMBL/Genbank·style·representation·of·a | 10287 | ······formatLocation·creates·an·EMBL/Genbank·style·representation·of·a |
| 10288 | ······Location. | 10288 | ······Location. |
| 10289 | ··formatOutput()·-·Method·in·class·org.biojava.bio.alignment.AlignmentPair | 10289 | ··formatOutput()·-·Method·in·class·org.biojava.bio.alignment.AlignmentPair |
| 10290 | ······ | 10290 | ······ |
| 10291 | ··formatOutput(int)·-·Method·in·class·org.biojava.bio.alignment.AlignmentPair | 10291 | ··formatOutput(int)·-·Method·in·class·org.biojava.bio.alignment.AlignmentPair |
| 10292 | ······This·method·provides·a·BLAST-like·formated·alignment·from·the·given | 10292 | ······This·method·provides·a·BLAST-like·formated·alignment·from·the·given |
| 10293 | ······Strings,·in·which·the·sequence·coordinates·and·the·information·"Query"·or | 10293 | ······Strings,·in·which·the·sequence·coordinates·and·the·information·"Query"·or |
| Offset 25060, 15 lines modified | Offset 25060, 15 lines modified | ||
| 25060 | ······ | 25060 | ······ |
| 25061 | ··parse(Object)·-·Method·in·class·org.biojava.bio.program.tagvalue.RegexParser | 25061 | ··parse(Object)·-·Method·in·class·org.biojava.bio.program.tagvalue.RegexParser |
| 25062 | ······ | 25062 | ······ |
| 25063 | ··parse(Object)·-·Method·in·interface | 25063 | ··parse(Object)·-·Method·in·interface |
| 25064 | ··org.biojava.bio.program.tagvalue.TagValueParser | 25064 | ··org.biojava.bio.program.tagvalue.TagValueParser |
| 25065 | ······ | 25065 | ······ |
| 25066 | ··parse(Readable,_ParseListener)·-·Method·in·class | 25066 | ··parse(Readable,_ParseListener)·-·Method·in·class |
| 25067 | ··org.biojava.bio.program.fastq. | 25067 | ··org.biojava.bio.program.fastq.SolexaFastqReader |
| 25068 | ······ | 25068 | ······ |
| 25069 | ··parse(Readable,_ParseListener)·-·Method·in·interface | 25069 | ··parse(Readable,_ParseListener)·-·Method·in·interface |
| 25070 | ··org.biojava.bio.program.fastq.FastqReader | 25070 | ··org.biojava.bio.program.fastq.FastqReader |
| 25071 | ······Parse·the·specified·readable. | 25071 | ······Parse·the·specified·readable. |
| 25072 | ··parse(String)·-·Method·in·class | 25072 | ··parse(String)·-·Method·in·class |
| 25073 | ··org.biojava.bio.program.sax.SequenceAlignmentSAXParser | 25073 | ··org.biojava.bio.program.sax.SequenceAlignmentSAXParser |
| 25074 | ······Full·implementation·of·interface·method. | 25074 | ······Full·implementation·of·interface·method. |
| Offset 26562, 27 lines modified | Offset 26562, 26 lines modified | ||
| 26562 | ······Reads·an·alignment·in·FASTA·format. | 26562 | ······Reads·an·alignment·in·FASTA·format. |
| 26563 | ··read(BufferedReader)·-·Method·in·class | 26563 | ··read(BufferedReader)·-·Method·in·class |
| 26564 | ··org.biojava.bio.seq.io.MSFAlignmentFormat | 26564 | ··org.biojava.bio.seq.io.MSFAlignmentFormat |
| 26565 | ······Reads·an·MSF·Alignment·File | 26565 | ······Reads·an·MSF·Alignment·File |
| 26566 | ··read(BufferedReader,_TagValueParser,_TagValueListener)·-·Method·in·class | 26566 | ··read(BufferedReader,_TagValueParser,_TagValueListener)·-·Method·in·class |
| 26567 | ··org.biojava.bio.program.tagvalue.Parser | 26567 | ··org.biojava.bio.program.tagvalue.Parser |
| 26568 | ······ | 26568 | ······ |
| 26569 | ··read(File)·-·Method·in·class·org.biojava.bio.program.fastq.SolexaFastqReader | ||
| 26569 | ··read(File)·-·Method·in·class | ||
| 26570 | ··org.biojava.bio.program.fastq.IlluminaFastqReader | ||
| 26571 | ······ | 26570 | ······ |
| 26572 | ··read(File)·-·Method·in·interface·org.biojava.bio.program.fastq.FastqReader | 26571 | ··read(File)·-·Method·in·interface·org.biojava.bio.program.fastq.FastqReader |
| 26573 | ······Read·zero·or·more·FASTQ·formatted·sequences·from·the·specified·file. | 26572 | ······Read·zero·or·more·FASTQ·formatted·sequences·from·the·specified·file. |
| 26574 | ··read(InputStream)·-·Method·in·class | 26573 | ··read(InputStream)·-·Method·in·class |
| 26575 | ··org.biojava.bio.program.fastq. | 26574 | ··org.biojava.bio.program.fastq.SolexaFastqReader |
| 26576 | ······ | 26575 | ······ |
| 26577 | ··read(InputStream)·-·Method·in·interface | 26576 | ··read(InputStream)·-·Method·in·interface |
| 26578 | ··org.biojava.bio.program.fastq.FastqReader | 26577 | ··org.biojava.bio.program.fastq.FastqReader |
| 26579 | ······Read·zero·or·more·FASTQ·formatted·sequences·from·the·specified·input | 26578 | ······Read·zero·or·more·FASTQ·formatted·sequences·from·the·specified·input |
| 26580 | ······stream. | 26579 | ······stream. |
| 26581 | ··read(URL)·-·Method·in·class·org.biojava.bio.program.fastq. | 26580 | ··read(URL)·-·Method·in·class·org.biojava.bio.program.fastq.SolexaFastqReader |
| 26582 | ······ | 26581 | ······ |
| 26583 | ··read(URL)·-·Method·in·interface·org.biojava.bio.program.fastq.FastqReader | 26582 | ··read(URL)·-·Method·in·interface·org.biojava.bio.program.fastq.FastqReader |
| 26584 | ······Read·zero·or·more·FASTQ·formatted·sequences·from·the·specified·url. | 26583 | ······Read·zero·or·more·FASTQ·formatted·sequences·from·the·specified·url. |
| 26585 | ··readableFileNames·-·Static·variable·in·class | 26584 | ··readableFileNames·-·Static·variable·in·class |
| 26586 | ··org.biojavax.bio.seq.io.EMBLFormat | 26585 | ··org.biojavax.bio.seq.io.EMBLFormat |
| 26587 | ······ | 26586 | ······ |
| 26588 | ··readableFiles·-·Static·variable·in·class·org.biojavax.bio.seq.io.FastaFormat | 26587 | ··readableFiles·-·Static·variable·in·class·org.biojavax.bio.seq.io.FastaFormat |
| Offset 35014, 15 lines modified | Offset 35013, 15 lines modified | ||
| 35014 | ··org.biojava.bio.seq.FeatureFilter.StrandFilter | 35013 | ··org.biojava.bio.seq.FeatureFilter.StrandFilter |
| 35015 | ······Build·a·new·filter·that·matches·all·features·of·a·given·strand. | 35014 | ······Build·a·new·filter·that·matches·all·features·of·a·given·strand. |
| 35016 | ··StrandParser·-·Class·in·org.biojava.bio.seq | 35015 | ··StrandParser·-·Class·in·org.biojava.bio.seq |
| 35017 | ······Process·strings·and·return·strand·objects. | 35016 | ······Process·strings·and·return·strand·objects. |
| 35018 | ··StrandParser()·-·Constructor·for·class·org.biojava.bio.seq.StrandParser | 35017 | ··StrandParser()·-·Constructor·for·class·org.biojava.bio.seq.StrandParser |
| 35019 | ······ | 35018 | ······ |
| 35020 | ··stream(Readable,_StreamListener)·-·Method·in·class | 35019 | ··stream(Readable,_StreamListener)·-·Method·in·class |
| 35021 | ··org.biojava.bio.program.fastq. | 35020 | ··org.biojava.bio.program.fastq.SolexaFastqReader |
| 35022 | ······ | 35021 | ······ |
| 35023 | ··stream(Readable,_StreamListener)·-·Method·in·interface | 35022 | ··stream(Readable,_StreamListener)·-·Method·in·interface |
| 35024 | ··org.biojava.bio.program.fastq.FastqReader | 35023 | ··org.biojava.bio.program.fastq.FastqReader |
| 35025 | ······Stream·the·specified·readable. | 35024 | ······Stream·the·specified·readable. |
| 35026 | ··StreamListener·-·Interface·in·org.biojava.bio.program.fastq | 35025 | ··StreamListener·-·Interface·in·org.biojava.bio.program.fastq |
| 35027 | ······Event·based·parser·callback. | 35026 | ······Event·based·parser·callback. |
| 35028 | ··streamNext(SeqIOListener)·-·Method·in·class | 35027 | ··streamNext(SeqIOListener)·-·Method·in·class |
| 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 | 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 14430, 40 lines modified | Offset 14430, 40 lines modified | ||
| 14430 | ····"l":·"forIndex(int)" | 14430 | ····"l":·"forIndex(int)" |
| 14431 | },·{ | 14431 | },·{ |
| 14432 | ····"p":·"org.biojava.bibliography", | 14432 | ····"p":·"org.biojava.bibliography", |
| 14433 | ····"c":·"BibRef", | 14433 | ····"c":·"BibRef", |
| 14434 | ····"l":·"format" | 14434 | ····"l":·"format" |
| 14435 | },·{ | 14435 | },·{ |
| 14436 | ····"p":·"org.biojava.bio.seq.io", | 14436 | ····"p":·"org.biojava.bio.seq.io", |
| 14437 | ····"c":·" | 14437 | ····"c":·"GenbankFileFormer", |
| 14438 | ····"l":·"formatLocation(Feature)", | 14438 | ····"l":·"formatLocation(Feature)", |
| 14439 | ····"u":·"formatLocation(org.biojava.bio.seq.Feature)" | 14439 | ····"u":·"formatLocation(org.biojava.bio.seq.Feature)" |
| 14440 | },·{ | 14440 | },·{ |
| 14441 | ····"p":·"org.biojava.bio.seq.io", | 14441 | ····"p":·"org.biojava.bio.seq.io", |
| 14442 | ····"c":·"SeqFileFormer", | 14442 | ····"c":·"SeqFileFormer", |
| 14443 | ····"l":·"formatLocation(Feature)", | 14443 | ····"l":·"formatLocation(Feature)", |
| 14444 | ····"u":·"formatLocation(org.biojava.bio.seq.Feature)" | 14444 | ····"u":·"formatLocation(org.biojava.bio.seq.Feature)" |
| 14445 | },·{ | 14445 | },·{ |
| 14446 | ····"p":·"org.biojava.bio.seq.io", | 14446 | ····"p":·"org.biojava.bio.seq.io", |
| 14447 | ····"c":·"SwissprotFileFormer", | 14447 | ····"c":·"SwissprotFileFormer", |
| 14448 | ····"l":·"formatLocation(Feature)", | 14448 | ····"l":·"formatLocation(Feature)", |
| 14449 | ····"u":·"formatLocation(org.biojava.bio.seq.Feature)" | 14449 | ····"u":·"formatLocation(org.biojava.bio.seq.Feature)" |
| 14450 | },·{ | 14450 | },·{ |
| 14451 | ····"p":·"org.biojava.bio.seq.io", | 14451 | ····"p":·"org.biojava.bio.seq.io", |
| 14452 | ····"c":·" | 14452 | ····"c":·"GenbankFileFormer", |
| 14453 | ····"l":·"formatLocation(Location,·StrandedFeature.Strand)", | 14453 | ····"l":·"formatLocation(Location,·StrandedFeature.Strand)", |
| 14454 | ····"u":·"formatLocation(org.biojava.bio.symbol.Location,org.biojava.bio.seq.StrandedFeature.Strand)" | 14454 | ····"u":·"formatLocation(org.biojava.bio.symbol.Location,org.biojava.bio.seq.StrandedFeature.Strand)" |
| 14455 | },·{ | 14455 | },·{ |
| 14456 | ····"p":·"org.biojava.bio.seq.io", | 14456 | ····"p":·"org.biojava.bio.seq.io", |
| 14457 | ····"c":·"SwissprotFileFormer", | 14457 | ····"c":·"SwissprotFileFormer", |
| 14458 | ····"l":·"formatLocation(StringBuffer,·Location)", | 14458 | ····"l":·"formatLocation(StringBuffer,·Location)", |
| 14459 | ····"u":·"formatLocation(java.lang.StringBuffer,org.biojava.bio.symbol.Location)" | 14459 | ····"u":·"formatLocation(java.lang.StringBuffer,org.biojava.bio.symbol.Location)" |
| 14460 | },·{ | 14460 | },·{ |
| 14461 | ····"p":·"org.biojava.bio.seq.io", | 14461 | ····"p":·"org.biojava.bio.seq.io", |
| 14462 | ····"c":·" | 14462 | ····"c":·"GenbankFileFormer", |
| 14463 | ····"l":·"formatLocation(StringBuffer,·Location,·StrandedFeature.Strand)", | 14463 | ····"l":·"formatLocation(StringBuffer,·Location,·StrandedFeature.Strand)", |
| 14464 | ····"u":·"formatLocation(java.lang.StringBuffer,org.biojava.bio.symbol.Location,org.biojava.bio.seq.StrandedFeature.Strand)" | 14464 | ····"u":·"formatLocation(java.lang.StringBuffer,org.biojava.bio.symbol.Location,org.biojava.bio.seq.StrandedFeature.Strand)" |
| 14465 | },·{ | 14465 | },·{ |
| 14466 | ····"p":·"org.biojava.bio.seq.io", | 14466 | ····"p":·"org.biojava.bio.seq.io", |
| 14467 | ····"c":·"SeqFileFormer", | 14467 | ····"c":·"SeqFileFormer", |
| 14468 | ····"l":·"formatLocation(StringBuffer,·Location,·StrandedFeature.Strand)", | 14468 | ····"l":·"formatLocation(StringBuffer,·Location,·StrandedFeature.Strand)", |
| 14469 | ····"u":·"formatLocation(java.lang.StringBuffer,org.biojava.bio.symbol.Location,org.biojava.bio.seq.StrandedFeature.Strand)" | 14469 | ····"u":·"formatLocation(java.lang.StringBuffer,org.biojava.bio.symbol.Location,org.biojava.bio.seq.StrandedFeature.Strand)" |
| Offset 36584, 15 lines modified | Offset 36584, 15 lines modified | ||
| 36584 | },·{ | 36584 | },·{ |
| 36585 | ····"p":·"org.biojavax.bio.phylo.io.phylip", | 36585 | ····"p":·"org.biojavax.bio.phylo.io.phylip", |
| 36586 | ····"c":·"PHYLIPFileFormat", | 36586 | ····"c":·"PHYLIPFileFormat", |
| 36587 | ····"l":·"parse(PHYLIPFileListener,·BufferedReader)", | 36587 | ····"l":·"parse(PHYLIPFileListener,·BufferedReader)", |
| 36588 | ····"u":·"parse(org.biojavax.bio.phylo.io.phylip.PHYLIPFileListener,java.io.BufferedReader)" | 36588 | ····"u":·"parse(org.biojavax.bio.phylo.io.phylip.PHYLIPFileListener,java.io.BufferedReader)" |
| 36589 | },·{ | 36589 | },·{ |
| 36590 | ····"p":·"org.biojava.bio.program.fastq", | 36590 | ····"p":·"org.biojava.bio.program.fastq", |
| 36591 | ····"c":·" | 36591 | ····"c":·"SolexaFastqReader", |
| 36592 | ····"l":·"parse(Readable,·ParseListener)", | 36592 | ····"l":·"parse(Readable,·ParseListener)", |
| 36593 | ····"u":·"parse(java.lang.Readable,org.biojava.bio.program.fastq.ParseListener)" | 36593 | ····"u":·"parse(java.lang.Readable,org.biojava.bio.program.fastq.ParseListener)" |
| 36594 | },·{ | 36594 | },·{ |
| 36595 | ····"p":·"org.biojava.bio.program.fastq", | 36595 | ····"p":·"org.biojava.bio.program.fastq", |
| 36596 | ····"c":·"FastqReader", | 36596 | ····"c":·"FastqReader", |
| 36597 | ····"l":·"parse(Readable,·ParseListener)", | 36597 | ····"l":·"parse(Readable,·ParseListener)", |
| 36598 | ····"u":·"parse(java.lang.Readable,org.biojava.bio.program.fastq.ParseListener)" | 36598 | ····"u":·"parse(java.lang.Readable,org.biojava.bio.program.fastq.ParseListener)" |
| Offset 38670, 35 lines modified | Offset 38670, 35 lines modified | ||
| 38670 | },·{ | 38670 | },·{ |
| 38671 | ····"p":·"org.biojava.utils.io", | 38671 | ····"p":·"org.biojava.utils.io", |
| 38672 | ····"c":·"RandomAccessReader", | 38672 | ····"c":·"RandomAccessReader", |
| 38673 | ····"l":·"read(char[],·int,·int)", | 38673 | ····"l":·"read(char[],·int,·int)", |
| 38674 | ····"u":·"read(char[],int,int)" | 38674 | ····"u":·"read(char[],int,int)" |
| 38675 | },·{ | 38675 | },·{ |
| 38676 | ····"p":·"org.biojava.bio.program.fastq", | 38676 | ····"p":·"org.biojava.bio.program.fastq", |
| 38677 | ····"c":·" | 38677 | ····"c":·"SolexaFastqReader", |
| 38678 | ····"l":·"read(File)", | 38678 | ····"l":·"read(File)", |
| 38679 | ····"u":·"read(java.io.File)" | 38679 | ····"u":·"read(java.io.File)" |
| 38680 | },·{ | 38680 | },·{ |
| 38681 | ····"p":·"org.biojava.bio.program.fastq", | 38681 | ····"p":·"org.biojava.bio.program.fastq", |
| 38682 | ····"c":·"FastqReader", | 38682 | ····"c":·"FastqReader", |
| 38683 | ····"l":·"read(File)", | 38683 | ····"l":·"read(File)", |
| 38684 | ····"u":·"read(java.io.File)" | 38684 | ····"u":·"read(java.io.File)" |
| 38685 | },·{ | 38685 | },·{ |
| 38686 | ····"p":·"org.biojava.bio.program.fastq", | 38686 | ····"p":·"org.biojava.bio.program.fastq", |
| 38687 | ····"c":·" | 38687 | ····"c":·"SolexaFastqReader", |
| 38688 | ····"l":·"read(InputStream)", | 38688 | ····"l":·"read(InputStream)", |
| 38689 | ····"u":·"read(java.io.InputStream)" | 38689 | ····"u":·"read(java.io.InputStream)" |
| 38690 | },·{ | 38690 | },·{ |
| 38691 | ····"p":·"org.biojava.bio.program.fastq", | 38691 | ····"p":·"org.biojava.bio.program.fastq", |
| 38692 | ····"c":·"FastqReader", | 38692 | ····"c":·"FastqReader", |
| 38693 | ····"l":·"read(InputStream)", | 38693 | ····"l":·"read(InputStream)", |
| 38694 | ····"u":·"read(java.io.InputStream)" | 38694 | ····"u":·"read(java.io.InputStream)" |
| 38695 | },·{ | 38695 | },·{ |
| 38696 | ····"p":·"org.biojava.bio.program.fastq", | 38696 | ····"p":·"org.biojava.bio.program.fastq", |
| 38697 | ····"c":·" | 38697 | ····"c":·"SolexaFastqReader", |
| 38698 | ····"l":·"read(URL)", | 38698 | ····"l":·"read(URL)", |
| 38699 | ····"u":·"read(java.net.URL)" | 38699 | ····"u":·"read(java.net.URL)" |
| 38700 | },·{ | 38700 | },·{ |
| 38701 | ····"p":·"org.biojava.bio.program.fastq", | 38701 | ····"p":·"org.biojava.bio.program.fastq", |
| 38702 | ····"c":·"FastqReader", | 38702 | ····"c":·"FastqReader", |
| 38703 | ····"l":·"read(URL)", | 38703 | ····"l":·"read(URL)", |
| 38704 | ····"u":·"read(java.net.URL)" | 38704 | ····"u":·"read(java.net.URL)" |
| Offset 50748, 15 lines modified | Offset 50748, 15 lines modified | ||
| 50748 | },·{ | 50748 | },·{ |
| 50749 | ····"p":·"org.biojava.bio.seq", | 50749 | ····"p":·"org.biojava.bio.seq", |
| 50750 | ····"c":·"StrandParser", | 50750 | ····"c":·"StrandParser", |
| 50751 | ····"l":·"StrandParser()", | 50751 | ····"l":·"StrandParser()", |
| 50752 | ····"u":·"%3Cinit%3E()" | 50752 | ····"u":·"%3Cinit%3E()" |
| 50753 | },·{ | 50753 | },·{ |
| 50754 | ····"p":·"org.biojava.bio.program.fastq", | 50754 | ····"p":·"org.biojava.bio.program.fastq", |
| 50755 | ····"c":·" | 50755 | ····"c":·"SolexaFastqReader", |
| 50756 | ····"l":·"stream(Readable,·StreamListener)", | 50756 | ····"l":·"stream(Readable,·StreamListener)", |
| 50757 | ····"u":·"stream(java.lang.Readable,org.biojava.bio.program.fastq.StreamListener)" | 50757 | ····"u":·"stream(java.lang.Readable,org.biojava.bio.program.fastq.StreamListener)" |
| 50758 | },·{ | 50758 | },·{ |
| 50759 | ····"p":·"org.biojava.bio.program.fastq", | 50759 | ····"p":·"org.biojava.bio.program.fastq", |
| 50760 | ····"c":·"FastqReader", | 50760 | ····"c":·"FastqReader", |
| 50761 | ····"l":·"stream(Readable,·StreamListener)", | 50761 | ····"l":·"stream(Readable,·StreamListener)", |
| 50762 | ····"u":·"stream(java.lang.Readable,org.biojava.bio.program.fastq.StreamListener)" | 50762 | ····"u":·"stream(java.lang.Readable,org.biojava.bio.program.fastq.StreamListener)" |