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| 3017 | <dd> | 3017 | <dd> |
| 3018 | <div·class="block">Create·a·bean·from·an·XML·file,·then·attempt·to·enter·it.</div> | 3018 | <div·class="block">Create·a·bean·from·an·XML·file,·then·attempt·to·enter·it.</div> |
| 3019 | </dd> | 3019 | </dd> |
| 3020 | <dt><a·href="org/biojava/utils/xml/AppBeanRunner.html#%3Cinit%3E()"·class="member-name-link">AppBeanRunner()</a>·-·Constructor·for·class·org.biojava.utils.xml.<a·href="org/biojava/utils/xml/AppBeanRunner.html"·title="class·in·org.biojava.utils.xml">AppBeanRunner</a></dt> | 3020 | <dt><a·href="org/biojava/utils/xml/AppBeanRunner.html#%3Cinit%3E()"·class="member-name-link">AppBeanRunner()</a>·-·Constructor·for·class·org.biojava.utils.xml.<a·href="org/biojava/utils/xml/AppBeanRunner.html"·title="class·in·org.biojava.utils.xml">AppBeanRunner</a></dt> |
| 3021 | <dd> </dd> | 3021 | <dd> </dd> |
| 3022 | <dt><a·href="org/biojava/utils/automata/NfaSubModel.html#append(org.biojava.utils.automata.NfaSubModel)"·class="member-name-link">append(NfaSubModel)</a>·-·Method·in·class·org.biojava.utils.automata.<a·href="org/biojava/utils/automata/NfaSubModel.html"·title="class·in·org.biojava.utils.automata">NfaSubModel</a></dt> | 3022 | <dt><a·href="org/biojava/utils/automata/NfaSubModel.html#append(org.biojava.utils.automata.NfaSubModel)"·class="member-name-link">append(NfaSubModel)</a>·-·Method·in·class·org.biojava.utils.automata.<a·href="org/biojava/utils/automata/NfaSubModel.html"·title="class·in·org.biojava.utils.automata">NfaSubModel</a></dt> |
| 3023 | <dd> </dd> | 3023 | <dd> </dd> |
| 3024 | <dt><a·href="org/biojava/bio/program/fastq/ | 3024 | <dt><a·href="org/biojava/bio/program/fastq/IlluminaFastqWriter.html#append(T,java.lang.Iterable)"·class="member-name-link">append(T,·Iterable<Fastq>)</a>·-·Method·in·class·org.biojava.bio.program.fastq.<a·href="org/biojava/bio/program/fastq/IlluminaFastqWriter.html"·title="class·in·org.biojav[·...·truncated·by·diffoscope;·len:·29,·SHA:·9e77e404da328ba858143229c08d1a780e77383d80c9e377cba8b0b7b5adc543·...·]FastqWriter</a></dt> |
| 3025 | <dd> </dd> | 3025 | <dd> </dd> |
| 3026 | <dt><a·href="org/biojava/bio/program/fastq/FastqWriter.html#append(T,java.lang.Iterable)"·class="member-name-link">append(T,·Iterable<Fastq>)</a>·-·Method·in·interface·org.biojava.bio.program.fastq.<a·href="org/biojava/bio/program/fastq/FastqWriter.html"·title="interface·in·org.biojava.bio.program.fastq">FastqWriter</a></dt> | 3026 | <dt><a·href="org/biojava/bio/program/fastq/FastqWriter.html#append(T,java.lang.Iterable)"·class="member-name-link">append(T,·Iterable<Fastq>)</a>·-·Method·in·interface·org.biojava.bio.program.fastq.<a·href="org/biojava/bio/program/fastq/FastqWriter.html"·title="interface·in·org.biojava.bio.program.fastq">FastqWriter</a></dt> |
| 3027 | <dd> | 3027 | <dd> |
| 3028 | <div·class="block">Append·the·specified·FASTQ·formatted·sequences·to·the·specified·appendable.</div> | 3028 | <div·class="block">Append·the·specified·FASTQ·formatted·sequences·to·the·specified·appendable.</div> |
| 3029 | </dd> | 3029 | </dd> |
| 3030 | <dt><a·href="org/biojava/bio/program/fastq/ | 3030 | <dt><a·href="org/biojava/bio/program/fastq/IlluminaFastqWriter.html#append(T,org.biojava.bio.program.fastq.Fastq...)"·class="member-name-link">append(T,·Fastq...)</a>·-·Method·in·class·org.biojava.bio.program.fastq.<a·href="org/biojava/bio/program/fastq/IlluminaFastqWriter.html"·title="class·in·org[·...·truncated·by·diffoscope;·len:·36,·SHA:·0db718adb3d279c17eafe445e2fd70bbeabb473173cea4ec5728f0ed571a1954·...·]FastqWriter</a></dt> |
| 3031 | <dd> </dd> | 3031 | <dd> </dd> |
| 3032 | <dt><a·href="org/biojava/bio/program/fastq/FastqWriter.html#append(T,org.biojava.bio.program.fastq.Fastq...)"·class="member-name-link">append(T,·Fastq...)</a>·-·Method·in·interface·org.biojava.bio.program.fastq.<a·href="org/biojava/bio/program/fastq/FastqWriter.html"·title="interface·in·org.biojava.bio.program.fastq">FastqWriter</a></dt> | 3032 | <dt><a·href="org/biojava/bio/program/fastq/FastqWriter.html#append(T,org.biojava.bio.program.fastq.Fastq...)"·class="member-name-link">append(T,·Fastq...)</a>·-·Method·in·interface·org.biojava.bio.program.fastq.<a·href="org/biojava/bio/program/fastq/FastqWriter.html"·title="interface·in·org.biojava.bio.program.fastq">FastqWriter</a></dt> |
| 3033 | <dd> | 3033 | <dd> |
| 3034 | <div·class="block">Append·the·specified·FASTQ·formatted·sequences·to·the·specified·appendable.</div> | 3034 | <div·class="block">Append·the·specified·FASTQ·formatted·sequences·to·the·specified·appendable.</div> |
| 3035 | </dd> | 3035 | </dd> |
| 3036 | <dt><a·href="org/biojavax/bio/phylo/io/nexus/CharactersBlock.html#appendMatrixData(java.lang.String,java.lang.Object)"·class="member-name-link">appendMatrixData(String,·Object)</a>·-·Method·in·class·org.biojavax.bio.phylo.io.nexus.<a·href="org/biojavax/bio/phylo/io/nexus/CharactersBlock.html"·title="class·in·org.biojavax.bio.phylo.io.nexus">CharactersBlock</a></dt> | 3036 | <dt><a·href="org/biojavax/bio/phylo/io/nexus/CharactersBlock.html#appendMatrixData(java.lang.String,java.lang.Object)"·class="member-name-link">appendMatrixData(String,·Object)</a>·-·Method·in·class·org.biojavax.bio.phylo.io.nexus.<a·href="org/biojavax/bio/phylo/io/nexus/CharactersBlock.html"·title="class·in·org.biojavax.bio.phylo.io.nexus">CharactersBlock</a></dt> |
| 3037 | <dd> </dd> | 3037 | <dd> </dd> |
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| 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/ProteinRefSeqFileFormer.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·or[·...·truncated·by·diffoscope;·len:·136,·SHA:·a7970d1c347eeb36de336d7295a0dc5107dea8857b9e672693d17131e36f2f6d·...·]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/ProteinRefSeqFileFormer.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/ProteinRefSeqFileFormer.html"·title="class·in·org.biojav[·...·truncated·by·diffoscope;·len:·27,·SHA:·fa5b48983d6c2e3e1b354e66ebb82a4552a42d2422270f1fc91d3c1f3bcf239e·...·]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/ProteinRefSeqFileFormer.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/bio[·...·truncated·by·diffoscope;·len:·99,·SHA:·fc6156a3b36476fb5274f693665b632b6c529620870217d758a804521c1e614d·...·]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 43108, 15 lines modified | Offset 43108, 15 lines modified | ||
| 43108 | <dd> | 43108 | <dd> |
| 43109 | <div·class="block">Takes·this·position·and·returns·a·copy·translated·by·'distance'·bases.</div> | 43109 | <div·class="block">Takes·this·position·and·returns·a·copy·translated·by·'distance'·bases.</div> |
| 43110 | </dd> | 43110 | </dd> |
| 43111 | <dt><a·href="org/biojavax/bio/seq/SimpleRichLocation.html#translate(int)"·class="member-name-link">translate(int)</a>·-·Method·in·class·org.biojavax.bio.seq.<a·href="org/biojavax/bio/seq/SimpleRichLocation.html"·title="class·in·org.biojavax.bio.seq">SimpleRichLocation</a></dt> | 43111 | <dt><a·href="org/biojavax/bio/seq/SimpleRichLocation.html#translate(int)"·class="member-name-link">translate(int)</a>·-·Method·in·class·org.biojavax.bio.seq.<a·href="org/biojavax/bio/seq/SimpleRichLocation.html"·title="class·in·org.biojavax.bio.seq">SimpleRichLocation</a></dt> |
| 43112 | <dd> | 43112 | <dd> |
| 43113 | <div·class="block">Create·a·location·that·is·a·translation·of·this·location.</div> | 43113 | <div·class="block">Create·a·location·that·is·a·translation·of·this·location.</div> |
| 43114 | </dd> | 43114 | </dd> |
| 43115 | <dt><a·href="org/biojava/bio/symbol/ | 43115 | <dt><a·href="org/biojava/bio/symbol/SimpleReversibleTranslationTable.html#translate(org.biojava.bio.symbol.Symbol)"·class="member-name-link">translate(Symbol)</a>·-·Method·in·class·org.biojava.bio.symbol.<a·href="org/biojava/bio/symbol/SimpleReversibleTranslationTable.html"·title="class·in·o[·...·truncated·by·diffoscope;·len:·38,·SHA:·58a540bdbcc332b72c50de72b16df7b4dc017d55cc1cf5aa6b9be7eef149b348·...·]eTranslationTable</a></dt> |
| 43116 | <dd> </dd> | 43116 | <dd> </dd> |
| 43117 | <dt><a·href="org/biojava/bio/symbol/TranslationTable.html#translate(org.biojava.bio.symbol.Symbol)"·class="member-name-link">translate(Symbol)</a>·-·Method·in·interface·org.biojava.bio.symbol.<a·href="org/biojava/bio/symbol/TranslationTable.html"·title="interface·in·org.biojava.bio.symbol">TranslationTable</a></dt> | 43117 | <dt><a·href="org/biojava/bio/symbol/TranslationTable.html#translate(org.biojava.bio.symbol.Symbol)"·class="member-name-link">translate(Symbol)</a>·-·Method·in·interface·org.biojava.bio.symbol.<a·href="org/biojava/bio/symbol/TranslationTable.html"·title="interface·in·org.biojava.bio.symbol">TranslationTable</a></dt> |
| 43118 | <dd> | 43118 | <dd> |
| 43119 | <div·class="block">Translate·a·single·symbol·from·source·alphabet·to·the·target·alphabet.</div> | 43119 | <div·class="block">Translate·a·single·symbol·from·source·alphabet·to·the·target·alphabet.</div> |
| 43120 | </dd> | 43120 | </dd> |
| 43121 | <dt><a·href="org/biojava/bio/seq/GeneticCodes.html#translate(org.biojava.bio.symbol.SymbolList)"·class="member-name-link">translate(SymbolList)</a>·-·Static·method·in·class·org.biojava.bio.seq.<a·href="org/biojava/bio/seq/GeneticCodes.html"·title="class·in·org.biojava.bio.seq">GeneticCodes</a></dt> | 43121 | <dt><a·href="org/biojava/bio/seq/GeneticCodes.html#translate(org.biojava.bio.symbol.SymbolList)"·class="member-name-link">translate(SymbolList)</a>·-·Static·method·in·class·org.biojava.bio.seq.<a·href="org/biojava/bio/seq/GeneticCodes.html"·title="class·in·org.biojava.bio.seq">GeneticCodes</a></dt> |
| 43122 | <dd> | 43122 | <dd> |
| Offset 44284, 39 lines modified | Offset 44284, 39 lines modified | ||
| 44284 | </dd> | 44284 | </dd> |
| 44285 | <dt><a·href="org/biojava/bio/symbol/CodonPrefTools.html#WORM_NUCLEAR"·class="member-name-link">WORM_NUCLEAR</a>·-·Static·variable·in·class·org.biojava.bio.symbol.<a·href="org/biojava/bio/symbol/CodonPrefTools.html"·title="class·in·org.biojava.bio.symbol">CodonPrefTools</a></dt> | 44285 | <dt><a·href="org/biojava/bio/symbol/CodonPrefTools.html#WORM_NUCLEAR"·class="member-name-link">WORM_NUCLEAR</a>·-·Static·variable·in·class·org.biojava.bio.symbol.<a·href="org/biojava/bio/symbol/CodonPrefTools.html"·title="class·in·org.biojava.bio.symbol">CodonPrefTools</a></dt> |
| 44286 | <dd> | 44286 | <dd> |
| 44287 | <div·class="block">Caenorhabditis·elegans·codon·preferences</div> | 44287 | <div·class="block">Caenorhabditis·elegans·codon·preferences</div> |
| 44288 | </dd> | 44288 | </dd> |
| 44289 | <dt><a·href="org/biojava/bio/program/ssaha/SearchListener.Wrapper.html#%3Cinit%3E(org.biojava.bio.program.ssaha.SearchListener)"·class="member-name-link">Wrapper(SearchListener)</a>·-·Constructor·for·class·org.biojava.bio.program.ssaha.<a·href="org/biojava/bio/program/ssaha/SearchListener.Wrapper.html"·title="class·in·org.biojava.bio.program.ssaha">SearchListener.Wrapper</a></dt> | 44289 | <dt><a·href="org/biojava/bio/program/ssaha/SearchListener.Wrapper.html#%3Cinit%3E(org.biojava.bio.program.ssaha.SearchListener)"·class="member-name-link">Wrapper(SearchListener)</a>·-·Constructor·for·class·org.biojava.bio.program.ssaha.<a·href="org/biojava/bio/program/ssaha/SearchListener.Wrapper.html"·title="class·in·org.biojava.bio.program.ssaha">SearchListener.Wrapper</a></dt> |
| 44290 | <dd> </dd> | 44290 | <dd> </dd> |
| 44291 | <dt><a·href="org/biojava/bio/program/fastq/ | 44291 | <dt><a·href="org/biojava/bio/program/fastq/IlluminaFastqWriter.html#write(java.io.File,java.lang.Iterable)"·class="member-name-link">write(File,·Iterable<Fastq>)</a>·-·Method·in·class·org.biojava.bio.program.fastq.<a·href="org/biojava/bio/program/fastq/IlluminaFastqWriter.html"·title="class·i[·...·truncated·by·diffoscope;·len:·41,·SHA:·53fbf549afaf766e1a362fffb6d8d9429bc7e0ef396806d038da2fd624235bac·...·]FastqWriter</a></dt> |
| 44292 | <dd> </dd> | 44292 | <dd> </dd> |
| 44293 | <dt><a·href="org/biojava/bio/program/fastq/FastqWriter.html#write(java.io.File,java.lang.Iterable)"·class="member-name-link">write(File,·Iterable<Fastq>)</a>·-·Method·in·interface·org.biojava.bio.program.fastq.<a·href="org/biojava/bio/program/fastq/FastqWriter.html"·title="interface·in·org.biojava.bio.program.fastq">FastqWriter</a></dt> | 44293 | <dt><a·href="org/biojava/bio/program/fastq/FastqWriter.html#write(java.io.File,java.lang.Iterable)"·class="member-name-link">write(File,·Iterable<Fastq>)</a>·-·Method·in·interface·org.biojava.bio.program.fastq.<a·href="org/biojava/bio/program/fastq/FastqWriter.html"·title="interface·in·org.biojava.bio.program.fastq">FastqWriter</a></dt> |
| 44294 | <dd> | 44294 | <dd> |
| 44295 | <div·class="block">Write·the·specified·FASTQ·formatted·sequences·to·the·specified·file.</div> | 44295 | <div·class="block">Write·the·specified·FASTQ·formatted·sequences·to·the·specified·file.</div> |
| 44296 | </dd> | 44296 | </dd> |
| 44297 | <dt><a·href="org/biojava/bio/program/fastq/ | 44297 | <dt><a·href="org/biojava/bio/program/fastq/IlluminaFastqWriter.html#write(java.io.File,org.biojava.bio.program.fastq.Fastq...)"·class="member-name-link">write(File,·Fastq...)</a>·-·Method·in·class·org.biojava.bio.program.fastq.<a·href="org/biojava/bio/program/fastq/IlluminaFastqWriter.html"·title="[·...·truncated·by·diffoscope;·len:·48,·SHA:·d90bf56424ea635868b053cb843a053d849dbadc31e852ed622eabff5c97e889·...·]FastqWriter</a></dt> |
| 44298 | <dd> </dd> | 44298 | <dd> </dd> |
| 44299 | <dt><a·href="org/biojava/bio/program/fastq/FastqWriter.html#write(java.io.File,org.biojava.bio.program.fastq.Fastq...)"·class="member-name-link">write(File,·Fastq...)</a>·-·Method·in·interface·org.biojava.bio.program.fastq.<a·href="org/biojava/bio/program/fastq/FastqWriter.html"·title="interface·in·org.biojava.bio.program.fastq">FastqWriter</a></dt> | 44299 | <dt><a·href="org/biojava/bio/program/fastq/FastqWriter.html#write(java.io.File,org.biojava.bio.program.fastq.Fastq...)"·class="member-name-link">write(File,·Fastq...)</a>·-·Method·in·interface·org.biojava.bio.program.fastq.<a·href="org/biojava/bio/program/fastq/FastqWriter.html"·title="interface·in·org.biojava.bio.program.fastq">FastqWriter</a></dt> |
| 44300 | <dd> | 44300 | <dd> |
| 44301 | <div·class="block">Write·the·specified·FASTQ·formatted·sequences·to·the·specified·file.</div> | 44301 | <div·class="block">Write·the·specified·FASTQ·formatted·sequences·to·the·specified·file.</div> |
| 44302 | </dd> | 44302 | </dd> |
| 44303 | <dt><a·href="org/biojava/bio/program/fastq/ | 44303 | <dt><a·href="org/biojava/bio/program/fastq/IlluminaFastqWriter.html#write(java.io.OutputStream,java.lang.Iterable)"·class="member-name-link">write(OutputStream,·Iterable<Fastq>)</a>·-·Method·in·class·org.biojava.bio.program.fastq.<a·href="org/biojava/bio/program/fastq/IlluminaFastqWriter.html[·...·truncated·by·diffoscope;·len:·57,·SHA:·771d3ec4ad618ff85a9557971e216c294d1521af88e2961247810637bf156b99·...·]FastqWriter</a></dt> |
| 44304 | <dd> </dd> | 44304 | <dd> </dd> |
| 44305 | <dt><a·href="org/biojava/bio/program/fastq/FastqWriter.html#write(java.io.OutputStream,java.lang.Iterable)"·class="member-name-link">write(OutputStream,·Iterable<Fastq>)</a>·-·Method·in·interface·org.biojava.bio.program.fastq.<a·href="org/biojava/bio/program/fastq/FastqWriter.html"·title="interface·in·org.biojava.bio.program.fastq">FastqWriter</a></dt> | 44305 | <dt><a·href="org/biojava/bio/program/fastq/FastqWriter.html#write(java.io.OutputStream,java.lang.Iterable)"·class="member-name-link">write(OutputStream,·Iterable<Fastq>)</a>·-·Method·in·interface·org.biojava.bio.program.fastq.<a·href="org/biojava/bio/program/fastq/FastqWriter.html"·title="interface·in·org.biojava.bio.program.fastq">FastqWriter</a></dt> |
| 44306 | <dd> | 44306 | <dd> |
| 44307 | <div·class="block">Write·the·specified·FASTQ·formatted·sequences·to·the·specified·output·stream.</div> | 44307 | <div·class="block">Write·the·specified·FASTQ·formatted·sequences·to·the·specified·output·stream.</div> |
| 44308 | </dd> | 44308 | </dd> |
| 44309 | <dt><a·href="org/biojava/bio/seq/io/FastaAlignmentFormat.html#write(java.io.OutputStream,org.biojava.bio.alignment.Alignment,int)"·class="member-name-link">write(OutputStream,·Alignment,·int)</a>·-·Method·in·class·org.biojava.bio.seq.io.<a·href="org/biojava/bio/seq/io/FastaAlignmentFormat.html"·title="class·in·org.biojava.bio.seq.io">FastaAlignmentFormat</a></dt> | 44309 | <dt><a·href="org/biojava/bio/seq/io/FastaAlignmentFormat.html#write(java.io.OutputStream,org.biojava.bio.alignment.Alignment,int)"·class="member-name-link">write(OutputStream,·Alignment,·int)</a>·-·Method·in·class·org.biojava.bio.seq.io.<a·href="org/biojava/bio/seq/io/FastaAlignmentFormat.html"·title="class·in·org.biojava.bio.seq.io">FastaAlignmentFormat</a></dt> |
| 44310 | <dd> | 44310 | <dd> |
| 44311 | <div·class="block">Writes·out·the·alignment·to·an·FASTA·file.</div> | 44311 | <div·class="block">Writes·out·the·alignment·to·an·FASTA·file.</div> |
| 44312 | </dd> | 44312 | </dd> |
| 44313 | <dt><a·href="org/biojava/bio/seq/io/MSFAlignmentFormat.html#write(java.io.OutputStream,org.biojava.bio.alignment.Alignment,int)"·class="member-name-link">write(OutputStream,·Alignment,·int)</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> | 44313 | <dt><a·href="org/biojava/bio/seq/io/MSFAlignmentFormat.html#write(java.io.OutputStream,org.biojava.bio.alignment.Alignment,int)"·class="member-name-link">write(OutputStream,·Alignment,·int)</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> |
| 44314 | <dd> </dd> | 44314 | <dd> </dd> |
| 44315 | <dt><a·href="org/biojava/bio/program/fastq/ | 44315 | <dt><a·href="org/biojava/bio/program/fastq/IlluminaFastqWriter.html#write(java.io.OutputStream,org.biojava.bio.program.fastq.Fastq...)"·class="member-name-link">write(OutputStream,·Fastq...)</a>·-·Method·in·class·org.biojava.bio.program.fastq.<a·href="org/biojava/bio/program/fastq/IlluminaFastqWrit[·...·truncated·by·diffoscope;·len:·64,·SHA:·f781b7919666a9eedd9032a985d958a3a5882a0a47375083dbfd511678ff48e5·...·]FastqWriter</a></dt> |
| 44316 | <dd> </dd> | 44316 | <dd> </dd> |
| 44317 | <dt><a·href="org/biojava/bio/program/fastq/FastqWriter.html#write(java.io.OutputStream,org.biojava.bio.program.fastq.Fastq...)"·class="member-name-link">write(OutputStream,·Fastq...)</a>·-·Method·in·interface·org.biojava.bio.program.fastq.<a·href="org/biojava/bio/program/fastq/FastqWriter.html"·title="interface·in·org.biojava.bio.program.fastq">FastqWriter</a></dt> | 44317 | <dt><a·href="org/biojava/bio/program/fastq/FastqWriter.html#write(java.io.OutputStream,org.biojava.bio.program.fastq.Fastq...)"·class="member-name-link">write(OutputStream,·Fastq...)</a>·-·Method·in·interface·org.biojava.bio.program.fastq.<a·href="org/biojava/bio/program/fastq/FastqWriter.html"·title="interface·in·org.biojava.bio.program.fastq">FastqWriter</a></dt> |
| 44318 | <dd> | 44318 | <dd> |
| 44319 | <div·class="block">Write·the·specified·FASTQ·formatted·sequences·to·the·specified·output·stream.</div> | 44319 | <div·class="block">Write·the·specified·FASTQ·formatted·sequences·to·the·specified·output·stream.</div> |
| 44320 | </dd> | 44320 | </dd> |
| 44321 | <dt><a·href="org/biojava/bio/seq/io/agave/AgaveWriter.html#write(org.biojava.bio.seq.Sequence)"·class="member-name-link">write(Sequence)</a>·-·Method·in·class·org.biojava.bio.seq.io.agave.<a·href="org/biojava/bio/seq/io/agave/AgaveWriter.html"·title="class·in·org.biojava.bio.seq.io.agave">AgaveWriter</a></dt> | 44321 | <dt><a·href="org/biojava/bio/seq/io/agave/AgaveWriter.html#write(org.biojava.bio.seq.Sequence)"·class="member-name-link">write(Sequence)</a>·-·Method·in·class·org.biojava.bio.seq.io.agave.<a·href="org/biojava/bio/seq/io/agave/AgaveWriter.html"·title="class·in·org.biojava.bio.seq.io.agave">AgaveWriter</a></dt> |
| 44322 | <dd> | 44322 | <dd> |
| Offset 2788, 22 lines modified | Offset 2788, 22 lines modified | ||
| 2788 | ··AppBeanRunner·-·Class·in·org.biojava.utils.xml | 2788 | ··AppBeanRunner·-·Class·in·org.biojava.utils.xml |
| 2789 | ······Create·a·bean·from·an·XML·file,·then·attempt·to·enter·it. | 2789 | ······Create·a·bean·from·an·XML·file,·then·attempt·to·enter·it. |
| 2790 | ··AppBeanRunner()·-·Constructor·for·class·org.biojava.utils.xml.AppBeanRunner | 2790 | ··AppBeanRunner()·-·Constructor·for·class·org.biojava.utils.xml.AppBeanRunner |
| 2791 | ······ | 2791 | ······ |
| 2792 | ··append(NfaSubModel)·-·Method·in·class·org.biojava.utils.automata.NfaSubModel | 2792 | ··append(NfaSubModel)·-·Method·in·class·org.biojava.utils.automata.NfaSubModel |
| 2793 | ······ | 2793 | ······ |
| 2794 | ··append(T,_Iterable<Fastq>)·-·Method·in·class | 2794 | ··append(T,_Iterable<Fastq>)·-·Method·in·class |
| 2795 | ··org.biojava.bio.program.fastq. | 2795 | ··org.biojava.bio.program.fastq.IlluminaFastqWriter |
| 2796 | ······ | 2796 | ······ |
| 2797 | ··append(T,_Iterable<Fastq>)·-·Method·in·interface | 2797 | ··append(T,_Iterable<Fastq>)·-·Method·in·interface |
| 2798 | ··org.biojava.bio.program.fastq.FastqWriter | 2798 | ··org.biojava.bio.program.fastq.FastqWriter |
| 2799 | ······Append·the·specified·FASTQ·formatted·sequences·to·the·specified | 2799 | ······Append·the·specified·FASTQ·formatted·sequences·to·the·specified |
| 2800 | ······appendable. | 2800 | ······appendable. |
| 2801 | ··append(T,_Fastq...)·-·Method·in·class | 2801 | ··append(T,_Fastq...)·-·Method·in·class |
| 2802 | ··org.biojava.bio.program.fastq. | 2802 | ··org.biojava.bio.program.fastq.IlluminaFastqWriter |
| 2803 | ······ | 2803 | ······ |
| 2804 | ··append(T,_Fastq...)·-·Method·in·interface | 2804 | ··append(T,_Fastq...)·-·Method·in·interface |
| 2805 | ··org.biojava.bio.program.fastq.FastqWriter | 2805 | ··org.biojava.bio.program.fastq.FastqWriter |
| 2806 | ······Append·the·specified·FASTQ·formatted·sequences·to·the·specified | 2806 | ······Append·the·specified·FASTQ·formatted·sequences·to·the·specified |
| 2807 | ······appendable. | 2807 | ······appendable. |
| 2808 | ··appendMatrixData(String,_Object)·-·Method·in·class | 2808 | ··appendMatrixData(String,_Object)·-·Method·in·class |
| 2809 | ··org.biojavax.bio.phylo.io.nexus.CharactersBlock | 2809 | ··org.biojavax.bio.phylo.io.nexus.CharactersBlock |
| 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.ProteinRefSeqFileFormer |
| 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.ProteinRefSeqFileFormer |
| 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.ProteinRefSeqFileFormer |
| 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 36764, 15 lines modified | Offset 36764, 15 lines modified | ||
| 36764 | ··translate(int)·-·Method·in·interface·org.biojavax.bio.seq.Position | 36764 | ··translate(int)·-·Method·in·interface·org.biojavax.bio.seq.Position |
| 36765 | ······Takes·this·position·and·returns·a·copy·translated·by·'distance'·bases. | 36765 | ······Takes·this·position·and·returns·a·copy·translated·by·'distance'·bases. |
| 36766 | ··translate(int)·-·Method·in·class·org.biojavax.bio.seq.SimplePosition | 36766 | ··translate(int)·-·Method·in·class·org.biojavax.bio.seq.SimplePosition |
| 36767 | ······Takes·this·position·and·returns·a·copy·translated·by·'distance'·bases. | 36767 | ······Takes·this·position·and·returns·a·copy·translated·by·'distance'·bases. |
| 36768 | ··translate(int)·-·Method·in·class·org.biojavax.bio.seq.SimpleRichLocation | 36768 | ··translate(int)·-·Method·in·class·org.biojavax.bio.seq.SimpleRichLocation |
| 36769 | ······Create·a·location·that·is·a·translation·of·this·location. | 36769 | ······Create·a·location·that·is·a·translation·of·this·location. |
| 36770 | ··translate(Symbol)·-·Method·in·class | 36770 | ··translate(Symbol)·-·Method·in·class |
| 36771 | ··org.biojava.bio.symbol. | 36771 | ··org.biojava.bio.symbol.SimpleReversibleTranslationTable |
| 36772 | ······ | 36772 | ······ |
| 36773 | ··translate(Symbol)·-·Method·in·interface | 36773 | ··translate(Symbol)·-·Method·in·interface |
| 36774 | ··org.biojava.bio.symbol.TranslationTable | 36774 | ··org.biojava.bio.symbol.TranslationTable |
| 36775 | ······Translate·a·single·symbol·from·source·alphabet·to·the·target·alphabet. | 36775 | ······Translate·a·single·symbol·from·source·alphabet·to·the·target·alphabet. |
| 36776 | ··translate(SymbolList)·-·Static·method·in·class | 36776 | ··translate(SymbolList)·-·Static·method·in·class |
| 36777 | ··org.biojava.bio.seq.GeneticCodes | 36777 | ··org.biojava.bio.seq.GeneticCodes |
| 36778 | ······Translate·RNA·into·protein·(with·termination·symbols). | 36778 | ······Translate·RNA·into·protein·(with·termination·symbols). |
| Offset 37689, 40 lines modified | Offset 37689, 40 lines modified | ||
| 37689 | ······width. | 37689 | ······width. |
| 37690 | ··WORM_NUCLEAR·-·Static·variable·in·class·org.biojava.bio.symbol.CodonPrefTools | 37690 | ··WORM_NUCLEAR·-·Static·variable·in·class·org.biojava.bio.symbol.CodonPrefTools |
| 37691 | ······Caenorhabditis·elegans·codon·preferences | 37691 | ······Caenorhabditis·elegans·codon·preferences |
| 37692 | ··Wrapper(SearchListener)·-·Constructor·for·class | 37692 | ··Wrapper(SearchListener)·-·Constructor·for·class |
| 37693 | ··org.biojava.bio.program.ssaha.SearchListener.Wrapper | 37693 | ··org.biojava.bio.program.ssaha.SearchListener.Wrapper |
| 37694 | ······ | 37694 | ······ |
| 37695 | ··write(File,_Iterable<Fastq>)·-·Method·in·class | 37695 | ··write(File,_Iterable<Fastq>)·-·Method·in·class |
| 37696 | ··org.biojava.bio.program.fastq. | 37696 | ··org.biojava.bio.program.fastq.IlluminaFastqWriter |
| 37697 | ······ | 37697 | ······ |
| 37698 | ··write(File,_Iterable<Fastq>)·-·Method·in·interface | 37698 | ··write(File,_Iterable<Fastq>)·-·Method·in·interface |
| 37699 | ··org.biojava.bio.program.fastq.FastqWriter | 37699 | ··org.biojava.bio.program.fastq.FastqWriter |
| 37700 | ······Write·the·specified·FASTQ·formatted·sequences·to·the·specified·file. | 37700 | ······Write·the·specified·FASTQ·formatted·sequences·to·the·specified·file. |
| 37701 | ··write(File,_Fastq...)·-·Method·in·class | 37701 | ··write(File,_Fastq...)·-·Method·in·class |
| 37702 | ··org.biojava.bio.program.fastq. | 37702 | ··org.biojava.bio.program.fastq.IlluminaFastqWriter |
| 37703 | ······ | 37703 | ······ |
| 37704 | ··write(File,_Fastq...)·-·Method·in·interface | 37704 | ··write(File,_Fastq...)·-·Method·in·interface |
| 37705 | ··org.biojava.bio.program.fastq.FastqWriter | 37705 | ··org.biojava.bio.program.fastq.FastqWriter |
| 37706 | ······Write·the·specified·FASTQ·formatted·sequences·to·the·specified·file. | 37706 | ······Write·the·specified·FASTQ·formatted·sequences·to·the·specified·file. |
| 37707 | ··write(OutputStream,_Iterable<Fastq>)·-·Method·in·class | 37707 | ··write(OutputStream,_Iterable<Fastq>)·-·Method·in·class |
| 37708 | ··org.biojava.bio.program.fastq. | 37708 | ··org.biojava.bio.program.fastq.IlluminaFastqWriter |
| 37709 | ······ | 37709 | ······ |
| 37710 | ··write(OutputStream,_Iterable<Fastq>)·-·Method·in·interface | 37710 | ··write(OutputStream,_Iterable<Fastq>)·-·Method·in·interface |
| 37711 | ··org.biojava.bio.program.fastq.FastqWriter | 37711 | ··org.biojava.bio.program.fastq.FastqWriter |
| 37712 | ······Write·the·specified·FASTQ·formatted·sequences·to·the·specified·output | 37712 | ······Write·the·specified·FASTQ·formatted·sequences·to·the·specified·output |
| 37713 | ······stream. | 37713 | ······stream. |
| 37714 | ··write(OutputStream,_Alignment,_int)·-·Method·in·class | 37714 | ··write(OutputStream,_Alignment,_int)·-·Method·in·class |
| 37715 | ··org.biojava.bio.seq.io.FastaAlignmentFormat | 37715 | ··org.biojava.bio.seq.io.FastaAlignmentFormat |
| 37716 | ······Writes·out·the·alignment·to·an·FASTA·file. | 37716 | ······Writes·out·the·alignment·to·an·FASTA·file. |
| 37717 | ··write(OutputStream,_Alignment,_int)·-·Method·in·class | 37717 | ··write(OutputStream,_Alignment,_int)·-·Method·in·class |
| 37718 | ··org.biojava.bio.seq.io.MSFAlignmentFormat | 37718 | ··org.biojava.bio.seq.io.MSFAlignmentFormat |
| 37719 | ······ | 37719 | ······ |
| 37720 | ··write(OutputStream,_Fastq...)·-·Method·in·class | 37720 | ··write(OutputStream,_Fastq...)·-·Method·in·class |
| 37721 | ··org.biojava.bio.program.fastq. | 37721 | ··org.biojava.bio.program.fastq.IlluminaFastqWriter |
| 37722 | ······ | 37722 | ······ |
| 37723 | ··write(OutputStream,_Fastq...)·-·Method·in·interface | 37723 | ··write(OutputStream,_Fastq...)·-·Method·in·interface |
| 37724 | ··org.biojava.bio.program.fastq.FastqWriter | 37724 | ··org.biojava.bio.program.fastq.FastqWriter |
| 37725 | ······Write·the·specified·FASTQ·formatted·sequences·to·the·specified·output | 37725 | ······Write·the·specified·FASTQ·formatted·sequences·to·the·specified·output |
| 37726 | ······stream. | 37726 | ······stream. |
| 37727 | ··write(Sequence)·-·Method·in·class·org.biojava.bio.seq.io.agave.AgaveWriter | 37727 | ··write(Sequence)·-·Method·in·class·org.biojava.bio.seq.io.agave.AgaveWriter |
| 37728 | ······Writing·Sequence. | 37728 | ······Writing·Sequence. |
| Offset 3994, 25 lines modified | Offset 3994, 25 lines modified | ||
| 3994 | },·{ | 3994 | },·{ |
| 3995 | ····"p":·"org.biojava.utils.automata", | 3995 | ····"p":·"org.biojava.utils.automata", |
| 3996 | ····"c":·"NfaSubModel", | 3996 | ····"c":·"NfaSubModel", |
| 3997 | ····"l":·"append(NfaSubModel)", | 3997 | ····"l":·"append(NfaSubModel)", |
| 3998 | ····"u":·"append(org.biojava.utils.automata.NfaSubModel)" | 3998 | ····"u":·"append(org.biojava.utils.automata.NfaSubModel)" |
| 3999 | },·{ | 3999 | },·{ |
| 4000 | ····"p":·"org.biojava.bio.program.fastq", | 4000 | ····"p":·"org.biojava.bio.program.fastq", |
| 4001 | ····"c":·" | 4001 | ····"c":·"IlluminaFastqWriter", |
| 4002 | ····"l":·"append(T,·Fastq...)", | 4002 | ····"l":·"append(T,·Fastq...)", |
| 4003 | ····"u":·"append(T,org.biojava.bio.program.fastq.Fastq...)" | 4003 | ····"u":·"append(T,org.biojava.bio.program.fastq.Fastq...)" |
| 4004 | },·{ | 4004 | },·{ |
| 4005 | ····"p":·"org.biojava.bio.program.fastq", | 4005 | ····"p":·"org.biojava.bio.program.fastq", |
| 4006 | ····"c":·"FastqWriter", | 4006 | ····"c":·"FastqWriter", |
| 4007 | ····"l":·"append(T,·Fastq...)", | 4007 | ····"l":·"append(T,·Fastq...)", |
| 4008 | ····"u":·"append(T,org.biojava.bio.program.fastq.Fastq...)" | 4008 | ····"u":·"append(T,org.biojava.bio.program.fastq.Fastq...)" |
| 4009 | },·{ | 4009 | },·{ |
| 4010 | ····"p":·"org.biojava.bio.program.fastq", | 4010 | ····"p":·"org.biojava.bio.program.fastq", |
| 4011 | ····"c":·" | 4011 | ····"c":·"IlluminaFastqWriter", |
| 4012 | ····"l":·"append(T,·Iterable<Fastq>)", | 4012 | ····"l":·"append(T,·Iterable<Fastq>)", |
| 4013 | ····"u":·"append(T,java.lang.Iterable)" | 4013 | ····"u":·"append(T,java.lang.Iterable)" |
| 4014 | },·{ | 4014 | },·{ |
| 4015 | ····"p":·"org.biojava.bio.program.fastq", | 4015 | ····"p":·"org.biojava.bio.program.fastq", |
| 4016 | ····"c":·"FastqWriter", | 4016 | ····"c":·"FastqWriter", |
| 4017 | ····"l":·"append(T,·Iterable<Fastq>)", | 4017 | ····"l":·"append(T,·Iterable<Fastq>)", |
| 4018 | ····"u":·"append(T,java.lang.Iterable)" | 4018 | ····"u":·"append(T,java.lang.Iterable)" |
| 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":·"ProteinRefSeqFileFormer", |
| 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":·"ProteinRefSeqFileFormer", |
| 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":·"ProteinRefSeqFileFormer", |
| 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 53366, 15 lines modified | Offset 53366, 15 lines modified | ||
| 53366 | ····"l":·"translate(int)" | 53366 | ····"l":·"translate(int)" |
| 53367 | },·{ | 53367 | },·{ |
| 53368 | ····"p":·"org.biojavax.bio.seq", | 53368 | ····"p":·"org.biojavax.bio.seq", |
| 53369 | ····"c":·"SimpleRichLocation", | 53369 | ····"c":·"SimpleRichLocation", |
| 53370 | ····"l":·"translate(int)" | 53370 | ····"l":·"translate(int)" |
| 53371 | },·{ | 53371 | },·{ |
| 53372 | ····"p":·"org.biojava.bio.symbol", | 53372 | ····"p":·"org.biojava.bio.symbol", |
| 53373 | ····"c":·" | 53373 | ····"c":·"SimpleReversibleTranslationTable", |
| 53374 | ····"l":·"translate(Symbol)", | 53374 | ····"l":·"translate(Symbol)", |
| 53375 | ····"u":·"translate(org.biojava.bio.symbol.Symbol)" | 53375 | ····"u":·"translate(org.biojava.bio.symbol.Symbol)" |
| 53376 | },·{ | 53376 | },·{ |
| 53377 | ····"p":·"org.biojava.bio.symbol", | 53377 | ····"p":·"org.biojava.bio.symbol", |
| 53378 | ····"c":·"TranslationTable", | 53378 | ····"c":·"TranslationTable", |
| 53379 | ····"l":·"translate(Symbol)", | 53379 | ····"l":·"translate(Symbol)", |
| 53380 | ····"u":·"translate(org.biojava.bio.symbol.Symbol)" | 53380 | ····"u":·"translate(org.biojava.bio.symbol.Symbol)" |
| Offset 54624, 25 lines modified | Offset 54624, 25 lines modified | ||
| 54624 | },·{ | 54624 | },·{ |
| 54625 | ····"p":·"org.biojava.bio.program.ssaha", | 54625 | ····"p":·"org.biojava.bio.program.ssaha", |
| 54626 | ····"c":·"SearchListener.Wrapper", | 54626 | ····"c":·"SearchListener.Wrapper", |
| 54627 | ····"l":·"Wrapper(SearchListener)", | 54627 | ····"l":·"Wrapper(SearchListener)", |
| 54628 | ····"u":·"%3Cinit%3E(org.biojava.bio.program.ssaha.SearchListener)" | 54628 | ····"u":·"%3Cinit%3E(org.biojava.bio.program.ssaha.SearchListener)" |
| 54629 | },·{ | 54629 | },·{ |
| 54630 | ····"p":·"org.biojava.bio.program.fastq", | 54630 | ····"p":·"org.biojava.bio.program.fastq", |
| 54631 | ····"c":·" | 54631 | ····"c":·"IlluminaFastqWriter", |
| 54632 | ····"l":·"write(File,·Fastq...)", | 54632 | ····"l":·"write(File,·Fastq...)", |
| 54633 | ····"u":·"write(java.io.File,org.biojava.bio.program.fastq.Fastq...)" | 54633 | ····"u":·"write(java.io.File,org.biojava.bio.program.fastq.Fastq...)" |
| 54634 | },·{ | 54634 | },·{ |
| 54635 | ····"p":·"org.biojava.bio.program.fastq", | 54635 | ····"p":·"org.biojava.bio.program.fastq", |
| 54636 | ····"c":·"FastqWriter", | 54636 | ····"c":·"FastqWriter", |
| 54637 | ····"l":·"write(File,·Fastq...)", | 54637 | ····"l":·"write(File,·Fastq...)", |
| 54638 | ····"u":·"write(java.io.File,org.biojava.bio.program.fastq.Fastq...)" | 54638 | ····"u":·"write(java.io.File,org.biojava.bio.program.fastq.Fastq...)" |
| 54639 | },·{ | 54639 | },·{ |
| 54640 | ····"p":·"org.biojava.bio.program.fastq", | 54640 | ····"p":·"org.biojava.bio.program.fastq", |
| 54641 | ····"c":·" | 54641 | ····"c":·"IlluminaFastqWriter", |
| 54642 | ····"l":·"write(File,·Iterable<Fastq>)", | 54642 | ····"l":·"write(File,·Iterable<Fastq>)", |
| 54643 | ····"u":·"write(java.io.File,java.lang.Iterable)" | 54643 | ····"u":·"write(java.io.File,java.lang.Iterable)" |
| 54644 | },·{ | 54644 | },·{ |
| 54645 | ····"p":·"org.biojava.bio.program.fastq", | 54645 | ····"p":·"org.biojava.bio.program.fastq", |
| 54646 | ····"c":·"FastqWriter", | 54646 | ····"c":·"FastqWriter", |
| 54647 | ····"l":·"write(File,·Iterable<Fastq>)", | 54647 | ····"l":·"write(File,·Iterable<Fastq>)", |
| 54648 | ····"u":·"write(java.io.File,java.lang.Iterable)" | 54648 | ····"u":·"write(java.io.File,java.lang.Iterable)" |
| Offset 54654, 25 lines modified | Offset 54654, 25 lines modified | ||
| 54654 | },·{ | 54654 | },·{ |
| 54655 | ····"p":·"org.biojava.bio.seq.io", | 54655 | ····"p":·"org.biojava.bio.seq.io", |
| 54656 | ····"c":·"MSFAlignmentFormat", | 54656 | ····"c":·"MSFAlignmentFormat", |
| 54657 | ····"l":·"write(OutputStream,·Alignment,·int)", | 54657 | ····"l":·"write(OutputStream,·Alignment,·int)", |
| 54658 | ····"u":·"write(java.io.OutputStream,org.biojava.bio.alignment.Alignment,int)" | 54658 | ····"u":·"write(java.io.OutputStream,org.biojava.bio.alignment.Alignment,int)" |
| 54659 | },·{ | 54659 | },·{ |
| 54660 | ····"p":·"org.biojava.bio.program.fastq", | 54660 | ····"p":·"org.biojava.bio.program.fastq", |
| 54661 | ····"c":·" | 54661 | ····"c":·"IlluminaFastqWriter", |
| 54662 | ····"l":·"write(OutputStream,·Fastq...)", | 54662 | ····"l":·"write(OutputStream,·Fastq...)", |
| 54663 | ····"u":·"write(java.io.OutputStream,org.biojava.bio.program.fastq.Fastq...)" | 54663 | ····"u":·"write(java.io.OutputStream,org.biojava.bio.program.fastq.Fastq...)" |
| 54664 | },·{ | 54664 | },·{ |
| 54665 | ····"p":·"org.biojava.bio.program.fastq", | 54665 | ····"p":·"org.biojava.bio.program.fastq", |
| 54666 | ····"c":·"FastqWriter", | 54666 | ····"c":·"FastqWriter", |
| 54667 | ····"l":·"write(OutputStream,·Fastq...)", | 54667 | ····"l":·"write(OutputStream,·Fastq...)", |
| 54668 | ····"u":·"write(java.io.OutputStream,org.biojava.bio.program.fastq.Fastq...)" | 54668 | ····"u":·"write(java.io.OutputStream,org.biojava.bio.program.fastq.Fastq...)" |
| 54669 | },·{ | 54669 | },·{ |
| 54670 | ····"p":·"org.biojava.bio.program.fastq", | 54670 | ····"p":·"org.biojava.bio.program.fastq", |
| 54671 | ····"c":·" | 54671 | ····"c":·"IlluminaFastqWriter", |
| Max diff block lines reached; 242/5228 bytes (4.63%) of diff not shown. | |||