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<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
<!-- NewPage -->
<html lang="en">
<head>
<!-- Generated by javadoc (version 1.7.0_65) on Tue Sep 02 20:47:33 CDT 2014 -->
<meta http-equiv="Content-Type" content="text/html" charset="UTF-8">
<title>All Classes (biojava-legacy 1.9.1 API)</title>
<meta name="date" content="2014-09-02">
<link rel="stylesheet" type="text/css" href="stylesheet.css" title="Style">
</head>
<body>
<h1 class="bar">All Classes</h1>
<div class="indexContainer">
<ul>
<li><a href="org/biojava/bio/proteomics/aaindex/AAindex.html" title="class in org.biojava.bio.proteomics.aaindex">AAindex</a></li>
<li><a href="org/biojava/bio/proteomics/aaindex/AAindexStreamReader.html" title="class in org.biojava.bio.proteomics.aaindex">AAindexStreamReader</a></li>
<li><a href="org/biojava/bio/program/abi/ABIFChromatogram.html" title="class in org.biojava.bio.program.abi">ABIFChromatogram</a></li>
<li><a href="org/biojava/bio/program/abi/ABIFParser.html" title="class in org.biojava.bio.program.abi">ABIFParser</a></li>
<li><a href="org/biojava/bio/program/abi/ABIFParser.DataAccess.html" title="interface in org.biojava.bio.program.abi"><i>ABIFParser.DataAccess</i></a></li>
<li><a href="org/biojava/bio/program/abi/ABIFParser.TaggedDataRecord.html" title="class in org.biojava.bio.program.abi">ABIFParser.TaggedDataRecord</a></li>
<li><a href="org/biojava/bio/program/abi/ABITools.html" title="class in org.biojava.bio.program.abi">ABITools</a></li>
<li><a href="org/biojava/bio/program/abi/ABITrace.html" title="class in org.biojava.bio.program.abi">ABITrace</a></li>
<li><a href="org/biojava/bio/gui/sequence/AbiTraceRenderer.html" title="class in org.biojava.bio.gui.sequence">AbiTraceRenderer</a></li>
<li><a href="org/biojava/bio/program/blast2html/AbstractAlignmentStyler.html" title="class in org.biojava.bio.program.blast2html">AbstractAlignmentStyler</a></li>
<li><a href="org/biojava/bio/symbol/AbstractAlphabet.html" title="class in org.biojava.bio.symbol">AbstractAlphabet</a></li>
<li><a href="org/biojava/bio/AbstractAnnotation.html" title="class in org.biojava.bio">AbstractAnnotation</a></li>
<li><a href="org/biojava/bio/gui/sequence/AbstractBeadRenderer.html" title="class in org.biojava.bio.gui.sequence">AbstractBeadRenderer</a></li>
<li><a href="org/biojavax/bio/db/AbstractBioEntryDB.html" title="class in org.biojavax.bio.db">AbstractBioEntryDB</a></li>
<li><a href="org/biojava/utils/AbstractChangeable.html" title="class in org.biojava.utils">AbstractChangeable</a></li>
<li><a href="org/biojava/bio/chromatogram/AbstractChromatogram.html" title="class in org.biojava.bio.chromatogram">AbstractChromatogram</a></li>
<li><a href="org/biojavax/ga/functions/AbstractCrossOverFunction.html" title="class in org.biojavax.ga.functions">AbstractCrossOverFunction</a></li>
<li><a href="org/biojava/bio/dist/AbstractDistribution.html" title="class in org.biojava.bio.dist">AbstractDistribution</a></li>
<li><a href="org/biojava/bio/seq/AbstractFeatureHolder.html" title="class in org.biojava.bio.seq">AbstractFeatureHolder</a></li>
<li><a href="org/biojavax/ga/impl/AbstractGeneticAlgorithm.html" title="class in org.biojavax.ga.impl">AbstractGeneticAlgorithm</a></li>
<li><a href="org/biojava/bio/symbol/AbstractLocation.html" title="class in org.biojava.bio.symbol">AbstractLocation</a></li>
<li><a href="org/biojava/bio/symbol/AbstractLocationDecorator.html" title="class in org.biojava.bio.symbol">AbstractLocationDecorator</a></li>
<li><a href="org/biojava/bio/symbol/AbstractManyToOneTranslationTable.html" title="class in org.biojava.bio.symbol">AbstractManyToOneTranslationTable</a></li>
<li><a href="org/biojava/bio/dp/twohead/AbstractMatrixPairDPCursor.html" title="class in org.biojava.bio.dp.twohead">AbstractMatrixPairDPCursor</a></li>
<li><a href="org/biojavax/ga/functions/AbstractMutationFunction.html" title="class in org.biojavax.ga.functions">AbstractMutationFunction</a></li>
<li><a href="org/biojava/bio/dist/AbstractOrderNDistribution.html" title="class in org.biojava.bio.dist">AbstractOrderNDistribution</a></li>
<li><a href="org/biojavax/ga/impl/AbstractOrganism.html" title="class in org.biojavax.ga.impl">AbstractOrganism</a></li>
<li><a href="org/biojava/bio/program/homologene/AbstractOrthologueSet.html" title="class in org.biojava.bio.program.homologene">AbstractOrthologueSet</a></li>
<li><a href="org/biojava/bio/program/homologene/AbstractOrthoPairCollection.html" title="class in org.biojava.bio.program.homologene">AbstractOrthoPairCollection</a></li>
<li><a href="org/biojava/bio/program/homologene/AbstractOrthoPairSet.html" title="class in org.biojava.bio.program.homologene">AbstractOrthoPairSet</a></li>
<li><a href="org/biojava/bio/gui/sequence/AbstractPeptideDigestRenderer.html" title="class in org.biojava.bio.gui.sequence">AbstractPeptideDigestRenderer</a></li>
<li><a href="org/biojavax/ga/impl/AbstractPopulation.html" title="class in org.biojavax.ga.impl">AbstractPopulation</a></li>
<li><a href="org/biojava/bio/symbol/AbstractRangeLocation.html" title="class in org.biojava.bio.symbol">AbstractRangeLocation</a></li>
<li><a href="org/biojava/bio/symbol/AbstractReversibleTranslationTable.html" title="class in org.biojava.bio.symbol">AbstractReversibleTranslationTable</a></li>
<li><a href="org/biojavax/bio/db/AbstractRichSequenceDB.html" title="class in org.biojavax.bio.db">AbstractRichSequenceDB</a></li>
<li><a href="org/biojava/bio/seq/db/AbstractSequenceDB.html" title="class in org.biojava.bio.seq.db">AbstractSequenceDB</a></li>
<li><a href="org/biojava/stats/svm/AbstractSVMClassifierModel.html" title="class in org.biojava.stats.svm">AbstractSVMClassifierModel</a></li>
<li><a href="org/biojava/stats/svm/AbstractSVMTarget.html" title="class in org.biojava.stats.svm">AbstractSVMTarget</a></li>
<li><a href="org/biojava/bio/symbol/AbstractSymbol.html" title="class in org.biojava.bio.symbol">AbstractSymbol</a></li>
<li><a href="org/biojava/bio/symbol/AbstractSymbolList.html" title="class in org.biojava.bio.symbol">AbstractSymbolList</a></li>
<li><a href="org/biojava/bio/taxa/AbstractTaxon.html" title="class in org.biojava.bio.taxa">AbstractTaxon</a></li>
<li><a href="org/biojava/ontology/AbstractTerm.html" title="class in org.biojava.ontology">AbstractTerm</a></li>
<li><a href="org/biojava/bio/dp/AbstractTrainer.html" title="class in org.biojava.bio.dp">AbstractTrainer</a></li>
<li><a href="org/biojava/bio/alignment/AbstractULAlignment.html" title="class in org.biojava.bio.alignment">AbstractULAlignment</a></li>
<li><a href="org/biojava/bio/program/tagvalue/AbstractWrapper.html" title="class in org.biojava.bio.program.tagvalue">AbstractWrapper</a></li>
<li><a href="org/biojava/bio/seq/db/emblcd/AcnumHitReader.html" title="class in org.biojava.bio.seq.db.emblcd">AcnumHitReader</a></li>
<li><a href="org/biojava/bio/seq/db/emblcd/AcnumTrgReader.html" title="class in org.biojava.bio.seq.db.emblcd">AcnumTrgReader</a></li>
<li><a href="org/biojava/utils/ActivityListener.html" title="interface in org.biojava.utils"><i>ActivityListener</i></a></li>
<li><a href="org/biojava/bio/seq/io/agave/Agave2AgaveAnnotFilter.html" title="class in org.biojava.bio.seq.io.agave">Agave2AgaveAnnotFilter</a></li>
<li><a href="org/biojava/bio/seq/io/agave/AGAVEAltIdsPropHandler.html" title="class in org.biojava.bio.seq.io.agave">AGAVEAltIdsPropHandler</a></li>
<li><a href="org/biojava/bio/seq/io/agave/AGAVEAnnotationsHandler.html" title="class in org.biojava.bio.seq.io.agave">AGAVEAnnotationsHandler</a></li>
<li><a href="org/biojava/bio/seq/io/agave/AGAVEAnnotFilter.html" title="interface in org.biojava.bio.seq.io.agave"><i>AGAVEAnnotFilter</i></a></li>
<li><a href="org/biojava/bio/seq/io/agave/AGAVEAnnotFilterFactory.html" title="interface in org.biojava.bio.seq.io.agave"><i>AGAVEAnnotFilterFactory</i></a></li>
<li><a href="org/biojava/bio/seq/io/agave/AGAVEAssemblyHandler.html" title="class in org.biojava.bio.seq.io.agave">AGAVEAssemblyHandler</a></li>
<li><a href="org/biojava/bio/seq/io/agave/AGAVEBioSeqCallbackItf.html" title="interface in org.biojava.bio.seq.io.agave"><i>AGAVEBioSeqCallbackItf</i></a></li>
<li><a href="org/biojava/bio/seq/io/agave/AGAVEBioSeqHandler.html" title="class in org.biojava.bio.seq.io.agave">AGAVEBioSeqHandler</a></li>
<li><a href="org/biojava/bio/seq/io/agave/AGAVEBioSequenceHandler.html" title="class in org.biojava.bio.seq.io.agave">AGAVEBioSequenceHandler</a></li>
<li><a href="org/biojava/bio/seq/io/agave/AGAVECallbackItf.html" title="interface in org.biojava.bio.seq.io.agave"><i>AGAVECallbackItf</i></a></li>
<li><a href="org/biojava/bio/seq/io/agave/AGAVECdsHandler.html" title="class in org.biojava.bio.seq.io.agave">AGAVECdsHandler</a></li>
<li><a href="org/biojava/bio/seq/io/agave/AGAVEChromosomeCallbackItf.html" title="interface in org.biojava.bio.seq.io.agave"><i>AGAVEChromosomeCallbackItf</i></a></li>
<li><a href="org/biojava/bio/seq/io/agave/AGAVEChromosomeHandler.html" title="class in org.biojava.bio.seq.io.agave">AGAVEChromosomeHandler</a></li>
<li><a href="org/biojava/bio/seq/io/agave/AGAVEClassificationHandler.html" title="class in org.biojava.bio.seq.io.agave">AGAVEClassificationHandler</a></li>
<li><a href="org/biojava/bio/seq/io/agave/AGAVECompResultHandler.html" title="class in org.biojava.bio.seq.io.agave">AGAVECompResultHandler</a></li>
<li><a href="org/biojava/bio/seq/io/agave/AGAVEComputationHandler.html" title="class in org.biojava.bio.seq.io.agave">AGAVEComputationHandler</a></li>
<li><a href="org/biojava/bio/seq/io/agave/AGAVEContigCallbackItf.html" title="interface in org.biojava.bio.seq.io.agave"><i>AGAVEContigCallbackItf</i></a></li>
<li><a href="org/biojava/bio/seq/io/agave/AGAVEContigHandler.html" title="class in org.biojava.bio.seq.io.agave">AGAVEContigHandler</a></li>
<li><a href="org/biojava/bio/seq/io/agave/AGAVEDbId.html" title="class in org.biojava.bio.seq.io.agave">AGAVEDbId</a></li>
<li><a href="org/biojava/bio/seq/io/agave/AGAVEDbIdCallbackItf.html" title="interface in org.biojava.bio.seq.io.agave"><i>AGAVEDbIdCallbackItf</i></a></li>
<li><a href="org/biojava/bio/seq/io/agave/AGAVEDbIdPropCallbackItf.html" title="interface in org.biojava.bio.seq.io.agave"><i>AGAVEDbIdPropCallbackItf</i></a></li>
<li><a href="org/biojava/bio/seq/io/agave/AGAVEDbIdPropHandler.html" title="class in org.biojava.bio.seq.io.agave">AGAVEDbIdPropHandler</a></li>
<li><a href="org/biojava/bio/seq/io/agave/AGAVEDescPropHandler.html" title="class in org.biojava.bio.seq.io.agave">AGAVEDescPropHandler</a></li>
<li><a href="org/biojava/bio/seq/io/agave/AGAVEElementIdPropHandler.html" title="class in org.biojava.bio.seq.io.agave">AGAVEElementIdPropHandler</a></li>
<li><a href="org/biojava/bio/seq/io/agave/AGAVEEvidenceCallbackItf.html" title="interface in org.biojava.bio.seq.io.agave"><i>AGAVEEvidenceCallbackItf</i></a></li>
<li><a href="org/biojava/bio/seq/io/agave/AGAVEEvidenceHandler.html" title="class in org.biojava.bio.seq.io.agave">AGAVEEvidenceHandler</a></li>
<li><a href="org/biojava/bio/seq/io/agave/AGAVEExonsPropHandler.html" title="class in org.biojava.bio.seq.io.agave">AGAVEExonsPropHandler</a></li>
<li><a href="org/biojava/bio/seq/io/agave/AGAVEFeatureCallbackItf.html" title="interface in org.biojava.bio.seq.io.agave"><i>AGAVEFeatureCallbackItf</i></a></li>
<li><a href="org/biojava/bio/seq/io/agave/AGAVEFragmentOrderHandler.html" title="class in org.biojava.bio.seq.io.agave">AGAVEFragmentOrderHandler</a></li>
<li><a href="org/biojava/bio/seq/io/agave/AGAVEFragmentOrientationHandler.html" title="class in org.biojava.bio.seq.io.agave">AGAVEFragmentOrientationHandler</a></li>
<li><a href="org/biojava/bio/seq/io/agave/AGAVEGeneHandler.html" title="class in org.biojava.bio.seq.io.agave">AGAVEGeneHandler</a></li>
<li><a href="org/biojava/bio/seq/io/agave/AGAVEHandler.html" title="class in org.biojava.bio.seq.io.agave">AGAVEHandler</a></li>
<li><a href="org/biojava/bio/seq/io/agave/AGAVEIdAlias.html" title="class in org.biojava.bio.seq.io.agave">AGAVEIdAlias</a></li>
<li><a href="org/biojava/bio/seq/io/agave/AGAVEIdAliasCallbackItf.html" title="interface in org.biojava.bio.seq.io.agave"><i>AGAVEIdAliasCallbackItf</i></a></li>
<li><a href="org/biojava/bio/seq/io/agave/AGAVEIdAliasPropHandler.html" title="class in org.biojava.bio.seq.io.agave">AGAVEIdAliasPropHandler</a></li>
<li><a href="org/biojava/bio/seq/io/agave/AGAVEKeywordPropHandler.html" title="class in org.biojava.bio.seq.io.agave">AGAVEKeywordPropHandler</a></li>
<li><a href="org/biojava/bio/seq/io/agave/AGAVEMapLocation.html" title="class in org.biojava.bio.seq.io.agave">AGAVEMapLocation</a></li>
<li><a href="org/biojava/bio/seq/io/agave/AGAVEMapLocationPropHandler.html" title="class in org.biojava.bio.seq.io.agave">AGAVEMapLocationPropHandler</a></li>
<li><a href="org/biojava/bio/seq/io/agave/AGAVEMapPosition.html" title="class in org.biojava.bio.seq.io.agave">AGAVEMapPosition</a></li>
<li><a href="org/biojava/bio/seq/io/agave/AGAVEMapPositionPropHandler.html" title="class in org.biojava.bio.seq.io.agave">AGAVEMapPositionPropHandler</a></li>
<li><a href="org/biojava/bio/seq/io/agave/AGAVEMatchAlignPropHandler.html" title="class in org.biojava.bio.seq.io.agave">AGAVEMatchAlignPropHandler</a></li>
<li><a href="org/biojava/bio/seq/io/agave/AGAVEMatchDescPropHandler.html" title="class in org.biojava.bio.seq.io.agave">AGAVEMatchDescPropHandler</a></li>
<li><a href="org/biojava/bio/seq/io/agave/AGAVEMatchRegion.html" title="class in org.biojava.bio.seq.io.agave">AGAVEMatchRegion</a></li>
<li><a href="org/biojava/bio/seq/io/agave/AGAVEMatchRegionPropHandler.html" title="class in org.biojava.bio.seq.io.agave">AGAVEMatchRegionPropHandler</a></li>
<li><a href="org/biojava/bio/seq/io/agave/AGAVEMrnaHandler.html" title="class in org.biojava.bio.seq.io.agave">AGAVEMrnaHandler</a></li>
<li><a href="org/biojava/bio/seq/io/agave/AGAVENotePropHandler.html" title="class in org.biojava.bio.seq.io.agave">AGAVENotePropHandler</a></li>
<li><a href="org/biojava/bio/seq/io/agave/AGAVEPredictedProteinHandler.html" title="class in org.biojava.bio.seq.io.agave">AGAVEPredictedProteinHandler</a></li>
<li><a href="org/biojava/bio/seq/io/agave/AGAVEProperty.html" title="class in org.biojava.bio.seq.io.agave">AGAVEProperty</a></li>
<li><a href="org/biojava/bio/seq/io/agave/AGAVEQualifierPropHandler.html" title="class in org.biojava.bio.seq.io.agave">AGAVEQualifierPropHandler</a></li>
<li><a href="org/biojava/bio/seq/io/agave/AGAVEQueryRegion.html" title="class in org.biojava.bio.seq.io.agave">AGAVEQueryRegion</a></li>
<li><a href="org/biojava/bio/seq/io/agave/AGAVEQueryRegionPropHandler.html" title="class in org.biojava.bio.seq.io.agave">AGAVEQueryRegionPropHandler</a></li>
<li><a href="org/biojava/bio/seq/io/agave/AGAVERelatedAnnot.html" title="class in org.biojava.bio.seq.io.agave">AGAVERelatedAnnot</a></li>
<li><a href="org/biojava/bio/seq/io/agave/AGAVERelatedAnnotPropHandler.html" title="class in org.biojava.bio.seq.io.agave">AGAVERelatedAnnotPropHandler</a></li>
<li><a href="org/biojava/bio/seq/io/agave/AGAVEResultGroupHandler.html" title="class in org.biojava.bio.seq.io.agave">AGAVEResultGroupHandler</a></li>
<li><a href="org/biojava/bio/seq/io/agave/AGAVEResultPropertyPropHandler.html" title="class in org.biojava.bio.seq.io.agave">AGAVEResultPropertyPropHandler</a></li>
<li><a href="org/biojava/bio/seq/io/agave/AGAVESciPropertyPropHandler.html" title="class in org.biojava.bio.seq.io.agave">AGAVESciPropertyPropHandler</a></li>
<li><a href="org/biojava/bio/seq/io/agave/AGAVESeqFeatureHandler.html" title="class in org.biojava.bio.seq.io.agave">AGAVESeqFeatureHandler</a></li>
<li><a href="org/biojava/bio/seq/io/agave/AGAVESeqLocationPropHandler.html" title="class in org.biojava.bio.seq.io.agave">AGAVESeqLocationPropHandler</a></li>
<li><a href="org/biojava/bio/seq/io/agave/AGAVESeqMapHandler.html" title="class in org.biojava.bio.seq.io.agave">AGAVESeqMapHandler</a></li>
<li><a href="org/biojava/bio/seq/io/agave/AGAVESeqPropHandler.html" title="class in org.biojava.bio.seq.io.agave">AGAVESeqPropHandler</a></li>
<li><a href="org/biojava/bio/seq/io/agave/AGAVETranscriptHandler.html" title="class in org.biojava.bio.seq.io.agave">AGAVETranscriptHandler</a></li>
<li><a href="org/biojava/bio/seq/io/agave/AGAVEUnorderedFragmentsHandler.html" title="class in org.biojava.bio.seq.io.agave">AGAVEUnorderedFragmentsHandler</a></li>
<li><a href="org/biojava/bio/seq/io/agave/AGAVEViewPropHandler.html" title="class in org.biojava.bio.seq.io.agave">AGAVEViewPropHandler</a></li>
<li><a href="org/biojava/bio/seq/io/agave/AgaveWriter.html" title="class in org.biojava.bio.seq.io.agave">AgaveWriter</a></li>
<li><a href="org/biojava/bio/seq/io/agave/AGAVEXref.html" title="class in org.biojava.bio.seq.io.agave">AGAVEXref</a></li>
<li><a href="org/biojava/bio/seq/io/agave/AGAVEXrefCallbackItf.html" title="interface in org.biojava.bio.seq.io.agave"><i>AGAVEXrefCallbackItf</i></a></li>
<li><a href="org/biojava/bio/seq/io/agave/AGAVEXrefPropHandler.html" title="class in org.biojava.bio.seq.io.agave">AGAVEXrefPropHandler</a></li>
<li><a href="org/biojava/bio/seq/io/agave/AGAVEXrefPropPropHandler.html" title="class in org.biojava.bio.seq.io.agave">AGAVEXrefPropPropHandler</a></li>
<li><a href="org/biojava/bio/seq/io/agave/AGAVEXrefs.html" title="class in org.biojava.bio.seq.io.agave">AGAVEXrefs</a></li>
<li><a href="org/biojava/bio/seq/io/agave/AGAVEXrefsPropHandler.html" title="class in org.biojava.bio.seq.io.agave">AGAVEXrefsPropHandler</a></li>
<li><a href="org/biojava/bio/program/tagvalue/Aggregator.html" title="class in org.biojava.bio.program.tagvalue">Aggregator</a></li>
<li><a href="org/biojava/bio/seq/io/AlignIOConstants.html" title="class in org.biojava.bio.seq.io">AlignIOConstants</a></li>
<li><a href="org/biojava/bio/alignment/Alignment.html" title="interface in org.biojava.bio.alignment"><i>Alignment</i></a></li>
<li><a href="org/biojava/bio/alignment/Alignment.SymbolListIterator.html" title="class in org.biojava.bio.alignment">Alignment.SymbolListIterator</a></li>
<li><a href="org/biojava/bio/alignment/AlignmentAlgorithm.html" title="class in org.biojava.bio.alignment">AlignmentAlgorithm</a></li>
<li><a href="org/biojava/bio/alignment/AlignmentElement.html" title="interface in org.biojava.bio.alignment"><i>AlignmentElement</i></a></li>
<li><a href="org/biojava/bio/seq/io/AlignmentFormat.html" title="interface in org.biojava.bio.seq.io"><i>AlignmentFormat</i></a></li>
<li><a href="org/biojava/bio/program/blast2html/AlignmentMarker.html" title="class in org.biojava.bio.program.blast2html">AlignmentMarker</a></li>
<li><a href="org/biojava/bio/alignment/AlignmentPair.html" title="class in org.biojava.bio.alignment">AlignmentPair</a></li>
<li><a href="org/biojava/bio/gui/sequence/AlignmentRenderer.html" title="class in org.biojava.bio.gui.sequence">AlignmentRenderer</a></li>
<li><a href="org/biojava/bio/program/ssbind/AlignmentStAXHandler.html" title="class in org.biojava.bio.program.ssbind">AlignmentStAXHandler</a></li>
<li><a href="org/biojava/bio/symbol/Alphabet.html" title="interface in org.biojava.bio.symbol"><i>Alphabet</i></a></li>
<li><a href="org/biojava/bio/symbol/AlphabetIndex.html" title="interface in org.biojava.bio.symbol"><i>AlphabetIndex</i></a></li>
<li><a href="org/biojava/bio/symbol/AlphabetManager.html" title="class in org.biojava.bio.symbol">AlphabetManager</a></li>
<li><a href="org/biojava/bio/program/ssbind/AlphabetResolver.html" title="class in org.biojava.bio.program.ssbind">AlphabetResolver</a></li>
<li><a href="org/biojava/ontology/AlreadyExistsException.html" title="class in org.biojava.ontology">AlreadyExistsException</a></li>
<li><a href="org/biojava/bio/seq/io/AlternateTokenization.html" title="class in org.biojava.bio.seq.io">AlternateTokenization</a></li>
<li><a href="org/biojava/bio/Annotatable.html" title="interface in org.biojava.bio"><i>Annotatable</i></a></li>
<li><a href="org/biojava/bio/Annotatable.AnnotationForwarder.html" title="class in org.biojava.bio">Annotatable.AnnotationForwarder</a></li>
<li><a href="org/biojava/bio/seq/db/AnnotatedSequenceDB.html" title="class in org.biojava.bio.seq.db">AnnotatedSequenceDB</a></li>
<li><a href="org/biojava/bio/Annotation.html" title="interface in org.biojava.bio"><i>Annotation</i></a></li>
<li><a href="org/biojava/bio/program/tagvalue/AnnotationBuilder.html" title="class in org.biojava.bio.program.tagvalue">AnnotationBuilder</a></li>
<li><a href="org/biojava/bio/AnnotationChanger.html" title="class in org.biojava.bio">AnnotationChanger</a></li>
<li><a href="org/biojava/bio/annodb/AnnotationDB.html" title="interface in org.biojava.bio.annodb"><i>AnnotationDB</i></a></li>
<li><a href="org/biojava/bio/program/ssbind/AnnotationFactory.html" title="class in org.biojava.bio.program.ssbind">AnnotationFactory</a></li>
<li><a href="org/biojava/bio/AnnotationRenamer.html" title="class in org.biojava.bio">AnnotationRenamer</a></li>
<li><a href="org/biojava/bio/AnnotationTools.html" title="class in org.biojava.bio">AnnotationTools</a></li>
<li><a href="org/biojava/bio/AnnotationType.html" title="interface in org.biojava.bio"><i>AnnotationType</i></a></li>
<li><a href="org/biojava/bio/AnnotationType.Abstract.html" title="class in org.biojava.bio">AnnotationType.Abstract</a></li>
<li><a href="org/biojava/bio/AnnotationType.Impl.html" title="class in org.biojava.bio">AnnotationType.Impl</a></li>
<li><a href="org/biojava/App.html" title="class in org.biojava">App</a></li>
<li><a href="org/biojava/utils/xml/AppBeanRunner.html" title="class in org.biojava.utils.xml">AppBeanRunner</a></li>
<li><a href="org/biojava/utils/xml/AppEntry.html" title="interface in org.biojava.utils.xml"><i>AppEntry</i></a></li>
<li><a href="org/biojava/utils/xml/AppException.html" title="class in org.biojava.utils.xml">AppException</a></li>
<li><a href="org/biojava/bio/alignment/ARAlignment.html" title="interface in org.biojava.bio.alignment"><i>ARAlignment</i></a></li>
<li><a href="org/biojava/utils/automata/ArrayStateMachineToolkit.html" title="class in org.biojava.utils.automata">ArrayStateMachineToolkit</a></li>
<li><a href="org/biojava/bio/gui/sequence/ArrowedFeatureRenderer.html" title="class in org.biojava.bio.gui.sequence">ArrowedFeatureRenderer</a></li>
<li><a href="org/biojava/bio/gui/glyph/ArrowGlyph.html" title="class in org.biojava.bio.gui.glyph">ArrowGlyph</a></li>
<li><a href="org/biojava/bio/seq/impl/AssembledSymbolList.html" title="class in org.biojava.bio.seq.impl">AssembledSymbolList</a></li>
<li><a href="org/biojava/utils/AssertionFailure.html" title="class in org.biojava.utils">AssertionFailure</a></li>
<li><a href="org/biojava/bio/symbol/AtomicSymbol.html" title="interface in org.biojava.bio.symbol"><i>AtomicSymbol</i></a></li>
<li><a href="org/biojava/utils/automata/AutomatonException.html" title="class in org.biojava.utils.automata">AutomatonException</a></li>
<li><a href="org/biojava/bio/dp/twohead/BackMatrixPairDPCursor.html" title="class in org.biojava.bio.dp.twohead">BackMatrixPairDPCursor</a></li>
<li><a href="org/biojava/bio/dp/BackPointer.html" title="class in org.biojava.bio.dp">BackPointer</a></li>
<li><a href="org/biojava/bio/gui/BarLogoPainter.html" title="class in org.biojava.bio.gui">BarLogoPainter</a></li>
<li><a href="org/biojava/bio/program/xml/BaseXMLWriter.html" title="class in org.biojava.bio.program.xml">BaseXMLWriter</a></li>
<li><a href="org/biojava/bio/gui/sequence/BasicFeatureRenderer.html" title="class in org.biojava.bio.gui.sequence">BasicFeatureRenderer</a></li>
<li><a href="org/biojava/bio/gui/sequence/BasicImapRenderer.html" title="class in org.biojava.bio.gui.sequence">BasicImapRenderer</a></li>
<li><a href="org/biojava/bio/program/xff/BasicXFFHelper.html" title="class in org.biojava.bio.program.xff">BasicXFFHelper</a></li>
<li><a href="org/biojava/bio/symbol/BasisSymbol.html" title="interface in org.biojava.bio.symbol"><i>BasisSymbol</i></a></li>
<li><a href="org/biojava/bio/dp/BaumWelchSampler.html" title="class in org.biojava.bio.dp">BaumWelchSampler</a></li>
<li><a href="org/biojava/bio/dp/BaumWelchTrainer.html" title="class in org.biojava.bio.dp">BaumWelchTrainer</a></li>
<li><a href="org/biojava/bio/gui/sequence/BeadFeatureRenderer.html" title="interface in org.biojava.bio.gui.sequence"><i>BeadFeatureRenderer</i></a></li>
<li><a href="org/biojava/bio/BeanAsAnnotation.html" title="class in org.biojava.bio">BeanAsAnnotation</a></li>
<li><a href="org/biojava/utils/BeanAsMap.html" title="class in org.biojava.utils">BeanAsMap</a></li>
<li><a href="org/biojava/bio/symbol/BetweenLocation.html" title="class in org.biojava.bio.symbol">BetweenLocation</a></li>
<li><a href="org/biojava/bibliography/BiblioArticle.html" title="class in org.biojava.bibliography">BiblioArticle</a></li>
<li><a href="org/biojava/bibliography/BiblioBook.html" title="class in org.biojava.bibliography">BiblioBook</a></li>
<li><a href="org/biojava/bibliography/BiblioBookArticle.html" title="class in org.biojava.bibliography">BiblioBookArticle</a></li>
<li><a href="org/biojava/bibliography/BiblioCriterion.html" title="class in org.biojava.bibliography">BiblioCriterion</a></li>
<li><a href="org/biojava/bibliography/BiblioDescription.html" title="class in org.biojava.bibliography">BiblioDescription</a></li>
<li><a href="org/biojava/bibliography/BiblioEntryStatus.html" title="class in org.biojava.bibliography">BiblioEntryStatus</a></li>
<li><a href="org/biojava/bibliography/BiblioJournal.html" title="class in org.biojava.bibliography">BiblioJournal</a></li>
<li><a href="org/biojava/bibliography/BiblioJournalArticle.html" title="class in org.biojava.bibliography">BiblioJournalArticle</a></li>
<li><a href="org/biojava/bibliography/BiblioOrganisation.html" title="class in org.biojava.bibliography">BiblioOrganisation</a></li>
<li><a href="org/biojava/bibliography/BiblioPatent.html" title="class in org.biojava.bibliography">BiblioPatent</a></li>
<li><a href="org/biojava/bibliography/BiblioPerson.html" title="class in org.biojava.bibliography">BiblioPerson</a></li>
<li><a href="org/biojava/bibliography/BiblioProceeding.html" title="class in org.biojava.bibliography">BiblioProceeding</a></li>
<li><a href="org/biojava/bibliography/BiblioProvider.html" title="class in org.biojava.bibliography">BiblioProvider</a></li>
<li><a href="org/biojava/bibliography/BiblioScope.html" title="class in org.biojava.bibliography">BiblioScope</a></li>
<li><a href="org/biojava/bibliography/BiblioService.html" title="class in org.biojava.bibliography">BiblioService</a></li>
<li><a href="org/biojava/bibliography/BiblioSubject.html" title="class in org.biojava.bibliography">BiblioSubject</a></li>
<li><a href="org/biojava/bibliography/BiblioTechReport.html" title="class in org.biojava.bibliography">BiblioTechReport</a></li>
<li><a href="org/biojava/bibliography/BiblioThesis.html" title="class in org.biojava.bibliography">BiblioThesis</a></li>
<li><a href="org/biojava/bibliography/BiblioWebResource.html" title="class in org.biojava.bibliography">BiblioWebResource</a></li>
<li><a href="org/biojava/bibliography/BibRef.html" title="class in org.biojava.bibliography">BibRef</a></li>
<li><a href="org/biojava/bibliography/BibRefException.html" title="class in org.biojava.bibliography">BibRefException</a></li>
<li><a href="org/biojava/bibliography/BibRefQuery.html" title="interface in org.biojava.bibliography"><i>BibRefQuery</i></a></li>
<li><a href="org/biojava/bibliography/BibRefSupport.html" title="interface in org.biojava.bibliography"><i>BibRefSupport</i></a></li>
<li><a href="org/biojava/utils/math/BinarySearch.html" title="class in org.biojava.utils.math">BinarySearch</a></li>
<li><a href="org/biojavax/bio/BioEntry.html" title="interface in org.biojavax.bio"><i>BioEntry</i></a></li>
<li><a href="org/biojavax/bio/db/BioEntryDB.html" title="interface in org.biojavax.bio.db"><i>BioEntryDB</i></a></li>
<li><a href="org/biojavax/bio/db/BioEntryDBLite.html" title="interface in org.biojavax.bio.db"><i>BioEntryDBLite</i></a></li>
<li><a href="org/biojavax/bio/BioEntryIterator.html" title="interface in org.biojavax.bio"><i>BioEntryIterator</i></a></li>
<li><a href="org/biojavax/bio/BioEntryRelationship.html" title="interface in org.biojavax.bio"><i>BioEntryRelationship</i></a></li>
<li><a href="org/biojava/bio/BioError.html" title="class in org.biojava.bio">BioError</a></li>
<li><a href="org/biojava/bio/BioException.html" title="class in org.biojava.bio">BioException</a></li>
<li><a href="org/biojava/bio/seq/db/biofetch/BioFetchSequenceDB.html" title="class in org.biojava.bio.seq.db.biofetch">BioFetchSequenceDB</a></li>
<li><a href="org/biojava/bio/seq/db/biofetch/BioFetchSequenceDBProvider.html" title="class in org.biojava.bio.seq.db.biofetch">BioFetchSequenceDBProvider</a></li>
<li><a href="org/biojava/bio/seq/db/BioIndex.html" title="class in org.biojava.bio.seq.db">BioIndex</a></li>
<li><a href="org/biojava/bio/search/BioMatcher.html" title="interface in org.biojava.bio.search"><i>BioMatcher</i></a></li>
<li><a href="org/biojava/bio/search/BioPattern.html" title="interface in org.biojava.bio.search"><i>BioPattern</i></a></li>
<li><a href="org/biojava/bio/BioRuntimeException.html" title="class in org.biojava.bio">BioRuntimeException</a></li>
<li><a href="org/biojavax/bio/db/biosql/BioSQLAcceptAllFilter.html" title="class in org.biojavax.bio.db.biosql">BioSQLAcceptAllFilter</a></li>
<li><a href="org/biojavax/bio/db/biosql/BioSQLAcceptNoneFilter.html" title="class in org.biojavax.bio.db.biosql">BioSQLAcceptNoneFilter</a></li>
<li><a href="org/biojavax/bio/db/biosql/BioSQLBioEntryDB.html" title="class in org.biojavax.bio.db.biosql">BioSQLBioEntryDB</a></li>
<li><a href="org/biojavax/bio/db/biosql/BioSQLCrossReferenceResolver.html" title="class in org.biojavax.bio.db.biosql">BioSQLCrossReferenceResolver</a></li>
<li><a href="org/biojavax/bio/db/biosql/BioSQLFeatureFilter.html" title="interface in org.biojavax.bio.db.biosql"><i>BioSQLFeatureFilter</i></a></li>
<li><a href="org/biojavax/bio/db/biosql/BioSQLFeatureFilter.And.html" title="class in org.biojavax.bio.db.biosql">BioSQLFeatureFilter.And</a></li>
<li><a href="org/biojavax/bio/db/biosql/BioSQLFeatureFilter.ByName.html" title="class in org.biojavax.bio.db.biosql">BioSQLFeatureFilter.ByName</a></li>
<li><a href="org/biojavax/bio/db/biosql/BioSQLFeatureFilter.ByNote.html" title="class in org.biojavax.bio.db.biosql">BioSQLFeatureFilter.ByNote</a></li>
<li><a href="org/biojavax/bio/db/biosql/BioSQLFeatureFilter.ByNoteTermOnly.html" title="class in org.biojavax.bio.db.biosql">BioSQLFeatureFilter.ByNoteTermOnly</a></li>
<li><a href="org/biojavax/bio/db/biosql/BioSQLFeatureFilter.ByRank.html" title="class in org.biojavax.bio.db.biosql">BioSQLFeatureFilter.ByRank</a></li>
<li><a href="org/biojavax/bio/db/biosql/BioSQLFeatureFilter.BySequenceName.html" title="class in org.biojavax.bio.db.biosql">BioSQLFeatureFilter.BySequenceName</a></li>
<li><a href="org/biojavax/bio/db/biosql/BioSQLFeatureFilter.BySourceTerm.html" title="class in org.biojavax.bio.db.biosql">BioSQLFeatureFilter.BySourceTerm</a></li>
<li><a href="org/biojavax/bio/db/biosql/BioSQLFeatureFilter.BySourceTermName.html" title="class in org.biojavax.bio.db.biosql">BioSQLFeatureFilter.BySourceTermName</a></li>
<li><a href="org/biojavax/bio/db/biosql/BioSQLFeatureFilter.ByStrand.html" title="class in org.biojavax.bio.db.biosql">BioSQLFeatureFilter.ByStrand</a></li>
<li><a href="org/biojavax/bio/db/biosql/BioSQLFeatureFilter.ByTypeTerm.html" title="class in org.biojavax.bio.db.biosql">BioSQLFeatureFilter.ByTypeTerm</a></li>
<li><a href="org/biojavax/bio/db/biosql/BioSQLFeatureFilter.ByTypeTermName.html" title="class in org.biojavax.bio.db.biosql">BioSQLFeatureFilter.ByTypeTermName</a></li>
<li><a href="org/biojavax/bio/db/biosql/BioSQLFeatureFilter.ContainedByRichLocation.html" title="class in org.biojavax.bio.db.biosql">BioSQLFeatureFilter.ContainedByRichLocation</a></li>
<li><a href="org/biojavax/bio/db/biosql/BioSQLFeatureFilter.HibernateFeatureFilter.html" title="class in org.biojavax.bio.db.biosql">BioSQLFeatureFilter.HibernateFeatureFilter</a></li>
<li><a href="org/biojavax/bio/db/biosql/BioSQLFeatureFilter.Not.html" title="class in org.biojavax.bio.db.biosql">BioSQLFeatureFilter.Not</a></li>
<li><a href="org/biojavax/bio/db/biosql/BioSQLFeatureFilter.Or.html" title="class in org.biojavax.bio.db.biosql">BioSQLFeatureFilter.Or</a></li>
<li><a href="org/biojavax/bio/db/biosql/BioSQLFeatureFilter.OverlapsRichLocation.html" title="class in org.biojavax.bio.db.biosql">BioSQLFeatureFilter.OverlapsRichLocation</a></li>
<li><a href="org/biojavax/bio/db/biosql/BioSQLFeatureFilter.Tools.html" title="class in org.biojavax.bio.db.biosql">BioSQLFeatureFilter.Tools</a></li>
<li><a href="org/biojavax/bio/db/biosql/BioSQLRichObjectBuilder.html" title="class in org.biojavax.bio.db.biosql">BioSQLRichObjectBuilder</a></li>
<li><a href="org/biojavax/bio/db/biosql/BioSQLRichSequenceDB.html" title="class in org.biojavax.bio.db.biosql">BioSQLRichSequenceDB</a></li>
<li><a href="org/biojavax/bio/db/biosql/BioSQLRichSequenceHandler.html" title="class in org.biojavax.bio.db.biosql">BioSQLRichSequenceHandler</a></li>
<li><a href="org/biojava/bio/seq/db/biosql/BioSQLSequenceDB.html" title="class in org.biojava.bio.seq.db.biosql">BioSQLSequenceDB</a></li>
<li><a href="org/biojava/bio/seq/db/biosql/BioSQLSequenceDBProvider.html" title="class in org.biojava.bio.seq.db.biosql">BioSQLSequenceDBProvider</a></li>
<li><a href="org/biojava/bio/program/indexdb/BioStore.html" title="class in org.biojava.bio.program.indexdb">BioStore</a></li>
<li><a href="org/biojava/bio/program/indexdb/BioStoreFactory.html" title="class in org.biojava.bio.program.indexdb">BioStoreFactory</a></li>
<li><a href="org/biojava/bio/program/blast2html/Blast2HTMLHandler.html" title="class in org.biojava.bio.program.blast2html">Blast2HTMLHandler</a></li>
<li><a href="org/biojava/bio/program/ssbind/BlastLikeHomologyBuilder.html" title="class in org.biojava.bio.program.ssbind">BlastLikeHomologyBuilder</a></li>
<li><a href="org/biojava/bio/program/sax/BlastLikeSAXParser.html" title="class in org.biojava.bio.program.sax">BlastLikeSAXParser</a></li>
<li><a href="org/biojava/bio/program/ssbind/BlastLikeSearchBuilder.html" title="class in org.biojava.bio.program.ssbind">BlastLikeSearchBuilder</a></li>
<li><a href="org/biojava/bio/search/BlastLikeSearchFilter.html" title="interface in org.biojava.bio.search"><i>BlastLikeSearchFilter</i></a></li>
<li><a href="org/biojava/bio/search/BlastLikeSearchFilter.AbstractBlastLikeSearchFilter.html" title="class in org.biojava.bio.search">BlastLikeSearchFilter.AbstractBlastLikeSearchFilter</a></li>
<li><a href="org/biojava/bio/search/BlastLikeSearchFilter.And.html" title="class in org.biojava.bio.search">BlastLikeSearchFilter.And</a></li>
<li><a href="org/biojava/bio/search/BlastLikeSearchFilter.ByHitProperty.html" title="class in org.biojava.bio.search">BlastLikeSearchFilter.ByHitProperty</a></li>
<li><a href="org/biojava/bio/search/BlastLikeSearchFilter.BySearchProperty.html" title="class in org.biojava.bio.search">BlastLikeSearchFilter.BySearchProperty</a></li>
<li><a href="org/biojava/bio/search/BlastLikeSearchFilter.BySubHitProperty.html" title="class in org.biojava.bio.search">BlastLikeSearchFilter.BySubHitProperty</a></li>
<li><a href="org/biojava/bio/search/BlastLikeSearchFilter.Node.html" title="interface in org.biojava.bio.search"><i>BlastLikeSearchFilter.Node</i></a></li>
<li><a href="org/biojava/bio/search/BlastLikeSearchFilter.Not.html" title="class in org.biojava.bio.search">BlastLikeSearchFilter.Not</a></li>
<li><a href="org/biojava/bio/search/BlastLikeSearchFilter.Or.html" title="class in org.biojava.bio.search">BlastLikeSearchFilter.Or</a></li>
<li><a href="org/biojava/bio/program/BlastLikeToXMLConverter.html" title="class in org.biojava.bio.program">BlastLikeToXMLConverter</a></li>
<li><a href="org/biojava/bio/program/sax/blastxml/BlastXMLParser.html" title="class in org.biojava.bio.program.sax.blastxml">BlastXMLParser</a></li>
<li><a href="org/biojava/bio/program/sax/blastxml/BlastXMLParserFacade.html" title="class in org.biojava.bio.program.sax.blastxml">BlastXMLParserFacade</a></li>
<li><a href="org/biojava/bio/gui/BlockPainter.html" title="interface in org.biojava.bio.gui"><i>BlockPainter</i></a></li>
<li><a href="org/biojava/utils/stax/BooleanElementHandlerBase.html" title="class in org.biojava.utils.stax">BooleanElementHandlerBase</a></li>
<li><a href="org/biojava/bio/program/tagvalue/BoundaryFinder.html" title="interface in org.biojava.bio.program.tagvalue"><i>BoundaryFinder</i></a></li>
<li><a href="org/biojava/bio/gui/sequence/BumpedRenderer.html" title="class in org.biojava.bio.gui.sequence">BumpedRenderer</a></li>
<li><a href="org/biojava/bio/seq/ByLocationMinMaxComparator.html" title="class in org.biojava.bio.seq">ByLocationMinMaxComparator</a></li>
<li><a href="org/biojava/bio/seq/ByLocationMinMaxFeatureComparator.html" title="class in org.biojava.bio.seq">ByLocationMinMaxFeatureComparator</a></li>
<li><a href="org/biojava/utils/bytecode/ByteCode.html" title="class in org.biojava.utils.bytecode">ByteCode</a></li>
<li><a href="org/biojava/utils/stax/ByteElementHandlerBase.html" title="class in org.biojava.utils.stax">ByteElementHandlerBase</a></li>
<li><a href="org/biojava/utils/cache/Cache.html" title="interface in org.biojava.utils.cache"><i>Cache</i></a></li>
<li><a href="org/biojava/utils/cache/CacheMap.html" title="interface in org.biojava.utils.cache"><i>CacheMap</i></a></li>
<li><a href="org/biojava/utils/cache/CacheReference.html" title="interface in org.biojava.utils.cache"><i>CacheReference</i></a></li>
<li><a href="org/biojava/utils/io/CachingInputStream.html" title="class in org.biojava.utils.io">CachingInputStream</a></li>
<li><a href="org/biojava/stats/svm/CachingKernel.html" title="class in org.biojava.stats.svm">CachingKernel</a></li>
<li><a href="org/biojava/bio/seq/db/CachingSequenceDB.html" title="class in org.biojava.bio.seq.db">CachingSequenceDB</a></li>
<li><a href="org/biojava/utils/candy/CandyEntry.html" title="class in org.biojava.utils.candy">CandyEntry</a></li>
<li><a href="org/biojava/utils/candy/CandyException.html" title="class in org.biojava.utils.candy">CandyException</a></li>
<li><a href="org/biojava/utils/candy/CandyFinder.html" title="interface in org.biojava.utils.candy"><i>CandyFinder</i></a></li>
<li><a href="org/biojava/utils/candy/CandyVocabulary.html" title="interface in org.biojava.utils.candy"><i>CandyVocabulary</i></a></li>
<li><a href="org/biojava/bio/CardinalityConstraint.html" title="class in org.biojava.bio">CardinalityConstraint</a></li>
<li><a href="org/biojava/bio/dp/twohead/Cell.html" title="class in org.biojava.bio.dp.twohead">Cell</a></li>
<li><a href="org/biojava/bio/dp/twohead/CellCalculator.html" title="interface in org.biojava.bio.dp.twohead"><i>CellCalculator</i></a></li>
<li><a href="org/biojava/bio/dp/twohead/CellCalculatorFactory.html" title="interface in org.biojava.bio.dp.twohead"><i>CellCalculatorFactory</i></a></li>
<li><a href="org/biojava/bio/dp/twohead/CellCalculatorFactoryMaker.html" title="interface in org.biojava.bio.dp.twohead"><i>CellCalculatorFactoryMaker</i></a></li>
<li><a href="org/biojava/utils/Changeable.html" title="interface in org.biojava.utils"><i>Changeable</i></a></li>
<li><a href="org/biojava/utils/cache/ChangeableCache.html" title="class in org.biojava.utils.cache">ChangeableCache</a></li>
<li><a href="org/biojava/utils/ChangeAdapter.html" title="class in org.biojava.utils">ChangeAdapter</a></li>
<li><a href="org/biojava/utils/ChangeEvent.html" title="class in org.biojava.utils">ChangeEvent</a></li>
<li><a href="org/biojava/utils/ChangeForwarder.html" title="class in org.biojava.utils">ChangeForwarder</a></li>
<li><a href="org/biojava/utils/ChangeForwarder.Retyper.html" title="class in org.biojava.utils">ChangeForwarder.Retyper</a></li>
<li><a href="org/biojava/utils/ChangeHub.html" title="interface in org.biojava.utils"><i>ChangeHub</i></a></li>
<li><a href="org/biojava/utils/ChangeListener.html" title="interface in org.biojava.utils"><i>ChangeListener</i></a></li>
<li><a href="org/biojava/utils/ChangeListener.AlwaysVetoListener.html" title="class in org.biojava.utils">ChangeListener.AlwaysVetoListener</a></li>
<li><a href="org/biojava/utils/ChangeListener.ChangeEventRecorder.html" title="class in org.biojava.utils">ChangeListener.ChangeEventRecorder</a></li>
<li><a href="org/biojava/utils/ChangeListener.LoggingListener.html" title="class in org.biojava.utils">ChangeListener.LoggingListener</a></li>
<li><a href="org/biojava/utils/ChangeSupport.html" title="class in org.biojava.utils">ChangeSupport</a></li>
<li><a href="org/biojava/bio/program/tagvalue/ChangeTable.html" title="class in org.biojava.bio.program.tagvalue">ChangeTable</a></li>
<li><a href="org/biojava/bio/program/tagvalue/ChangeTable.ChainedChanger.html" title="class in org.biojava.bio.program.tagvalue">ChangeTable.ChainedChanger</a></li>
<li><a href="org/biojava/bio/program/tagvalue/ChangeTable.Changer.html" title="interface in org.biojava.bio.program.tagvalue"><i>ChangeTable.Changer</i></a></li>
<li><a href="org/biojava/bio/program/tagvalue/ChangeTable.Splitter.html" title="interface in org.biojava.bio.program.tagvalue"><i>ChangeTable.Splitter</i></a></li>
<li><a href="org/biojava/utils/ChangeType.html" title="class in org.biojava.utils">ChangeType</a></li>
<li><a href="org/biojava/utils/ChangeVetoException.html" title="class in org.biojava.utils">ChangeVetoException</a></li>
<li><a href="org/biojavax/bio/phylo/io/nexus/CharactersBlock.html" title="class in org.biojavax.bio.phylo.io.nexus">CharactersBlock</a></li>
<li><a href="org/biojavax/bio/phylo/io/nexus/CharactersBlockBuilder.html" title="class in org.biojavax.bio.phylo.io.nexus">CharactersBlockBuilder</a></li>
<li><a href="org/biojavax/bio/phylo/io/nexus/CharactersBlockListener.html" title="interface in org.biojavax.bio.phylo.io.nexus"><i>CharactersBlockListener</i></a></li>
<li><a href="org/biojavax/bio/phylo/io/nexus/CharactersBlockParser.html" title="class in org.biojavax.bio.phylo.io.nexus">CharactersBlockParser</a></li>
<li><a href="org/biojava/bio/seq/io/CharacterTokenization.html" title="class in org.biojava.bio.seq.io">CharacterTokenization</a></li>
<li><a href="org/biojava/utils/stax/CharElementHandlerBase.html" title="class in org.biojava.utils.stax">CharElementHandlerBase</a></li>
<li><a href="org/biojava/bio/chromatogram/Chromatogram.html" title="interface in org.biojava.bio.chromatogram"><i>Chromatogram</i></a></li>
<li><a href="org/biojava/bio/chromatogram/ChromatogramFactory.html" title="class in org.biojava.bio.chromatogram">ChromatogramFactory</a></li>
<li><a href="org/biojava/bio/chromatogram/graphic/ChromatogramGraphic.html" title="class in org.biojava.bio.chromatogram.graphic">ChromatogramGraphic</a></li>
<li><a href="org/biojava/bio/chromatogram/graphic/ChromatogramGraphic.Option.html" title="class in org.biojava.bio.chromatogram.graphic">ChromatogramGraphic.Option</a></li>
<li><a href="org/biojava/bio/chromatogram/graphic/ChromatogramNonlinearScaler.html" title="interface in org.biojava.bio.chromatogram.graphic"><i>ChromatogramNonlinearScaler</i></a></li>
<li><a href="org/biojava/bio/chromatogram/graphic/ChromatogramNonlinearScaler.Identity.html" title="class in org.biojava.bio.chromatogram.graphic">ChromatogramNonlinearScaler.Identity</a></li>
<li><a href="org/biojava/bio/chromatogram/ChromatogramTools.html" title="class in org.biojava.bio.chromatogram">ChromatogramTools</a></li>
<li><a href="org/biojava/bio/symbol/ChunkedSymbolList.html" title="class in org.biojava.bio.symbol">ChunkedSymbolList</a></li>
<li><a href="org/biojava/bio/seq/io/ChunkedSymbolListFactory.html" title="class in org.biojava.bio.seq.io">ChunkedSymbolListFactory</a></li>
<li><a href="org/biojava/bio/gui/sequence/CircularFeatureFilteringRenderer.html" title="class in org.biojava.bio.gui.sequence">CircularFeatureFilteringRenderer</a></li>
<li><a href="org/biojava/bio/gui/sequence/CircularFeatureRenderer.html" title="interface in org.biojava.bio.gui.sequence"><i>CircularFeatureRenderer</i></a></li>
<li><a href="org/biojava/bio/gui/sequence/CircularFeaturesRenderer.html" title="class in org.biojava.bio.gui.sequence">CircularFeaturesRenderer</a></li>
<li><a href="org/biojava/bio/symbol/CircularLocation.html" title="class in org.biojava.bio.symbol">CircularLocation</a></li>
<li><a href="org/biojava/bio/gui/sequence/CircularMLR.html" title="class in org.biojava.bio.gui.sequence">CircularMLR</a></li>
<li><a href="org/biojava/bio/gui/sequence/CircularPaddedRenderer.html" title="class in org.biojava.bio.gui.sequence">CircularPaddedRenderer</a></li>
<li><a href="org/biojava/bio/taxa/CircularReferenceException.html" title="class in org.biojava.bio.taxa">CircularReferenceException</a></li>
<li><a href="org/biojava/bio/gui/sequence/CircularRenderer.html" title="interface in org.biojava.bio.gui.sequence"><i>CircularRenderer</i></a></li>
<li><a href="org/biojava/bio/gui/sequence/CircularRendererContext.html" title="interface in org.biojava.bio.gui.sequence"><i>CircularRendererContext</i></a></li>
<li><a href="org/biojava/bio/gui/sequence/CircularRendererPanel.html" title="class in org.biojava.bio.gui.sequence">CircularRendererPanel</a></li>
<li><a href="org/biojava/bio/seq/CircularView.html" title="class in org.biojava.bio.seq">CircularView</a></li>
<li><a href="org/biojava/stats/svm/tools/ClassifierExample.html" title="class in org.biojava.stats.svm.tools">ClassifierExample</a></li>
<li><a href="org/biojava/stats/svm/tools/ClassifierExample.PointClassifier.html" title="class in org.biojava.stats.svm.tools">ClassifierExample.PointClassifier</a></li>
<li><a href="org/biojava/stats/svm/tools/Classify.html" title="class in org.biojava.stats.svm.tools">Classify</a></li>
<li><a href="org/biojava/utils/ClassTools.html" title="class in org.biojava.utils">ClassTools</a></li>
<li><a href="org/biojava/bio/program/sax/ClustalWAlignmentSAXParser.html" title="class in org.biojava.bio.program.sax">ClustalWAlignmentSAXParser</a></li>
<li><a href="org/biojava/utils/bytecode/CodeClass.html" title="interface in org.biojava.utils.bytecode"><i>CodeClass</i></a></li>
<li><a href="org/biojava/utils/bytecode/CodeContext.html" title="interface in org.biojava.utils.bytecode"><i>CodeContext</i></a></li>
<li><a href="org/biojava/utils/bytecode/CodeException.html" title="class in org.biojava.utils.bytecode">CodeException</a></li>
<li><a href="org/biojava/utils/bytecode/CodeField.html" title="class in org.biojava.utils.bytecode">CodeField</a></li>
<li><a href="org/biojava/utils/bytecode/CodeGenerator.html" title="interface in org.biojava.utils.bytecode"><i>CodeGenerator</i></a></li>
<li><a href="org/biojava/utils/bytecode/CodeMethod.html" title="interface in org.biojava.utils.bytecode"><i>CodeMethod</i></a></li>
<li><a href="org/biojava/utils/bytecode/CodeUtils.html" title="class in org.biojava.utils.bytecode">CodeUtils</a></li>
<li><a href="org/biojava/bio/symbol/CodonPref.html" title="interface in org.biojava.bio.symbol"><i>CodonPref</i></a></li>
<li><a href="org/biojava/bio/symbol/CodonPrefFilter.html" title="interface in org.biojava.bio.symbol"><i>CodonPrefFilter</i></a></li>
<li><a href="org/biojava/bio/symbol/CodonPrefFilter.AcceptAll.html" title="class in org.biojava.bio.symbol">CodonPrefFilter.AcceptAll</a></li>
<li><a href="org/biojava/bio/symbol/CodonPrefFilter.ByName.html" title="class in org.biojava.bio.symbol">CodonPrefFilter.ByName</a></li>
<li><a href="org/biojava/bio/symbol/CodonPrefFilter.EverythingToXML.html" title="class in org.biojava.bio.symbol">CodonPrefFilter.EverythingToXML</a></li>
<li><a href="org/biojava/bio/symbol/CodonPrefTools.html" title="class in org.biojava.bio.symbol">CodonPrefTools</a></li>
<li><a href="org/biojava/bio/CollectionConstraint.html" title="interface in org.biojava.bio"><i>CollectionConstraint</i></a></li>
<li><a href="org/biojava/bio/CollectionConstraint.AllValuesIn.html" title="class in org.biojava.bio">CollectionConstraint.AllValuesIn</a></li>
<li><a href="org/biojava/bio/CollectionConstraint.And.html" title="class in org.biojava.bio">CollectionConstraint.And</a></li>
<li><a href="org/biojava/bio/CollectionConstraint.Contains.html" title="class in org.biojava.bio">CollectionConstraint.Contains</a></li>
<li><a href="org/biojava/bio/CollectionConstraint.Or.html" title="class in org.biojava.bio">CollectionConstraint.Or</a></li>
<li><a href="org/biojava/bio/program/blast2html/ColourCommand.html" title="interface in org.biojava.bio.program.blast2html"><i>ColourCommand</i></a></li>
<li><a href="org/biojavax/Comment.html" title="interface in org.biojavax"><i>Comment</i></a></li>
<li><a href="org/biojava/utils/Commitable.html" title="interface in org.biojava.utils"><i>Commitable</i></a></li>
<li><a href="org/biojava/utils/CommitFailure.html" title="class in org.biojava.utils">CommitFailure</a></li>
<li><a href="org/biojava/bio/program/ssaha/CompactedDataStore.html" title="class in org.biojava.bio.program.ssaha">CompactedDataStore</a></li>
<li><a href="org/biojava/bio/program/ssaha/CompactedDataStoreFactory.html" title="class in org.biojava.bio.program.ssaha">CompactedDataStoreFactory</a></li>
<li><a href="org/biojavax/ontology/ComparableOntology.html" title="interface in org.biojavax.ontology"><i>ComparableOntology</i></a></li>
<li><a href="org/biojavax/ontology/ComparableTerm.html" title="interface in org.biojavax.ontology"><i>ComparableTerm</i></a></li>
<li><a href="org/biojavax/ontology/ComparableTriple.html" title="interface in org.biojavax.ontology"><i>ComparableTriple</i></a></li>
<li><a href="org/biojava/bio/seq/ComponentFeature.html" title="interface in org.biojava.bio.seq"><i>ComponentFeature</i></a></li>
<li><a href="org/biojava/bio/seq/ComponentFeature.Template.html" title="class in org.biojava.bio.seq">ComponentFeature.Template</a></li>
<li><a href="org/biojava/bio/molbio/Composition.html" title="class in org.biojava.bio.molbio">Composition</a></li>
<li><a href="org/biojavax/bio/seq/CompoundRichLocation.html" title="class in org.biojavax.bio.seq">CompoundRichLocation</a></li>
<li><a href="org/biojava/utils/math/ComputeObject.html" title="interface in org.biojava.utils.math"><i>ComputeObject</i></a></li>
<li><a href="org/biojava/utils/bytecode/ConstantPool.html" title="class in org.biojava.utils.bytecode">ConstantPool</a></li>
<li><a href="org/biojava/utils/Constants.html" title="class in org.biojava.utils">Constants</a></li>
<li><a href="org/biojava/bio/dist/Count.html" title="interface in org.biojava.bio.dist"><i>Count</i></a></li>
<li><a href="org/biojava/utils/io/CountedBufferedReader.html" title="class in org.biojava.utils.io">CountedBufferedReader</a></li>
<li><a href="org/biojavax/utils/CRC64Checksum.html" title="class in org.biojavax.utils">CRC64Checksum</a></li>
<li><a href="org/biojava/bio/gui/sequence/CrosshairRenderer.html" title="class in org.biojava.bio.gui.sequence">CrosshairRenderer</a></li>
<li><a href="org/biojavax/ga/functions/CrossOverFunction.html" title="interface in org.biojavax.ga.functions"><i>CrossOverFunction</i></a></li>
<li><a href="org/biojavax/ga/functions/CrossOverFunction.NoCross.html" title="class in org.biojavax.ga.functions">CrossOverFunction.NoCross</a></li>
<li><a href="org/biojava/bio/seq/io/CrossProductTokenization.html" title="class in org.biojava.bio.seq.io">CrossProductTokenization</a></li>
<li><a href="org/biojavax/CrossRef.html" title="interface in org.biojavax"><i>CrossRef</i></a></li>
<li><a href="org/biojavax/CrossReferenceResolutionException.html" title="class in org.biojavax">CrossReferenceResolutionException</a></li>
<li><a href="org/biojavax/CrossReferenceResolver.html" title="interface in org.biojavax"><i>CrossReferenceResolver</i></a></li>
<li><a href="org/biojava/bio/program/blast2html/DatabaseURLGenerator.html" title="interface in org.biojava.bio.program.blast2html"><i>DatabaseURLGenerator</i></a></li>
<li><a href="org/biojavax/bio/phylo/io/nexus/DataBlock.html" title="class in org.biojavax.bio.phylo.io.nexus">DataBlock</a></li>
<li><a href="org/biojavax/bio/phylo/io/nexus/DataBlockBuilder.html" title="class in org.biojavax.bio.phylo.io.nexus">DataBlockBuilder</a></li>
<li><a href="org/biojavax/bio/phylo/io/nexus/DataBlockListener.html" title="interface in org.biojavax.bio.phylo.io.nexus"><i>DataBlockListener</i></a></li>
<li><a href="org/biojavax/bio/phylo/io/nexus/DataBlockParser.html" title="class in org.biojavax.bio.phylo.io.nexus">DataBlockParser</a></li>
<li><a href="org/biojava/bio/program/ssaha/DataStore.html" title="interface in org.biojava.bio.program.ssaha"><i>DataStore</i></a></li>
<li><a href="org/biojava/bio/program/ssaha/DataStoreFactory.html" title="interface in org.biojava.bio.program.ssaha"><i>DataStoreFactory</i></a></li>
<li><a href="org/biojava/bio/seq/db/biosql/DBHelper.html" title="class in org.biojava.bio.seq.db.biosql">DBHelper</a></li>
<li><a href="org/biojava/bio/seq/db/biosql/DBHelper.BioSequenceStyle.html" title="class in org.biojava.bio.seq.db.biosql">DBHelper.BioSequenceStyle</a></li>
<li><a href="org/biojava/bio/seq/db/biosql/DBHelper.DeleteStyle.html" title="class in org.biojava.bio.seq.db.biosql">DBHelper.DeleteStyle</a></li>
<li><a href="org/biojava/bio/seq/db/biosql/DBHelper.JoinStyle.html" title="class in org.biojava.bio.seq.db.biosql">DBHelper.JoinStyle</a></li>
<li><a href="org/biojavax/bio/seq/io/DebuggingRichSeqIOListener.html" title="class in org.biojavax.bio.seq.io">DebuggingRichSeqIOListener</a></li>
<li><a href="org/biojava/ontology/DefaultOps.html" title="class in org.biojava.ontology">DefaultOps</a></li>
<li><a href="org/biojava/bio/program/blast2html/DefaultURLGeneratorFactory.html" title="class in org.biojava.bio.program.blast2html">DefaultURLGeneratorFactory</a></li>
<li><a href="org/biojava/bio/seq/io/agave/DelegationManager.html" title="interface in org.biojava.bio.seq.io.agave"><i>DelegationManager</i></a></li>
<li><a href="org/biojava/utils/stax/DelegationManager.html" title="interface in org.biojava.utils.stax"><i>DelegationManager</i></a></li>
<li><a href="org/biojava/utils/automata/DfaBuilder.html" title="class in org.biojava.utils.automata">DfaBuilder</a></li>
<li><a href="org/biojava/stats/svm/DiagonalAddKernel.html" title="class in org.biojava.stats.svm">DiagonalAddKernel</a></li>
<li><a href="org/biojava/stats/svm/DiagonalCachingKernel.html" title="class in org.biojava.stats.svm">DiagonalCachingKernel</a></li>
<li><a href="org/biojava/bio/proteomics/Digest.html" title="class in org.biojava.bio.proteomics">Digest</a></li>
<li><a href="org/biojavax/bio/phylo/DistanceBasedTreeMethod.html" title="class in org.biojavax.bio.phylo">DistanceBasedTreeMethod</a></li>
<li><a href="org/biojavax/bio/phylo/io/nexus/DistancesBlock.html" title="class in org.biojavax.bio.phylo.io.nexus">DistancesBlock</a></li>
<li><a href="org/biojavax/bio/phylo/io/nexus/DistancesBlockBuilder.html" title="class in org.biojavax.bio.phylo.io.nexus">DistancesBlockBuilder</a></li>
<li><a href="org/biojavax/bio/phylo/io/nexus/DistancesBlockListener.html" title="interface in org.biojavax.bio.phylo.io.nexus"><i>DistancesBlockListener</i></a></li>
<li><a href="org/biojavax/bio/phylo/io/nexus/DistancesBlockParser.html" title="class in org.biojavax.bio.phylo.io.nexus">DistancesBlockParser</a></li>
<li><a href="org/biojava/bio/seq/distributed/DistDataSource.html" title="interface in org.biojava.bio.seq.distributed"><i>DistDataSource</i></a></li>
<li><a href="org/biojava/bio/seq/distributed/DistributedSequenceDB.html" title="class in org.biojava.bio.seq.distributed">DistributedSequenceDB</a></li>
<li><a href="org/biojava/bio/dist/Distribution.html" title="interface in org.biojava.bio.dist"><i>Distribution</i></a></li>
<li><a href="org/biojava/bio/dist/Distribution.NullModelForwarder.html" title="class in org.biojava.bio.dist">Distribution.NullModelForwarder</a></li>
<li><a href="org/biojava/bio/dist/DistributionFactory.html" title="interface in org.biojava.bio.dist"><i>DistributionFactory</i></a></li>
<li><a href="org/biojava/bio/dist/DistributionFactory.DefaultDistributionFactory.html" title="class in org.biojava.bio.dist">DistributionFactory.DefaultDistributionFactory</a></li>
<li><a href="org/biojava/bio/gui/DistributionLogo.html" title="class in org.biojava.bio.gui">DistributionLogo</a></li>
<li><a href="org/biojava/bio/dist/DistributionTools.html" title="class in org.biojava.bio.dist">DistributionTools</a></li>
<li><a href="org/biojava/bio/dist/DistributionTrainer.html" title="interface in org.biojava.bio.dist"><i>DistributionTrainer</i></a></li>
<li><a href="org/biojava/bio/dist/DistributionTrainerContext.html" title="interface in org.biojava.bio.dist"><i>DistributionTrainerContext</i></a></li>
<li><a href="org/biojava/bio/seq/db/emblcd/DivisionLkpReader.html" title="class in org.biojava.bio.seq.db.emblcd">DivisionLkpReader</a></li>
<li><a href="org/biojava/bio/symbol/DNAAmbPack.html" title="class in org.biojava.bio.symbol">DNAAmbPack</a></li>
<li><a href="org/biojava/bio/molbio/DNAComposition.html" title="class in org.biojava.bio.molbio">DNAComposition</a></li>
<li><a href="org/biojava/bio/symbol/DNANoAmbPack.html" title="class in org.biojava.bio.symbol">DNANoAmbPack</a></li>
<li><a href="org/biojava/bio/gui/DNAStyle.html" title="class in org.biojava.bio.gui">DNAStyle</a></li>
<li><a href="org/biojava/bio/seq/DNATools.html" title="class in org.biojava.bio.seq">DNATools</a></li>
<li><a href="org/biojavax/DocRef.html" title="interface in org.biojavax"><i>DocRef</i></a></li>
<li><a href="org/biojavax/DocRefAuthor.html" title="interface in org.biojavax"><i>DocRefAuthor</i></a></li>
<li><a href="org/biojavax/DocRefAuthor.Tools.html" title="class in org.biojavax">DocRefAuthor.Tools</a></li>
<li><a href="org/biojava/bio/dp/DotState.html" title="interface in org.biojava.bio.dp"><i>DotState</i></a></li>
<li><a href="org/biojava/bio/symbol/DoubleAlphabet.html" title="class in org.biojava.bio.symbol">DoubleAlphabet</a></li>
<li><a href="org/biojava/bio/symbol/DoubleAlphabet.DoubleRange.html" title="class in org.biojava.bio.symbol">DoubleAlphabet.DoubleRange</a></li>
<li><a href="org/biojava/bio/symbol/DoubleAlphabet.DoubleSymbol.html" title="class in org.biojava.bio.symbol">DoubleAlphabet.DoubleSymbol</a></li>
<li><a href="org/biojava/bio/symbol/DoubleAlphabet.SubDoubleAlphabet.html" title="class in org.biojava.bio.symbol">DoubleAlphabet.SubDoubleAlphabet</a></li>
<li><a href="org/biojava/utils/stax/DoubleElementHandlerBase.html" title="class in org.biojava.utils.stax">DoubleElementHandlerBase</a></li>
<li><a href="org/biojava/bio/seq/io/DoubleTokenization.html" title="class in org.biojava.bio.seq.io">DoubleTokenization</a></li>
<li><a href="org/biojava/bio/dp/DP.html" title="class in org.biojava.bio.dp">DP</a></li>
<li><a href="org/biojava/bio/dp/DP.ReverseIterator.html" title="class in org.biojava.bio.dp">DP.ReverseIterator</a></li>
<li><a href="org/biojava/bio/dp/twohead/DPCompiler.html" title="class in org.biojava.bio.dp.twohead">DPCompiler</a></li>
<li><a href="org/biojava/bio/dp/onehead/DPCursor.html" title="interface in org.biojava.bio.dp.onehead"><i>DPCursor</i></a></li>
<li><a href="org/biojava/bio/dp/DPFactory.html" title="interface in org.biojava.bio.dp"><i>DPFactory</i></a></li>
<li><a href="org/biojava/bio/dp/DPFactory.DefaultFactory.html" title="class in org.biojava.bio.dp">DPFactory.DefaultFactory</a></li>
<li><a href="org/biojava/bio/dp/twohead/DPInterpreter.html" title="class in org.biojava.bio.dp.twohead">DPInterpreter</a></li>
<li><a href="org/biojava/bio/dp/twohead/DPInterpreter.Maker.html" title="class in org.biojava.bio.dp.twohead">DPInterpreter.Maker</a></li>
<li><a href="org/biojava/bio/dp/DPMatrix.html" title="interface in org.biojava.bio.dp"><i>DPMatrix</i></a></li>
<li><a href="org/biojavax/DummyCrossReferenceResolver.html" title="class in org.biojavax">DummyCrossReferenceResolver</a></li>
<li><a href="org/biojavax/bio/seq/DummyRichSequenceHandler.html" title="class in org.biojavax.bio.seq">DummyRichSequenceHandler</a></li>
<li><a href="org/biojava/bio/seq/impl/DummySequence.html" title="class in org.biojava.bio.seq.impl">DummySequence</a></li>
<li><a href="org/biojava/bio/seq/db/DummySequenceDB.html" title="class in org.biojava.bio.seq.db">DummySequenceDB</a></li>
<li><a href="org/biojava/bio/seq/db/DummySequenceDBInstallation.html" title="class in org.biojava.bio.seq.db">DummySequenceDBInstallation</a></li>
<li><a href="org/biojava/bio/symbol/DummySymbolList.html" title="class in org.biojava.bio.symbol">DummySymbolList</a></li>
<li><a href="org/biojava/bio/program/homologene/DuplicateTaxonException.html" title="class in org.biojava.bio.program.homologene">DuplicateTaxonException</a></li>
<li><a href="org/biojava/bio/program/blast2html/EbiDatabaseURLGenerator.html" title="class in org.biojava.bio.program.blast2html">EbiDatabaseURLGenerator</a></li>
<li><a href="org/biojava/bio/taxa/EbiFormat.html" title="class in org.biojava.bio.taxa">EbiFormat</a></li>
<li><a href="org/biojava/bio/program/tagvalue/Echo.html" title="class in org.biojava.bio.program.tagvalue">Echo</a></li>
<li><a href="org/biojava/bio/EcNumber.html" title="interface in org.biojava.bio"><i>EcNumber</i></a></li>
<li><a href="org/biojava/bio/EcNumber.Impl.html" title="class in org.biojava.bio">EcNumber.Impl</a></li>
<li><a href="org/biojava/bio/symbol/Edit.html" title="class in org.biojava.bio.symbol">Edit</a></li>
<li><a href="org/biojava/bio/alignment/EditableAlignment.html" title="interface in org.biojava.bio.alignment"><i>EditableAlignment</i></a></li>
<li><a href="org/biojava/bio/program/xff/ElementRecognizer.html" title="interface in org.biojava.bio.program.xff"><i>ElementRecognizer</i></a></li>
<li><a href="org/biojava/bio/seq/io/agave/ElementRecognizer.html" title="interface in org.biojava.bio.seq.io.agave"><i>ElementRecognizer</i></a></li>
<li><a href="org/biojava/bio/seq/io/game/ElementRecognizer.html" title="interface in org.biojava.bio.seq.io.game"><i>ElementRecognizer</i></a></li>
<li><a href="org/biojava/bio/program/xff/ElementRecognizer.AllElementRecognizer.html" title="class in org.biojava.bio.program.xff">ElementRecognizer.AllElementRecognizer</a></li>
<li><a href="org/biojava/bio/seq/io/agave/ElementRecognizer.AllElementRecognizer.html" title="class in org.biojava.bio.seq.io.agave">ElementRecognizer.AllElementRecognizer</a></li>
<li><a href="org/biojava/bio/seq/io/game/ElementRecognizer.AllElementRecognizer.html" title="class in org.biojava.bio.seq.io.game">ElementRecognizer.AllElementRecognizer</a></li>
<li><a href="org/biojava/bio/program/xff/ElementRecognizer.ByLocalName.html" title="class in org.biojava.bio.program.xff">ElementRecognizer.ByLocalName</a></li>
<li><a href="org/biojava/bio/seq/io/agave/ElementRecognizer.ByLocalName.html" title="class in org.biojava.bio.seq.io.agave">ElementRecognizer.ByLocalName</a></li>
<li><a href="org/biojava/bio/seq/io/game/ElementRecognizer.ByLocalName.html" title="class in org.biojava.bio.seq.io.game">ElementRecognizer.ByLocalName</a></li>
<li><a href="org/biojava/bio/program/xff/ElementRecognizer.ByNSName.html" title="class in org.biojava.bio.program.xff">ElementRecognizer.ByNSName</a></li>
<li><a href="org/biojava/bio/seq/io/agave/ElementRecognizer.ByNSName.html" title="class in org.biojava.bio.seq.io.agave">ElementRecognizer.ByNSName</a></li>
<li><a href="org/biojava/bio/seq/io/game/ElementRecognizer.ByNSName.html" title="class in org.biojava.bio.seq.io.game">ElementRecognizer.ByNSName</a></li>
<li><a href="org/biojava/bio/program/xff/ElementRecognizer.HasAttribute.html" title="class in org.biojava.bio.program.xff">ElementRecognizer.HasAttribute</a></li>
<li><a href="org/biojava/bio/seq/io/agave/ElementRecognizer.HasAttribute.html" title="class in org.biojava.bio.seq.io.agave">ElementRecognizer.HasAttribute</a></li>
<li><a href="org/biojava/bio/seq/io/game/ElementRecognizer.HasAttribute.html" title="class in org.biojava.bio.seq.io.game">ElementRecognizer.HasAttribute</a></li>
<li><a href="org/biojava/bio/gui/sequence/EllipticalBeadRenderer.html" title="class in org.biojava.bio.gui.sequence">EllipticalBeadRenderer</a></li>
<li><a href="org/biojava/bio/program/formats/Embl.html" title="class in org.biojava.bio.program.formats">Embl</a></li>
<li><a href="org/biojava/bio/seq/io/agave/Embl2AgaveAnnotFilter.html" title="class in org.biojava.bio.seq.io.agave">Embl2AgaveAnnotFilter</a></li>
<li><a href="org/biojava/bio/seq/db/emblcd/EmblCDROMIndexReader.html" title="class in org.biojava.bio.seq.db.emblcd">EmblCDROMIndexReader</a></li>
<li><a href="org/biojava/bio/seq/db/EmblCDROMIndexStore.html" title="class in org.biojava.bio.seq.db">EmblCDROMIndexStore</a></li>
<li><a href="org/biojava/bio/seq/db/emblcd/EmblCDROMRandomAccess.html" title="class in org.biojava.bio.seq.db.emblcd">EmblCDROMRandomAccess</a></li>
<li><a href="org/biojava/bio/seq/io/EmblFileFormer.html" title="class in org.biojava.bio.seq.io">EmblFileFormer</a></li>
<li><a href="org/biojavax/bio/seq/io/EMBLFormat.html" title="class in org.biojavax.bio.seq.io">EMBLFormat</a></li>
<li><a href="org/biojavax/bio/seq/io/EMBLFormat.Terms.html" title="class in org.biojavax.bio.seq.io">EMBLFormat.Terms</a></li>
<li><a href="org/biojava/bio/seq/io/EmblLikeFormat.html" title="class in org.biojava.bio.seq.io">EmblLikeFormat</a></li>
<li><a href="org/biojava/bio/seq/io/EmblLikeLocationParser.html" title="class in org.biojava.bio.seq.io">EmblLikeLocationParser</a></li>
<li><a href="org/biojava/bio/seq/io/EmblProcessor.html" title="class in org.biojava.bio.seq.io">EmblProcessor</a></li>
<li><a href="org/biojava/bio/seq/io/EmblProcessor.Factory.html" title="class in org.biojava.bio.seq.io">EmblProcessor.Factory</a></li>
<li><a href="org/biojava/bio/seq/io/EmblReferenceComparator.html" title="class in org.biojava.bio.seq.io">EmblReferenceComparator</a></li>
<li><a href="org/biojavax/bio/seq/io/EMBLxmlFormat.html" title="class in org.biojavax.bio.seq.io">EMBLxmlFormat</a></li>
<li><a href="org/biojavax/bio/seq/io/EMBLxmlFormat.Terms.html" title="class in org.biojavax.bio.seq.io">EMBLxmlFormat.Terms</a></li>
<li><a href="org/biojava/bio/dp/twohead/EmissionCache.html" title="class in org.biojava.bio.dp.twohead">EmissionCache</a></li>
<li><a href="org/biojava/bio/dp/EmissionState.html" title="interface in org.biojava.bio.dp"><i>EmissionState</i></a></li>
<li><a href="org/biojavax/EmptyRichAnnotation.html" title="class in org.biojavax">EmptyRichAnnotation</a></li>
<li><a href="org/biojavax/bio/seq/EmptyRichLocation.html" title="class in org.biojavax.bio.seq">EmptyRichLocation</a></li>
<li><a href="org/biojava/bio/seq/db/emblcd/EntryNamIdxReader.html" title="class in org.biojava.bio.seq.db.emblcd">EntryNamIdxReader</a></li>
<li><a href="org/biojava/bio/seq/db/emblcd/EntryNamRandomAccess.html" title="class in org.biojava.bio.seq.db.emblcd">EntryNamRandomAccess</a></li>
<li><a href="org/biojava/bio/program/formats/Enzyme.html" title="class in org.biojava.bio.program.formats">Enzyme</a></li>
<li><a href="org/biojava/utils/ExecRunner.html" title="class in org.biojava.utils">ExecRunner</a></li>
<li><a href="org/biojava/utils/process/ExternalProcess.html" title="class in org.biojava.utils.process">ExternalProcess</a></li>
<li><a href="org/biojava/bio/seq/io/FastaAlignmentFormat.html" title="class in org.biojava.bio.seq.io">FastaAlignmentFormat</a></li>
<li><a href="org/biojava/bio/seq/io/FastaDescriptionLineParser.html" title="class in org.biojava.bio.seq.io">FastaDescriptionLineParser</a></li>
<li><a href="org/biojava/bio/seq/io/FastaDescriptionLineParser.Factory.html" title="class in org.biojava.bio.seq.io">FastaDescriptionLineParser.Factory</a></li>
<li><a href="org/biojava/bio/seq/io/FastaFormat.html" title="class in org.biojava.bio.seq.io">FastaFormat</a></li>
<li><a href="org/biojavax/bio/seq/io/FastaFormat.html" title="class in org.biojavax.bio.seq.io">FastaFormat</a></li>
<li><a href="org/biojavax/bio/seq/io/FastaHeader.html" title="class in org.biojavax.bio.seq.io">FastaHeader</a></li>
<li><a href="org/biojava/bio/program/sax/FastaSearchSAXParser.html" title="class in org.biojava.bio.program.sax">FastaSearchSAXParser</a></li>
<li><a href="org/biojava/bio/program/sax/FastaSequenceSAXParser.html" title="class in org.biojava.bio.program.sax">FastaSequenceSAXParser</a></li>
<li><a href="org/biojava/bio/program/fastq/Fastq.html" title="class in org.biojava.bio.program.fastq">Fastq</a></li>
<li><a href="org/biojava/bio/program/fastq/FastqBuilder.html" title="class in org.biojava.bio.program.fastq">FastqBuilder</a></li>
<li><a href="org/biojava/bio/program/fastq/FastqReader.html" title="interface in org.biojava.bio.program.fastq"><i>FastqReader</i></a></li>
<li><a href="org/biojava/bio/program/fastq/FastqTools.html" title="class in org.biojava.bio.program.fastq">FastqTools</a></li>
<li><a href="org/biojava/bio/program/fastq/FastqVariant.html" title="enum in org.biojava.bio.program.fastq">FastqVariant</a></li>
<li><a href="org/biojava/bio/program/fastq/FastqWriter.html" title="interface in org.biojava.bio.program.fastq"><i>FastqWriter</i></a></li>
<li><a href="org/biojava/utils/xml/FastXMLWriter.html" title="class in org.biojava.utils.xml">FastXMLWriter</a></li>
<li><a href="org/biojava/bio/seq/Feature.html" title="interface in org.biojava.bio.seq"><i>Feature</i></a></li>
<li><a href="org/biojava/bio/seq/Feature.ByLocationComparator.html" title="class in org.biojava.bio.seq">Feature.ByLocationComparator</a></li>
<li><a href="org/biojava/bio/seq/Feature.Template.html" title="class in org.biojava.bio.seq">Feature.Template</a></li>
<li><a href="org/biojava/bio/gui/sequence/FeatureBlockSequenceRenderer.html" title="class in org.biojava.bio.gui.sequence">FeatureBlockSequenceRenderer</a></li>
<li><a href="org/biojava/bio/seq/FeatureFilter.html" title="interface in org.biojava.bio.seq"><i>FeatureFilter</i></a></li>
<li><a href="org/biojava/bio/seq/FeatureFilter.And.html" title="class in org.biojava.bio.seq">FeatureFilter.And</a></li>
<li><a href="org/biojava/bio/seq/FeatureFilter.AnnotationContains.html" title="class in org.biojava.bio.seq">FeatureFilter.AnnotationContains</a></li>
<li><a href="org/biojava/bio/seq/FeatureFilter.ByAncestor.html" title="class in org.biojava.bio.seq">FeatureFilter.ByAncestor</a></li>
<li><a href="org/biojava/bio/seq/FeatureFilter.ByAnnotation.html" title="class in org.biojava.bio.seq">FeatureFilter.ByAnnotation</a></li>
<li><a href="org/biojava/bio/seq/FeatureFilter.ByAnnotationType.html" title="class in org.biojava.bio.seq">FeatureFilter.ByAnnotationType</a></li>
<li><a href="org/biojava/bio/seq/FeatureFilter.ByChild.html" title="class in org.biojava.bio.seq">FeatureFilter.ByChild</a></li>
<li><a href="org/biojava/bio/seq/FeatureFilter.ByClass.html" title="class in org.biojava.bio.seq">FeatureFilter.ByClass</a></li>
<li><a href="org/biojava/bio/seq/FeatureFilter.ByComponentName.html" title="class in org.biojava.bio.seq">FeatureFilter.ByComponentName</a></li>
<li><a href="org/biojava/bio/seq/FeatureFilter.ByDescendant.html" title="class in org.biojava.bio.seq">FeatureFilter.ByDescendant</a></li>
<li><a href="org/biojava/bio/seq/FeatureFilter.ByFeature.html" title="class in org.biojava.bio.seq">FeatureFilter.ByFeature</a></li>
<li><a href="org/biojava/bio/seq/FeatureFilter.ByPairwiseScore.html" title="class in org.biojava.bio.seq">FeatureFilter.ByPairwiseScore</a></li>
<li><a href="org/biojava/bio/seq/FeatureFilter.ByParent.html" title="class in org.biojava.bio.seq">FeatureFilter.ByParent</a></li>
<li><a href="org/biojava/bio/seq/FeatureFilter.BySequenceName.html" title="class in org.biojava.bio.seq">FeatureFilter.BySequenceName</a></li>
<li><a href="org/biojava/bio/seq/FeatureFilter.BySource.html" title="class in org.biojava.bio.seq">FeatureFilter.BySource</a></li>
<li><a href="org/biojava/bio/seq/FeatureFilter.ByType.html" title="class in org.biojava.bio.seq">FeatureFilter.ByType</a></li>
<li><a href="org/biojava/bio/seq/FeatureFilter.ContainedByLocation.html" title="class in org.biojava.bio.seq">FeatureFilter.ContainedByLocation</a></li>
<li><a href="org/biojava/bio/seq/FeatureFilter.FrameFilter.html" title="class in org.biojava.bio.seq">FeatureFilter.FrameFilter</a></li>
<li><a href="org/biojava/bio/seq/FeatureFilter.HasAnnotation.html" title="class in org.biojava.bio.seq">FeatureFilter.HasAnnotation</a></li>
<li><a href="org/biojava/bio/seq/FeatureFilter.Not.html" title="class in org.biojava.bio.seq">FeatureFilter.Not</a></li>
<li><a href="org/biojava/bio/seq/FeatureFilter.OnlyChildren.html" title="class in org.biojava.bio.seq">FeatureFilter.OnlyChildren</a></li>
<li><a href="org/biojava/bio/seq/FeatureFilter.OnlyDescendants.html" title="class in org.biojava.bio.seq">FeatureFilter.OnlyDescendants</a></li>
<li><a href="org/biojava/bio/seq/FeatureFilter.Or.html" title="class in org.biojava.bio.seq">FeatureFilter.Or</a></li>
<li><a href="org/biojava/bio/seq/FeatureFilter.OverlapsLocation.html" title="class in org.biojava.bio.seq">FeatureFilter.OverlapsLocation</a></li>
<li><a href="org/biojava/bio/seq/FeatureFilter.ShadowContainedByLocation.html" title="class in org.biojava.bio.seq">FeatureFilter.ShadowContainedByLocation</a></li>
<li><a href="org/biojava/bio/seq/FeatureFilter.ShadowOverlapsLocation.html" title="class in org.biojava.bio.seq">FeatureFilter.ShadowOverlapsLocation</a></li>
<li><a href="org/biojava/bio/seq/FeatureFilter.StrandFilter.html" title="class in org.biojava.bio.seq">FeatureFilter.StrandFilter</a></li>
<li><a href="org/biojava/bio/program/xff/FeatureHandler.html" title="class in org.biojava.bio.program.xff">FeatureHandler</a></li>
<li><a href="org/biojava/bio/seq/FeatureHolder.html" title="interface in org.biojava.bio.seq"><i>FeatureHolder</i></a></li>
<li><a href="org/biojava/bio/seq/FeatureHolder.EmptyFeatureHolder.html" title="class in org.biojava.bio.seq">FeatureHolder.EmptyFeatureHolder</a></li>
<li><a href="org/biojava/bio/seq/FeatureHolderUtils.html" title="class in org.biojava.bio.seq">FeatureHolderUtils</a></li>
<li><a href="org/biojava/bio/seq/impl/FeatureImpl.html" title="class in org.biojava.bio.seq.impl">FeatureImpl</a></li>
<li><a href="org/biojava/bio/gui/sequence/FeatureLabelRenderer.html" title="class in org.biojava.bio.gui.sequence">FeatureLabelRenderer</a></li>
<li><a href="org/biojava/bio/gui/sequence/FeatureLabelRenderer.AnnotationLabelMaker.html" title="class in org.biojava.bio.gui.sequence">FeatureLabelRenderer.AnnotationLabelMaker</a></li>
<li><a href="org/biojava/bio/gui/sequence/FeatureLabelRenderer.LabelMaker.html" title="interface in org.biojava.bio.gui.sequence"><i>FeatureLabelRenderer.LabelMaker</i></a></li>
<li><a href="org/biojava/bio/gui/sequence/FeatureLabelRenderer.SourceLabelMaker.html" title="class in org.biojava.bio.gui.sequence">FeatureLabelRenderer.SourceLabelMaker</a></li>
<li><a href="org/biojava/bio/gui/sequence/FeatureLabelRenderer.TypeLabelMaker.html" title="class in org.biojava.bio.gui.sequence">FeatureLabelRenderer.TypeLabelMaker</a></li>
<li><a href="org/biojava/bio/seq/FeatureRealizer.html" title="interface in org.biojava.bio.seq"><i>FeatureRealizer</i></a></li>
<li><a href="org/biojava/bio/gui/sequence/FeatureRenderer.html" title="interface in org.biojava.bio.gui.sequence"><i>FeatureRenderer</i></a></li>
<li><a href="org/biojava/bio/gui/sequence/FeatureSource.html" title="interface in org.biojava.bio.gui.sequence"><i>FeatureSource</i></a></li>
<li><a href="org/biojava/bio/seq/io/FeatureTableParser.html" title="class in org.biojava.bio.seq.io">FeatureTableParser</a></li>
<li><a href="org/biojava/bio/gui/FeatureTree.html" title="class in org.biojava.bio.gui">FeatureTree</a></li>
<li><a href="org/biojava/bio/seq/FeatureTypes.html" title="class in org.biojava.bio.seq">FeatureTypes</a></li>
<li><a href="org/biojava/bio/seq/FeatureTypes.Repository.html" title="interface in org.biojava.bio.seq"><i>FeatureTypes.Repository</i></a></li>
<li><a href="org/biojava/bio/seq/FeatureTypes.RepositoryImpl.html" title="class in org.biojava.bio.seq">FeatureTypes.RepositoryImpl</a></li>
<li><a href="org/biojava/bio/seq/FeatureTypes.Type.html" title="interface in org.biojava.bio.seq"><i>FeatureTypes.Type</i></a></li>
<li><a href="org/biojava/bio/seq/db/FetchURL.html" title="class in org.biojava.bio.seq.db">FetchURL</a></li>
<li><a href="org/biojava/utils/FileAsList.html" title="class in org.biojava.utils">FileAsList</a></li>
<li><a href="org/biojava/bio/search/FilteringContentHandler.html" title="class in org.biojava.bio.search">FilteringContentHandler</a></li>
<li><a href="org/biojava/bio/gui/sequence/FilteringRenderer.html" title="class in org.biojava.bio.gui.sequence">FilteringRenderer</a></li>
<li><a href="org/biojava/bio/search/FilterTest.html" title="interface in org.biojava.bio.search"><i>FilterTest</i></a></li>
<li><a href="org/biojava/bio/search/FilterTest.Equals.html" title="class in org.biojava.bio.search">FilterTest.Equals</a></li>
<li><a href="org/biojava/bio/search/FilterTest.FindRegex.html" title="class in org.biojava.bio.search">FilterTest.FindRegex</a></li>
<li><a href="org/biojava/bio/search/FilterTest.GreaterThan.html" title="class in org.biojava.bio.search">FilterTest.GreaterThan</a></li>
<li><a href="org/biojava/bio/search/FilterTest.LessThan.html" title="class in org.biojava.bio.search">FilterTest.LessThan</a></li>
<li><a href="org/biojava/bio/search/FilterTest.MatchRegex.html" title="class in org.biojava.bio.search">FilterTest.MatchRegex</a></li>
<li><a href="org/biojava/bio/seq/filter/FilterTransformer.html" title="class in org.biojava.bio.seq.filter">FilterTransformer</a></li>
<li><a href="org/biojava/bio/seq/FilterUtils.html" title="class in org.biojava.bio.seq">FilterUtils</a></li>
<li><a href="org/biojava/bio/seq/FilterUtils.FilterTransformer.html" title="interface in org.biojava.bio.seq"><i>FilterUtils.FilterTransformer</i></a></li>
<li><a href="org/biojava/bio/symbol/FiniteAlphabet.html" title="interface in org.biojava.bio.symbol"><i>FiniteAlphabet</i></a></li>
<li><a href="org/biojava/utils/automata/FiniteAutomaton.html" title="class in org.biojava.utils.automata">FiniteAutomaton</a></li>
<li><a href="org/biojavax/ga/functions/FitnessFunction.html" title="interface in org.biojavax.ga.functions"><i>FitnessFunction</i></a></li>
<li><a href="org/biojava/bio/chromatogram/graphic/FixedBaseWidthScaler.html" title="class in org.biojava.bio.chromatogram.graphic">FixedBaseWidthScaler</a></li>
<li><a href="org/biojava/utils/cache/FixedSizeCache.html" title="class in org.biojava.utils.cache">FixedSizeCache</a></li>
<li><a href="org/biojava/utils/cache/FixedSizeMap.html" title="class in org.biojava.utils.cache">FixedSizeMap</a></li>
<li><a href="org/biojava/utils/io/FlatFileCache.html" title="class in org.biojava.utils.io">FlatFileCache</a></li>
<li><a href="org/biojava/bio/program/unigene/FlatFileUnigeneFactory.html" title="class in org.biojava.bio.program.unigene">FlatFileUnigeneFactory</a></li>
<li><a href="org/biojava/bio/seq/db/flat/FlatSequenceDB.html" title="class in org.biojava.bio.seq.db.flat">FlatSequenceDB</a></li>
<li><a href="org/biojava/bio/seq/db/flat/FlatSequenceDBProvider.html" title="class in org.biojava.bio.seq.db.flat">FlatSequenceDBProvider</a></li>
<li><a href="org/biojava/bio/alignment/FlexibleAlignment.html" title="class in org.biojava.bio.alignment">FlexibleAlignment</a></li>
<li><a href="org/biojava/utils/stax/FloatElementHandlerBase.html" title="class in org.biojava.utils.stax">FloatElementHandlerBase</a></li>
<li><a href="org/biojava/bio/program/formats/Format.html" title="interface in org.biojava.bio.program.formats"><i>Format</i></a></li>
<li><a href="org/biojava/bio/program/tagvalue/Formats.html" title="class in org.biojava.bio.program.tagvalue">Formats</a></li>
<li><a href="org/biojava/bio/program/formats/FormatTools.html" title="class in org.biojava.bio.program.formats">FormatTools</a></li>
<li><a href="org/biojava/bio/seq/Frame.html" title="interface in org.biojava.bio.seq"><i>Frame</i></a></li>
<li><a href="org/biojava/bio/seq/FramedFeature.html" title="interface in org.biojava.bio.seq"><i>FramedFeature</i></a></li>
<li><a href="org/biojava/bio/seq/FramedFeature.ReadingFrame.html" title="class in org.biojava.bio.seq">FramedFeature.ReadingFrame</a></li>
<li><a href="org/biojava/bio/seq/FramedFeature.Template.html" title="class in org.biojava.bio.seq">FramedFeature.Template</a></li>
<li><a href="org/biojava/bio/program/hmmer/FullHmmerProfileHMM.html" title="class in org.biojava.bio.program.hmmer">FullHmmerProfileHMM</a></li>
<li><a href="org/biojava/bio/symbol/FundamentalAtomicSymbol.html" title="class in org.biojava.bio.symbol">FundamentalAtomicSymbol</a></li>
<li><a href="org/biojava/bio/symbol/FuzzyLocation.html" title="class in org.biojava.bio.symbol">FuzzyLocation</a></li>
<li><a href="org/biojava/bio/symbol/FuzzyLocation.RangeResolver.html" title="interface in org.biojava.bio.symbol"><i>FuzzyLocation.RangeResolver</i></a></li>
<li><a href="org/biojava/bio/symbol/FuzzyPointLocation.html" title="class in org.biojava.bio.symbol">FuzzyPointLocation</a></li>
<li><a href="org/biojava/bio/symbol/FuzzyPointLocation.PointResolver.html" title="interface in org.biojava.bio.symbol"><i>FuzzyPointLocation.PointResolver</i></a></li>
<li><a href="org/biojavax/ga/functions/GACross.html" title="interface in org.biojavax.ga.functions"><i>GACross</i></a></li>
<li><a href="org/biojavax/ga/functions/GACrossResult.html" title="interface in org.biojavax.ga.functions"><i>GACrossResult</i></a></li>
<li><a href="org/biojava/bio/seq/io/game/GAMEAnnotationHandler.html" title="class in org.biojava.bio.seq.io.game">GAMEAnnotationHandler</a></li>
<li><a href="org/biojava/bio/seq/io/game12/GAMEAnnotationHandler.html" title="class in org.biojava.bio.seq.io.game12">GAMEAnnotationHandler</a></li>
<li><a href="org/biojava/bio/seq/io/game12/GAMEAspectHandler.html" title="class in org.biojava.bio.seq.io.game12">GAMEAspectHandler</a></li>
<li><a href="org/biojava/bio/seq/io/game/GAMEAspectPropHandler.html" title="class in org.biojava.bio.seq.io.game">GAMEAspectPropHandler</a></li>
<li><a href="org/biojava/bio/seq/io/game12/GAMEDbxrefHandler.html" title="class in org.biojava.bio.seq.io.game12">GAMEDbxrefHandler</a></li>
<li><a href="org/biojava/bio/seq/io/game/GAMEDbxrefPropHandler.html" title="class in org.biojava.bio.seq.io.game">GAMEDbxrefPropHandler</a></li>
<li><a href="org/biojava/bio/seq/io/game/GAMEDescriptionPropHandler.html" title="class in org.biojava.bio.seq.io.game">GAMEDescriptionPropHandler</a></li>
<li><a href="org/biojava/bio/seq/io/game/GAMEFeatureCallbackItf.html" title="interface in org.biojava.bio.seq.io.game"><i>GAMEFeatureCallbackItf</i></a></li>
<li><a href="org/biojava/bio/seq/io/game/GAMEFeatureSetHandler.html" title="class in org.biojava.bio.seq.io.game">GAMEFeatureSetHandler</a></li>
<li><a href="org/biojava/bio/seq/io/game12/GAMEFeatureSetHandler.html" title="class in org.biojava.bio.seq.io.game12">GAMEFeatureSetHandler</a></li>
<li><a href="org/biojava/bio/seq/io/game/GAMEFeatureSetPropHandler.html" title="class in org.biojava.bio.seq.io.game">GAMEFeatureSetPropHandler</a></li>
<li><a href="org/biojava/bio/seq/io/game/GAMEFeatureSpanHandler.html" title="class in org.biojava.bio.seq.io.game">GAMEFeatureSpanHandler</a></li>
<li><a href="org/biojava/bio/seq/io/game12/GAMEFeatureSpanHandler.html" title="class in org.biojava.bio.seq.io.game12">GAMEFeatureSpanHandler</a></li>
<li><a href="org/biojava/bio/seq/io/GAMEFormat.html" title="class in org.biojava.bio.seq.io">GAMEFormat</a></li>
<li><a href="org/biojava/bio/seq/io/game12/GAMEGeneHandler.html" title="class in org.biojava.bio.seq.io.game12">GAMEGeneHandler</a></li>
<li><a href="org/biojava/bio/seq/io/game/GAMEGenePropHandler.html" title="class in org.biojava.bio.seq.io.game">GAMEGenePropHandler</a></li>
<li><a href="org/biojava/bio/seq/io/game/GAMEHandler.html" title="class in org.biojava.bio.seq.io.game">GAMEHandler</a></li>
<li><a href="org/biojava/bio/seq/io/game12/GAMEHandler.html" title="class in org.biojava.bio.seq.io.game12">GAMEHandler</a></li>
<li><a href="org/biojava/bio/seq/io/game/GAMEMapPosPropHandler.html" title="class in org.biojava.bio.seq.io.game">GAMEMapPosPropHandler</a></li>
<li><a href="org/biojava/bio/seq/io/game/GAMENameCallbackItf.html" title="interface in org.biojava.bio.seq.io.game"><i>GAMENameCallbackItf</i></a></li>
<li><a href="org/biojava/bio/seq/io/game/GAMENamePropHandler.html" title="class in org.biojava.bio.seq.io.game">GAMENamePropHandler</a></li>
<li><a href="org/biojava/bio/seq/io/game12/GAMEPropertyHandler.html" title="class in org.biojava.bio.seq.io.game12">GAMEPropertyHandler</a></li>
<li><a href="org/biojava/bio/seq/io/game/GAMEResiduesPropHandler.html" title="class in org.biojava.bio.seq.io.game">GAMEResiduesPropHandler</a></li>
<li><a href="org/biojava/bio/seq/io/game12/GAMESeqHandler.html" title="class in org.biojava.bio.seq.io.game12">GAMESeqHandler</a></li>
<li><a href="org/biojava/bio/seq/io/game/GAMESeqPropHandler.html" title="class in org.biojava.bio.seq.io.game">GAMESeqPropHandler</a></li>
<li><a href="org/biojava/bio/seq/io/game12/GAMESeqRelHandler.html" title="class in org.biojava.bio.seq.io.game12">GAMESeqRelHandler</a></li>
<li><a href="org/biojava/bio/seq/io/game/GAMESeqRelPropHandler.html" title="class in org.biojava.bio.seq.io.game">GAMESeqRelPropHandler</a></li>
<li><a href="org/biojava/bio/seq/io/game12/GAMESpanHandler.html" title="class in org.biojava.bio.seq.io.game12">GAMESpanHandler</a></li>
<li><a href="org/biojava/bio/seq/io/game/GAMESpanPropHandler.html" title="class in org.biojava.bio.seq.io.game">GAMESpanPropHandler</a></li>
<li><a href="org/biojava/bio/seq/io/game/GAMETranscriptCallbackItf.html" title="interface in org.biojava.bio.seq.io.game"><i>GAMETranscriptCallbackItf</i></a></li>
<li><a href="org/biojava/bio/seq/io/game/GAMETypePropHandler.html" title="class in org.biojava.bio.seq.io.game">GAMETypePropHandler</a></li>
<li><a href="org/biojava/bio/dist/GapDistribution.html" title="class in org.biojava.bio.dist">GapDistribution</a></li>
<li><a href="org/biojava/bio/gui/sequence/GappedRenderer.html" title="class in org.biojava.bio.gui.sequence">GappedRenderer</a></li>
<li><a href="org/biojava/bio/seq/GappedSequence.html" title="interface in org.biojava.bio.seq"><i>GappedSequence</i></a></li>
<li><a href="org/biojava/bio/symbol/GappedSymbolList.html" title="interface in org.biojava.bio.symbol"><i>GappedSymbolList</i></a></li>
<li><a href="org/biojavax/ga/GAStoppingCriteria.html" title="interface in org.biojavax.ga"><i>GAStoppingCriteria</i></a></li>
<li><a href="org/biojavax/ga/GAStoppingCriteria.MaximumGeneration.html" title="class in org.biojavax.ga">GAStoppingCriteria.MaximumGeneration</a></li>
<li><a href="org/biojavax/ga/util/GATools.html" title="class in org.biojavax.ga.util">GATools</a></li>
<li><a href="org/biojava/bio/seq/io/GenbankFileFormer.html" title="class in org.biojava.bio.seq.io">GenbankFileFormer</a></li>
<li><a href="org/biojava/bio/seq/io/GenbankFormat.html" title="class in org.biojava.bio.seq.io">GenbankFormat</a></li>
<li><a href="org/biojavax/bio/seq/io/GenbankFormat.html" title="class in org.biojavax.bio.seq.io">GenbankFormat</a></li>
<li><a href="org/biojavax/bio/seq/io/GenbankFormat.Terms.html" title="class in org.biojavax.bio.seq.io">GenbankFormat.Terms</a></li>
<li><a href="org/biojavax/bio/seq/io/GenbankLocationParser.html" title="class in org.biojavax.bio.seq.io">GenbankLocationParser</a></li>
<li><a href="org/biojava/bio/seq/io/GenbankProcessor.html" title="class in org.biojava.bio.seq.io">GenbankProcessor</a></li>
<li><a href="org/biojava/bio/seq/io/GenbankProcessor.Factory.html" title="class in org.biojava.bio.seq.io">GenbankProcessor.Factory</a></li>
<li><a href="org/biojavax/bio/db/ncbi/GenbankRichSequenceDB.html" title="class in org.biojavax.bio.db.ncbi">GenbankRichSequenceDB</a></li>
<li><a href="org/biojava/bio/seq/db/GenbankSequenceDB.html" title="class in org.biojava.bio.seq.db">GenbankSequenceDB</a></li>
<li><a href="org/biojava/bio/seq/io/GenbankXmlFormat.html" title="class in org.biojava.bio.seq.io">GenbankXmlFormat</a></li>
<li><a href="org/biojava/bio/seq/io/GenEmblFeatureComparator.html" title="class in org.biojava.bio.seq.io">GenEmblFeatureComparator</a></li>
<li><a href="org/biojava/bio/seq/io/GenEmblPropertyComparator.html" title="class in org.biojava.bio.seq.io">GenEmblPropertyComparator</a></li>
<li><a href="org/biojava/utils/bytecode/GeneratedClassLoader.html" title="class in org.biojava.utils.bytecode">GeneratedClassLoader</a></li>
<li><a href="org/biojava/utils/bytecode/GeneratedCodeClass.html" title="class in org.biojava.utils.bytecode">GeneratedCodeClass</a></li>
<li><a href="org/biojava/utils/bytecode/GeneratedCodeMethod.html" title="class in org.biojava.utils.bytecode">GeneratedCodeMethod</a></li>
<li><a href="org/biojavax/ga/GeneticAlgorithm.html" title="interface in org.biojavax.ga"><i>GeneticAlgorithm</i></a></li>
<li><a href="org/biojava/bio/seq/GeneticCodes.html" title="class in org.biojava.bio.seq">GeneticCodes</a></li>
<li><a href="org/biojava/bio/seq/io/GenpeptFormat.html" title="class in org.biojava.bio.seq.io">GenpeptFormat</a></li>
<li><a href="org/biojavax/bio/db/ncbi/GenpeptRichSequenceDB.html" title="class in org.biojavax.bio.db.ncbi">GenpeptRichSequenceDB</a></li>
<li><a href="org/biojava/bio/seq/db/GenpeptSequenceDB.html" title="class in org.biojava.bio.seq.db">GenpeptSequenceDB</a></li>
<li><a href="org/biojava/bio/program/gff3/GFF3DocumentHandler.html" title="interface in org.biojava.bio.program.gff3"><i>GFF3DocumentHandler</i></a></li>
<li><a href="org/biojava/bio/program/gff3/GFF3Parser.html" title="class in org.biojava.bio.program.gff3">GFF3Parser</a></li>
<li><a href="org/biojava/bio/program/gff3/GFF3Record.html" title="interface in org.biojava.bio.program.gff3"><i>GFF3Record</i></a></li>
<li><a href="org/biojava/bio/program/gff3/GFF3Record.Impl.html" title="class in org.biojava.bio.program.gff3">GFF3Record.Impl</a></li>
<li><a href="org/biojava/bio/seq/distributed/GFFDataSource.html" title="class in org.biojava.bio.seq.distributed">GFFDataSource</a></li>
<li><a href="org/biojava/bio/program/gff/GFFDocumentHandler.html" title="interface in org.biojava.bio.program.gff"><i>GFFDocumentHandler</i></a></li>
<li><a href="org/biojava/bio/program/gff/GFFEntrySet.html" title="class in org.biojava.bio.program.gff">GFFEntrySet</a></li>
<li><a href="org/biojava/bio/program/gff/GFFErrorHandler.html" title="interface in org.biojava.bio.program.gff"><i>GFFErrorHandler</i></a></li>
<li><a href="org/biojava/bio/program/gff/GFFErrorHandler.AbortErrorHandler.html" title="class in org.biojava.bio.program.gff">GFFErrorHandler.AbortErrorHandler</a></li>
<li><a href="org/biojava/bio/program/gff/GFFErrorHandler.SkipRecordErrorHandler.html" title="class in org.biojava.bio.program.gff">GFFErrorHandler.SkipRecordErrorHandler</a></li>
<li><a href="org/biojava/bio/program/gff/GFFFilterer.html" title="class in org.biojava.bio.program.gff">GFFFilterer</a></li>
<li><a href="org/biojava/bio/program/gff/GFFParser.html" title="class in org.biojava.bio.program.gff">GFFParser</a></li>
<li><a href="org/biojava/bio/program/gff/GFFRecord.html" title="interface in org.biojava.bio.program.gff"><i>GFFRecord</i></a></li>
<li><a href="org/biojava/bio/program/gff/GFFRecordFilter.html" title="interface in org.biojava.bio.program.gff"><i>GFFRecordFilter</i></a></li>
<li><a href="org/biojava/bio/program/gff/GFFRecordFilter.AcceptAll.html" title="class in org.biojava.bio.program.gff">GFFRecordFilter.AcceptAll</a></li>
<li><a href="org/biojava/bio/program/gff/GFFRecordFilter.FeatureFilter.html" title="class in org.biojava.bio.program.gff">GFFRecordFilter.FeatureFilter</a></li>
<li><a href="org/biojava/bio/program/gff/GFFRecordFilter.FrameFilter.html" title="class in org.biojava.bio.program.gff">GFFRecordFilter.FrameFilter</a></li>
<li><a href="org/biojava/bio/program/gff/GFFRecordFilter.NotFilter.html" title="class in org.biojava.bio.program.gff">GFFRecordFilter.NotFilter</a></li>
<li><a href="org/biojava/bio/program/gff/GFFRecordFilter.SequenceFilter.html" title="class in org.biojava.bio.program.gff">GFFRecordFilter.SequenceFilter</a></li>
<li><a href="org/biojava/bio/program/gff/GFFRecordFilter.SourceFilter.html" title="class in org.biojava.bio.program.gff">GFFRecordFilter.SourceFilter</a></li>
<li><a href="org/biojava/bio/program/gff/GFFRecordFilter.StrandFilter.html" title="class in org.biojava.bio.program.gff">GFFRecordFilter.StrandFilter</a></li>
<li><a href="org/biojava/bio/program/gff/GFFTools.html" title="class in org.biojava.bio.program.gff">GFFTools</a></li>
<li><a href="org/biojava/bio/program/gff/GFFWriter.html" title="class in org.biojava.bio.program.gff">GFFWriter</a></li>
<li><a href="org/biojava/bio/gui/glyph/Glyph.html" title="interface in org.biojava.bio.gui.glyph"><i>Glyph</i></a></li>
<li><a href="org/biojava/bio/gui/sequence/GlyphFeatureRenderer.html" title="class in org.biojava.bio.gui.sequence">GlyphFeatureRenderer</a></li>
<li><a href="org/biojava/bio/gui/glyph/GlyphUtils.html" title="class in org.biojava.bio.gui.glyph">GlyphUtils</a></li>
<li><a href="org/biojava/ontology/io/GOParser.html" title="class in org.biojava.ontology.io">GOParser</a></li>
<li><a href="org/biojava/bio/gui/sequence/GUITools.html" title="class in org.biojava.bio.gui.sequence">GUITools</a></li>
<li><a href="org/biojavax/bio/db/HashBioEntryDB.html" title="class in org.biojavax.bio.db">HashBioEntryDB</a></li>
<li><a href="org/biojavax/bio/seq/io/HashedFastaIterator.html" title="class in org.biojavax.bio.seq.io">HashedFastaIterator</a></li>
<li><a href="org/biojavax/bio/db/HashRichSequenceDB.html" title="class in org.biojavax.bio.db">HashRichSequenceDB</a></li>
<li><a href="org/biojava/bio/seq/db/HashSequenceDB.html" title="class in org.biojava.bio.seq.db">HashSequenceDB</a></li>
<li><a href="org/biojava/bio/program/ssbind/HeaderStAXHandler.html" title="class in org.biojava.bio.program.ssbind">HeaderStAXHandler</a></li>
<li><a href="org/biojava/bio/gui/sequence/HeadlessRenderContext.html" title="class in org.biojava.bio.gui.sequence">HeadlessRenderContext</a></li>
<li><a href="org/biojava/bio/gui/glyph/HelixGlyph.html" title="class in org.biojava.bio.gui.glyph">HelixGlyph</a></li>
<li><a href="org/biojava/bio/program/ssaha/HitMerger.html" title="class in org.biojava.bio.program.ssaha">HitMerger</a></li>
<li><a href="org/biojava/bio/program/ssbind/HitStAXHandler.html" title="class in org.biojava.bio.program.ssbind">HitStAXHandler</a></li>
<li><a href="org/biojava/bio/program/hmmer/HmmerProfileHMM.html" title="class in org.biojava.bio.program.hmmer">HmmerProfileHMM</a></li>
<li><a href="org/biojava/bio/program/hmmer/HmmerProfileParser.html" title="class in org.biojava.bio.program.hmmer">HmmerProfileParser</a></li>
<li><a href="org/biojava/bio/dp/HMMTrainer.html" title="interface in org.biojava.bio.dp"><i>HMMTrainer</i></a></li>
<li><a href="org/biojava/bio/program/homologene/HomologeneBuilder.html" title="interface in org.biojava.bio.program.homologene"><i>HomologeneBuilder</i></a></li>
<li><a href="org/biojava/bio/program/homologene/HomologeneDB.html" title="interface in org.biojava.bio.program.homologene"><i>HomologeneDB</i></a></li>
<li><a href="org/biojava/bio/program/homologene/HomologeneTools.html" title="class in org.biojava.bio.program.homologene">HomologeneTools</a></li>
<li><a href="org/biojava/bio/seq/homol/Homology.html" title="interface in org.biojava.bio.seq.homol"><i>Homology</i></a></li>
<li><a href="org/biojava/bio/seq/homol/HomologyDB.html" title="interface in org.biojava.bio.seq.homol"><i>HomologyDB</i></a></li>
<li><a href="org/biojava/bio/seq/homol/HomologyFeature.html" title="interface in org.biojava.bio.seq.homol"><i>HomologyFeature</i></a></li>
<li><a href="org/biojava/bio/seq/homol/HomologyFeature.Template.html" title="class in org.biojava.bio.seq.homol">HomologyFeature.Template</a></li>
<li><a href="org/biojava/bio/program/ssbind/HSPStAXHandler.html" title="class in org.biojava.bio.program.ssbind">HSPStAXHandler</a></li>
<li><a href="org/biojava/bio/program/ssbind/HSPSummaryStAXHandler.html" title="class in org.biojava.bio.program.ssbind">HSPSummaryStAXHandler</a></li>
<li><a href="org/biojava/bio/program/blast2html/HTMLRenderer.html" title="class in org.biojava.bio.program.blast2html">HTMLRenderer</a></li>
<li><a href="org/biojava/bio/seq/db/biosql/HypersonicDBHelper.html" title="class in org.biojava.bio.seq.db.biosql">HypersonicDBHelper</a></li>
<li><a href="org/biojava/utils/lsid/Identifiable.html" title="interface in org.biojava.utils.lsid"><i>Identifiable</i></a></li>
<li><a href="org/biojava/bio/seq/db/IDMaker.html" title="interface in org.biojava.bio.seq.db"><i>IDMaker</i></a></li>
<li><a href="org/biojava/bio/seq/db/IDMaker.ByName.html" title="class in org.biojava.bio.seq.db">IDMaker.ByName</a></li>
<li><a href="org/biojava/bio/seq/db/IDMaker.ByURN.html" title="class in org.biojava.bio.seq.db">IDMaker.ByURN</a></li>
<li><a href="org/biojava/utils/bytecode/IfExpression.html" title="class in org.biojava.utils.bytecode">IfExpression</a></li>
<li><a href="org/biojava/bio/dist/IgnoreCountsTrainer.html" title="class in org.biojava.bio.dist">IgnoreCountsTrainer</a></li>
<li><a href="org/biojava/bio/program/gff/IgnoreRecordException.html" title="class in org.biojava.bio.program.gff">IgnoreRecordException</a></li>
<li><a href="org/biojava/bio/alignment/IllegalAlignmentEditException.html" title="class in org.biojava.bio.alignment">IllegalAlignmentEditException</a></li>
<li><a href="org/biojava/bio/symbol/IllegalAlphabetException.html" title="class in org.biojava.bio.symbol">IllegalAlphabetException</a></li>
<li><a href="org/biojava/bio/seq/db/IllegalIDException.html" title="class in org.biojava.bio.seq.db">IllegalIDException</a></li>
<li><a href="org/biojavax/ga/exception/IllegalOrganismException.html" title="class in org.biojavax.ga.exception">IllegalOrganismException</a></li>
<li><a href="org/biojava/bio/symbol/IllegalSymbolException.html" title="class in org.biojava.bio.symbol">IllegalSymbolException</a></li>
<li><a href="org/biojava/bio/dp/IllegalTransitionException.html" title="class in org.biojava.bio.dp">IllegalTransitionException</a></li>
<li><a href="org/biojava/bio/program/fastq/IlluminaFastqReader.html" title="class in org.biojava.bio.program.fastq">IlluminaFastqReader</a></li>
<li><a href="org/biojava/bio/program/fastq/IlluminaFastqWriter.html" title="class in org.biojava.bio.program.fastq">IlluminaFastqWriter</a></li>
<li><a href="org/biojava/bio/gui/sequence/ImageMap.html" title="interface in org.biojava.bio.gui.sequence"><i>ImageMap</i></a></li>
<li><a href="org/biojava/bio/gui/sequence/ImageMap.ClientSide.html" title="class in org.biojava.bio.gui.sequence">ImageMap.ClientSide</a></li>
<li><a href="org/biojava/bio/gui/sequence/ImageMap.HotSpot.html" title="class in org.biojava.bio.gui.sequence">ImageMap.HotSpot</a></li>
<li><a href="org/biojava/bio/gui/sequence/ImageMap.ServerSide.html" title="class in org.biojava.bio.gui.sequence">ImageMap.ServerSide</a></li>
<li><a href="org/biojava/bio/gui/sequence/ImageMapRenderer.html" title="interface in org.biojava.bio.gui.sequence"><i>ImageMapRenderer</i></a></li>
<li><a href="org/biojava/bio/seq/db/Index.html" title="interface in org.biojava.bio.seq.db"><i>Index</i></a></li>
<li><a href="org/biojava/bio/program/tagvalue/Index2Model.html" title="class in org.biojava.bio.program.tagvalue">Index2Model</a></li>
<li><a href="org/biojava/bio/annodb/IndexedAnnotationDB.html" title="class in org.biojava.bio.annodb">IndexedAnnotationDB</a></li>
<li><a href="org/biojava/bio/annodb/IndexedAnnotationDB.ParserListenerFactory.html" title="interface in org.biojava.bio.annodb"><i>IndexedAnnotationDB.ParserListenerFactory</i></a></li>
<li><a href="org/biojava/bio/annodb/IndexedAnnotationDB.StaticMethodRPFactory.html" title="class in org.biojava.bio.annodb">IndexedAnnotationDB.StaticMethodRPFactory</a></li>
<li><a href="org/biojava/utils/IndexedChangeHub.html" title="class in org.biojava.utils">IndexedChangeHub</a></li>
<li><a href="org/biojava/bio/dist/IndexedCount.html" title="class in org.biojava.bio.dist">IndexedCount</a></li>
<li><a href="org/biojava/bio/seq/db/IndexedSequenceDB.html" title="class in org.biojava.bio.seq.db">IndexedSequenceDB</a></li>
<li><a href="org/biojava/bio/program/tagvalue/Indexer.html" title="class in org.biojava.bio.program.tagvalue">Indexer</a></li>
<li><a href="org/biojava/bio/program/tagvalue/Indexer2.html" title="class in org.biojava.bio.program.tagvalue">Indexer2</a></li>
<li><a href="org/biojava/bio/program/indexdb/IndexStore.html" title="interface in org.biojava.bio.program.indexdb"><i>IndexStore</i></a></li>
<li><a href="org/biojava/bio/seq/db/IndexStore.html" title="interface in org.biojava.bio.seq.db"><i>IndexStore</i></a></li>
<li><a href="org/biojava/bio/program/indexdb/IndexTools.html" title="class in org.biojava.bio.program.indexdb">IndexTools</a></li>
<li><a href="org/biojavax/bio/seq/InfinitelyAmbiguousSymbolList.html" title="class in org.biojavax.bio.seq">InfinitelyAmbiguousSymbolList</a></li>
<li><a href="org/biojava/utils/xml/Initializable.html" title="interface in org.biojava.utils.xml"><i>Initializable</i></a></li>
<li><a href="org/biojava/utils/process/InputHandler.html" title="interface in org.biojava.utils.process"><i>InputHandler</i></a></li>
<li><a href="org/biojava/utils/io/InputStreamProvider.html" title="class in org.biojava.utils.io">InputStreamProvider</a></li>
<li><a href="org/biojavax/bio/seq/io/INSDseqFormat.html" title="class in org.biojavax.bio.seq.io">INSDseqFormat</a></li>
<li><a href="org/biojavax/bio/seq/io/INSDseqFormat.Terms.html" title="class in org.biojavax.bio.seq.io">INSDseqFormat.Terms</a></li>
<li><a href="org/biojava/utils/bytecode/Instruction.html" title="interface in org.biojava.utils.bytecode"><i>Instruction</i></a></li>
<li><a href="org/biojava/utils/bytecode/InstructionVector.html" title="class in org.biojava.utils.bytecode">InstructionVector</a></li>
<li><a href="org/biojava/bio/symbol/IntegerAlphabet.html" title="class in org.biojava.bio.symbol">IntegerAlphabet</a></li>
<li><a href="org/biojava/bio/symbol/IntegerAlphabet.IntegerSymbol.html" title="class in org.biojava.bio.symbol">IntegerAlphabet.IntegerSymbol</a></li>
<li><a href="org/biojava/bio/symbol/IntegerAlphabet.SubIntegerAlphabet.html" title="class in org.biojava.bio.symbol">IntegerAlphabet.SubIntegerAlphabet</a></li>
<li><a href="org/biojava/ontology/IntegerOntology.html" title="class in org.biojava.ontology">IntegerOntology</a></li>
<li><a href="org/biojava/bio/seq/io/IntegerTokenization.html" title="class in org.biojava.bio.seq.io">IntegerTokenization</a></li>
<li><a href="org/biojava/utils/stax/IntElementHandlerBase.html" title="class in org.biojava.utils.stax">IntElementHandlerBase</a></li>
<li><a href="org/biojava/utils/bytecode/IntrospectedCodeClass.html" title="class in org.biojava.utils.bytecode">IntrospectedCodeClass</a></li>
<li><a href="org/biojava/ontology/InvalidTermException.html" title="class in org.biojava.ontology">InvalidTermException</a></li>
<li><a href="org/biojava/bio/proteomics/IsoelectricPointCalc.html" title="class in org.biojava.bio.proteomics">IsoelectricPointCalc</a></li>
<li><a href="org/biojava/stats/svm/ItemValue.html" title="interface in org.biojava.stats.svm"><i>ItemValue</i></a></li>
<li><a href="org/biojava/utils/JDBCConnectionPool.html" title="class in org.biojava.utils">JDBCConnectionPool</a></li>
<li><a href="org/biojava/utils/JDBCPooledDataSource.html" title="class in org.biojava.utils">JDBCPooledDataSource</a></li>
<li><a href="org/biojava/utils/cache/KeyedWeakReference.html" title="class in org.biojava.utils.cache">KeyedWeakReference</a></li>
<li><a href="org/biojava/bio/search/KnuthMorrisPrattSearch.html" title="class in org.biojava.bio.search">KnuthMorrisPrattSearch</a></li>
<li><a href="org/biojava/utils/bytecode/Label.html" title="class in org.biojava.utils.bytecode">Label</a></li>
<li><a href="org/biojava/bio/gui/sequence/LabelledSequenceRenderer.html" title="class in org.biojava.bio.gui.sequence">LabelledSequenceRenderer</a></li>
<li><a href="org/biojava/bio/gui/sequence/LabelRenderer.html" title="interface in org.biojava.bio.gui.sequence"><i>LabelRenderer</i></a></li>
<li><a href="org/biojava/bio/gui/sequence/LabelRenderer.RenderNothing.html" title="class in org.biojava.bio.gui.sequence">LabelRenderer.RenderNothing</a></li>
<li><a href="org/biojava/utils/io/LargeBuffer.html" title="class in org.biojava.utils.io">LargeBuffer</a></li>
<li><a href="org/biojava/bio/gui/sequence/LayeredRenderer.html" title="class in org.biojava.bio.gui.sequence">LayeredRenderer</a></li>
<li><a href="org/biojava/bio/seq/LazyFeatureHolder.html" title="class in org.biojava.bio.seq">LazyFeatureHolder</a></li>
<li><a href="org/biojava/bio/annodb/LazyFilteredAnnotationDB.html" title="class in org.biojava.bio.annodb">LazyFilteredAnnotationDB</a></li>
<li><a href="org/biojava/bio/seq/impl/LazyFilterFeatureHolder.html" title="class in org.biojava.bio.seq.impl">LazyFilterFeatureHolder</a></li>
<li><a href="org/biojava/bio/annodb/LazySearchedAnnotationDB.html" title="class in org.biojava.bio.annodb">LazySearchedAnnotationDB</a></li>
<li><a href="org/biojava/utils/lsid/LifeScienceIdentifier.html" title="class in org.biojava.utils.lsid">LifeScienceIdentifier</a></li>
<li><a href="org/biojava/utils/lsid/LifeScienceIdentifierParseException.html" title="class in org.biojava.utils.lsid">LifeScienceIdentifierParseException</a></li>
<li><a href="org/biojava/bio/program/formats/Ligand.html" title="class in org.biojava.bio.program.formats">Ligand</a></li>
<li><a href="org/biojava/bio/program/formats/Ligand.Compound.html" title="class in org.biojava.bio.program.formats">Ligand.Compound</a></li>
<li><a href="org/biojava/bio/program/formats/Ligand.Enzyme.html" title="class in org.biojava.bio.program.formats">Ligand.Enzyme</a></li>
<li><a href="org/biojava/bio/program/formats/Ligand.Reaction.html" title="class in org.biojava.bio.program.formats">Ligand.Reaction</a></li>
<li><a href="org/biojava/bio/dp/twohead/LightPairDPCursor.html" title="class in org.biojava.bio.dp.twohead">LightPairDPCursor</a></li>
<li><a href="org/biojava/stats/svm/LinearKernel.html" title="class in org.biojava.stats.svm">LinearKernel</a></li>
<li><a href="org/biojava/bio/gui/sequence/LineInfo.html" title="class in org.biojava.bio.gui.sequence">LineInfo</a></li>
<li><a href="org/biojava/bio/program/tagvalue/LineSplitParser.html" title="class in org.biojava.bio.program.tagvalue">LineSplitParser</a></li>
<li><a href="org/biojava/stats/svm/ListSumKernel.html" title="class in org.biojava.stats.svm">ListSumKernel</a></li>
<li><a href="org/biojava/utils/ListTools.html" title="class in org.biojava.utils">ListTools</a></li>
<li><a href="org/biojava/utils/ListTools.Doublet.html" title="class in org.biojava.utils">ListTools.Doublet</a></li>
<li><a href="org/biojava/utils/ListTools.Mapper.html" title="interface in org.biojava.utils"><i>ListTools.Mapper</i></a></li>
<li><a href="org/biojava/utils/ListTools.SeriesList.html" title="class in org.biojava.utils">ListTools.SeriesList</a></li>
<li><a href="org/biojava/utils/ListTools.Triplet.html" title="class in org.biojava.utils">ListTools.Triplet</a></li>
<li><a href="org/biojava/utils/bytecode/LocalVariable.html" title="class in org.biojava.utils.bytecode">LocalVariable</a></li>
<li><a href="org/biojava/bio/symbol/Location.html" title="interface in org.biojava.bio.symbol"><i>Location</i></a></li>
<li><a href="org/biojava/bio/program/xff/LocationHandlerBase.html" title="class in org.biojava.bio.program.xff">LocationHandlerBase</a></li>
<li><a href="org/biojava/bio/symbol/LocationTools.html" title="class in org.biojava.bio.symbol">LocationTools</a></li>
<li><a href="org/biojava/bio/gui/LogoContext.html" title="interface in org.biojava.bio.gui"><i>LogoContext</i></a></li>
<li><a href="org/biojava/bio/gui/LogoPainter.html" title="interface in org.biojava.bio.gui"><i>LogoPainter</i></a></li>
<li><a href="org/biojava/utils/stax/LongElementHandlerBase.html" title="class in org.biojava.utils.stax">LongElementHandlerBase</a></li>
<li><a href="org/biojava/bio/dp/MagicalState.html" title="class in org.biojava.bio.dp">MagicalState</a></li>
<li><a href="org/biojava/bio/symbol/ManyToOneTranslationTable.html" title="interface in org.biojava.bio.symbol"><i>ManyToOneTranslationTable</i></a></li>
<li><a href="org/biojava/bio/program/ssaha/MappedDataStoreFactory.html" title="class in org.biojava.bio.program.ssaha">MappedDataStoreFactory</a></li>
<li><a href="org/biojava/utils/bytecode/MarkLabel.html" title="class in org.biojava.utils.bytecode">MarkLabel</a></li>
<li><a href="org/biojava/bio/dp/MarkovModel.html" title="interface in org.biojava.bio.dp"><i>MarkovModel</i></a></li>
<li><a href="org/biojava/bio/proteomics/MassCalc.html" title="class in org.biojava.bio.proteomics">MassCalc</a></li>
<li><a href="org/biojava/utils/regex/Matcher.html" title="class in org.biojava.utils.regex">Matcher</a></li>
<li><a href="org/biojava/bio/dp/twohead/MatrixPairDPCursor.html" title="class in org.biojava.bio.dp.twohead">MatrixPairDPCursor</a></li>
<li><a href="org/biojava/bio/search/MaxMismatchMatcher.html" title="class in org.biojava.bio.search">MaxMismatchMatcher</a></li>
<li><a href="org/biojava/bio/search/MaxMismatchPattern.html" title="class in org.biojava.bio.search">MaxMismatchPattern</a></li>
<li><a href="org/biojava/bio/program/Meme.html" title="class in org.biojava.bio.program">Meme</a></li>
<li><a href="org/biojava/bio/MergeAnnotation.html" title="class in org.biojava.bio">MergeAnnotation</a></li>
<li><a href="org/biojava/bio/seq/MergeFeatureHolder.html" title="class in org.biojava.bio.seq">MergeFeatureHolder</a></li>
<li><a href="org/biojava/bio/symbol/MergeLocation.html" title="class in org.biojava.bio.symbol">MergeLocation</a></li>
<li><a href="org/biojava/bio/annodb/MergingAnnotationDB.html" title="class in org.biojava.bio.annodb">MergingAnnotationDB</a></li>
<li><a href="org/biojava/utils/MergingIterator.html" title="class in org.biojava.utils">MergingIterator</a></li>
<li><a href="org/biojava/utils/MergingSet.html" title="class in org.biojava.utils">MergingSet</a></li>
<li><a href="org/biojava/bio/dp/ModelInState.html" title="interface in org.biojava.bio.dp"><i>ModelInState</i></a></li>
<li><a href="org/biojava/bio/dp/ModelTrainer.html" title="interface in org.biojava.bio.dp"><i>ModelTrainer</i></a></li>
<li><a href="org/biojava/bio/symbol/MotifTools.html" title="class in org.biojava.bio.symbol">MotifTools</a></li>
<li><a href="org/biojava/bio/seq/io/MSFAlignmentFormat.html" title="class in org.biojava.bio.seq.io">MSFAlignmentFormat</a></li>
<li><a href="org/biojava/bio/gui/sequence/MultiLineRenderer.html" title="class in org.biojava.bio.gui.sequence">MultiLineRenderer</a></li>
<li><a href="org/biojavax/bio/phylo/MultipleHitCorrection.html" title="class in org.biojavax.bio.phylo">MultipleHitCorrection</a></li>
<li><a href="org/biojavax/bio/seq/MultiSourceCompoundRichLocation.html" title="class in org.biojavax.bio.seq">MultiSourceCompoundRichLocation</a></li>
<li><a href="org/biojava/bio/program/tagvalue/MultiTagger.html" title="class in org.biojava.bio.program.tagvalue">MultiTagger</a></li>
<li><a href="org/biojavax/ga/functions/MutationFunction.html" title="interface in org.biojavax.ga.functions"><i>MutationFunction</i></a></li>
<li><a href="org/biojavax/ga/functions/MutationFunction.NoMutation.html" title="class in org.biojavax.ga.functions">MutationFunction.NoMutation</a></li>
<li><a href="org/biojava/bio/seq/db/biosql/MySQLDBHelper.html" title="class in org.biojava.bio.seq.db.biosql">MySQLDBHelper</a></li>
<li><a href="org/biojavax/Namespace.html" title="interface in org.biojavax"><i>Namespace</i></a></li>
<li><a href="org/biojava/bio/seq/io/NameTokenization.html" title="class in org.biojava.bio.seq.io">NameTokenization</a></li>
<li><a href="org/biojava/bio/program/blast2html/NcbiDatabaseURLGenerator.html" title="class in org.biojava.bio.program.blast2html">NcbiDatabaseURLGenerator</a></li>
<li><a href="org/biojava/bio/seq/db/NCBISequenceDB.html" title="class in org.biojava.bio.seq.db">NCBISequenceDB</a></li>
<li><a href="org/biojavax/bio/taxa/NCBITaxon.html" title="interface in org.biojavax.bio.taxa"><i>NCBITaxon</i></a></li>
<li><a href="org/biojavax/bio/taxa/io/NCBITaxonomyLoader.html" title="interface in org.biojavax.bio.taxa.io"><i>NCBITaxonomyLoader</i></a></li>
<li><a href="org/biojava/bio/alignment/NeedlemanWunsch.html" title="class in org.biojava.bio.alignment">NeedlemanWunsch</a></li>
<li><a href="org/biojava/stats/svm/NestedKernel.html" title="class in org.biojava.stats.svm">NestedKernel</a></li>
<li><a href="org/biojava/bio/seq/impl/NewAssembledSymbolList.html" title="class in org.biojava.bio.seq.impl">NewAssembledSymbolList</a></li>
<li><a href="org/biojava/bio/seq/NewSimpleAssembly.html" title="class in org.biojava.bio.seq">NewSimpleAssembly</a></li>
<li><a href="org/biojavax/bio/phylo/io/nexus/NexusBlock.html" title="interface in org.biojavax.bio.phylo.io.nexus"><i>NexusBlock</i></a></li>
<li><a href="org/biojavax/bio/phylo/io/nexus/NexusBlock.Abstract.html" title="class in org.biojavax.bio.phylo.io.nexus">NexusBlock.Abstract</a></li>
<li><a href="org/biojavax/bio/phylo/io/nexus/NexusBlockBuilder.html" title="interface in org.biojavax.bio.phylo.io.nexus"><i>NexusBlockBuilder</i></a></li>
<li><a href="org/biojavax/bio/phylo/io/nexus/NexusBlockBuilder.Abstract.html" title="class in org.biojavax.bio.phylo.io.nexus">NexusBlockBuilder.Abstract</a></li>
<li><a href="org/biojavax/bio/phylo/io/nexus/NexusBlockListener.html" title="interface in org.biojavax.bio.phylo.io.nexus"><i>NexusBlockListener</i></a></li>
<li><a href="org/biojavax/bio/phylo/io/nexus/NexusBlockParser.html" title="interface in org.biojavax.bio.phylo.io.nexus"><i>NexusBlockParser</i></a></li>
<li><a href="org/biojavax/bio/phylo/io/nexus/NexusBlockParser.Abstract.html" title="class in org.biojavax.bio.phylo.io.nexus">NexusBlockParser.Abstract</a></li>
<li><a href="org/biojavax/bio/phylo/io/nexus/NexusComment.html" title="class in org.biojavax.bio.phylo.io.nexus">NexusComment</a></li>
<li><a href="org/biojavax/bio/phylo/io/nexus/NexusFile.html" title="class in org.biojavax.bio.phylo.io.nexus">NexusFile</a></li>
<li><a href="org/biojavax/bio/phylo/io/nexus/NexusFileBuilder.html" title="class in org.biojavax.bio.phylo.io.nexus">NexusFileBuilder</a></li>
<li><a href="org/biojavax/bio/phylo/io/nexus/NexusFileFormat.html" title="class in org.biojavax.bio.phylo.io.nexus">NexusFileFormat</a></li>
<li><a href="org/biojavax/bio/phylo/io/nexus/NexusFileListener.html" title="interface in org.biojavax.bio.phylo.io.nexus"><i>NexusFileListener</i></a></li>
<li><a href="org/biojavax/bio/phylo/io/nexus/NexusFileListener.Abstract.html" title="class in org.biojavax.bio.phylo.io.nexus">NexusFileListener.Abstract</a></li>
<li><a href="org/biojavax/bio/phylo/io/nexus/NexusObject.html" title="interface in org.biojavax.bio.phylo.io.nexus"><i>NexusObject</i></a></li>
<li><a href="org/biojava/utils/automata/Nfa.html" title="class in org.biojava.utils.automata">Nfa</a></li>
<li><a href="org/biojava/utils/automata/NfaBuilder.html" title="interface in org.biojava.utils.automata"><i>NfaBuilder</i></a></li>
<li><a href="org/biojava/utils/automata/NfaSubModel.html" title="class in org.biojava.utils.automata">NfaSubModel</a></li>
<li><a href="org/biojava/bio/program/ssaha/NIODataStoreFactory.html" title="class in org.biojava.bio.program.ssaha">NIODataStoreFactory</a></li>
<li><a href="org/biojava/stats/svm/NormalizingKernel.html" title="class in org.biojava.stats.svm">NormalizingKernel</a></li>
<li><a href="org/biojavax/Note.html" title="interface in org.biojavax"><i>Note</i></a></li>
<li><a href="org/biojava/bio/seq/NucleotideTools.html" title="class in org.biojava.bio.seq">NucleotideTools</a></li>
<li><a href="org/biojava/naming/ObdaContext.html" title="class in org.biojava.naming">ObdaContext</a></li>
<li><a href="org/biojava/naming/ObdaInitialContextFactory.html" title="class in org.biojava.naming">ObdaInitialContextFactory</a></li>
<li><a href="org/biojava/directory/OBDARegistryParser.html" title="class in org.biojava.directory">OBDARegistryParser</a></li>
<li><a href="org/biojava/naming/ObdaUriParser.html" title="class in org.biojava.naming">ObdaUriParser</a></li>
<li><a href="org/biojava/utils/ObjectUtil.html" title="class in org.biojava.utils">ObjectUtil</a></li>
<li><a href="org/biojava/ontology/obo/OboFileEventListener.html" title="interface in org.biojava.ontology.obo"><i>OboFileEventListener</i></a></li>
<li><a href="org/biojava/ontology/obo/OboFileHandler.html" title="class in org.biojava.ontology.obo">OboFileHandler</a></li>
<li><a href="org/biojava/ontology/obo/OboFileParser.html" title="class in org.biojava.ontology.obo">OboFileParser</a></li>
<li><a href="org/biojava/ontology/obo/OboFileParser.SOPair.html" title="class in org.biojava.ontology.obo">OboFileParser.SOPair</a></li>
<li><a href="org/biojava/ontology/io/OboParser.html" title="class in org.biojava.ontology.io">OboParser</a></li>
<li><a href="org/biojava/bio/gui/sequence/OffsetRulerRenderer.html" title="class in org.biojava.bio.gui.sequence">OffsetRulerRenderer</a></li>
<li><a href="org/biojava/ontology/Ontology.html" title="interface in org.biojava.ontology"><i>Ontology</i></a></li>
<li><a href="org/biojava/ontology/Ontology.Impl.html" title="class in org.biojava.ontology">Ontology.Impl</a></li>
<li><a href="org/biojava/ontology/OntologyException.html" title="class in org.biojava.ontology">OntologyException</a></li>
<li><a href="org/biojava/ontology/OntologyFactory.html" title="interface in org.biojava.ontology"><i>OntologyFactory</i></a></li>
<li><a href="org/biojava/ontology/OntologyOps.html" title="interface in org.biojava.ontology"><i>OntologyOps</i></a></li>
<li><a href="org/biojava/ontology/OntologyTerm.html" title="interface in org.biojava.ontology"><i>OntologyTerm</i></a></li>
<li><a href="org/biojava/ontology/OntologyTerm.Impl.html" title="class in org.biojava.ontology">OntologyTerm.Impl</a></li>
<li><a href="org/biojava/ontology/OntoTools.html" title="class in org.biojava.ontology">OntoTools</a></li>
<li><a href="org/biojava/bio/seq/OptimizableFilter.html" title="interface in org.biojava.bio.seq"><i>OptimizableFilter</i></a></li>
<li><a href="org/biojava/bio/seq/db/biosql/OracleDBHelper.html" title="class in org.biojava.bio.seq.db.biosql">OracleDBHelper</a></li>
<li><a href="org/biojavax/ga/functions/OrderCrossover.html" title="class in org.biojavax.ga.functions">OrderCrossover</a></li>
<li><a href="org/biojava/bio/dist/OrderNDistribution.html" title="interface in org.biojava.bio.dist"><i>OrderNDistribution</i></a></li>
<li><a href="org/biojava/bio/dist/OrderNDistributionFactory.html" title="class in org.biojava.bio.dist">OrderNDistributionFactory</a></li>
<li><a href="org/biojavax/ga/Organism.html" title="interface in org.biojavax.ga"><i>Organism</i></a></li>
<li><a href="org/biojava/bio/seq/io/OrganismParser.html" title="class in org.biojava.bio.seq.io">OrganismParser</a></li>
<li><a href="org/biojava/bio/seq/io/OrganismParser.Factory.html" title="class in org.biojava.bio.seq.io">OrganismParser.Factory</a></li>
<li><a href="org/biojava/bio/program/homologene/Orthologue.html" title="interface in org.biojava.bio.program.homologene"><i>Orthologue</i></a></li>
<li><a href="org/biojava/bio/program/homologene/OrthologueFilter.html" title="interface in org.biojava.bio.program.homologene"><i>OrthologueFilter</i></a></li>
<li><a href="org/biojava/bio/program/homologene/OrthologueFilter.AcceptAll.html" title="class in org.biojava.bio.program.homologene">OrthologueFilter.AcceptAll</a></li>
<li><a href="org/biojava/bio/program/homologene/OrthologueFilter.And.html" title="class in org.biojava.bio.program.homologene">OrthologueFilter.And</a></li>
<li><a href="org/biojava/bio/program/homologene/OrthologueFilter.ByAccession.html" title="class in org.biojava.bio.program.homologene">OrthologueFilter.ByAccession</a></li>
<li><a href="org/biojava/bio/program/homologene/OrthologueFilter.ByHomologeneID.html" title="class in org.biojava.bio.program.homologene">OrthologueFilter.ByHomologeneID</a></li>
<li><a href="org/biojava/bio/program/homologene/OrthologueFilter.ByLocusID.html" title="class in org.biojava.bio.program.homologene">OrthologueFilter.ByLocusID</a></li>
<li><a href="org/biojava/bio/program/homologene/OrthologueFilter.ByTaxon.html" title="class in org.biojava.bio.program.homologene">OrthologueFilter.ByTaxon</a></li>
<li><a href="org/biojava/bio/program/homologene/OrthologueFilter.ByTaxonID.html" title="class in org.biojava.bio.program.homologene">OrthologueFilter.ByTaxonID</a></li>
<li><a href="org/biojava/bio/program/homologene/OrthologueFilter.ByTitle.html" title="class in org.biojava.bio.program.homologene">OrthologueFilter.ByTitle</a></li>
<li><a href="org/biojava/bio/program/homologene/OrthologueFilter.Not.html" title="class in org.biojava.bio.program.homologene">OrthologueFilter.Not</a></li>
<li><a href="org/biojava/bio/program/homologene/OrthologueFilter.Or.html" title="class in org.biojava.bio.program.homologene">OrthologueFilter.Or</a></li>
<li><a href="org/biojava/bio/program/homologene/OrthologueFilter.Xor.html" title="class in org.biojava.bio.program.homologene">OrthologueFilter.Xor</a></li>
<li><a href="org/biojava/bio/program/homologene/OrthologueSet.html" title="interface in org.biojava.bio.program.homologene"><i>OrthologueSet</i></a></li>
<li><a href="org/biojava/bio/program/homologene/OrthologueSet.Iterator.html" title="interface in org.biojava.bio.program.homologene"><i>OrthologueSet.Iterator</i></a></li>
<li><a href="org/biojava/bio/program/homologene/OrthoPair.html" title="interface in org.biojava.bio.program.homologene"><i>OrthoPair</i></a></li>
<li><a href="org/biojava/bio/program/homologene/OrthoPairCollection.html" title="interface in org.biojava.bio.program.homologene"><i>OrthoPairCollection</i></a></li>
<li><a href="org/biojava/bio/program/homologene/OrthoPairCollection.Iterator.html" title="interface in org.biojava.bio.program.homologene"><i>OrthoPairCollection.Iterator</i></a></li>
<li><a href="org/biojava/bio/program/homologene/OrthoPairFilter.html" title="interface in org.biojava.bio.program.homologene"><i>OrthoPairFilter</i></a></li>
<li><a href="org/biojava/bio/program/homologene/OrthoPairFilter.AcceptAll.html" title="class in org.biojava.bio.program.homologene">OrthoPairFilter.AcceptAll</a></li>
<li><a href="org/biojava/bio/program/homologene/OrthoPairFilter.And.html" title="class in org.biojava.bio.program.homologene">OrthoPairFilter.And</a></li>
<li><a href="org/biojava/bio/program/homologene/OrthoPairFilter.ByMaxIdentity.html" title="class in org.biojava.bio.program.homologene">OrthoPairFilter.ByMaxIdentity</a></li>
<li><a href="org/biojava/bio/program/homologene/OrthoPairFilter.ByMinIdentity.html" title="class in org.biojava.bio.program.homologene">OrthoPairFilter.ByMinIdentity</a></li>
<li><a href="org/biojava/bio/program/homologene/OrthoPairFilter.ByRef.html" title="class in org.biojava.bio.program.homologene">OrthoPairFilter.ByRef</a></li>
<li><a href="org/biojava/bio/program/homologene/OrthoPairFilter.BySimilarityType.html" title="class in org.biojava.bio.program.homologene">OrthoPairFilter.BySimilarityType</a></li>
<li><a href="org/biojava/bio/program/homologene/OrthoPairFilter.Not.html" title="class in org.biojava.bio.program.homologene">OrthoPairFilter.Not</a></li>
<li><a href="org/biojava/bio/program/homologene/OrthoPairFilter.Or.html" title="class in org.biojava.bio.program.homologene">OrthoPairFilter.Or</a></li>
<li><a href="org/biojava/bio/program/homologene/OrthoPairFilter.Xor.html" title="class in org.biojava.bio.program.homologene">OrthoPairFilter.Xor</a></li>
<li><a href="org/biojava/bio/program/homologene/OrthoPairSet.html" title="interface in org.biojava.bio.program.homologene"><i>OrthoPairSet</i></a></li>
<li><a href="org/biojava/bio/program/homologene/OrthoPairSet.Iterator.html" title="interface in org.biojava.bio.program.homologene"><i>OrthoPairSet.Iterator</i></a></li>
<li><a href="org/biojava/bio/program/homologene/OrthoPairSetFilter.html" title="interface in org.biojava.bio.program.homologene"><i>OrthoPairSetFilter</i></a></li>
<li><a href="org/biojava/bio/program/homologene/OrthoPairSetFilter.AcceptAll.html" title="class in org.biojava.bio.program.homologene">OrthoPairSetFilter.AcceptAll</a></li>
<li><a href="org/biojava/bio/program/homologene/OrthoPairSetFilter.AllPairsInCollection.html" title="class in org.biojava.bio.program.homologene">OrthoPairSetFilter.AllPairsInCollection</a></li>
<li><a href="org/biojava/bio/program/homologene/OrthoPairSetFilter.And.html" title="class in org.biojava.bio.program.homologene">OrthoPairSetFilter.And</a></li>
<li><a href="org/biojava/bio/program/homologene/OrthoPairSetFilter.ByMinIdentity.html" title="class in org.biojava.bio.program.homologene">OrthoPairSetFilter.ByMinIdentity</a></li>
<li><a href="org/biojava/bio/program/homologene/OrthoPairSetFilter.ByTaxon.html" title="class in org.biojava.bio.program.homologene">OrthoPairSetFilter.ByTaxon</a></li>
<li><a href="org/biojava/bio/program/homologene/OrthoPairSetFilter.Not.html" title="class in org.biojava.bio.program.homologene">OrthoPairSetFilter.Not</a></li>
<li><a href="org/biojava/bio/program/homologene/OrthoPairSetFilter.Or.html" title="class in org.biojava.bio.program.homologene">OrthoPairSetFilter.Or</a></li>
<li><a href="org/biojava/bio/program/homologene/OrthoPairSetFilter.SomePairsInCollection.html" title="class in org.biojava.bio.program.homologene">OrthoPairSetFilter.SomePairsInCollection</a></li>
<li><a href="org/biojava/bio/program/homologene/OrthoPairSetFilter.Xor.html" title="class in org.biojava.bio.program.homologene">OrthoPairSetFilter.Xor</a></li>
<li><a href="org/biojava/utils/process/OutputHandler.html" title="interface in org.biojava.utils.process"><i>OutputHandler</i></a></li>
<li><a href="org/biojava/bio/OverlayAnnotation.html" title="class in org.biojava.bio">OverlayAnnotation</a></li>
<li><a href="org/biojava/utils/OverlayMap.html" title="class in org.biojava.utils">OverlayMap</a></li>
<li><a href="org/biojava/bio/gui/sequence/OverlayMarker.html" title="interface in org.biojava.bio.gui.sequence"><i>OverlayMarker</i></a></li>
<li><a href="org/biojava/bio/gui/sequence/OverlayRendererWrapper.html" title="class in org.biojava.bio.gui.sequence">OverlayRendererWrapper</a></li>
<li><a href="org/biojava/bio/symbol/PackedSymbolList.html" title="class in org.biojava.bio.symbol">PackedSymbolList</a></li>
<li><a href="org/biojava/bio/symbol/PackedSymbolListFactory.html" title="class in org.biojava.bio.symbol">PackedSymbolListFactory</a></li>
<li><a href="org/biojava/bio/symbol/Packing.html" title="interface in org.biojava.bio.symbol"><i>Packing</i></a></li>
<li><a href="org/biojava/bio/symbol/PackingFactory.html" title="class in org.biojava.bio.symbol">PackingFactory</a></li>
<li><a href="org/biojava/bio/gui/sequence/PaddingRenderer.html" title="class in org.biojava.bio.gui.sequence">PaddingRenderer</a></li>
<li><a href="org/biojava/bio/dist/PairDistribution.html" title="class in org.biojava.bio.dist">PairDistribution</a></li>
<li><a href="org/biojava/bio/dp/twohead/PairDPCursor.html" title="interface in org.biojava.bio.dp.twohead"><i>PairDPCursor</i></a></li>
<li><a href="org/biojava/bio/dp/twohead/PairDPMatrix.html" title="class in org.biojava.bio.dp.twohead">PairDPMatrix</a></li>
<li><a href="org/biojava/bio/gui/sequence/PairwiseDiagonalRenderer.html" title="class in org.biojava.bio.gui.sequence">PairwiseDiagonalRenderer</a></li>
<li><a href="org/biojava/bio/dp/twohead/PairwiseDP.html" title="class in org.biojava.bio.dp.twohead">PairwiseDP</a></li>
<li><a href="org/biojava/bio/gui/sequence/PairwiseFilteringRenderer.html" title="class in org.biojava.bio.gui.sequence">PairwiseFilteringRenderer</a></li>
<li><a href="org/biojava/bio/gui/sequence/PairwiseOverlayRenderer.html" title="class in org.biojava.bio.gui.sequence">PairwiseOverlayRenderer</a></li>
<li><a href="org/biojava/bio/gui/sequence/PairwiseRenderContext.html" title="interface in org.biojava.bio.gui.sequence"><i>PairwiseRenderContext</i></a></li>
<li><a href="org/biojava/bio/gui/sequence/PairwiseSequencePanel.html" title="class in org.biojava.bio.gui.sequence">PairwiseSequencePanel</a></li>
<li><a href="org/biojava/bio/gui/sequence/PairwiseSequenceRenderer.html" title="interface in org.biojava.bio.gui.sequence"><i>PairwiseSequenceRenderer</i></a></li>
<li><a href="org/biojava/bio/gui/sequence/PairwiseSequenceRenderer.PairwiseRendererForwarder.html" title="class in org.biojava.bio.gui.sequence">PairwiseSequenceRenderer.PairwiseRendererForwarder</a></li>
<li><a href="org/biojava/utils/bytecode/ParametricCodeGenerator.html" title="interface in org.biojava.utils.bytecode"><i>ParametricCodeGenerator</i></a></li>
<li><a href="org/biojava/utils/bytecode/ParametricType.html" title="class in org.biojava.utils.bytecode">ParametricType</a></li>
<li><a href="org/biojava/utils/ParseErrorEvent.html" title="class in org.biojava.utils">ParseErrorEvent</a></li>
<li><a href="org/biojava/utils/ParseErrorListener.html" title="interface in org.biojava.utils"><i>ParseErrorListener</i></a></li>
<li><a href="org/biojava/utils/ParseErrorSource.html" title="interface in org.biojava.utils"><i>ParseErrorSource</i></a></li>
<li><a href="org/biojava/bio/seq/io/ParseException.html" title="class in org.biojava.bio.seq.io">ParseException</a></li>
<li><a href="org/biojava/bio/program/fastq/ParseListener.html" title="interface in org.biojava.bio.program.fastq"><i>ParseListener</i></a></li>
<li><a href="org/biojava/bio/program/tagvalue/Parser.html" title="class in org.biojava.bio.program.tagvalue">Parser</a></li>
<li><a href="org/biojava/utils/ParserException.html" title="class in org.biojava.utils">ParserException</a></li>
<li><a href="org/biojava/bio/program/tagvalue/ParserListener.html" title="class in org.biojava.bio.program.tagvalue">ParserListener</a></li>
<li><a href="org/biojavax/bio/phylo/ParsimonyTreeMethod.html" title="class in org.biojavax.bio.phylo">ParsimonyTreeMethod</a></li>
<li><a href="org/biojava/utils/regex/Pattern.html" title="class in org.biojava.utils.regex">Pattern</a></li>
<li><a href="org/biojava/utils/automata/PatternBlitz.html" title="class in org.biojava.utils.automata">PatternBlitz</a></li>
<li><a href="org/biojava/utils/regex/PatternFactory.html" title="class in org.biojava.utils.regex">PatternFactory</a></li>
<li><a href="org/biojava/utils/automata/PatternListener.html" title="interface in org.biojava.utils.automata"><i>PatternListener</i></a></li>
<li><a href="org/biojava/utils/automata/PatternMaker.html" title="class in org.biojava.utils.automata">PatternMaker</a></li>
<li><a href="org/biojava/bio/program/sax/PdbSAXParser.html" title="class in org.biojava.bio.program.sax">PdbSAXParser</a></li>
<li><a href="org/biojava/bio/program/PdbToXMLConverter.html" title="class in org.biojava.bio.program">PdbToXMLConverter</a></li>
<li><a href="org/biojava/bio/gui/sequence/PeptideDigestRenderer.html" title="class in org.biojava.bio.gui.sequence">PeptideDigestRenderer</a></li>
<li><a href="org/biojava/bio/program/phred/PhredFormat.html" title="class in org.biojava.bio.program.phred">PhredFormat</a></li>
<li><a href="org/biojava/bio/program/phred/PhredSequence.html" title="class in org.biojava.bio.program.phred">PhredSequence</a></li>
<li><a href="org/biojava/bio/program/phred/PhredTools.html" title="class in org.biojava.bio.program.phred">PhredTools</a></li>
<li><a href="org/biojavax/bio/phylo/io/phylip/PHYLIPFileBuilder.html" title="class in org.biojavax.bio.phylo.io.phylip">PHYLIPFileBuilder</a></li>
<li><a href="org/biojavax/bio/phylo/io/phylip/PHYLIPFileFormat.html" title="class in org.biojavax.bio.phylo.io.phylip">PHYLIPFileFormat</a></li>
<li><a href="org/biojavax/bio/phylo/io/phylip/PHYLIPFileListener.html" title="interface in org.biojavax.bio.phylo.io.phylip"><i>PHYLIPFileListener</i></a></li>
<li><a href="org/biojava/bio/gui/PlainBlock.html" title="class in org.biojava.bio.gui">PlainBlock</a></li>
<li><a href="org/biojava/bio/gui/PlainStyle.html" title="class in org.biojava.bio.gui">PlainStyle</a></li>
<li><a href="org/biojava/bio/symbol/PointLocation.html" title="class in org.biojava.bio.symbol">PointLocation</a></li>
<li><a href="org/biojava/stats/svm/PolynomialKernel.html" title="class in org.biojava.stats.svm">PolynomialKernel</a></li>
<li><a href="org/biojavax/ga/Population.html" title="interface in org.biojavax.ga"><i>Population</i></a></li>
<li><a href="org/biojavax/bio/seq/Position.html" title="interface in org.biojavax.bio.seq"><i>Position</i></a></li>
<li><a href="org/biojavax/bio/seq/PositionResolver.html" title="interface in org.biojavax.bio.seq"><i>PositionResolver</i></a></li>
<li><a href="org/biojavax/bio/seq/PositionResolver.AverageResolver.html" title="class in org.biojavax.bio.seq">PositionResolver.AverageResolver</a></li>
<li><a href="org/biojavax/bio/seq/PositionResolver.MaximalResolver.html" title="class in org.biojavax.bio.seq">PositionResolver.MaximalResolver</a></li>
<li><a href="org/biojavax/bio/seq/PositionResolver.MinimalResolver.html" title="class in org.biojavax.bio.seq">PositionResolver.MinimalResolver</a></li>
<li><a href="org/biojava/bio/seq/db/biosql/PostgreSQLDBHelper.html" title="class in org.biojava.bio.seq.db.biosql">PostgreSQLDBHelper</a></li>
<li><a href="org/biojava/utils/bytecode/PParametricCodeGenerator.html" title="interface in org.biojava.utils.bytecode"><i>PParametricCodeGenerator</i></a></li>
<li><a href="org/biojava/utils/xml/PrettyXMLWriter.html" title="class in org.biojava.utils.xml">PrettyXMLWriter</a></li>
<li><a href="org/biojava/utils/ProcessTimeoutException.html" title="class in org.biojava.utils">ProcessTimeoutException</a></li>
<li><a href="org/biojava/utils/ProcessTools.html" title="class in org.biojava.utils">ProcessTools</a></li>
<li><a href="org/biojava/bio/program/hmmer/ProfileEmissionState.html" title="class in org.biojava.bio.program.hmmer">ProfileEmissionState</a></li>
<li><a href="org/biojava/bio/dp/ProfileHMM.html" title="class in org.biojava.bio.dp">ProfileHMM</a></li>
<li><a href="org/biojava/bio/seq/projection/ProjectedFeature.html" title="class in org.biojava.bio.seq.projection">ProjectedFeature</a></li>
<li><a href="org/biojava/bio/seq/projection/ProjectedFeatureHolder.html" title="class in org.biojava.bio.seq.projection">ProjectedFeatureHolder</a></li>
<li><a href="org/biojava/bio/seq/projection/Projection.html" title="interface in org.biojava.bio.seq.projection"><i>Projection</i></a></li>
<li><a href="org/biojava/bio/seq/projection/ProjectionContext.html" title="interface in org.biojava.bio.seq.projection"><i>ProjectionContext</i></a></li>
<li><a href="org/biojava/bio/seq/projection/ProjectionEngine.html" title="class in org.biojava.bio.seq.projection">ProjectionEngine</a></li>
<li><a href="org/biojava/bio/seq/projection/ProjectionEngine.Instantiator.html" title="interface in org.biojava.bio.seq.projection"><i>ProjectionEngine.Instantiator</i></a></li>
<li><a href="org/biojava/bio/seq/projection/ProjectionEngine.TemplateProjector.html" title="interface in org.biojava.bio.seq.projection"><i>ProjectionEngine.TemplateProjector</i></a></li>
<li><a href="org/biojava/bio/seq/projection/ProjectionUtils.html" title="class in org.biojava.bio.seq.projection">ProjectionUtils</a></li>
<li><a href="org/biojava/bio/program/xff/PropDetailHandler.html" title="class in org.biojava.bio.program.xff">PropDetailHandler</a></li>
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