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<!DOCTYPE HTML>
<!-- NewPage -->
<html lang="en">
<head>
<!-- Generated by javadoc (11.0.16) on Fri Oct 28 16:15:48 PDT 2022 -->
<title>All Classes (biojava 6.1.0 API)</title>
<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
<meta name="dc.created" content="2022-10-28">
<link rel="stylesheet" type="text/css" href="stylesheet.css" title="Style">
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<body>
<h1 class="bar">All Classes</h1>
<main role="main" class="indexContainer">
<ul>
<li><a href="org/biojava/nbio/core/alignment/matrices/AAindexFactory.html" title="class in org.biojava.nbio.core.alignment.matrices">AAindexFactory</a></li>
<li><a href="org/biojava/nbio/core/alignment/matrices/AAIndexFileParser.html" title="class in org.biojava.nbio.core.alignment.matrices">AAIndexFileParser</a></li>
<li><a href="org/biojava/nbio/core/alignment/matrices/AAIndexProvider.html" title="interface in org.biojava.nbio.core.alignment.matrices"><span class="interfaceName">AAIndexProvider</span></a></li>
<li><a href="org/biojava/nbio/core/sequence/io/ABITrace.html" title="class in org.biojava.nbio.core.sequence.io">ABITrace</a></li>
<li><a href="org/biojava/nbio/core/sequence/compound/ABITracerCompoundSet.html" title="class in org.biojava.nbio.core.sequence.compound">ABITracerCompoundSet</a></li>
<li><a href="org/biojava/nbio/structure/align/gui/AboutDialog.html" title="class in org.biojava.nbio.structure.align.gui">AboutDialog</a></li>
<li><a href="org/biojava/nbio/structure/align/gui/jmol/AbstractAlignmentJmol.html" title="class in org.biojava.nbio.structure.align.gui.jmol">AbstractAlignmentJmol</a></li>
<li><a href="org/biojava/nbio/ontology/utils/AbstractAnnotation.html" title="class in org.biojava.nbio.ontology.utils">AbstractAnnotation</a></li>
<li><a href="org/biojava/nbio/structure/io/cif/AbstractCifFileSupplier.html" title="class in org.biojava.nbio.structure.io.cif">AbstractCifFileSupplier</a></li>
<li><a href="org/biojava/nbio/structure/io/cif/AbstractCifFileSupplier.WrappedAtom.html" title="class in org.biojava.nbio.structure.io.cif">AbstractCifFileSupplier.WrappedAtom</a></li>
<li><a href="org/biojava/nbio/core/sequence/template/AbstractCompound.html" title="class in org.biojava.nbio.core.sequence.template">AbstractCompound</a></li>
<li><a href="org/biojava/nbio/core/sequence/template/AbstractCompoundSet.html" title="class in org.biojava.nbio.core.sequence.template">AbstractCompoundSet</a></li>
<li><a href="org/biojava/nbio/core/sequence/template/AbstractCompoundTranslator.html" title="class in org.biojava.nbio.core.sequence.template">AbstractCompoundTranslator</a></li>
<li><a href="org/biojava/nbio/core/sequence/features/AbstractFeature.html" title="class in org.biojava.nbio.core.sequence.features">AbstractFeature</a></li>
<li><a href="org/biojava/nbio/core/sequence/location/template/AbstractLocation.html" title="class in org.biojava.nbio.core.sequence.location.template">AbstractLocation</a></li>
<li><a href="org/biojava/nbio/alignment/template/AbstractMatrixAligner.html" title="class in org.biojava.nbio.alignment.template">AbstractMatrixAligner</a></li>
<li><a href="org/biojava/nbio/core/sequence/template/AbstractNucleotideCompoundSet.html" title="class in org.biojava.nbio.core.sequence.template">AbstractNucleotideCompoundSet</a></li>
<li><a href="org/biojava/nbio/alignment/template/AbstractPairwiseSequenceAligner.html" title="class in org.biojava.nbio.alignment.template">AbstractPairwiseSequenceAligner</a></li>
<li><a href="org/biojava/nbio/alignment/template/AbstractProfileProfileAligner.html" title="class in org.biojava.nbio.alignment.template">AbstractProfileProfileAligner</a></li>
<li><a href="org/biojava/nbio/core/sequence/reference/AbstractReference.html" title="class in org.biojava.nbio.core.sequence.reference">AbstractReference</a></li>
<li><a href="org/biojava/nbio/alignment/template/AbstractScorer.html" title="class in org.biojava.nbio.alignment.template">AbstractScorer</a></li>
<li><a href="org/biojava/nbio/structure/align/multiple/AbstractScoresCache.html" title="class in org.biojava.nbio.structure.align.multiple">AbstractScoresCache</a></li>
<li><a href="org/biojava/nbio/core/sequence/template/AbstractSequence.html" title="class in org.biojava.nbio.core.sequence.template">AbstractSequence</a></li>
<li><a href="org/biojava/nbio/core/sequence/template/AbstractSequence.AnnotationType.html" title="enum in org.biojava.nbio.core.sequence.template">AbstractSequence.AnnotationType</a></li>
<li><a href="org/biojava/nbio/structure/align/AbstractStructureAlignment.html" title="class in org.biojava.nbio.structure.align">AbstractStructureAlignment</a></li>
<li><a href="org/biojava/nbio/ontology/AbstractTerm.html" title="class in org.biojava.nbio.ontology">AbstractTerm</a></li>
<li><a href="org/biojava/nbio/structure/align/ce/AbstractUserArgumentProcessor.html" title="class in org.biojava.nbio.structure.align.ce">AbstractUserArgumentProcessor</a></li>
<li><a href="org/biojava/nbio/core/sequence/location/template/AccesionedLocation.html" title="interface in org.biojava.nbio.core.sequence.location.template"><span class="interfaceName">AccesionedLocation</span></a></li>
<li><a href="org/biojava/nbio/core/sequence/template/Accessioned.html" title="interface in org.biojava.nbio.core.sequence.template"><span class="interfaceName">Accessioned</span></a></li>
<li><a href="org/biojava/nbio/core/sequence/AccessionID.html" title="class in org.biojava.nbio.core.sequence">AccessionID</a></li>
<li><a href="org/biojava/nbio/structure/align/model/AFP.html" title="class in org.biojava.nbio.structure.align.model">AFP</a></li>
<li><a href="org/biojava/nbio/structure/align/util/AFPAlignmentDisplay.html" title="class in org.biojava.nbio.structure.align.util">AFPAlignmentDisplay</a></li>
<li><a href="org/biojava/nbio/structure/align/fatcat/calc/AFPCalculator.html" title="class in org.biojava.nbio.structure.align.fatcat.calc">AFPCalculator</a></li>
<li><a href="org/biojava/nbio/structure/align/model/AFPChain.html" title="class in org.biojava.nbio.structure.align.model">AFPChain</a></li>
<li><a href="org/biojava/nbio/structure/align/gui/aligpanel/AFPChainCoordManager.html" title="class in org.biojava.nbio.structure.align.gui.aligpanel">AFPChainCoordManager</a></li>
<li><a href="org/biojava/nbio/structure/align/fatcat/calc/AFPChainer.html" title="class in org.biojava.nbio.structure.align.fatcat.calc">AFPChainer</a></li>
<li><a href="org/biojava/nbio/structure/align/xml/AFPChainFlipper.html" title="class in org.biojava.nbio.structure.align.xml">AFPChainFlipper</a></li>
<li><a href="org/biojava/nbio/structure/align/util/AFPChainScorer.html" title="class in org.biojava.nbio.structure.align.util">AFPChainScorer</a></li>
<li><a href="org/biojava/nbio/structure/align/model/AfpChainWriter.html" title="class in org.biojava.nbio.structure.align.model">AfpChainWriter</a></li>
<li><a href="org/biojava/nbio/structure/align/xml/AFPChainXMLConverter.html" title="class in org.biojava.nbio.structure.align.xml">AFPChainXMLConverter</a></li>
<li><a href="org/biojava/nbio/structure/align/xml/AFPChainXMLParser.html" title="class in org.biojava.nbio.structure.align.xml">AFPChainXMLParser</a></li>
<li><a href="demo/AFPFromFasta.html" title="class in demo">AFPFromFasta</a></li>
<li><a href="org/biojava/nbio/structure/align/fatcat/calc/AFPOptimizer.html" title="class in org.biojava.nbio.structure.align.fatcat.calc">AFPOptimizer</a></li>
<li><a href="org/biojava/nbio/structure/align/fatcat/calc/AFPPostProcessor.html" title="class in org.biojava.nbio.structure.align.fatcat.calc">AFPPostProcessor</a></li>
<li><a href="org/biojava/nbio/structure/align/AFPTwister.html" title="class in org.biojava.nbio.structure.align">AFPTwister</a></li>
<li><a href="org/biojava/nbio/survival/cox/stats/AgScore.html" title="class in org.biojava.nbio.survival.cox.stats">AgScore</a></li>
<li><a href="org/biojava/nbio/structure/align/helper/AligMatEl.html" title="class in org.biojava.nbio.structure.align.helper">AligMatEl</a></li>
<li><a href="org/biojava/nbio/structure/align/pairwise/Alignable.html" title="interface in org.biojava.nbio.structure.align.pairwise"><span class="interfaceName">Alignable</span></a></li>
<li><a href="org/biojava/nbio/structure/gui/util/AlignedPosition.html" title="class in org.biojava.nbio.structure.gui.util">AlignedPosition</a></li>
<li><a href="org/biojava/nbio/core/alignment/template/AlignedSequence.html" title="interface in org.biojava.nbio.core.alignment.template"><span class="interfaceName">AlignedSequence</span></a></li>
<li><a href="org/biojava/nbio/core/alignment/template/AlignedSequence.Step.html" title="enum in org.biojava.nbio.core.alignment.template">AlignedSequence.Step</a></li>
<li><a href="org/biojava/nbio/alignment/template/Aligner.html" title="interface in org.biojava.nbio.alignment.template"><span class="interfaceName">Aligner</span></a></li>
<li><a href="org/biojava/nbio/alignment/routines/AlignerHelper.html" title="class in org.biojava.nbio.alignment.routines">AlignerHelper</a></li>
<li><a href="org/biojava/nbio/alignment/routines/AlignerHelper.Anchor.html" title="class in org.biojava.nbio.alignment.routines">AlignerHelper.Anchor</a></li>
<li><a href="org/biojava/nbio/alignment/routines/AlignerHelper.Anchor.QueryIndexComparator.html" title="class in org.biojava.nbio.alignment.routines">AlignerHelper.Anchor.QueryIndexComparator</a></li>
<li><a href="org/biojava/nbio/alignment/routines/AlignerHelper.Cut.html" title="class in org.biojava.nbio.alignment.routines">AlignerHelper.Cut</a></li>
<li><a href="org/biojava/nbio/alignment/routines/AlignerHelper.Last.html" title="enum in org.biojava.nbio.alignment.routines">AlignerHelper.Last</a></li>
<li><a href="org/biojava/nbio/alignment/routines/AlignerHelper.Subproblem.html" title="class in org.biojava.nbio.alignment.routines">AlignerHelper.Subproblem</a></li>
<li><a href="org/biojava/nbio/structure/align/gui/AlignmentCalc.html" title="class in org.biojava.nbio.structure.align.gui">AlignmentCalc</a></li>
<li><a href="org/biojava/nbio/structure/gui/util/AlignmentCalc.html" title="class in org.biojava.nbio.structure.gui.util">AlignmentCalc</a></li>
<li><a href="org/biojava/nbio/structure/align/gui/AlignmentCalculationRunnable.html" title="interface in org.biojava.nbio.structure.align.gui"><span class="interfaceName">AlignmentCalculationRunnable</span></a></li>
<li><a href="org/biojava/nbio/structure/align/gui/AlignmentGui.html" title="class in org.biojava.nbio.structure.align.gui">AlignmentGui</a></li>
<li><a href="demo/AlignmentGuiDemo.html" title="class in demo">AlignmentGuiDemo</a></li>
<li><a href="org/biojava/nbio/structure/gui/events/AlignmentPositionListener.html" title="interface in org.biojava.nbio.structure.gui.events"><span class="interfaceName">AlignmentPositionListener</span></a></li>
<li><a href="org/biojava/nbio/structure/align/pairwise/AlignmentProgressListener.html" title="class in org.biojava.nbio.structure.align.pairwise">AlignmentProgressListener</a></li>
<li><a href="org/biojava/nbio/structure/align/pairwise/AlignmentResult.html" title="class in org.biojava.nbio.structure.align.pairwise">AlignmentResult</a></li>
<li><a href="org/biojava/nbio/alignment/Alignments.html" title="class in org.biojava.nbio.alignment">Alignments</a></li>
<li><a href="org/biojava/nbio/alignment/Alignments.PairInProfileScorerType.html" title="enum in org.biojava.nbio.alignment">Alignments.PairInProfileScorerType</a></li>
<li><a href="org/biojava/nbio/alignment/Alignments.PairwiseSequenceAlignerType.html" title="enum in org.biojava.nbio.alignment">Alignments.PairwiseSequenceAlignerType</a></li>
<li><a href="org/biojava/nbio/alignment/Alignments.PairwiseSequenceScorerType.html" title="enum in org.biojava.nbio.alignment">Alignments.PairwiseSequenceScorerType</a></li>
<li><a href="org/biojava/nbio/alignment/Alignments.ProfileProfileAlignerType.html" title="enum in org.biojava.nbio.alignment">Alignments.ProfileProfileAlignerType</a></li>
<li><a href="org/biojava/nbio/alignment/Alignments.RefinerType.html" title="enum in org.biojava.nbio.alignment">Alignments.RefinerType</a></li>
<li><a href="org/biojava/nbio/structure/align/gui/AlignmentTextPanel.html" title="class in org.biojava.nbio.structure.align.gui">AlignmentTextPanel</a></li>
<li><a href="org/biojava/nbio/structure/align/util/AlignmentTools.html" title="class in org.biojava.nbio.structure.align.util">AlignmentTools</a></li>
<li><a href="org/biojava/nbio/structure/align/util/AlignmentTools.IdentityMap.html" title="class in org.biojava.nbio.structure.align.util">AlignmentTools.IdentityMap</a></li>
<li><a href="org/biojava/nbio/structure/align/pairwise/AligNPE.html" title="class in org.biojava.nbio.structure.align.pairwise">AligNPE</a></li>
<li><a href="org/biojava/nbio/structure/align/helper/AlignUtils.html" title="class in org.biojava.nbio.structure.align.helper">AlignUtils</a></li>
<li><a href="org/biojava/nbio/structure/align/gui/aligpanel/AligPanel.html" title="class in org.biojava.nbio.structure.align.gui.aligpanel">AligPanel</a></li>
<li><a href="org/biojava/nbio/structure/align/gui/aligpanel/AligPanelMouseMotionListener.html" title="class in org.biojava.nbio.structure.align.gui.aligpanel">AligPanelMouseMotionListener</a></li>
<li><a href="org/biojava/nbio/structure/align/webstart/AligUIManager.html" title="class in org.biojava.nbio.structure.align.webstart">AligUIManager</a></li>
<li><a href="org/biojava/nbio/structure/chem/AllChemCompProvider.html" title="class in org.biojava.nbio.structure.chem">AllChemCompProvider</a></li>
<li><a href="org/biojava/nbio/ontology/AlreadyExistsException.html" title="class in org.biojava.nbio.ontology">AlreadyExistsException</a></li>
<li><a href="org/biojava/nbio/structure/align/pairwise/AltAligComparator.html" title="class in org.biojava.nbio.structure.align.pairwise">AltAligComparator</a></li>
<li><a href="org/biojava/nbio/structure/align/pairwise/AlternativeAlignment.html" title="class in org.biojava.nbio.structure.align.pairwise">AlternativeAlignment</a></li>
<li><a href="org/biojava/nbio/structure/gui/util/AlternativeAlignmentFrame.html" title="class in org.biojava.nbio.structure.gui.util">AlternativeAlignmentFrame</a></li>
<li><a href="org/biojava/nbio/core/sequence/compound/AmbiguityDNACompoundSet.html" title="class in org.biojava.nbio.core.sequence.compound">AmbiguityDNACompoundSet</a></li>
<li><a href="org/biojava/nbio/core/sequence/compound/AmbiguityDNARNAHybridCompoundSet.html" title="class in org.biojava.nbio.core.sequence.compound">AmbiguityDNARNAHybridCompoundSet</a></li>
<li><a href="org/biojava/nbio/core/sequence/compound/AmbiguityRNACompoundSet.html" title="class in org.biojava.nbio.core.sequence.compound">AmbiguityRNACompoundSet</a></li>
<li><a href="org/biojava/nbio/structure/AminoAcid.html" title="interface in org.biojava.nbio.structure"><span class="interfaceName">AminoAcid</span></a></li>
<li><a href="org/biojava/nbio/aaproperties/xml/AminoAcidComposition.html" title="class in org.biojava.nbio.aaproperties.xml">AminoAcidComposition</a></li>
<li><a href="org/biojava/nbio/aaproperties/xml/AminoAcidCompositionTable.html" title="class in org.biojava.nbio.aaproperties.xml">AminoAcidCompositionTable</a></li>
<li><a href="org/biojava/nbio/core/sequence/compound/AminoAcidCompound.html" title="class in org.biojava.nbio.core.sequence.compound">AminoAcidCompound</a></li>
<li><a href="org/biojava/nbio/core/sequence/compound/AminoAcidCompoundSet.html" title="class in org.biojava.nbio.core.sequence.compound">AminoAcidCompoundSet</a></li>
<li><a href="org/biojava/nbio/structure/AminoAcidImpl.html" title="class in org.biojava.nbio.structure">AminoAcidImpl</a></li>
<li><a href="org/biojava/nbio/aaproperties/AminoAcidProperties.html" title="class in org.biojava.nbio.aaproperties">AminoAcidProperties</a></li>
<li><a href="org/biojava/nbio/alignment/routines/AnchoredPairwiseSequenceAligner.html" title="class in org.biojava.nbio.alignment.routines">AnchoredPairwiseSequenceAligner</a></li>
<li><a href="org/biojava/nbio/structure/symmetry/internal/AngleOrderDetectorPlus.html" title="class in org.biojava.nbio.structure.symmetry.internal">AngleOrderDetectorPlus</a></li>
<li><a href="org/biojava/nbio/ontology/utils/Annotatable.html" title="interface in org.biojava.nbio.ontology.utils"><span class="interfaceName">Annotatable</span></a></li>
<li><a href="org/biojava/nbio/ontology/utils/Annotation.html" title="interface in org.biojava.nbio.ontology.utils"><span class="interfaceName">Annotation</span></a></li>
<li><a href="org/biojava/nbio/genome/App.html" title="class in org.biojava.nbio.genome">App</a></li>
<li><a href="org/biojava/nbio/ontology/App.html" title="class in org.biojava.nbio.ontology">App</a></li>
<li><a href="org/biojava/nbio/core/sequence/loader/ArrayListProxySequenceReader.html" title="class in org.biojava.nbio.core.sequence.loader">ArrayListProxySequenceReader</a></li>
<li><a href="org/biojava/nbio/core/sequence/storage/ArrayListSequenceReader.html" title="class in org.biojava.nbio.core.sequence.storage">ArrayListSequenceReader</a></li>
<li><a href="org/biojava/nbio/structure/asa/AsaCalculator.html" title="class in org.biojava.nbio.structure.asa">AsaCalculator</a></li>
<li><a href="org/biojava/nbio/ontology/utils/AssertionFailure.html" title="class in org.biojava.nbio.ontology.utils">AssertionFailure</a></li>
<li><a href="org/biojava/nbio/structure/scop/Astral.html" title="class in org.biojava.nbio.structure.scop">Astral</a></li>
<li><a href="org/biojava/nbio/structure/scop/Astral.AstralSet.html" title="enum in org.biojava.nbio.structure.scop">Astral.AstralSet</a></li>
<li><a href="org/biojava/nbio/structure/Atom.html" title="interface in org.biojava.nbio.structure"><span class="interfaceName">Atom</span></a></li>
<li><a href="org/biojava/nbio/structure/align/util/AtomCache.html" title="class in org.biojava.nbio.structure.align.util">AtomCache</a></li>
<li><a href="org/biojava/nbio/structure/contact/AtomContact.html" title="class in org.biojava.nbio.structure.contact">AtomContact</a></li>
<li><a href="org/biojava/nbio/structure/contact/AtomContactSet.html" title="class in org.biojava.nbio.structure.contact">AtomContactSet</a></li>
<li><a href="org/biojava/nbio/structure/contact/AtomIdentifier.html" title="class in org.biojava.nbio.structure.contact">AtomIdentifier</a></li>
<li><a href="org/biojava/nbio/structure/AtomImpl.html" title="class in org.biojava.nbio.structure">AtomImpl</a></li>
<li><a href="org/biojava/nbio/structure/align/gui/jmol/AtomInfo.html" title="class in org.biojava.nbio.structure.align.gui.jmol">AtomInfo</a></li>
<li><a href="org/biojava/nbio/structure/align/gui/jmol/AtomInfoParser.html" title="class in org.biojava.nbio.structure.align.gui.jmol">AtomInfoParser</a></li>
<li><a href="org/biojava/nbio/structure/AtomIterator.html" title="class in org.biojava.nbio.structure">AtomIterator</a></li>
<li><a href="org/biojava/nbio/structure/AtomPositionMap.html" title="class in org.biojava.nbio.structure">AtomPositionMap</a></li>
<li><a href="org/biojava/nbio/structure/AtomPositionMap.GroupMatcher.html" title="interface in org.biojava.nbio.structure"><span class="interfaceName">AtomPositionMap.GroupMatcher</span></a></li>
<li><a href="org/biojava/nbio/structure/AugmentedResidueRange.html" title="class in org.biojava.nbio.structure">AugmentedResidueRange</a></li>
<li><a href="org/biojava/nbio/structure/Author.html" title="class in org.biojava.nbio.structure">Author</a></li>
<li><a href="org/biojava/nbio/structure/align/gui/autosuggest/AutoSuggestProvider.html" title="interface in org.biojava.nbio.structure.align.gui.autosuggest"><span class="interfaceName">AutoSuggestProvider</span></a></li>
<li><a href="org/biojava/nbio/structure/symmetry/axis/AxisAligner.html" title="class in org.biojava.nbio.structure.symmetry.axis">AxisAligner</a></li>
<li><a href="org/biojava/nbio/structure/basepairs/BasePairParameters.html" title="class in org.biojava.nbio.structure.basepairs">BasePairParameters</a></li>
<li><a href="org/biojava/nbio/core/sequence/BasicSequence.html" title="class in org.biojava.nbio.core.sequence">BasicSequence</a></li>
<li><a href="org/biojava/nbio/structure/io/BcifFileReader.html" title="class in org.biojava.nbio.structure.io">BcifFileReader</a></li>
<li><a href="org/biojava/nbio/structure/scop/BerkeleyScopInstallation.html" title="class in org.biojava.nbio.structure.scop">BerkeleyScopInstallation</a></li>
<li><a href="org/biojava/nbio/structure/secstruc/BetaBridge.html" title="class in org.biojava.nbio.structure.secstruc">BetaBridge</a></li>
<li><a href="org/biojava/nbio/structure/BioAssemblyIdentifier.html" title="class in org.biojava.nbio.structure">BioAssemblyIdentifier</a></li>
<li><a href="org/biojava/nbio/structure/quaternary/BioAssemblyInfo.html" title="class in org.biojava.nbio.structure.quaternary">BioAssemblyInfo</a></li>
<li><a href="org/biojava/nbio/structure/quaternary/BioAssemblyTools.html" title="class in org.biojava.nbio.structure.quaternary">BioAssemblyTools</a></li>
<li><a href="demo/BioJavaAADemo.html" title="class in demo">BioJavaAADemo</a></li>
<li><a href="org/biojava/nbio/structure/gui/BiojavaJmol.html" title="class in org.biojava.nbio.structure.gui">BiojavaJmol</a></li>
<li><a href="org/biojava/nbio/structure/align/BioJavaStructureAlignment.html" title="class in org.biojava.nbio.structure.align">BioJavaStructureAlignment</a></li>
<li><a href="org/biojava/nbio/structure/quaternary/BiologicalAssemblyBuilder.html" title="class in org.biojava.nbio.structure.quaternary">BiologicalAssemblyBuilder</a></li>
<li><a href="org/biojava/nbio/structure/quaternary/BiologicalAssemblyTransformation.html" title="class in org.biojava.nbio.structure.quaternary">BiologicalAssemblyTransformation</a></li>
<li><a href="org/biojava/nbio/core/sequence/storage/BitSequenceReader.html" title="class in org.biojava.nbio.core.sequence.storage">BitSequenceReader</a></li>
<li><a href="org/biojava/nbio/core/sequence/storage/BitSequenceReader.BitArrayWorker.html" title="class in org.biojava.nbio.core.sequence.storage">BitSequenceReader.BitArrayWorker</a></li>
<li><a href="org/biojava/nbio/ws/alignment/qblast/BlastAlignmentParameterEnum.html" title="enum in org.biojava.nbio.ws.alignment.qblast">BlastAlignmentParameterEnum</a></li>
<li><a href="org/biojava/nbio/structure/symmetry/utils/BlastClustReader.html" title="class in org.biojava.nbio.structure.symmetry.utils">BlastClustReader</a></li>
<li><a href="org/biojava/nbio/core/search/io/blast/BlastHitBuilder.html" title="class in org.biojava.nbio.core.search.io.blast">BlastHitBuilder</a></li>
<li><a href="org/biojava/nbio/genome/homology/BlastHomologyHits.html" title="class in org.biojava.nbio.genome.homology">BlastHomologyHits</a></li>
<li><a href="org/biojava/nbio/core/search/io/blast/BlastHspBuilder.html" title="class in org.biojava.nbio.core.search.io.blast">BlastHspBuilder</a></li>
<li><a href="org/biojava/nbio/ws/alignment/qblast/BlastJob.html" title="class in org.biojava.nbio.ws.alignment.qblast">BlastJob</a></li>
<li><a href="org/biojava/nbio/ws/alignment/qblast/BlastMatrixEnum.html" title="enum in org.biojava.nbio.ws.alignment.qblast">BlastMatrixEnum</a></li>
<li><a href="org/biojava/nbio/ws/alignment/qblast/BlastOutputAlignmentFormatEnum.html" title="enum in org.biojava.nbio.ws.alignment.qblast">BlastOutputAlignmentFormatEnum</a></li>
<li><a href="org/biojava/nbio/ws/alignment/qblast/BlastOutputFormatEnum.html" title="enum in org.biojava.nbio.ws.alignment.qblast">BlastOutputFormatEnum</a></li>
<li><a href="org/biojava/nbio/ws/alignment/qblast/BlastOutputParameterEnum.html" title="enum in org.biojava.nbio.ws.alignment.qblast">BlastOutputParameterEnum</a></li>
<li><a href="org/biojava/nbio/ws/alignment/qblast/BlastProgramEnum.html" title="enum in org.biojava.nbio.ws.alignment.qblast">BlastProgramEnum</a></li>
<li><a href="org/biojava/nbio/core/search/io/blast/BlastResult.html" title="class in org.biojava.nbio.core.search.io.blast">BlastResult</a></li>
<li><a href="org/biojava/nbio/core/search/io/blast/BlastResultBuilder.html" title="class in org.biojava.nbio.core.search.io.blast">BlastResultBuilder</a></li>
<li><a href="org/biojava/nbio/core/search/io/blast/BlastTabularParser.html" title="class in org.biojava.nbio.core.search.io.blast">BlastTabularParser</a></li>
<li><a href="org/biojava/nbio/core/search/io/blast/BlastXMLParser.html" title="class in org.biojava.nbio.core.search.io.blast">BlastXMLParser</a></li>
<li><a href="org/biojava/nbio/genome/query/BlastXMLQuery.html" title="class in org.biojava.nbio.genome.query">BlastXMLQuery</a></li>
<li><a href="org/biojava/nbio/structure/align/multiple/Block.html" title="interface in org.biojava.nbio.structure.align.multiple"><span class="interfaceName">Block</span></a></li>
<li><a href="org/biojava/nbio/structure/align/multiple/BlockImpl.html" title="class in org.biojava.nbio.structure.align.multiple">BlockImpl</a></li>
<li><a href="org/biojava/nbio/structure/align/multiple/BlockSet.html" title="interface in org.biojava.nbio.structure.align.multiple"><span class="interfaceName">BlockSet</span></a></li>
<li><a href="org/biojava/nbio/structure/align/multiple/BlockSetImpl.html" title="class in org.biojava.nbio.structure.align.multiple">BlockSetImpl</a></li>
<li><a href="org/biojava/nbio/structure/Bond.html" title="interface in org.biojava.nbio.structure"><span class="interfaceName">Bond</span></a></li>
<li><a href="org/biojava/nbio/structure/BondImpl.html" title="class in org.biojava.nbio.structure">BondImpl</a></li>
<li><a href="org/biojava/nbio/structure/io/BondMaker.html" title="class in org.biojava.nbio.structure.io">BondMaker</a></li>
<li><a href="org/biojava/nbio/structure/BondType.html" title="enum in org.biojava.nbio.structure">BondType</a></li>
<li><a href="org/biojava/nbio/structure/contact/BoundingBox.html" title="class in org.biojava.nbio.structure.contact">BoundingBox</a></li>
<li><a href="org/biojava/nbio/structure/xtal/BravaisLattice.html" title="enum in org.biojava.nbio.structure.xtal">BravaisLattice</a></li>
<li><a href="org/biojava/nbio/structure/secstruc/BridgeType.html" title="enum in org.biojava.nbio.structure.secstruc">BridgeType</a></li>
<li><a href="org/biojava/nbio/structure/align/webstart/BrowserOpener.html" title="class in org.biojava.nbio.structure.align.webstart">BrowserOpener</a></li>
<li><a href="org/biojava/nbio/core/sequence/io/BufferedReaderBytesRead.html" title="class in org.biojava.nbio.core.sequence.io">BufferedReaderBytesRead</a></li>
<li><a href="org/biojava/nbio/structure/symmetry/core/C2RotationSolver.html" title="class in org.biojava.nbio.structure.symmetry.core">C2RotationSolver</a></li>
<li><a href="org/biojava/nbio/structure/io/CAConverter.html" title="class in org.biojava.nbio.structure.io">CAConverter</a></li>
<li><a href="org/biojava/nbio/structure/Calc.html" title="class in org.biojava.nbio.structure">Calc</a></li>
<li><a href="org/biojava/nbio/structure/geometry/CalcPoint.html" title="class in org.biojava.nbio.structure.geometry">CalcPoint</a></li>
<li><a href="org/biojava/nbio/alignment/template/CallablePairwiseSequenceAligner.html" title="class in org.biojava.nbio.alignment.template">CallablePairwiseSequenceAligner</a></li>
<li><a href="org/biojava/nbio/alignment/template/CallablePairwiseSequenceScorer.html" title="class in org.biojava.nbio.alignment.template">CallablePairwiseSequenceScorer</a></li>
<li><a href="org/biojava/nbio/alignment/template/CallableProfileProfileAligner.html" title="class in org.biojava.nbio.alignment.template">CallableProfileProfileAligner</a></li>
<li><a href="org/biojava/nbio/structure/align/CallableStructureAlignment.html" title="class in org.biojava.nbio.structure.align">CallableStructureAlignment</a></li>
<li><a href="org/biojava/nbio/structure/quaternary/CartesianProduct.html" title="class in org.biojava.nbio.structure.quaternary">CartesianProduct</a></li>
<li><a href="org/biojava/nbio/aaproperties/xml/CaseFreeAminoAcidCompoundSet.html" title="class in org.biojava.nbio.aaproperties.xml">CaseFreeAminoAcidCompoundSet</a></li>
<li><a href="org/biojava/nbio/core/sequence/transcription/CaseInsensitiveCompound.html" title="class in org.biojava.nbio.core.sequence.transcription">CaseInsensitiveCompound</a></li>
<li><a href="org/biojava/nbio/core/sequence/io/CasePreservingProteinSequenceCreator.html" title="class in org.biojava.nbio.core.sequence.io">CasePreservingProteinSequenceCreator</a></li>
<li><a href="org/biojava/nbio/structure/cath/CathCategory.html" title="enum in org.biojava.nbio.structure.cath">CathCategory</a></li>
<li><a href="org/biojava/nbio/structure/cath/CathDatabase.html" title="interface in org.biojava.nbio.structure.cath"><span class="interfaceName">CathDatabase</span></a></li>
<li><a href="org/biojava/nbio/structure/cath/CathDomain.html" title="class in org.biojava.nbio.structure.cath">CathDomain</a></li>
<li><a href="org/biojava/nbio/structure/cath/CathFactory.html" title="class in org.biojava.nbio.structure.cath">CathFactory</a></li>
<li><a href="org/biojava/nbio/structure/cath/CathFragment.html" title="class in org.biojava.nbio.structure.cath">CathFragment</a></li>
<li><a href="org/biojava/nbio/structure/cath/CathInstallation.html" title="class in org.biojava.nbio.structure.cath">CathInstallation</a></li>
<li><a href="org/biojava/nbio/structure/cath/CathNode.html" title="class in org.biojava.nbio.structure.cath">CathNode</a></li>
<li><a href="org/biojava/nbio/structure/cath/CathSegment.html" title="class in org.biojava.nbio.structure.cath">CathSegment</a></li>
<li><a href="org/biojava/nbio/core/sequence/CDSComparator.html" title="class in org.biojava.nbio.core.sequence">CDSComparator</a></li>
<li><a href="org/biojava/nbio/core/sequence/CDSSequence.html" title="class in org.biojava.nbio.core.sequence">CDSSequence</a></li>
<li><a href="org/biojava/nbio/structure/align/ce/CECalculator.html" title="class in org.biojava.nbio.structure.align.ce">CECalculator</a></li>
<li><a href="org/biojava/nbio/structure/align/ce/CeCalculatorEnhanced.html" title="class in org.biojava.nbio.structure.align.ce">CeCalculatorEnhanced</a></li>
<li><a href="org/biojava/nbio/structure/align/ce/CeCPMain.html" title="class in org.biojava.nbio.structure.align.ce">CeCPMain</a></li>
<li><a href="org/biojava/nbio/structure/align/ce/CeCPMain.CPRange.html" title="class in org.biojava.nbio.structure.align.ce">CeCPMain.CPRange</a></li>
<li><a href="org/biojava/nbio/structure/align/ce/CECPParameters.html" title="class in org.biojava.nbio.structure.align.ce">CECPParameters</a></li>
<li><a href="org/biojava/nbio/structure/align/ce/CECPParameters.DuplicationHint.html" title="enum in org.biojava.nbio.structure.align.ce">CECPParameters.DuplicationHint</a></li>
<li><a href="org/biojava/nbio/structure/align/ce/CeCPUserArgumentProcessor.html" title="class in org.biojava.nbio.structure.align.ce">CeCPUserArgumentProcessor</a></li>
<li><a href="org/biojava/nbio/structure/align/ce/CeMain.html" title="class in org.biojava.nbio.structure.align.ce">CeMain</a></li>
<li><a href="org/biojava/nbio/survival/kaplanmeier/figure/CensorStatus.html" title="class in org.biojava.nbio.survival.kaplanmeier.figure">CensorStatus</a></li>
<li><a href="org/biojava/nbio/survival/kaplanmeier/figure/CensorStatusSelect.html" title="interface in org.biojava.nbio.survival.kaplanmeier.figure"><span class="interfaceName">CensorStatusSelect</span></a></li>
<li><a href="org/biojava/nbio/structure/align/ce/CeParameters.html" title="class in org.biojava.nbio.structure.align.ce">CeParameters</a></li>
<li><a href="org/biojava/nbio/structure/align/ce/CeParameters.ScoringStrategy.html" title="enum in org.biojava.nbio.structure.align.ce">CeParameters.ScoringStrategy</a></li>
<li><a href="org/biojava/nbio/structure/align/ce/CeSideChainMain.html" title="class in org.biojava.nbio.structure.align.ce">CeSideChainMain</a></li>
<li><a href="org/biojava/nbio/structure/align/ce/CeSideChainUserArgumentProcessor.html" title="class in org.biojava.nbio.structure.align.ce">CeSideChainUserArgumentProcessor</a></li>
<li><a href="org/biojava/nbio/structure/symmetry/internal/CeSymm.html" title="class in org.biojava.nbio.structure.symmetry.internal">CeSymm</a></li>
<li><a href="org/biojava/nbio/structure/symmetry/internal/CeSymmIterative.html" title="class in org.biojava.nbio.structure.symmetry.internal">CeSymmIterative</a></li>
<li><a href="org/biojava/nbio/structure/symmetry/internal/CESymmParameters.html" title="class in org.biojava.nbio.structure.symmetry.internal">CESymmParameters</a></li>
<li><a href="org/biojava/nbio/structure/symmetry/internal/CESymmParameters.OrderDetectorMethod.html" title="enum in org.biojava.nbio.structure.symmetry.internal">CESymmParameters.OrderDetectorMethod</a></li>
<li><a href="org/biojava/nbio/structure/symmetry/internal/CESymmParameters.RefineMethod.html" title="enum in org.biojava.nbio.structure.symmetry.internal">CESymmParameters.RefineMethod</a></li>
<li><a href="org/biojava/nbio/structure/symmetry/internal/CESymmParameters.SymmetryType.html" title="enum in org.biojava.nbio.structure.symmetry.internal">CESymmParameters.SymmetryType</a></li>
<li><a href="org/biojava/nbio/structure/symmetry/internal/CeSymmResult.html" title="class in org.biojava.nbio.structure.symmetry.internal">CeSymmResult</a></li>
<li><a href="org/biojava/nbio/structure/align/ce/CeUserArgumentProcessor.html" title="class in org.biojava.nbio.structure.align.ce">CeUserArgumentProcessor</a></li>
<li><a href="org/biojava/nbio/structure/align/ce/CeUserArgumentProcessor.CeStartupParams.html" title="class in org.biojava.nbio.structure.align.ce">CeUserArgumentProcessor.CeStartupParams</a></li>
<li><a href="org/biojava/nbio/structure/Chain.html" title="interface in org.biojava.nbio.structure"><span class="interfaceName">Chain</span></a></li>
<li><a href="org/biojava/nbio/structure/ChainImpl.html" title="class in org.biojava.nbio.structure">ChainImpl</a></li>
<li><a href="org/biojava/nbio/structure/symmetry/misc/ChainSignature.html" title="class in org.biojava.nbio.structure.symmetry.misc">ChainSignature</a></li>
<li><a href="org/biojava/nbio/survival/data/ChangeValue.html" title="interface in org.biojava.nbio.survival.data"><span class="interfaceName">ChangeValue</span></a></li>
<li><a href="org/biojava/nbio/structure/io/ChargeAdder.html" title="class in org.biojava.nbio.structure.io">ChargeAdder</a></li>
<li><a href="org/biojava/nbio/structure/chem/ChemComp.html" title="class in org.biojava.nbio.structure.chem">ChemComp</a></li>
<li><a href="org/biojava/nbio/structure/chem/ChemCompAtom.html" title="class in org.biojava.nbio.structure.chem">ChemCompAtom</a></li>
<li><a href="org/biojava/nbio/structure/chem/ChemCompBond.html" title="class in org.biojava.nbio.structure.chem">ChemCompBond</a></li>
<li><a href="org/biojava/nbio/structure/io/cif/ChemCompConsumer.html" title="interface in org.biojava.nbio.structure.io.cif"><span class="interfaceName">ChemCompConsumer</span></a></li>
<li><a href="org/biojava/nbio/structure/io/cif/ChemCompConsumerImpl.html" title="class in org.biojava.nbio.structure.io.cif">ChemCompConsumerImpl</a></li>
<li><a href="org/biojava/nbio/structure/io/cif/ChemCompConverter.html" title="class in org.biojava.nbio.structure.io.cif">ChemCompConverter</a></li>
<li><a href="org/biojava/nbio/structure/chem/ChemCompDescriptor.html" title="class in org.biojava.nbio.structure.chem">ChemCompDescriptor</a></li>
<li><a href="demo/ChemCompDistribution.html" title="class in demo">ChemCompDistribution</a></li>
<li><a href="org/biojava/nbio/structure/chem/ChemCompGroupFactory.html" title="class in org.biojava.nbio.structure.chem">ChemCompGroupFactory</a></li>
<li><a href="org/biojava/nbio/structure/chem/ChemCompProvider.html" title="interface in org.biojava.nbio.structure.chem"><span class="interfaceName">ChemCompProvider</span></a></li>
<li><a href="org/biojava/nbio/structure/chem/ChemCompTools.html" title="class in org.biojava.nbio.structure.chem">ChemCompTools</a></li>
<li><a href="org/biojava/nbio/structure/chem/ChemicalComponentDictionary.html" title="class in org.biojava.nbio.structure.chem">ChemicalComponentDictionary</a></li>
<li><a href="org/biojava/nbio/survival/cox/stats/ChiSq.html" title="class in org.biojava.nbio.survival.cox.stats">ChiSq</a></li>
<li><a href="org/biojava/nbio/survival/cox/stats/Cholesky2.html" title="class in org.biojava.nbio.survival.cox.stats">Cholesky2</a></li>
<li><a href="org/biojava/nbio/structure/jama/CholeskyDecomposition.html" title="class in org.biojava.nbio.structure.jama">CholeskyDecomposition</a></li>
<li><a href="org/biojava/nbio/structure/align/gui/ChooseDirAction.html" title="class in org.biojava.nbio.structure.align.gui">ChooseDirAction</a></li>
<li><a href="org/biojava/nbio/genome/util/ChromosomeMappingTools.html" title="class in org.biojava.nbio.genome.util">ChromosomeMappingTools</a></li>
<li><a href="org/biojava/nbio/core/sequence/ChromosomeSequence.html" title="class in org.biojava.nbio.core.sequence">ChromosomeSequence</a></li>
<li><a href="org/biojava/nbio/genome/parsers/genename/ChromPos.html" title="class in org.biojava.nbio.genome.parsers.genename">ChromPos</a></li>
<li><a href="org/biojava/nbio/survival/cox/stats/Chsolve2.html" title="class in org.biojava.nbio.survival.cox.stats">Chsolve2</a></li>
<li><a href="org/biojava/nbio/structure/io/cif/CifBean.html" title="interface in org.biojava.nbio.structure.io.cif"><span class="interfaceName">CifBean</span></a></li>
<li><a href="org/biojava/nbio/structure/io/cif/CifChainSupplierImpl.html" title="class in org.biojava.nbio.structure.io.cif">CifChainSupplierImpl</a></li>
<li><a href="org/biojava/nbio/structure/io/cif/CifFileConsumer.html" title="interface in org.biojava.nbio.structure.io.cif"><span class="interfaceName">CifFileConsumer</span></a></li>
<li><a href="org/biojava/nbio/structure/io/CifFileReader.html" title="class in org.biojava.nbio.structure.io">CifFileReader</a></li>
<li><a href="org/biojava/nbio/structure/io/cif/CifFileSupplier.html" title="interface in org.biojava.nbio.structure.io.cif"><span class="interfaceName">CifFileSupplier</span></a></li>
<li><a href="org/biojava/nbio/structure/io/cif/CifStructureConsumer.html" title="interface in org.biojava.nbio.structure.io.cif"><span class="interfaceName">CifStructureConsumer</span></a></li>
<li><a href="org/biojava/nbio/structure/io/cif/CifStructureConsumerImpl.html" title="class in org.biojava.nbio.structure.io.cif">CifStructureConsumerImpl</a></li>
<li><a href="org/biojava/nbio/structure/io/cif/CifStructureConverter.html" title="class in org.biojava.nbio.structure.io.cif">CifStructureConverter</a></li>
<li><a href="org/biojava/nbio/structure/io/cif/CifStructureSupplierImpl.html" title="class in org.biojava.nbio.structure.io.cif">CifStructureSupplierImpl</a></li>
<li><a href="org/biojava/nbio/core/sequence/io/util/ClasspathResource.html" title="class in org.biojava.nbio.core.sequence.io.util">ClasspathResource</a></li>
<li><a href="org/biojava/nbio/survival/kaplanmeier/metadata/ClinicalMetaDataOutcome.html" title="class in org.biojava.nbio.survival.kaplanmeier.metadata">ClinicalMetaDataOutcome</a></li>
<li><a href="org/biojava/nbio/structure/align/util/CliTools.html" title="class in org.biojava.nbio.structure.align.util">CliTools</a></li>
<li><a href="org/biojava/nbio/structure/align/ClusterAltAligs.html" title="class in org.biojava.nbio.structure.align">ClusterAltAligs</a></li>
<li><a href="org/biojava/nbio/structure/domain/pdp/ClusterDomains.html" title="class in org.biojava.nbio.structure.domain.pdp">ClusterDomains</a></li>
<li><a href="org/biojava/nbio/core/sequence/compound/CodonCompound.html" title="class in org.biojava.nbio.core.sequence.compound">CodonCompound</a></li>
<li><a href="org/biojava/nbio/structure/align/util/CollectionTools.html" title="class in org.biojava.nbio.structure.align.util">CollectionTools</a></li>
<li><a href="org/biojava/nbio/structure/symmetry/jmolScript/ColorConverter.html" title="class in org.biojava.nbio.structure.symmetry.jmolScript">ColorConverter</a></li>
<li><a href="org/biojava/nbio/structure/gui/util/color/ColorInterpolator.html" title="interface in org.biojava.nbio.structure.gui.util.color"><span class="interfaceName">ColorInterpolator</span></a></li>
<li><a href="org/biojava/nbio/structure/gui/util/color/ColorUtils.html" title="class in org.biojava.nbio.structure.gui.util.color">ColorUtils</a></li>
<li><a href="org/biojava/nbio/aaproperties/CommandPrompt.html" title="class in org.biojava.nbio.aaproperties">CommandPrompt</a></li>
<li><a href="org/biojava/nbio/aaproperties/CommandPrompt.PropertyName.html" title="enum in org.biojava.nbio.aaproperties">CommandPrompt.PropertyName</a></li>
<li><a href="org/biojava/nbio/survival/data/CompactCharSequence.html" title="class in org.biojava.nbio.survival.data">CompactCharSequence</a></li>
<li><a href="org/biojava/nbio/phylo/Comparison.html" title="class in org.biojava.nbio.phylo">Comparison</a></li>
<li><a href="org/biojava/nbio/core/sequence/template/ComplementCompound.html" title="interface in org.biojava.nbio.core.sequence.template"><span class="interfaceName">ComplementCompound</span></a></li>
<li><a href="org/biojava/nbio/core/sequence/views/ComplementSequenceView.html" title="class in org.biojava.nbio.core.sequence.views">ComplementSequenceView</a></li>
<li><a href="org/biojava/nbio/protmod/Component.html" title="class in org.biojava.nbio.protmod">Component</a></li>
<li><a href="org/biojava/nbio/protmod/io/ComponentXMLConverter.html" title="class in org.biojava.nbio.protmod.io">ComponentXMLConverter</a></li>
<li><a href="org/biojava/nbio/core/sequence/template/Compound.html" title="interface in org.biojava.nbio.core.sequence.template"><span class="interfaceName">Compound</span></a></li>
<li><a href="org/biojava/nbio/core/exceptions/CompoundNotFoundException.html" title="class in org.biojava.nbio.core.exceptions">CompoundNotFoundException</a></li>
<li><a href="org/biojava/nbio/core/sequence/template/CompoundSet.html" title="interface in org.biojava.nbio.core.sequence.template"><span class="interfaceName">CompoundSet</span></a></li>
<li><a href="org/biojava/nbio/core/sequence/template/CompoundTranslator.html" title="interface in org.biojava.nbio.core.sequence.template"><span class="interfaceName">CompoundTranslator</span></a></li>
<li><a href="org/biojava/nbio/core/util/ConcurrencyTools.html" title="class in org.biojava.nbio.core.util">ConcurrencyTools</a></li>
<li><a href="org/biojava/nbio/structure/align/gui/ConfigPDBInstallPanel.html" title="class in org.biojava.nbio.structure.align.gui">ConfigPDBInstallPanel</a></li>
<li><a href="org/biojava/nbio/structure/align/ce/ConfigStrucAligParams.html" title="interface in org.biojava.nbio.structure.align.ce"><span class="interfaceName">ConfigStrucAligParams</span></a></li>
<li><a href="org/biojava/nbio/structure/align/util/ConfigurationException.html" title="class in org.biojava.nbio.structure.align.util">ConfigurationException</a></li>
<li><a href="org/biojava/nbio/structure/align/webstart/ConfigXMLHandler.html" title="class in org.biojava.nbio.structure.align.webstart">ConfigXMLHandler</a></li>
<li><a href="org/biojava/nbio/aaproperties/Constraints.html" title="class in org.biojava.nbio.aaproperties">Constraints</a></li>
<li><a href="org/biojava/nbio/structure/contact/Contact.html" title="class in org.biojava.nbio.structure.contact">Contact</a></li>
<li><a href="org/biojava/nbio/structure/gui/util/color/ContinuousColorMapper.html" title="interface in org.biojava.nbio.structure.gui.util.color"><span class="interfaceName">ContinuousColorMapper</span></a></li>
<li><a href="org/biojava/nbio/structure/gui/util/color/ContinuousColorMapperTransform.html" title="class in org.biojava.nbio.structure.gui.util.color">ContinuousColorMapperTransform</a></li>
<li><a href="org/biojava/nbio/aaproperties/profeat/convertor/Convert2Charge.html" title="class in org.biojava.nbio.aaproperties.profeat.convertor">Convert2Charge</a></li>
<li><a href="org/biojava/nbio/aaproperties/profeat/convertor/Convert2Hydrophobicity.html" title="class in org.biojava.nbio.aaproperties.profeat.convertor">Convert2Hydrophobicity</a></li>
<li><a href="org/biojava/nbio/aaproperties/profeat/convertor/Convert2NormalizedVanDerWaalsVolume.html" title="class in org.biojava.nbio.aaproperties.profeat.convertor">Convert2NormalizedVanDerWaalsVolume</a></li>
<li><a href="org/biojava/nbio/aaproperties/profeat/convertor/Convert2Polarity.html" title="class in org.biojava.nbio.aaproperties.profeat.convertor">Convert2Polarity</a></li>
<li><a href="org/biojava/nbio/aaproperties/profeat/convertor/Convert2Polarizability.html" title="class in org.biojava.nbio.aaproperties.profeat.convertor">Convert2Polarizability</a></li>
<li><a href="org/biojava/nbio/aaproperties/profeat/convertor/Convert2SecondaryStructure.html" title="class in org.biojava.nbio.aaproperties.profeat.convertor">Convert2SecondaryStructure</a></li>
<li><a href="org/biojava/nbio/aaproperties/profeat/convertor/Convert2SolventAccessibility.html" title="class in org.biojava.nbio.aaproperties.profeat.convertor">Convert2SolventAccessibility</a></li>
<li><a href="org/biojava/nbio/aaproperties/profeat/convertor/Convertor.html" title="class in org.biojava.nbio.aaproperties.profeat.convertor">Convertor</a></li>
<li><a href="demo/CookBook.html" title="class in demo">CookBook</a></li>
<li><a href="demo/CookbookMSA.html" title="class in demo">CookbookMSA</a></li>
<li><a href="org/biojava/nbio/structure/gui/util/CoordManager.html" title="class in org.biojava.nbio.structure.gui.util">CoordManager</a></li>
<li><a href="org/biojava/nbio/structure/align/multiple/util/CoreSuperimposer.html" title="class in org.biojava.nbio.structure.align.multiple.util">CoreSuperimposer</a></li>
<li><a href="org/biojava/nbio/survival/cox/CoxCC.html" title="class in org.biojava.nbio.survival.cox">CoxCC</a></li>
<li><a href="org/biojava/nbio/survival/cox/CoxCoefficient.html" title="class in org.biojava.nbio.survival.cox">CoxCoefficient</a></li>
<li><a href="org/biojava/nbio/survival/cox/comparators/CoxComparatorInterface.html" title="interface in org.biojava.nbio.survival.cox.comparators"><span class="interfaceName">CoxComparatorInterface</span></a></li>
<li><a href="org/biojava/nbio/survival/cox/CoxHelper.html" title="class in org.biojava.nbio.survival.cox">CoxHelper</a></li>
<li><a href="org/biojava/nbio/survival/cox/CoxInfo.html" title="class in org.biojava.nbio.survival.cox">CoxInfo</a></li>
<li><a href="org/biojava/nbio/survival/cox/CoxMart.html" title="class in org.biojava.nbio.survival.cox">CoxMart</a></li>
<li><a href="org/biojava/nbio/survival/cox/CoxMethod.html" title="enum in org.biojava.nbio.survival.cox">CoxMethod</a></li>
<li><a href="org/biojava/nbio/survival/cox/CoxR.html" title="class in org.biojava.nbio.survival.cox">CoxR</a></li>
<li><a href="org/biojava/nbio/survival/cox/CoxScore.html" title="class in org.biojava.nbio.survival.cox">CoxScore</a></li>
<li><a href="org/biojava/nbio/survival/cox/CoxVariables.html" title="class in org.biojava.nbio.survival.cox">CoxVariables</a></li>
<li><a href="org/biojava/nbio/survival/cox/comparators/CoxVariablesOverallModelFitComparator.html" title="class in org.biojava.nbio.survival.cox.comparators">CoxVariablesOverallModelFitComparator</a></li>
<li><a href="org/biojava/nbio/survival/cox/comparators/CoxVariablesVariableComparator.html" title="class in org.biojava.nbio.survival.cox.comparators">CoxVariablesVariableComparator</a></li>
<li><a href="org/biojava/nbio/core/util/CRC64Checksum.html" title="class in org.biojava.nbio.core.util">CRC64Checksum</a></li>
<li><a href="org/biojava/nbio/structure/xtal/CrystalBuilder.html" title="class in org.biojava.nbio.structure.xtal">CrystalBuilder</a></li>
<li><a href="org/biojava/nbio/structure/xtal/CrystalCell.html" title="class in org.biojava.nbio.structure.xtal">CrystalCell</a></li>
<li><a href="org/biojava/nbio/structure/xtal/CrystalTransform.html" title="class in org.biojava.nbio.structure.xtal">CrystalTransform</a></li>
<li><a href="org/biojava/nbio/structure/domain/pdp/Cut.html" title="class in org.biojava.nbio.structure.domain.pdp">Cut</a></li>
<li><a href="org/biojava/nbio/structure/domain/pdp/CutDomain.html" title="class in org.biojava.nbio.structure.domain.pdp">CutDomain</a></li>
<li><a href="org/biojava/nbio/structure/domain/pdp/CutSites.html" title="class in org.biojava.nbio.structure.domain.pdp">CutSites</a></li>
<li><a href="org/biojava/nbio/structure/domain/pdp/CutValues.html" title="class in org.biojava.nbio.structure.domain.pdp">CutValues</a></li>
<li><a href="org/biojava/nbio/genome/parsers/cytoband/Cytoband.html" title="class in org.biojava.nbio.genome.parsers.cytoband">Cytoband</a></li>
<li><a href="org/biojava/nbio/genome/parsers/cytoband/CytobandParser.html" title="class in org.biojava.nbio.genome.parsers.cytoband">CytobandParser</a></li>
<li><a href="org/biojava/nbio/structure/DatabasePDBRevRecord.html" title="class in org.biojava.nbio.structure">DatabasePDBRevRecord</a></li>
<li><a href="org/biojava/nbio/core/sequence/features/DatabaseReferenceInterface.html" title="interface in org.biojava.nbio.core.sequence.features"><span class="interfaceName">DatabaseReferenceInterface</span></a></li>
<li><a href="org/biojava/nbio/phosphosite/Dataset.html" title="class in org.biojava.nbio.phosphosite">Dataset</a></li>
<li><a href="org/biojava/nbio/core/sequence/DataSource.html" title="enum in org.biojava.nbio.core.sequence">DataSource</a></li>
<li><a href="org/biojava/nbio/structure/DBRef.html" title="class in org.biojava.nbio.structure">DBRef</a></li>
<li><a href="org/biojava/nbio/core/sequence/features/DBReferenceInfo.html" title="class in org.biojava.nbio.core.sequence.features">DBReferenceInfo</a></li>
<li><a href="org/biojava/nbio/core/alignment/matrices/DefaultAAIndexProvider.html" title="class in org.biojava.nbio.core.alignment.matrices">DefaultAAIndexProvider</a></li>
<li><a href="org/biojava/nbio/structure/align/gui/autosuggest/DefaultAutoSuggestProvider.html" title="class in org.biojava.nbio.structure.align.gui.autosuggest">DefaultAutoSuggestProvider</a></li>
<li><a href="org/biojava/nbio/structure/gui/util/color/DefaultMatrixMapper.html" title="class in org.biojava.nbio.structure.gui.util.color">DefaultMatrixMapper</a></li>
<li><a href="org/biojava/nbio/ontology/DefaultOps.html" title="class in org.biojava.nbio.ontology">DefaultOps</a></li>
<li><a href="demo/DemoAlignmentFromFasta.html" title="class in demo">DemoAlignmentFromFasta</a></li>
<li><a href="demo/DemoAlignProteins.html" title="class in demo">DemoAlignProteins</a></li>
<li><a href="demo/DemoAsa.html" title="class in demo">DemoAsa</a></li>
<li><a href="demo/DemoAtomCache.html" title="class in demo">DemoAtomCache</a></li>
<li><a href="demo/DemoBerkeleyScop.html" title="class in demo">DemoBerkeleyScop</a></li>
<li><a href="demo/DemoBioAssemblies.html" title="class in demo">DemoBioAssemblies</a></li>
<li><a href="demo/DemoCATH.html" title="class in demo">DemoCATH</a></li>
<li><a href="demo/DemoCE.html" title="class in demo">DemoCE</a></li>
<li><a href="demo/DemoCeSymm.html" title="class in demo">DemoCeSymm</a></li>
<li><a href="demo/DemoChangeChemCompProvider.html" title="class in demo">DemoChangeChemCompProvider</a></li>
<li><a href="demo/DemoCommandLineStartup.html" title="class in demo">DemoCommandLineStartup</a></li>
<li><a href="demo/DemoContacts.html" title="class in demo">DemoContacts</a></li>
<li><a href="demo/DemoCrystalInterfaces.html" title="class in demo">DemoCrystalInterfaces</a></li>
<li><a href="demo/DemoDistanceTree.html" title="class in demo">DemoDistanceTree</a></li>
<li><a href="demo/DemoDomainsplit.html" title="class in demo">DemoDomainsplit</a></li>
<li><a href="demo/DemoFATCAT.html" title="class in demo">DemoFATCAT</a></li>
<li><a href="demo/DemoLoadSecStruc.html" title="class in demo">DemoLoadSecStruc</a></li>
<li><a href="demo/DemoLoadStructure.html" title="class in demo">DemoLoadStructure</a></li>
<li><a href="demo/DemoLoadSubstMax.html" title="class in demo">DemoLoadSubstMax</a></li>
<li><a href="demo/DemoMMCIFReader.html" title="class in demo">DemoMMCIFReader</a></li>
<li><a href="demo/DemoMmcifToPdbConverter.html" title="class in demo">DemoMmcifToPdbConverter</a></li>
<li><a href="demo/DemoMmtfReader.html" title="class in demo">DemoMmtfReader</a></li>
<li><a href="demo/DemoMmtfWriter.html" title="class in demo">DemoMmtfWriter</a></li>
<li><a href="demo/DemoMultipleMC.html" title="class in demo">DemoMultipleMC</a></li>
<li><a href="demo/DemoNWALignment.html" title="class in demo">DemoNWALignment</a></li>
<li><a href="demo/DemoQsAlign.html" title="class in demo">DemoQsAlign</a></li>
<li><a href="demo/DemoQuatSymmetryJmol.html" title="class in demo">DemoQuatSymmetryJmol</a></li>
<li><a href="demo/DemoRotationAxis.html" title="class in demo">DemoRotationAxis</a></li>
<li><a href="demo/DemoSCOP.html" title="class in demo">DemoSCOP</a></li>
<li><a href="demo/DemoSecStrucCalc.html" title="class in demo">DemoSecStrucCalc</a></li>
<li><a href="demo/DemoShowBiolAssembly.html" title="class in demo">DemoShowBiolAssembly</a></li>
<li><a href="demo/DemoShowCATHDomain.html" title="class in demo">DemoShowCATHDomain</a></li>
<li><a href="demo/DemoShowLargeAssembly.html" title="class in demo">DemoShowLargeAssembly</a></li>
<li><a href="demo/DemoSixFrameTranslation.html" title="class in demo">DemoSixFrameTranslation</a></li>
<li><a href="demo/DemoStructureFromFasta.html" title="class in demo">DemoStructureFromFasta</a></li>
<li><a href="demo/DemoSW3DAligner.html" title="class in demo">DemoSW3DAligner</a></li>
<li><a href="demo/DemoSymmetry.html" title="class in demo">DemoSymmetry</a></li>
<li><a href="org/biojava/nbio/survival/kaplanmeier/metadata/DiscreteQuantizerInterface.html" title="interface in org.biojava.nbio.survival.kaplanmeier.metadata"><span class="interfaceName">DiscreteQuantizerInterface</span></a></li>
<li><a href="org/biojava/nbio/structure/align/gui/DisplayAFP.html" title="class in org.biojava.nbio.structure.align.gui">DisplayAFP</a></li>
<li><a href="org/biojava/nbio/structure/symmetry/geometry/DistanceBox.html" title="class in org.biojava.nbio.structure.symmetry.geometry">DistanceBox</a></li>
<li><a href="org/biojava/nbio/phylo/DistanceMatrixCalculator.html" title="class in org.biojava.nbio.phylo">DistanceMatrixCalculator</a></li>
<li><a href="org/biojava/nbio/phylo/DistanceTreeEvaluator.html" title="class in org.biojava.nbio.phylo">DistanceTreeEvaluator</a></li>
<li><a href="org/biojava/nbio/core/sequence/compound/DNACompoundSet.html" title="class in org.biojava.nbio.core.sequence.compound">DNACompoundSet</a></li>
<li><a href="org/biojava/nbio/core/sequence/DNASequence.html" title="class in org.biojava.nbio.core.sequence">DNASequence</a></li>
<li><a href="org/biojava/nbio/core/sequence/DNASequence.DNAType.html" title="enum in org.biojava.nbio.core.sequence">DNASequence.DNAType</a></li>
<li><a href="org/biojava/nbio/core/sequence/io/DNASequenceCreator.html" title="class in org.biojava.nbio.core.sequence.io">DNASequenceCreator</a></li>
<li><a href="org/biojava/nbio/core/sequence/transcription/DNAToRNATranslator.html" title="class in org.biojava.nbio.core.sequence.transcription">DNAToRNATranslator</a></li>
<li><a href="org/biojava/nbio/structure/domain/pdp/Domain.html" title="class in org.biojava.nbio.structure.domain.pdp">Domain</a></li>
<li><a href="org/biojava/nbio/structure/domain/DomainProvider.html" title="interface in org.biojava.nbio.structure.domain"><span class="interfaceName">DomainProvider</span></a></li>
<li><a href="org/biojava/nbio/structure/align/gui/DotPlotPanel.html" title="class in org.biojava.nbio.structure.align.gui">DotPlotPanel</a></li>
<li><a href="org/biojava/nbio/structure/chem/DownloadChemCompProvider.html" title="class in org.biojava.nbio.structure.chem">DownloadChemCompProvider</a></li>
<li><a href="org/biojava/nbio/structure/secstruc/DSSPParser.html" title="class in org.biojava.nbio.structure.secstruc">DSSPParser</a></li>
<li><a href="org/biojava/nbio/structure/ecod/EcodDatabase.html" title="interface in org.biojava.nbio.structure.ecod"><span class="interfaceName">EcodDatabase</span></a></li>
<li><a href="org/biojava/nbio/structure/ecod/EcodDomain.html" title="class in org.biojava.nbio.structure.ecod">EcodDomain</a></li>
<li><a href="org/biojava/nbio/structure/ecod/EcodFactory.html" title="class in org.biojava.nbio.structure.ecod">EcodFactory</a></li>
<li><a href="org/biojava/nbio/structure/ecod/EcodInstallation.html" title="class in org.biojava.nbio.structure.ecod">EcodInstallation</a></li>
<li><a href="org/biojava/nbio/structure/ecod/EcodInstallation.EcodParser.html" title="class in org.biojava.nbio.structure.ecod">EcodInstallation.EcodParser</a></li>
<li><a href="org/biojava/nbio/core/sequence/edits/Edit.html" title="interface in org.biojava.nbio.core.sequence.edits"><span class="interfaceName">Edit</span></a></li>
<li><a href="org/biojava/nbio/core/sequence/edits/Edit.AbstractEdit.html" title="class in org.biojava.nbio.core.sequence.edits">Edit.AbstractEdit</a></li>
<li><a href="org/biojava/nbio/core/sequence/edits/Edit.Delete.html" title="class in org.biojava.nbio.core.sequence.edits">Edit.Delete</a></li>
<li><a href="org/biojava/nbio/core/sequence/edits/Edit.Insert.html" title="class in org.biojava.nbio.core.sequence.edits">Edit.Insert</a></li>
<li><a href="org/biojava/nbio/core/sequence/edits/Edit.Substitute.html" title="class in org.biojava.nbio.core.sequence.edits">Edit.Substitute</a></li>
<li><a href="org/biojava/nbio/structure/jama/EigenvalueDecomposition.html" title="class in org.biojava.nbio.structure.jama">EigenvalueDecomposition</a></li>
<li><a href="org/biojava/nbio/aaproperties/xml/Element.html" title="class in org.biojava.nbio.aaproperties.xml">Element</a></li>
<li><a href="org/biojava/nbio/structure/Element.html" title="enum in org.biojava.nbio.structure">Element</a></li>
<li><a href="org/biojava/nbio/aaproperties/xml/ElementTable.html" title="class in org.biojava.nbio.aaproperties.xml">ElementTable</a></li>
<li><a href="org/biojava/nbio/structure/ElementType.html" title="enum in org.biojava.nbio.structure">ElementType</a></li>
<li><a href="org/biojava/nbio/core/sequence/io/embl/EmblId.html" title="class in org.biojava.nbio.core.sequence.io.embl">EmblId</a></li>
<li><a href="org/biojava/nbio/core/sequence/io/embl/EmblReader.html" title="class in org.biojava.nbio.core.sequence.io.embl">EmblReader</a></li>
<li><a href="org/biojava/nbio/core/sequence/io/embl/EmblRecord.html" title="class in org.biojava.nbio.core.sequence.io.embl">EmblRecord</a></li>
<li><a href="org/biojava/nbio/core/sequence/io/embl/EmblReference.html" title="class in org.biojava.nbio.core.sequence.io.embl">EmblReference</a></li>
<li><a href="org/biojava/nbio/structure/io/EntityFinder.html" title="class in org.biojava.nbio.structure.io">EntityFinder</a></li>
<li><a href="org/biojava/nbio/structure/EntityInfo.html" title="class in org.biojava.nbio.structure">EntityInfo</a></li>
<li><a href="org/biojava/nbio/structure/EntityType.html" title="enum in org.biojava.nbio.structure">EntityType</a></li>
<li><a href="org/biojava/nbio/core/util/Equals.html" title="class in org.biojava.nbio.core.util">Equals</a></li>
<li><a href="org/biojava/nbio/core/sequence/ExonComparator.html" title="class in org.biojava.nbio.core.sequence">ExonComparator</a></li>
<li><a href="org/biojava/nbio/core/sequence/ExonSequence.html" title="class in org.biojava.nbio.core.sequence">ExonSequence</a></li>
<li><a href="org/biojava/nbio/structure/ExperimentalTechnique.html" title="enum in org.biojava.nbio.structure">ExperimentalTechnique</a></li>
<li><a href="org/biojava/nbio/survival/kaplanmeier/figure/ExpressionFigure.html" title="class in org.biojava.nbio.survival.kaplanmeier.figure">ExpressionFigure</a></li>
<li><a href="org/biojava/nbio/structure/io/FastaAFPChainConverter.html" title="class in org.biojava.nbio.structure.io">FastaAFPChainConverter</a></li>
<li><a href="org/biojava/nbio/core/sequence/io/FastaGeneWriter.html" title="class in org.biojava.nbio.core.sequence.io">FastaGeneWriter</a></li>
<li><a href="org/biojava/nbio/core/sequence/io/template/FastaHeaderFormatInterface.html" title="interface in org.biojava.nbio.core.sequence.io.template"><span class="interfaceName">FastaHeaderFormatInterface</span></a></li>
<li><a href="org/biojava/nbio/core/sequence/io/FastaReader.html" title="class in org.biojava.nbio.core.sequence.io">FastaReader</a></li>
<li><a href="org/biojava/nbio/core/sequence/io/FastaReaderHelper.html" title="class in org.biojava.nbio.core.sequence.io">FastaReaderHelper</a></li>
<li><a href="org/biojava/nbio/data/sequence/FastaSequence.html" title="class in org.biojava.nbio.data.sequence">FastaSequence</a></li>
<li><a href="org/biojava/nbio/core/sequence/io/FastaSequenceParser.html" title="class in org.biojava.nbio.core.sequence.io">FastaSequenceParser</a></li>
<li><a href="org/biojava/nbio/structure/io/FastaStructureParser.html" title="class in org.biojava.nbio.structure.io">FastaStructureParser</a></li>
<li><a href="org/biojava/nbio/core/sequence/io/FastaWriter.html" title="class in org.biojava.nbio.core.sequence.io">FastaWriter</a></li>
<li><a href="org/biojava/nbio/core/sequence/io/FastaWriterHelper.html" title="class in org.biojava.nbio.core.sequence.io">FastaWriterHelper</a></li>
<li><a href="org/biojava/nbio/genome/io/fastq/Fastq.html" title="class in org.biojava.nbio.genome.io.fastq">Fastq</a></li>
<li><a href="org/biojava/nbio/genome/io/fastq/FastqBuilder.html" title="class in org.biojava.nbio.genome.io.fastq">FastqBuilder</a></li>
<li><a href="org/biojava/nbio/genome/io/fastq/FastqReader.html" title="interface in org.biojava.nbio.genome.io.fastq"><span class="interfaceName">FastqReader</span></a></li>
<li><a href="org/biojava/nbio/genome/io/fastq/FastqTools.html" title="class in org.biojava.nbio.genome.io.fastq">FastqTools</a></li>
<li><a href="org/biojava/nbio/genome/io/fastq/FastqVariant.html" title="enum in org.biojava.nbio.genome.io.fastq">FastqVariant</a></li>
<li><a href="org/biojava/nbio/genome/io/fastq/FastqWriter.html" title="interface in org.biojava.nbio.genome.io.fastq"><span class="interfaceName">FastqWriter</span></a></li>
<li><a href="org/biojava/nbio/structure/align/fatcat/FatCat.html" title="class in org.biojava.nbio.structure.align.fatcat">FatCat</a></li>
<li><a href="org/biojava/nbio/structure/align/fatcat/calc/FatCatAligner.html" title="class in org.biojava.nbio.structure.align.fatcat.calc">FatCatAligner</a></li>
<li><a href="org/biojava/nbio/structure/align/fatcat/FatCatFlexible.html" title="class in org.biojava.nbio.structure.align.fatcat">FatCatFlexible</a></li>
<li><a href="org/biojava/nbio/structure/align/fatcat/calc/FatCatParameters.html" title="class in org.biojava.nbio.structure.align.fatcat.calc">FatCatParameters</a></li>
<li><a href="org/biojava/nbio/structure/align/fatcat/FatCatRigid.html" title="class in org.biojava.nbio.structure.align.fatcat">FatCatRigid</a></li>
<li><a href="org/biojava/nbio/structure/align/fatcat/FatCatUserArgumentProcessor.html" title="class in org.biojava.nbio.structure.align.fatcat">FatCatUserArgumentProcessor</a></li>
<li><a href="org/biojava/nbio/structure/align/fatcat/calc/FCAlignHelper.html" title="class in org.biojava.nbio.structure.align.fatcat.calc">FCAlignHelper</a></li>
<li><a href="org/biojava/nbio/genome/parsers/gff/Feature.html" title="class in org.biojava.nbio.genome.parsers.gff">Feature</a></li>
<li><a href="org/biojava/nbio/core/sequence/features/FeatureDbReferenceInfo.html" title="class in org.biojava.nbio.core.sequence.features">FeatureDbReferenceInfo</a></li>
<li><a href="org/biojava/nbio/genome/parsers/gff/FeatureHelper.html" title="class in org.biojava.nbio.genome.parsers.gff">FeatureHelper</a></li>
<li><a href="org/biojava/nbio/genome/parsers/gff/FeatureI.html" title="interface in org.biojava.nbio.genome.parsers.gff"><span class="interfaceName">FeatureI</span></a></li>
<li><a href="org/biojava/nbio/core/sequence/features/FeatureInterface.html" title="interface in org.biojava.nbio.core.sequence.features"><span class="interfaceName">FeatureInterface</span></a></li>
<li><a href="org/biojava/nbio/genome/parsers/gff/FeatureList.html" title="class in org.biojava.nbio.genome.parsers.gff">FeatureList</a></li>
<li><a href="org/biojava/nbio/core/sequence/features/FeatureRetriever.html" title="interface in org.biojava.nbio.core.sequence.features"><span class="interfaceName">FeatureRetriever</span></a></li>
<li><a href="org/biojava/nbio/core/sequence/features/FeaturesKeyWordInterface.html" title="interface in org.biojava.nbio.core.sequence.features"><span class="interfaceName">FeaturesKeyWordInterface</span></a></li>
<li><a href="org/biojava/nbio/structure/io/FileConvert.html" title="class in org.biojava.nbio.structure.io">FileConvert</a></li>
<li><a href="org/biojava/nbio/core/util/FileDownloadUtils.html" title="class in org.biojava.nbio.core.util">FileDownloadUtils</a></li>
<li><a href="org/biojava/nbio/structure/io/FileParsingParameters.html" title="class in org.biojava.nbio.structure.io">FileParsingParameters</a></li>
<li><a href="org/biojava/nbio/core/sequence/io/FileProxyDNASequenceCreator.html" title="class in org.biojava.nbio.core.sequence.io">FileProxyDNASequenceCreator</a></li>
<li><a href="org/biojava/nbio/core/sequence/io/FileProxyProteinSequenceCreator.html" title="class in org.biojava.nbio.core.sequence.io">FileProxyProteinSequenceCreator</a></li>
<li><a href="org/biojava/nbio/core/sequence/io/FileProxyRNASequenceCreator.html" title="class in org.biojava.nbio.core.sequence.io">FileProxyRNASequenceCreator</a></li>
<li><a href="org/biojava/nbio/core/util/FlatFileCache.html" title="class in org.biojava.nbio.core.util">FlatFileCache</a></li>
<li><a href="org/biojava/nbio/phylo/ForesterWrapper.html" title="class in org.biojava.nbio.phylo">ForesterWrapper</a></li>
<li><a href="org/biojava/nbio/core/sequence/storage/FourBitSequenceReader.html" title="class in org.biojava.nbio.core.sequence.storage">FourBitSequenceReader</a></li>
<li><a href="org/biojava/nbio/core/sequence/storage/FourBitSequenceReader.FourBitArrayWorker.html" title="class in org.biojava.nbio.core.sequence.storage">FourBitSequenceReader.FourBitArrayWorker</a></li>
<li><a href="org/biojava/nbio/alignment/FractionalIdentityInProfileScorer.html" title="class in org.biojava.nbio.alignment">FractionalIdentityInProfileScorer</a></li>
<li><a href="org/biojava/nbio/alignment/FractionalIdentityScorer.html" title="class in org.biojava.nbio.alignment">FractionalIdentityScorer</a></li>
<li><a href="org/biojava/nbio/alignment/FractionalSimilarityInProfileScorer.html" title="class in org.biojava.nbio.alignment">FractionalSimilarityInProfileScorer</a></li>
<li><a href="org/biojava/nbio/alignment/FractionalSimilarityScorer.html" title="class in org.biojava.nbio.alignment">FractionalSimilarityScorer</a></li>
<li><a href="org/biojava/nbio/structure/align/pairwise/FragmentJoiner.html" title="class in org.biojava.nbio.structure.align.pairwise">FragmentJoiner</a></li>
<li><a href="org/biojava/nbio/structure/align/pairwise/FragmentPair.html" title="class in org.biojava.nbio.structure.align.pairwise">FragmentPair</a></li>
<li><a href="org/biojava/nbio/core/sequence/transcription/Frame.html" title="enum in org.biojava.nbio.core.sequence.transcription">Frame</a></li>
<li><a href="org/biojava/nbio/core/sequence/location/FuzzyPoint.html" title="class in org.biojava.nbio.core.sequence.location">FuzzyPoint</a></li>
<li><a href="org/biojava/nbio/structure/align/helper/GapArray.html" title="class in org.biojava.nbio.structure.align.helper">GapArray</a></li>
<li><a href="org/biojava/nbio/alignment/template/GapPenalty.html" title="interface in org.biojava.nbio.alignment.template"><span class="interfaceName">GapPenalty</span></a></li>
<li><a href="org/biojava/nbio/alignment/template/GapPenalty.Type.html" title="enum in org.biojava.nbio.alignment.template">GapPenalty.Type</a></li>
<li><a href="org/biojava/nbio/genome/parsers/gff/GCStats.html" title="class in org.biojava.nbio.genome.parsers.gff">GCStats</a></li>
<li><a href="org/biojava/nbio/core/sequence/io/template/GenbankHeaderFormatInterface.html" title="interface in org.biojava.nbio.core.sequence.io.template"><span class="interfaceName">GenbankHeaderFormatInterface</span></a></li>
<li><a href="org/biojava/nbio/core/sequence/loader/GenbankProxySequenceReader.html" title="class in org.biojava.nbio.core.sequence.loader">GenbankProxySequenceReader</a></li>
<li><a href="org/biojava/nbio/core/sequence/io/GenbankReader.html" title="class in org.biojava.nbio.core.sequence.io">GenbankReader</a></li>
<li><a href="org/biojava/nbio/core/sequence/io/GenbankReaderHelper.html" title="class in org.biojava.nbio.core.sequence.io">GenbankReaderHelper</a></li>
<li><a href="org/biojava/nbio/core/sequence/reference/GenbankReference.html" title="class in org.biojava.nbio.core.sequence.reference">GenbankReference</a></li>
<li><a href="org/biojava/nbio/core/sequence/io/GenbankSequenceParser.html" title="class in org.biojava.nbio.core.sequence.io">GenbankSequenceParser</a></li>
<li><a href="org/biojava/nbio/core/sequence/io/GenbankWriter.html" title="class in org.biojava.nbio.core.sequence.io">GenbankWriter</a></li>
<li><a href="org/biojava/nbio/core/sequence/io/GenbankWriterHelper.html" title="class in org.biojava.nbio.core.sequence.io">GenbankWriterHelper</a></li>
<li><a href="org/biojava/nbio/genome/parsers/genename/GeneChromosomePosition.html" title="class in org.biojava.nbio.genome.parsers.genename">GeneChromosomePosition</a></li>
<li><a href="org/biojava/nbio/genome/parsers/genename/GeneChromosomePositionParser.html" title="class in org.biojava.nbio.genome.parsers.genename">GeneChromosomePositionParser</a></li>
<li><a href="org/biojava/nbio/genome/GeneFeatureHelper.html" title="class in org.biojava.nbio.genome">GeneFeatureHelper</a></li>
<li><a href="org/biojava/nbio/genome/parsers/gff/GeneIDGFF2Reader.html" title="class in org.biojava.nbio.genome.parsers.gff">GeneIDGFF2Reader</a></li>
<li><a href="org/biojava/nbio/genome/parsers/geneid/GeneIDXMLReader.html" title="class in org.biojava.nbio.genome.parsers.geneid">GeneIDXMLReader</a></li>
<li><a href="org/biojava/nbio/genome/parsers/gff/GeneMarkGTFReader.html" title="class in org.biojava.nbio.genome.parsers.gff">GeneMarkGTFReader</a></li>
<li><a href="org/biojava/nbio/genome/parsers/genename/GeneName.html" title="class in org.biojava.nbio.genome.parsers.genename">GeneName</a></li>
<li><a href="org/biojava/nbio/genome/parsers/genename/GeneNamesParser.html" title="class in org.biojava.nbio.genome.parsers.genename">GeneNamesParser</a></li>
<li><a href="org/biojava/nbio/core/sequence/io/GenericFastaHeaderFormat.html" title="class in org.biojava.nbio.core.sequence.io">GenericFastaHeaderFormat</a></li>
<li><a href="org/biojava/nbio/core/sequence/io/GenericFastaHeaderParser.html" title="class in org.biojava.nbio.core.sequence.io">GenericFastaHeaderParser</a></li>
<li><a href="org/biojava/nbio/core/sequence/io/GenericGenbankHeaderFormat.html" title="class in org.biojava.nbio.core.sequence.io">GenericGenbankHeaderFormat</a></li>
<li><a href="org/biojava/nbio/core/sequence/io/GenericGenbankHeaderParser.html" title="class in org.biojava.nbio.core.sequence.io">GenericGenbankHeaderParser</a></li>
<li><a href="org/biojava/nbio/core/sequence/io/GenericInsdcHeaderFormat.html" title="class in org.biojava.nbio.core.sequence.io">GenericInsdcHeaderFormat</a></li>
<li><a href="org/biojava/nbio/core/sequence/GeneSequence.html" title="class in org.biojava.nbio.core.sequence">GeneSequence</a></li>
<li><a href="org/biojava/nbio/structure/domain/pdp/GetDistanceMatrix.html" title="class in org.biojava.nbio.structure.domain.pdp">GetDistanceMatrix</a></li>
<li><a href="org/biojava/nbio/genome/homology/GFF3FromUniprotBlastHits.html" title="class in org.biojava.nbio.genome.homology">GFF3FromUniprotBlastHits</a></li>
<li><a href="org/biojava/nbio/genome/parsers/gff/GFF3Reader.html" title="class in org.biojava.nbio.genome.parsers.gff">GFF3Reader</a></li>
<li><a href="org/biojava/nbio/genome/parsers/gff/GFF3Writer.html" title="class in org.biojava.nbio.genome.parsers.gff">GFF3Writer</a></li>
<li><a href="org/biojava/nbio/ontology/io/GOParser.html" title="class in org.biojava.nbio.ontology.io">GOParser</a></li>
<li><a href="org/biojava/nbio/structure/align/pairwise/Gotoh.html" title="class in org.biojava.nbio.structure.align.pairwise">Gotoh</a></li>
<li><a href="org/biojava/nbio/structure/gui/util/color/GradientMapper.html" title="class in org.biojava.nbio.structure.gui.util.color">GradientMapper</a></li>
<li><a href="org/biojava/nbio/structure/gui/util/color/GradientPanel.html" title="class in org.biojava.nbio.structure.gui.util.color">GradientPanel</a></li>
<li><a href="org/biojava/nbio/structure/symmetry/internal/GraphComponentOrderDetector.html" title="class in org.biojava.nbio.structure.symmetry.internal">GraphComponentOrderDetector</a></li>
<li><a href="org/biojava/nbio/structure/symmetry/internal/GraphComponentRefiner.html" title="class in org.biojava.nbio.structure.symmetry.internal">GraphComponentRefiner</a></li>
<li><a href="org/biojava/nbio/structure/contact/Grid.html" title="class in org.biojava.nbio.structure.contact">Grid</a></li>
<li><a href="org/biojava/nbio/structure/contact/GridCell.html" title="class in org.biojava.nbio.structure.contact">GridCell</a></li>
<li><a href="org/biojava/nbio/structure/Group.html" title="interface in org.biojava.nbio.structure"><span class="interfaceName">Group</span></a></li>
<li><a href="org/biojava/nbio/structure/asa/GroupAsa.html" title="class in org.biojava.nbio.structure.asa">GroupAsa</a></li>
<li><a href="org/biojava/nbio/structure/contact/GroupContact.html" title="class in org.biojava.nbio.structure.contact">GroupContact</a></li>
<li><a href="org/biojava/nbio/structure/contact/GroupContactSet.html" title="class in org.biojava.nbio.structure.contact">GroupContactSet</a></li>
<li><a href="org/biojava/nbio/structure/GroupIterator.html" title="class in org.biojava.nbio.structure">GroupIterator</a></li>
<li><a href="org/biojava/nbio/survival/kaplanmeier/figure/GroupResults.html" title="class in org.biojava.nbio.survival.kaplanmeier.figure">GroupResults</a></li>
<li><a href="org/biojava/nbio/structure/io/GroupToSDF.html" title="class in org.biojava.nbio.structure.io">GroupToSDF</a></li>
<li><a href="org/biojava/nbio/structure/GroupType.html" title="enum in org.biojava.nbio.structure">GroupType</a></li>
<li><a href="org/biojava/nbio/alignment/routines/GuanUberbacher.html" title="class in org.biojava.nbio.alignment.routines">GuanUberbacher</a></li>
<li><a href="org/biojava/nbio/alignment/GuideTree.html" title="class in org.biojava.nbio.alignment">GuideTree</a></li>
<li><a href="org/biojava/nbio/alignment/template/GuideTreeNode.html" title="interface in org.biojava.nbio.alignment.template"><span class="interfaceName">GuideTreeNode</span></a></li>
<li><a href="org/biojava/nbio/structure/align/ce/GuiWrapper.html" title="class in org.biojava.nbio.structure.align.ce">GuiWrapper</a></li>
<li><a href="org/biojava/nbio/core/util/Hashcoder.html" title="class in org.biojava.nbio.core.util">Hashcoder</a></li>
<li><a href="org/biojava/nbio/structure/secstruc/HBond.html" title="class in org.biojava.nbio.structure.secstruc">HBond</a></li>
<li><a href="org/biojava/nbio/survival/data/HeaderInfo.html" title="class in org.biojava.nbio.survival.data">HeaderInfo</a></li>
<li><a href="org/biojava/nbio/structure/symmetry/core/HelicalRepeatUnit.html" title="class in org.biojava.nbio.structure.symmetry.core">HelicalRepeatUnit</a></li>
<li><a href="org/biojava/nbio/structure/symmetry/core/Helix.html" title="class in org.biojava.nbio.structure.symmetry.core">Helix</a></li>
<li><a href="org/biojava/nbio/structure/symmetry/axis/HelixAxisAligner.html" title="class in org.biojava.nbio.structure.symmetry.axis">HelixAxisAligner</a></li>
<li><a href="org/biojava/nbio/structure/symmetry/core/HelixExtender.html" title="class in org.biojava.nbio.structure.symmetry.core">HelixExtender</a></li>
<li><a href="org/biojava/nbio/structure/symmetry/core/HelixLayers.html" title="class in org.biojava.nbio.structure.symmetry.core">HelixLayers</a></li>
<li><a href="org/biojava/nbio/structure/symmetry/core/HelixSolver.html" title="class in org.biojava.nbio.structure.symmetry.core">HelixSolver</a></li>
<li><a href="org/biojava/nbio/proteincomparisontool/HelloWorld.html" title="class in org.biojava.nbio.proteincomparisontool">HelloWorld</a></li>
<li><a href="org/biojava/nbio/structure/align/gui/HelpDialog.html" title="class in org.biojava.nbio.structure.align.gui">HelpDialog</a></li>
<li><a href="org/biojava/nbio/structure/HetatomImpl.html" title="class in org.biojava.nbio.structure">HetatomImpl</a></li>
<li><a href="org/biojava/nbio/structure/HetatomImpl.PerformanceBehavior.html" title="enum in org.biojava.nbio.structure">HetatomImpl.PerformanceBehavior</a></li>
<li><a href="org/biojava/nbio/alignment/template/HierarchicalClusterer.html" title="interface in org.biojava.nbio.alignment.template"><span class="interfaceName">HierarchicalClusterer</span></a></li>
<li><a href="org/biojava/nbio/core/search/io/Hit.html" title="class in org.biojava.nbio.core.search.io">Hit</a></li>
<li><a href="demo/HmmerDemo.html" title="class in demo">HmmerDemo</a></li>
<li><a href="org/biojava/nbio/ws/hmmer/HmmerDomain.html" title="class in org.biojava.nbio.ws.hmmer">HmmerDomain</a></li>
<li><a href="org/biojava/nbio/ws/hmmer/HmmerResult.html" title="class in org.biojava.nbio.ws.hmmer">HmmerResult</a></li>
<li><a href="org/biojava/nbio/ws/hmmer/HmmerScan.html" title="interface in org.biojava.nbio.ws.hmmer"><span class="interfaceName">HmmerScan</span></a></li>
<li><a href="org/biojava/nbio/core/search/io/Hsp.html" title="class in org.biojava.nbio.core.search.io">Hsp</a></li>
<li><a href="org/biojava/nbio/structure/gui/util/color/HSVColorSpace.html" title="class in org.biojava.nbio.structure.gui.util.color">HSVColorSpace</a></li>
<li><a href="org/biojava/nbio/structure/symmetry/geometry/IcosahedralSampler.html" title="class in org.biojava.nbio.structure.symmetry.geometry">IcosahedralSampler</a></li>
<li><a href="org/biojava/nbio/structure/symmetry/geometry/Icosahedron.html" title="class in org.biojava.nbio.structure.symmetry.geometry">Icosahedron</a></li>
<li><a href="org/biojava/nbio/structure/align/helper/IdxComparator.html" title="class in org.biojava.nbio.structure.align.helper">IdxComparator</a></li>
<li><a href="org/biojava/nbio/genome/io/fastq/IlluminaFastqReader.html" title="class in org.biojava.nbio.genome.io.fastq">IlluminaFastqReader</a></li>
<li><a href="org/biojava/nbio/genome/io/fastq/IlluminaFastqWriter.html" title="class in org.biojava.nbio.genome.io.fastq">IlluminaFastqWriter</a></li>
<li><a href="org/biojava/nbio/structure/align/helper/IndexPair.html" title="class in org.biojava.nbio.structure.align.helper">IndexPair</a></li>
<li><a href="org/biojava/nbio/core/util/InputStreamProvider.html" title="class in org.biojava.nbio.core.util">InputStreamProvider</a></li>
<li><a href="org/biojava/nbio/core/sequence/location/InsdcLocations.html" title="class in org.biojava.nbio.core.sequence.location">InsdcLocations</a></li>
<li><a href="org/biojava/nbio/core/sequence/location/InsdcLocations.BondLocation.html" title="class in org.biojava.nbio.core.sequence.location">InsdcLocations.BondLocation</a></li>
<li><a href="org/biojava/nbio/core/sequence/location/InsdcLocations.GroupLocation.html" title="class in org.biojava.nbio.core.sequence.location">InsdcLocations.GroupLocation</a></li>
<li><a href="org/biojava/nbio/core/sequence/location/InsdcLocations.OneOfLocation.html" title="class in org.biojava.nbio.core.sequence.location">InsdcLocations.OneOfLocation</a></li>
<li><a href="org/biojava/nbio/core/sequence/location/InsdcLocations.OrderLocation.html" title="class in org.biojava.nbio.core.sequence.location">InsdcLocations.OrderLocation</a></li>
<li><a href="org/biojava/nbio/core/sequence/location/InsdcParser.html" title="class in org.biojava.nbio.core.sequence.location">InsdcParser</a></li>
<li><a href="org/biojava/nbio/ontology/IntegerOntology.html" title="class in org.biojava.nbio.ontology">IntegerOntology</a></li>
<li><a href="org/biojava/nbio/structure/contact/InterfaceFinder.html" title="class in org.biojava.nbio.structure.contact">InterfaceFinder</a></li>
<li><a href="org/biojava/nbio/core/sequence/IntronSequence.html" title="class in org.biojava.nbio.core.sequence">IntronSequence</a></li>
<li><a href="org/biojava/nbio/ontology/InvalidTermException.html" title="class in org.biojava.nbio.ontology">InvalidTermException</a></li>
<li><a href="org/biojava/nbio/core/sequence/io/util/IOUtils.html" title="class in org.biojava.nbio.core.sequence.io.util">IOUtils</a></li>
<li><a href="org/biojava/nbio/core/sequence/io/util/IOUtils.ReaderProcessor.html" title="interface in org.biojava.nbio.core.sequence.io.util"><span class="interfaceName">IOUtils.ReaderProcessor</span></a></li>
<li><a href="org/biojava/nbio/aaproperties/IPeptideProperties.html" title="interface in org.biojava.nbio.aaproperties"><span class="interfaceName">IPeptideProperties</span></a></li>
<li><a href="org/biojava/nbio/aaproperties/profeat/IProfeatProperties.html" title="interface in org.biojava.nbio.aaproperties.profeat"><span class="interfaceName">IProfeatProperties</span></a></li>
<li><a href="org/biojava/nbio/aaproperties/profeat/IProfeatProperties.ATTRIBUTE.html" title="enum in org.biojava.nbio.aaproperties.profeat">IProfeatProperties.ATTRIBUTE</a></li>
<li><a href="org/biojava/nbio/aaproperties/profeat/IProfeatProperties.DISTRIBUTION.html" title="enum in org.biojava.nbio.aaproperties.profeat">IProfeatProperties.DISTRIBUTION</a></li>
<li><a href="org/biojava/nbio/aaproperties/profeat/IProfeatProperties.GROUPING.html" title="enum in org.biojava.nbio.aaproperties.profeat">IProfeatProperties.GROUPING</a></li>
<li><a href="org/biojava/nbio/aaproperties/profeat/IProfeatProperties.TRANSITION.html" title="enum in org.biojava.nbio.aaproperties.profeat">IProfeatProperties.TRANSITION</a></li>
<li><a href="org/biojava/nbio/aaproperties/xml/Isotope.html" title="class in org.biojava.nbio.aaproperties.xml">Isotope</a></li>
<li><a href="org/biojava/nbio/core/sequence/io/IUPACParser.html" title="class in org.biojava.nbio.core.sequence.io">IUPACParser</a></li>
<li><a href="org/biojava/nbio/core/sequence/io/IUPACParser.IUPACTable.html" title="class in org.biojava.nbio.core.sequence.io">IUPACParser.IUPACTable</a></li>
<li><a href="org/biojava/nbio/structure/align/gui/autosuggest/JAutoSuggest.html" title="class in org.biojava.nbio.structure.align.gui.autosuggest">JAutoSuggest</a></li>
<li><a href="org/biojava/nbio/structure/gui/JMatrixPanel.html" title="class in org.biojava.nbio.structure.gui">JMatrixPanel</a></li>
<li><a href="org/biojava/nbio/structure/gui/events/JmolAlignedPositionListener.html" title="class in org.biojava.nbio.structure.gui.events">JmolAlignedPositionListener</a></li>
<li><a href="org/biojava/nbio/structure/align/gui/jmol/JmolPanel.html" title="class in org.biojava.nbio.structure.align.gui.jmol">JmolPanel</a></li>
<li><a href="org/biojava/nbio/structure/align/gui/jmol/JmolPanel.JmolLoggerAdapter.html" title="class in org.biojava.nbio.structure.align.gui.jmol">JmolPanel.JmolLoggerAdapter</a></li>
<li><a href="org/biojava/nbio/structure/symmetry/jmolScript/JmolSymmetryScriptGenerator.html" title="class in org.biojava.nbio.structure.symmetry.jmolScript">JmolSymmetryScriptGenerator</a></li>
<li><a href="org/biojava/nbio/structure/symmetry/jmolScript/JmolSymmetryScriptGeneratorC1.html" title="class in org.biojava.nbio.structure.symmetry.jmolScript">JmolSymmetryScriptGeneratorC1</a></li>
<li><a href="org/biojava/nbio/structure/symmetry/jmolScript/JmolSymmetryScriptGeneratorCn.html" title="class in org.biojava.nbio.structure.symmetry.jmolScript">JmolSymmetryScriptGeneratorCn</a></li>
<li><a href="org/biojava/nbio/structure/symmetry/jmolScript/JmolSymmetryScriptGeneratorDn.html" title="class in org.biojava.nbio.structure.symmetry.jmolScript">JmolSymmetryScriptGeneratorDn</a></li>
<li><a href="org/biojava/nbio/structure/symmetry/jmolScript/JmolSymmetryScriptGeneratorH.html" title="class in org.biojava.nbio.structure.symmetry.jmolScript">JmolSymmetryScriptGeneratorH</a></li>
<li><a href="org/biojava/nbio/structure/symmetry/jmolScript/JmolSymmetryScriptGeneratorI.html" title="class in org.biojava.nbio.structure.symmetry.jmolScript">JmolSymmetryScriptGeneratorI</a></li>
<li><a href="org/biojava/nbio/structure/symmetry/jmolScript/JmolSymmetryScriptGeneratorO.html" title="class in org.biojava.nbio.structure.symmetry.jmolScript">JmolSymmetryScriptGeneratorO</a></li>
<li><a href="org/biojava/nbio/structure/symmetry/jmolScript/JmolSymmetryScriptGeneratorPointGroup.html" title="class in org.biojava.nbio.structure.symmetry.jmolScript">JmolSymmetryScriptGeneratorPointGroup</a></li>
<li><a href="org/biojava/nbio/structure/symmetry/jmolScript/JmolSymmetryScriptGeneratorT.html" title="class in org.biojava.nbio.structure.symmetry.jmolScript">JmolSymmetryScriptGeneratorT</a></li>
<li><a href="org/biojava/nbio/structure/align/gui/jmol/JmolTools.html" title="class in org.biojava.nbio.structure.align.gui.jmol">JmolTools</a></li>
<li><a href="org/biojava/nbio/structure/gui/JmolViewerImpl.html" title="class in org.biojava.nbio.structure.gui">JmolViewerImpl</a></li>
<li><a href="org/biojava/nbio/structure/align/webstart/JNLPProxy.html" title="class in org.biojava.nbio.structure.align.webstart">JNLPProxy</a></li>
<li><a href="org/biojava/nbio/core/sequence/storage/JoiningSequenceReader.html" title="class in org.biojava.nbio.core.sequence.storage">JoiningSequenceReader</a></li>
<li><a href="org/biojava/nbio/structure/align/helper/JointFragments.html" title="class in org.biojava.nbio.structure.align.helper">JointFragments</a></li>
<li><a href="org/biojava/nbio/structure/JournalArticle.html" title="class in org.biojava.nbio.structure">JournalArticle</a></li>
<li><a href="org/biojava/nbio/structure/align/gui/JPrintPanel.html" title="class in org.biojava.nbio.structure.align.gui">JPrintPanel</a></li>
<li><a href="org/biojava/nbio/ronn/Jronn.html" title="class in org.biojava.nbio.ronn">Jronn</a></li>
<li><a href="org/biojava/nbio/ronn/Jronn.Range.html" title="class in org.biojava.nbio.ronn">Jronn.Range</a></li>
<li><a href="org/biojava/nbio/survival/kaplanmeier/figure/KaplanMeierFigure.html" title="class in org.biojava.nbio.survival.kaplanmeier.figure">KaplanMeierFigure</a></li>
<li><a href="org/biojava/nbio/ontology/utils/KeyedWeakReference.html" title="class in org.biojava.nbio.ontology.utils">KeyedWeakReference</a></li>
<li><a href="org/biojava/nbio/survival/kaplanmeier/figure/KMFigureInfo.html" title="class in org.biojava.nbio.survival.kaplanmeier.figure">KMFigureInfo</a></li>
<li><a href="org/biojava/nbio/structure/secstruc/Ladder.html" title="class in org.biojava.nbio.structure.secstruc">Ladder</a></li>
<li><a href="org/biojava/nbio/core/sequence/template/LightweightProfile.html" title="interface in org.biojava.nbio.core.sequence.template"><span class="interfaceName">LightweightProfile</span></a></li>
<li><a href="org/biojava/nbio/core/sequence/template/LightweightProfile.StringFormat.html" title="enum in org.biojava.nbio.core.sequence.template">LightweightProfile.StringFormat</a></li>
<li><a href="org/biojava/nbio/structure/gui/util/color/LinearColorInterpolator.html" title="class in org.biojava.nbio.structure.gui.util.color">LinearColorInterpolator</a></li>
<li><a href="org/biojava/nbio/structure/gui/util/color/LinearColorInterpolator.InterpolationDirection.html" title="enum in org.biojava.nbio.structure.gui.util.color">LinearColorInterpolator.InterpolationDirection</a></li>
<li><a href="org/biojava/nbio/structure/io/LocalPDBDirectory.html" title="class in org.biojava.nbio.structure.io">LocalPDBDirectory</a></li>
<li><a href="org/biojava/nbio/structure/io/LocalPDBDirectory.FetchBehavior.html" title="enum in org.biojava.nbio.structure.io">LocalPDBDirectory.FetchBehavior</a></li>
<li><a href="org/biojava/nbio/structure/io/LocalPDBDirectory.ObsoleteBehavior.html" title="enum in org.biojava.nbio.structure.io">LocalPDBDirectory.ObsoleteBehavior</a></li>
<li><a href="org/biojava/nbio/structure/domain/LocalProteinDomainParser.html" title="class in org.biojava.nbio.structure.domain">LocalProteinDomainParser</a></li>
<li><a href="org/biojava/nbio/structure/scop/LocalScopDatabase.html" title="interface in org.biojava.nbio.structure.scop"><span class="interfaceName">LocalScopDatabase</span></a></li>
<li><a href="org/biojava/nbio/core/sequence/location/template/Location.html" title="interface in org.biojava.nbio.core.sequence.location.template"><span class="interfaceName">Location</span></a></li>
<li><a href="org/biojava/nbio/genome/parsers/gff/Location.html" title="class in org.biojava.nbio.genome.parsers.gff">Location</a></li>
<li><a href="org/biojava/nbio/core/sequence/location/template/Location.Tools.html" title="class in org.biojava.nbio.core.sequence.location.template">Location.Tools</a></li>
<li><a href="org/biojava/nbio/core/sequence/location/LocationHelper.html" title="class in org.biojava.nbio.core.sequence.location">LocationHelper</a></li>
<li><a href="org/biojava/nbio/genome/parsers/gff/LocIterator.html" title="class in org.biojava.nbio.genome.parsers.gff">LocIterator</a></li>
<li><a href="org/biojava/nbio/structure/gui/util/color/LogColorMapper.html" title="class in org.biojava.nbio.structure.gui.util.color">LogColorMapper</a></li>
<li><a href="org/biojava/nbio/structure/jama/LUDecomposition.html" title="class in org.biojava.nbio.structure.jama">LUDecomposition</a></li>
<li><a href="org/biojava/nbio/ws/alignment/qblast/MapToStringTransformer.html" title="class in org.biojava.nbio.ws.alignment.qblast">MapToStringTransformer</a></li>
<li><a href="org/biojava/nbio/structure/jama/Maths.html" title="class in org.biojava.nbio.structure.jama">Maths</a></li>
<li><a href="org/biojava/nbio/structure/geometry/Matrices.html" title="class in org.biojava.nbio.structure.geometry">Matrices</a></li>
<li><a href="org/biojava/nbio/structure/jama/Matrix.html" title="class in org.biojava.nbio.structure.jama">Matrix</a></li>
<li><a href="org/biojava/nbio/survival/cox/matrix/Matrix.html" title="class in org.biojava.nbio.survival.cox.matrix">Matrix</a></li>
<li><a href="org/biojava/nbio/alignment/template/MatrixAligner.html" title="interface in org.biojava.nbio.alignment.template"><span class="interfaceName">MatrixAligner</span></a></li>
<li><a href="org/biojava/nbio/structure/align/ce/MatrixListener.html" title="interface in org.biojava.nbio.structure.align.ce"><span class="interfaceName">MatrixListener</span></a></li>
<li><a href="org/biojava/nbio/survival/cox/comparators/MeanModelComparator.html" title="class in org.biojava.nbio.survival.cox.comparators">MeanModelComparator</a></li>
<li><a href="org/biojava/nbio/survival/kaplanmeier/metadata/MeanQuantizer.html" title="class in org.biojava.nbio.survival.kaplanmeier.metadata">MeanQuantizer</a></li>
<li><a href="org/biojava/nbio/structure/align/gui/MemoryMonitor.html" title="class in org.biojava.nbio.structure.align.gui">MemoryMonitor</a></li>
<li><a href="org/biojava/nbio/structure/align/gui/MenuCreator.html" title="class in org.biojava.nbio.structure.align.gui">MenuCreator</a></li>
<li><a href="org/biojava/nbio/structure/gui/util/MenuCreator.html" title="class in org.biojava.nbio.structure.gui.util">MenuCreator</a></li>
<li><a href="org/biojava/nbio/structure/align/gui/MenuCreator.DotPlotListener.html" title="class in org.biojava.nbio.structure.align.gui">MenuCreator.DotPlotListener</a></li>
<li><a href="org/biojava/nbio/core/exceptions/Messages.html" title="class in org.biojava.nbio.core.exceptions">Messages</a></li>
<li><a href="org/biojava/nbio/survival/kaplanmeier/metadata/MetaDataInfo.html" title="class in org.biojava.nbio.survival.kaplanmeier.metadata">MetaDataInfo</a></li>
<li><a href="org/biojava/nbio/structure/io/cif/MetalBondConsumer.html" title="interface in org.biojava.nbio.structure.io.cif"><span class="interfaceName">MetalBondConsumer</span></a></li>
<li><a href="org/biojava/nbio/structure/io/cif/MetalBondConsumerImpl.html" title="class in org.biojava.nbio.structure.io.cif">MetalBondConsumerImpl</a></li>
<li><a href="org/biojava/nbio/structure/io/cif/MetalBondConverter.html" title="class in org.biojava.nbio.structure.io.cif">MetalBondConverter</a></li>
<li><a href="org/biojava/nbio/structure/chem/MetalBondDistance.html" title="class in org.biojava.nbio.structure.chem">MetalBondDistance</a></li>
<li><a href="org/biojava/nbio/structure/basepairs/MismatchedBasePairParameters.html" title="class in org.biojava.nbio.structure.basepairs">MismatchedBasePairParameters</a></li>
<li><a href="org/biojava/nbio/structure/io/mmtf/MmtfActions.html" title="class in org.biojava.nbio.structure.io.mmtf">MmtfActions</a></li>
<li><a href="org/biojava/nbio/structure/io/MMTFFileReader.html" title="class in org.biojava.nbio.structure.io">MMTFFileReader</a></li>
<li><a href="org/biojava/nbio/structure/io/mmtf/MmtfStructureReader.html" title="class in org.biojava.nbio.structure.io.mmtf">MmtfStructureReader</a></li>
<li><a href="org/biojava/nbio/structure/io/mmtf/MmtfStructureWriter.html" title="class in org.biojava.nbio.structure.io.mmtf">MmtfStructureWriter</a></li>
<li><a href="org/biojava/nbio/structure/io/mmtf/MmtfSummaryDataBean.html" title="class in org.biojava.nbio.structure.io.mmtf">MmtfSummaryDataBean</a></li>
<li><a href="org/biojava/nbio/structure/io/mmtf/MmtfUtils.html" title="class in org.biojava.nbio.structure.io.mmtf">MmtfUtils</a></li>
<li><a href="org/biojava/nbio/structure/Model.html" title="class in org.biojava.nbio.structure">Model</a></li>
<li><a href="org/biojava/nbio/ronn/ModelLoader.html" title="class in org.biojava.nbio.ronn">ModelLoader</a></li>
<li><a href="org/biojava/nbio/ronn/ModelLoader.Model.html" title="class in org.biojava.nbio.ronn">ModelLoader.Model</a></li>
<li><a href="org/biojava/nbio/ronn/ModelLoader.Threshold.html" title="class in org.biojava.nbio.ronn">ModelLoader.Threshold</a></li>
<li><a href="org/biojava/nbio/protmod/ModificationCategory.html" title="enum in org.biojava.nbio.protmod">ModificationCategory</a></li>
<li><a href="org/biojava/nbio/protmod/ModificationCondition.html" title="interface in org.biojava.nbio.protmod"><span class="interfaceName">ModificationCondition</span></a></li>
<li><a href="org/biojava/nbio/protmod/ModificationConditionImpl.html" title="class in org.biojava.nbio.protmod">ModificationConditionImpl</a></li>
<li><a href="org/biojava/nbio/protmod/ModificationLinkage.html" title="class in org.biojava.nbio.protmod">ModificationLinkage</a></li>
<li><a href="org/biojava/nbio/protmod/ModificationOccurrenceType.html" title="enum in org.biojava.nbio.protmod">ModificationOccurrenceType</a></li>
<li><a href="org/biojava/nbio/aaproperties/xml/ModifiedAminoAcidCompoundSet.html" title="class in org.biojava.nbio.aaproperties.xml">ModifiedAminoAcidCompoundSet</a></li>
<li><a href="org/biojava/nbio/protmod/structure/ModifiedCompound.html" title="interface in org.biojava.nbio.protmod.structure"><span class="interfaceName">ModifiedCompound</span></a></li>
<li><a href="org/biojava/nbio/protmod/structure/ModifiedCompoundImpl.html" title="class in org.biojava.nbio.protmod.structure">ModifiedCompoundImpl</a></li>
<li><a href="org/biojava/nbio/protmod/io/ModifiedCompoundXMLConverter.html" title="class in org.biojava.nbio.protmod.io">ModifiedCompoundXMLConverter</a></li>
<li><a href="org/biojava/nbio/structure/geometry/MomentsOfInertia.html" title="class in org.biojava.nbio.structure.geometry">MomentsOfInertia</a></li>
<li><a href="org/biojava/nbio/structure/geometry/MomentsOfInertia.SymmetryClass.html" title="enum in org.biojava.nbio.structure.geometry">MomentsOfInertia.SymmetryClass</a></li>
<li><a href="org/biojava/nbio/structure/align/multiple/MultipleAlignment.html" title="interface in org.biojava.nbio.structure.align.multiple"><span class="interfaceName">MultipleAlignment</span></a></li>
<li><a href="org/biojava/nbio/structure/align/gui/MultipleAlignmentCalc.html" title="class in org.biojava.nbio.structure.align.gui">MultipleAlignmentCalc</a></li>
<li><a href="org/biojava/nbio/structure/align/gui/aligpanel/MultipleAlignmentCoordManager.html" title="class in org.biojava.nbio.structure.align.gui.aligpanel">MultipleAlignmentCoordManager</a></li>
<li><a href="org/biojava/nbio/structure/align/multiple/util/MultipleAlignmentDisplay.html" title="class in org.biojava.nbio.structure.align.multiple.util">MultipleAlignmentDisplay</a></li>
<li><a href="org/biojava/nbio/structure/align/multiple/MultipleAlignmentEnsemble.html" title="interface in org.biojava.nbio.structure.align.multiple"><span class="interfaceName">MultipleAlignmentEnsemble</span></a></li>
<li><a href="org/biojava/nbio/structure/align/multiple/MultipleAlignmentEnsembleImpl.html" title="class in org.biojava.nbio.structure.align.multiple">MultipleAlignmentEnsembleImpl</a></li>
<li><a href="org/biojava/nbio/structure/align/gui/MultipleAlignmentGUI.html" title="class in org.biojava.nbio.structure.align.gui">MultipleAlignmentGUI</a></li>
<li><a href="org/biojava/nbio/structure/align/multiple/MultipleAlignmentImpl.html" title="class in org.biojava.nbio.structure.align.multiple">MultipleAlignmentImpl</a></li>
<li><a href="org/biojava/nbio/structure/align/gui/jmol/MultipleAlignmentJmol.html" title="class in org.biojava.nbio.structure.align.gui.jmol">MultipleAlignmentJmol</a></li>
<li><a href="org/biojava/nbio/structure/align/gui/MultipleAlignmentJmolDisplay.html" title="class in org.biojava.nbio.structure.align.gui">MultipleAlignmentJmolDisplay</a></li>
<li><a href="org/biojava/nbio/structure/align/multiple/util/MultipleAlignmentScorer.html" title="class in org.biojava.nbio.structure.align.multiple.util">MultipleAlignmentScorer</a></li>
<li><a href="org/biojava/nbio/structure/align/multiple/util/MultipleAlignmentTools.html" title="class in org.biojava.nbio.structure.align.multiple.util">MultipleAlignmentTools</a></li>
<li><a href="org/biojava/nbio/structure/align/multiple/util/MultipleAlignmentWriter.html" title="class in org.biojava.nbio.structure.align.multiple.util">MultipleAlignmentWriter</a></li>
<li><a href="org/biojava/nbio/structure/align/xml/MultipleAlignmentXMLConverter.html" title="class in org.biojava.nbio.structure.align.xml">MultipleAlignmentXMLConverter</a></li>
<li><a href="org/biojava/nbio/structure/align/xml/MultipleAlignmentXMLParser.html" title="class in org.biojava.nbio.structure.align.xml">MultipleAlignmentXMLParser</a></li>
<li><a href="org/biojava/nbio/structure/align/gui/aligpanel/MultipleAligPanel.html" title="class in org.biojava.nbio.structure.align.gui.aligpanel">MultipleAligPanel</a></li>
<li><a href="org/biojava/nbio/structure/align/gui/aligpanel/MultipleAligPanelMouseMotionListener.html" title="class in org.biojava.nbio.structure.align.gui.aligpanel">MultipleAligPanelMouseMotionListener</a></li>
<li><a href="org/biojava/nbio/structure/align/multiple/mc/MultipleMcMain.html" title="class in org.biojava.nbio.structure.align.multiple.mc">MultipleMcMain</a></li>
<li><a href="org/biojava/nbio/structure/align/multiple/mc/MultipleMcOptimizer.html" title="class in org.biojava.nbio.structure.align.multiple.mc">MultipleMcOptimizer</a></li>
<li><a href="org/biojava/nbio/structure/align/multiple/mc/MultipleMcParameters.html" title="class in org.biojava.nbio.structure.align.multiple.mc">MultipleMcParameters</a></li>
<li><a href="org/biojava/nbio/core/sequence/MultipleSequenceAlignment.html" title="class in org.biojava.nbio.core.sequence">MultipleSequenceAlignment</a></li>
<li><a href="org/biojava/nbio/structure/align/gui/aligpanel/MultipleStatusDisplay.html" title="class in org.biojava.nbio.structure.align.gui.aligpanel">MultipleStatusDisplay</a></li>
<li><a href="org/biojava/nbio/structure/align/MultipleStructureAligner.html" title="interface in org.biojava.nbio.structure.align"><span class="interfaceName">MultipleStructureAligner</span></a></li>
<li><a href="org/biojava/nbio/structure/align/multiple/util/MultipleSuperimposer.html" title="interface in org.biojava.nbio.structure.align.multiple.util"><span class="interfaceName">MultipleSuperimposer</span></a></li>
<li><a href="org/biojava/nbio/core/alignment/template/MutableAlignedSequence.html" title="interface in org.biojava.nbio.core.alignment.template"><span class="interfaceName">MutableAlignedSequence</span></a></li>
<li><a href="org/biojava/nbio/core/alignment/template/MutableProfile.html" title="interface in org.biojava.nbio.core.alignment.template"><span class="interfaceName">MutableProfile</span></a></li>
<li><a href="org/biojava/nbio/core/alignment/template/MutableProfilePair.html" title="interface in org.biojava.nbio.core.alignment.template"><span class="interfaceName">MutableProfilePair</span></a></li>
<li><a href="org/biojava/nbio/core/alignment/template/MutableSequencePair.html" title="interface in org.biojava.nbio.core.alignment.template"><span class="interfaceName">MutableSequencePair</span></a></li>
<li><a href="org/biojava/nbio/structure/Mutator.html" title="class in org.biojava.nbio.structure">Mutator</a></li>
<li><a href="org/biojava/nbio/structure/align/gui/MyAlignmentLoadListener.html" title="class in org.biojava.nbio.structure.align.gui">MyAlignmentLoadListener</a></li>
<li><a href="org/biojava/nbio/structure/align/gui/MyDistMaxListener.html" title="class in org.biojava.nbio.structure.align.gui">MyDistMaxListener</a></li>
<li><a href="org/biojava/nbio/structure/align/gui/MyExportListener.html" title="class in org.biojava.nbio.structure.align.gui">MyExportListener</a></li>
<li><a href="org/biojava/nbio/structure/align/gui/jmol/MyJmolStatusListener.html" title="class in org.biojava.nbio.structure.align.gui.jmol">MyJmolStatusListener</a></li>
<li><a href="org/biojava/nbio/structure/align/gui/MyOpenPdbFileListener.html" title="class in org.biojava.nbio.structure.align.gui">MyOpenPdbFileListener</a></li>
<li><a href="org/biojava/nbio/structure/align/gui/MySaveFileListener.html" title="class in org.biojava.nbio.structure.align.gui">MySaveFileListener</a></li>
<li><a href="org/biojava/nbio/structure/align/gui/MyTableRowSorter.html" title="class in org.biojava.nbio.structure.align.gui">MyTableRowSorter</a></li>
<li><a href="org/biojava/nbio/aaproperties/xml/MyValidationEventHandler.html" title="class in org.biojava.nbio.aaproperties.xml">MyValidationEventHandler</a></li>
<li><a href="org/biojava/nbio/aaproperties/xml/Name2Count.html" title="class in org.biojava.nbio.aaproperties.xml">Name2Count</a></li>
<li><a href="org/biojava/nbio/ws/alignment/qblast/NCBIQBlastAlignmentProperties.html" title="class in org.biojava.nbio.ws.alignment.qblast">NCBIQBlastAlignmentProperties</a></li>
<li><a href="org/biojava/nbio/ws/alignment/qblast/NCBIQBlastOutputProperties.html" title="class in org.biojava.nbio.ws.alignment.qblast">NCBIQBlastOutputProperties</a></li>
<li><a href="org/biojava/nbio/ws/alignment/qblast/NCBIQBlastService.html" title="class in org.biojava.nbio.ws.alignment.qblast">NCBIQBlastService</a></li>
<li><a href="demo/NCBIQBlastServiceDemo.html" title="class in demo">NCBIQBlastServiceDemo</a></li>
<li><a href="org/biojava/nbio/alignment/NeedlemanWunsch.html" title="class in org.biojava.nbio.alignment">NeedlemanWunsch</a></li>
<li><a href="org/biojava/nbio/core/sequence/compound/NucleotideCompound.html" title="class in org.biojava.nbio.core.sequence.compound">NucleotideCompound</a></li>
<li><a href="org/biojava/nbio/structure/NucleotideImpl.html" title="class in org.biojava.nbio.structure">NucleotideImpl</a></li>
<li><a href="org/biojava/nbio/ronn/NullOutputStream.html" title="class in org.biojava.nbio.ronn">NullOutputStream</a></li>
<li><a href="org/biojava/nbio/survival/kaplanmeier/figure/NumbersAtRiskPanel.html" title="class in org.biojava.nbio.survival.kaplanmeier.figure">NumbersAtRiskPanel</a></li>
<li><a href="org/biojava/nbio/ontology/obo/OboFileEventListener.html" title="interface in org.biojava.nbio.ontology.obo"><span class="interfaceName">OboFileEventListener</span></a></li>
<li><a href="org/biojava/nbio/ontology/obo/OboFileHandler.html" title="class in org.biojava.nbio.ontology.obo">OboFileHandler</a></li>
<li><a href="org/biojava/nbio/ontology/obo/OboFileParser.html" title="class in org.biojava.nbio.ontology.obo">OboFileParser</a></li>
<li><a href="org/biojava/nbio/ontology/obo/OboFileParser.SOPair.html" title="class in org.biojava.nbio.ontology.obo">OboFileParser.SOPair</a></li>
<li><a href="org/biojava/nbio/ontology/io/OboParser.html" title="class in org.biojava.nbio.ontology.io">OboParser</a></li>
<li><a href="org/biojava/nbio/structure/symmetry/geometry/Octahedron.html" title="class in org.biojava.nbio.structure.symmetry.geometry">Octahedron</a></li>
<li><a href="org/biojava/nbio/ontology/Ontology.html" title="interface in org.biojava.nbio.ontology"><span class="interfaceName">Ontology</span></a></li>
<li><a href="org/biojava/nbio/ontology/Ontology.Impl.html" title="class in org.biojava.nbio.ontology">Ontology.Impl</a></li>
<li><a href="org/biojava/nbio/ontology/OntologyException.html" title="class in org.biojava.nbio.ontology">OntologyException</a></li>
<li><a href="org/biojava/nbio/ontology/OntologyFactory.html" title="interface in org.biojava.nbio.ontology"><span class="interfaceName">OntologyFactory</span></a></li>
<li><a href="org/biojava/nbio/ontology/OntologyOps.html" title="interface in org.biojava.nbio.ontology"><span class="interfaceName">OntologyOps</span></a></li>
<li><a href="org/biojava/nbio/ontology/OntologyTerm.html" title="interface in org.biojava.nbio.ontology"><span class="interfaceName">OntologyTerm</span></a></li>
<li><a href="org/biojava/nbio/ontology/OntologyTerm.Impl.html" title="class in org.biojava.nbio.ontology">OntologyTerm.Impl</a></li>
<li><a href="org/biojava/nbio/ontology/OntoTools.html" title="class in org.biojava.nbio.ontology">OntoTools</a></li>
<li><a href="org/biojava/nbio/structure/quaternary/OperatorResolver.html" title="class in org.biojava.nbio.structure.quaternary">OperatorResolver</a></li>
<li><a href="org/biojava/nbio/structure/align/ce/OptimalCECPMain.html" title="class in org.biojava.nbio.structure.align.ce">OptimalCECPMain</a></li>
<li><a href="org/biojava/nbio/structure/align/ce/OptimalCECPParameters.html" title="class in org.biojava.nbio.structure.align.ce">OptimalCECPParameters</a></li>
<li><a href="org/biojava/nbio/structure/symmetry/internal/OrderDetector.html" title="interface in org.biojava.nbio.structure.symmetry.internal"><span class="interfaceName">OrderDetector</span></a></li>
<li><a href="org/biojava/nbio/structure/quaternary/OrderedPair.html" title="class in org.biojava.nbio.structure.quaternary">OrderedPair</a></li>
<li><a href="org/biojava/nbio/ronn/ORonn.html" title="class in org.biojava.nbio.ronn">ORonn</a></li>
<li><a href="org/biojava/nbio/ronn/ORonnModel.html" title="class in org.biojava.nbio.ronn">ORonnModel</a></li>
<li><a href="org/biojava/nbio/genome/query/OutputHitsGFF.html" title="class in org.biojava.nbio.genome.query">OutputHitsGFF</a></li>
<li><a href="org/biojava/nbio/structure/contact/Pair.html" title="class in org.biojava.nbio.structure.contact">Pair</a></li>
<li><a href="org/biojava/nbio/alignment/template/PairInProfileScorer.html" title="interface in org.biojava.nbio.alignment.template"><span class="interfaceName">PairInProfileScorer</span></a></li>
<li><a href="org/biojava/nbio/alignment/template/PairwiseSequenceAligner.html" title="interface in org.biojava.nbio.alignment.template"><span class="interfaceName">PairwiseSequenceAligner</span></a></li>
<li><a href="org/biojava/nbio/alignment/template/PairwiseSequenceScorer.html" title="interface in org.biojava.nbio.alignment.template"><span class="interfaceName">PairwiseSequenceScorer</span></a></li>
<li><a href="org/biojava/nbio/structure/align/gui/ParameterGUI.html" title="class in org.biojava.nbio.structure.align.gui">ParameterGUI</a></li>
<li><a href="demo/ParseFastaFileDemo.html" title="class in demo">ParseFastaFileDemo</a></li>
<li><a href="demo/ParseGO.html" title="class in demo">ParseGO</a></li>
<li><a href="org/biojava/nbio/genome/io/fastq/ParseListener.html" title="interface in org.biojava.nbio.genome.io.fastq"><span class="interfaceName">ParseListener</span></a></li>
<li><a href="org/biojava/nbio/core/exceptions/ParserException.html" title="class in org.biojava.nbio.core.exceptions">ParserException</a></li>
<li><a href="org/biojava/nbio/alignment/template/PartitionRefiner.html" title="interface in org.biojava.nbio.alignment.template"><span class="interfaceName">PartitionRefiner</span></a></li>
<li><a href="org/biojava/nbio/structure/PassthroughIdentifier.html" title="class in org.biojava.nbio.structure">PassthroughIdentifier</a></li>
<li><a href="org/biojava/nbio/structure/io/PDBBioAssemblyParser.html" title="class in org.biojava.nbio.structure.io">PDBBioAssemblyParser</a></li>
<li><a href="org/biojava/nbio/structure/PDBCrystallographicInfo.html" title="class in org.biojava.nbio.structure">PDBCrystallographicInfo</a></li>
<li><a href="org/biojava/nbio/structure/gui/util/PDBDirPanel.html" title="class in org.biojava.nbio.structure.gui.util">PDBDirPanel</a></li>
<li><a href="org/biojava/nbio/structure/io/PDBFileParser.html" title="class in org.biojava.nbio.structure.io">PDBFileParser</a></li>
<li><a href="org/biojava/nbio/structure/io/PDBFileReader.html" title="class in org.biojava.nbio.structure.io">PDBFileReader</a></li>
<li><a href="org/biojava/nbio/structure/PDBHeader.html" title="class in org.biojava.nbio.structure">PDBHeader</a></li>
<li><a href="org/biojava/nbio/structure/PdbId.html" title="class in org.biojava.nbio.structure">PdbId</a></li>
<li><a href="org/biojava/nbio/structure/align/client/PdbPair.html" title="class in org.biojava.nbio.structure.align.client">PdbPair</a></li>
<li><a href="org/biojava/nbio/structure/align/xml/PdbPairsMessage.html" title="class in org.biojava.nbio.structure.align.xml">PdbPairsMessage</a></li>
<li><a href="org/biojava/nbio/structure/align/xml/PdbPairXMLConverter.html" title="class in org.biojava.nbio.structure.align.xml">PdbPairXMLConverter</a></li>
<li><a href="org/biojava/nbio/structure/io/PDBParseException.html" title="class in org.biojava.nbio.structure.io">PDBParseException</a></li>
<li><a href="org/biojava/nbio/structure/PDBRecord.html" title="interface in org.biojava.nbio.structure"><span class="interfaceName">PDBRecord</span></a></li>
<li><a href="org/biojava/nbio/structure/gui/util/PDBServerPanel.html" title="class in org.biojava.nbio.structure.gui.util">PDBServerPanel</a></li>
<li><a href="org/biojava/nbio/structure/PDBStatus.html" title="class in org.biojava.nbio.structure">PDBStatus</a></li>
<li><a href="org/biojava/nbio/structure/PDBStatus.Status.html" title="enum in org.biojava.nbio.structure">PDBStatus.Status</a></li>
<li><a href="org/biojava/nbio/structure/io/util/PDBTemporaryStorageUtils.html" title="class in org.biojava.nbio.structure.io.util">PDBTemporaryStorageUtils</a></li>
<li><a href="org/biojava/nbio/structure/io/util/PDBTemporaryStorageUtils.LinkRecord.html" title="class in org.biojava.nbio.structure.io.util">PDBTemporaryStorageUtils.LinkRecord</a></li>
<li><a href="org/biojava/nbio/structure/gui/util/PDBUploadPanel.html" title="class in org.biojava.nbio.structure.gui.util">PDBUploadPanel</a></li>
<li><a href="org/biojava/nbio/structure/domain/pdp/PDPDistanceMatrix.html" title="class in org.biojava.nbio.structure.domain.pdp">PDPDistanceMatrix</a></li>
<li><a href="org/biojava/nbio/structure/domain/pdp/PDPParameters.html" title="class in org.biojava.nbio.structure.domain.pdp">PDPParameters</a></li>
<li><a href="org/biojava/nbio/aaproperties/PeptideProperties.html" title="class in org.biojava.nbio.aaproperties">PeptideProperties</a></li>
<li><a href="org/biojava/nbio/aaproperties/PeptideProperties.SingleLetterAACode.html" title="enum in org.biojava.nbio.aaproperties">PeptideProperties.SingleLetterAACode</a></li>
<li><a href="org/biojava/nbio/aaproperties/PeptidePropertiesImpl.html" title="class in org.biojava.nbio.aaproperties">PeptidePropertiesImpl</a></li>
<li><a href="org/biojava/nbio/structure/symmetry/utils/PermutationGenerator.html" title="class in org.biojava.nbio.structure.symmetry.utils">PermutationGenerator</a></li>
<li><a href="org/biojava/nbio/structure/symmetry/core/PermutationGroup.html" title="class in org.biojava.nbio.structure.symmetry.core">PermutationGroup</a></li>
<li><a href="org/biojava/nbio/core/sequence/io/PlainFastaHeaderParser.html" title="class in org.biojava.nbio.core.sequence.io">PlainFastaHeaderParser</a></li>
<li><a href="org/biojava/nbio/core/sequence/location/template/Point.html" title="interface in org.biojava.nbio.core.sequence.location.template"><span class="interfaceName">Point</span></a></li>
<li><a href="org/biojava/nbio/core/sequence/location/template/Point.Resolver.html" title="interface in org.biojava.nbio.core.sequence.location.template"><span class="interfaceName">Point.Resolver</span></a></li>
<li><a href="org/biojava/nbio/structure/symmetry/geometry/Polyhedron.html" title="interface in org.biojava.nbio.structure.symmetry.geometry"><span class="interfaceName">Polyhedron</span></a></li>
<li><a href="org/biojava/nbio/structure/chem/PolymerType.html" title="enum in org.biojava.nbio.structure.chem">PolymerType</a></li>
<li><a href="org/biojava/nbio/structure/symmetry/utils/PowerSet.html" title="class in org.biojava.nbio.structure.symmetry.utils">PowerSet</a></li>
<li><a href="demo/PredictDisorder.html" title="class in demo">PredictDisorder</a></li>
<li><a href="org/biojava/nbio/core/util/PrettyXMLWriter.html" title="class in org.biojava.nbio.core.util">PrettyXMLWriter</a></li>
<li><a href="org/biojava/nbio/structure/symmetry/geometry/Prism.html" title="class in org.biojava.nbio.structure.symmetry.geometry">Prism</a></li>
<li><a href="org/biojava/nbio/aaproperties/profeat/ProfeatProperties.html" title="class in org.biojava.nbio.aaproperties.profeat">ProfeatProperties</a></li>
<li><a href="org/biojava/nbio/aaproperties/profeat/ProfeatPropertiesImpl.html" title="class in org.biojava.nbio.aaproperties.profeat">ProfeatPropertiesImpl</a></li>
<li><a href="org/biojava/nbio/core/alignment/template/Profile.html" title="interface in org.biojava.nbio.core.alignment.template"><span class="interfaceName">Profile</span></a></li>
<li><a href="org/biojava/nbio/core/alignment/template/Profile.StringFormat.html" title="enum in org.biojava.nbio.core.alignment.template">Profile.StringFormat</a></li>
<li><a href="org/biojava/nbio/core/alignment/template/ProfilePair.html" title="interface in org.biojava.nbio.core.alignment.template"><span class="interfaceName">ProfilePair</span></a></li>
<li><a href="org/biojava/nbio/alignment/template/ProfileProfileAligner.html" title="interface in org.biojava.nbio.alignment.template"><span class="interfaceName">ProfileProfileAligner</span></a></li>
<li><a href="org/biojava/nbio/alignment/template/ProfileProfileScorer.html" title="interface in org.biojava.nbio.alignment.template"><span class="interfaceName">ProfileProfileScorer</span></a></li>
<li><a href="org/biojava/nbio/core/alignment/template/ProfileView.html" title="interface in org.biojava.nbio.core.alignment.template"><span class="interfaceName">ProfileView</span></a></li>
<li><a href="org/biojava/nbio/structure/symmetry/misc/ProteinComplexSignature.html" title="class in org.biojava.nbio.structure.symmetry.misc">ProteinComplexSignature</a></li>
<li><a href="org/biojava/nbio/genome/util/ProteinMappingTools.html" title="class in org.biojava.nbio.genome.util">ProteinMappingTools</a></li>
<li><a href="org/biojava/nbio/protmod/ProteinModification.html" title="interface in org.biojava.nbio.protmod"><span class="interfaceName">ProteinModification</span></a></li>
<li><a href="org/biojava/nbio/protmod/structure/ProteinModificationIdentifier.html" title="class in org.biojava.nbio.protmod.structure">ProteinModificationIdentifier</a></li>
<li><a href="org/biojava/nbio/protmod/ProteinModificationImpl.html" title="class in org.biojava.nbio.protmod">ProteinModificationImpl</a></li>
<li><a href="org/biojava/nbio/protmod/ProteinModificationImpl.Builder.html" title="class in org.biojava.nbio.protmod">ProteinModificationImpl.Builder</a></li>
<li><a href="org/biojava/nbio/protmod/ProteinModificationRegistry.html" title="class in org.biojava.nbio.protmod">ProteinModificationRegistry</a></li>
<li><a href="org/biojava/nbio/protmod/io/ProteinModificationXmlReader.html" title="class in org.biojava.nbio.protmod.io">ProteinModificationXmlReader</a></li>
<li><a href="org/biojava/nbio/core/sequence/ProteinSequence.html" title="class in org.biojava.nbio.core.sequence">ProteinSequence</a></li>
<li><a href="org/biojava/nbio/core/sequence/io/ProteinSequenceCreator.html" title="class in org.biojava.nbio.core.sequence.io">ProteinSequenceCreator</a></li>
<li><a href="org/biojava/nbio/core/sequence/template/ProxySequenceReader.html" title="interface in org.biojava.nbio.core.sequence.template"><span class="interfaceName">ProxySequenceReader</span></a></li>
<li><a href="org/biojava/nbio/structure/jama/QRDecomposition.html" title="class in org.biojava.nbio.structure.jama">QRDecomposition</a></li>
<li><a href="org/biojava/nbio/structure/align/quaternary/QsAlign.html" title="class in org.biojava.nbio.structure.align.quaternary">QsAlign</a></li>
<li><a href="org/biojava/nbio/structure/align/quaternary/QsAlignParameters.html" title="class in org.biojava.nbio.structure.align.quaternary">QsAlignParameters</a></li>
<li><a href="org/biojava/nbio/structure/align/quaternary/QsAlignResult.html" title="class in org.biojava.nbio.structure.align.quaternary">QsAlignResult</a></li>
<li><a href="org/biojava/nbio/structure/align/quaternary/QsRelation.html" title="enum in org.biojava.nbio.structure.align.quaternary">QsRelation</a></li>
<li><a href="org/biojava/nbio/core/sequence/features/Qualifier.html" title="class in org.biojava.nbio.core.sequence.features">Qualifier</a></li>
<li><a href="org/biojava/nbio/core/sequence/features/QualityFeature.html" title="class in org.biojava.nbio.core.sequence.features">QualityFeature</a></li>
<li><a href="org/biojava/nbio/core/sequence/features/QuantityFeature.html" title="class in org.biojava.nbio.core.sequence.features">QuantityFeature</a></li>
<li><a href="org/biojava/nbio/structure/symmetry/core/QuatSuperpositionScorer.html" title="class in org.biojava.nbio.structure.symmetry.core">QuatSuperpositionScorer</a></li>
<li><a href="org/biojava/nbio/structure/symmetry/core/QuatSymmetryDetector.html" title="class in org.biojava.nbio.structure.symmetry.core">QuatSymmetryDetector</a></li>
<li><a href="org/biojava/nbio/structure/symmetry/core/QuatSymmetryParameters.html" title="class in org.biojava.nbio.structure.symmetry.core">QuatSymmetryParameters</a></li>
<li><a href="org/biojava/nbio/structure/symmetry/core/QuatSymmetryResults.html" title="class in org.biojava.nbio.structure.symmetry.core">QuatSymmetryResults</a></li>
<li><a href="org/biojava/nbio/structure/symmetry/core/QuatSymmetryScores.html" title="class in org.biojava.nbio.structure.symmetry.core">QuatSymmetryScores</a></li>
<li><a href="org/biojava/nbio/structure/symmetry/core/QuatSymmetrySolver.html" title="interface in org.biojava.nbio.structure.symmetry.core"><span class="interfaceName">QuatSymmetrySolver</span></a></li>
<li><a href="org/biojava/nbio/structure/symmetry/core/QuatSymmetrySubunits.html" title="class in org.biojava.nbio.structure.symmetry.core">QuatSymmetrySubunits</a></li>
<li><a href="org/biojava/nbio/structure/align/gui/jmol/RasmolCommandListener.html" title="class in org.biojava.nbio.structure.align.gui.jmol">RasmolCommandListener</a></li>
<li><a href="org/biojava/nbio/structure/symmetry/geometry/RectangularPrism.html" title="class in org.biojava.nbio.structure.symmetry.geometry">RectangularPrism</a></li>
<li><a href="org/biojava/nbio/structure/chem/ReducedChemCompProvider.html" title="class in org.biojava.nbio.structure.chem">ReducedChemCompProvider</a></li>
<li><a href="org/biojava/nbio/core/sequence/reference/ReferenceInterface.html" title="interface in org.biojava.nbio.core.sequence.reference"><span class="interfaceName">ReferenceInterface</span></a></li>
<li><a href="org/biojava/nbio/structure/align/multiple/util/ReferenceSuperimposer.html" title="class in org.biojava.nbio.structure.align.multiple.util">ReferenceSuperimposer</a></li>
<li><a href="org/biojava/nbio/structure/symmetry/internal/RefinerFailedException.html" title="class in org.biojava.nbio.structure.symmetry.internal">RefinerFailedException</a></li>
<li><a href="org/biojava/nbio/ws/hmmer/RemoteHmmerScan.html" title="class in org.biojava.nbio.ws.hmmer">RemoteHmmerScan</a></li>
<li><a href="org/biojava/nbio/ws/alignment/RemotePairwiseAlignmentOutputProperties.html" title="interface in org.biojava.nbio.ws.alignment"><span class="interfaceName">RemotePairwiseAlignmentOutputProperties</span></a></li>
<li><a href="org/biojava/nbio/ws/alignment/RemotePairwiseAlignmentProperties.html" title="interface in org.biojava.nbio.ws.alignment"><span class="interfaceName">RemotePairwiseAlignmentProperties</span></a></li>
<li><a href="org/biojava/nbio/ws/alignment/RemotePairwiseAlignmentService.html" title="interface in org.biojava.nbio.ws.alignment"><span class="interfaceName">RemotePairwiseAlignmentService</span></a></li>
<li><a href="org/biojava/nbio/ontology/RemoteTerm.html" title="interface in org.biojava.nbio.ontology"><span class="interfaceName">RemoteTerm</span></a></li>
<li><a href="org/biojava/nbio/ontology/RemoteTerm.Impl.html" title="class in org.biojava.nbio.ontology">RemoteTerm.Impl</a></li>
<li><a href="org/biojava/nbio/structure/gui/RenderStyle.html" title="enum in org.biojava.nbio.structure.gui">RenderStyle</a></li>
<li><a href="org/biojava/nbio/alignment/template/RescoreRefiner.html" title="interface in org.biojava.nbio.alignment.template"><span class="interfaceName">RescoreRefiner</span></a></li>
<li><a href="org/biojava/nbio/survival/cox/ResidualsCoxph.html" title="class in org.biojava.nbio.survival.cox">ResidualsCoxph</a></li>
<li><a href="org/biojava/nbio/survival/cox/ResidualsCoxph.Type.html" title="enum in org.biojava.nbio.survival.cox">ResidualsCoxph.Type</a></li>
<li><a href="org/biojava/nbio/structure/symmetry/internal/ResidueGroup.html" title="class in org.biojava.nbio.structure.symmetry.internal">ResidueGroup</a></li>
<li><a href="org/biojava/nbio/structure/ResidueNumber.html" title="class in org.biojava.nbio.structure">ResidueNumber</a></li>
<li><a href="org/biojava/nbio/structure/ResidueRange.html" title="class in org.biojava.nbio.structure">ResidueRange</a></li>
<li><a href="org/biojava/nbio/structure/ResidueRangeAndLength.html" title="class in org.biojava.nbio.structure">ResidueRangeAndLength</a></li>
<li><a href="org/biojava/nbio/structure/chem/ResidueType.html" title="enum in org.biojava.nbio.structure.chem">ResidueType</a></li>
<li><a href="org/biojava/nbio/structure/align/util/ResourceManager.html" title="class in org.biojava.nbio.structure.align.util">ResourceManager</a></li>
<li><a href="org/biojava/nbio/core/search/io/Result.html" title="class in org.biojava.nbio.core.search.io">Result</a></li>
<li><a href="org/biojava/nbio/core/search/io/ResultFactory.html" title="interface in org.biojava.nbio.core.search.io"><span class="interfaceName">ResultFactory</span></a></li>
<li><a href="org/biojava/nbio/core/sequence/views/ReversedSequenceView.html" title="class in org.biojava.nbio.core.sequence.views">ReversedSequenceView</a></li>
<li><a href="org/biojava/nbio/survival/cox/RiskInfo.html" title="class in org.biojava.nbio.survival.cox">RiskInfo</a></li>
<li><a href="org/biojava/nbio/core/sequence/compound/RNACompoundSet.html" title="class in org.biojava.nbio.core.sequence.compound">RNACompoundSet</a></li>
<li><a href="org/biojava/nbio/core/sequence/RNASequence.html" title="class in org.biojava.nbio.core.sequence">RNASequence</a></li>
<li><a href="org/biojava/nbio/core/sequence/io/RNASequenceCreator.html" title="class in org.biojava.nbio.core.sequence.io">RNASequenceCreator</a></li>
<li><a href="org/biojava/nbio/core/sequence/views/RnaSequenceView.html" title="class in org.biojava.nbio.core.sequence.views">RnaSequenceView</a></li>
<li><a href="org/biojava/nbio/core/sequence/transcription/RNAToAminoAcidTranslator.html" title="class in org.biojava.nbio.core.sequence.transcription">RNAToAminoAcidTranslator</a></li>
<li><a href="org/biojava/nbio/ronn/RonnConstraint.html" title="class in org.biojava.nbio.ronn">RonnConstraint</a></li>
<li><a href="org/biojava/nbio/ronn/RonnConstraint.Threshold.html" title="enum in org.biojava.nbio.ronn">RonnConstraint.Threshold</a></li>
<li><a href="org/biojava/nbio/structure/symmetry/core/Rotation.html" title="class in org.biojava.nbio.structure.symmetry.core">Rotation</a></li>
<li><a href="org/biojava/nbio/structure/align/util/RotationAxis.html" title="class in org.biojava.nbio.structure.align.util">RotationAxis</a></li>
<li><a href="org/biojava/nbio/structure/symmetry/axis/RotationAxisAligner.html" title="class in org.biojava.nbio.structure.symmetry.axis">RotationAxisAligner</a></li>
<li><a href="org/biojava/nbio/structure/symmetry/core/RotationGroup.html" title="class in org.biojava.nbio.structure.symmetry.core">RotationGroup</a></li>
<li><a href="org/biojava/nbio/structure/symmetry/core/RotationSolver.html" title="class in org.biojava.nbio.structure.symmetry.core">RotationSolver</a></li>
<li><a href="org/biojava/nbio/genome/io/fastq/SangerFastqReader.html" title="class in org.biojava.nbio.genome.io.fastq">SangerFastqReader</a></li>
<li><a href="org/biojava/nbio/genome/io/fastq/SangerFastqWriter.html" title="class in org.biojava.nbio.genome.io.fastq">SangerFastqWriter</a></li>
<li><a href="org/biojava/nbio/structure/gui/ScaleableMatrixPanel.html" title="class in org.biojava.nbio.structure.gui">ScaleableMatrixPanel</a></li>
<li><a href="org/biojava/nbio/core/alignment/matrices/ScaledSubstitutionMatrix.html" title="class in org.biojava.nbio.core.alignment.matrices">ScaledSubstitutionMatrix</a></li>
<li><a href="org/biojava/nbio/aaproperties/xml/SchemaGenerator.html" title="class in org.biojava.nbio.aaproperties.xml">SchemaGenerator</a></li>
<li><a href="org/biojava/nbio/structure/align/gui/autosuggest/SCOPAutoSuggestProvider.html" title="class in org.biojava.nbio.structure.align.gui.autosuggest">SCOPAutoSuggestProvider</a></li>
<li><a href="org/biojava/nbio/structure/scop/ScopCategory.html" title="enum in org.biojava.nbio.structure.scop">ScopCategory</a></li>
<li><a href="org/biojava/nbio/structure/scop/ScopDatabase.html" title="interface in org.biojava.nbio.structure.scop"><span class="interfaceName">ScopDatabase</span></a></li>
<li><a href="org/biojava/nbio/structure/scop/ScopDescription.html" title="class in org.biojava.nbio.structure.scop">ScopDescription</a></li>
<li><a href="org/biojava/nbio/structure/scop/ScopDomain.html" title="class in org.biojava.nbio.structure.scop">ScopDomain</a></li>
<li><a href="org/biojava/nbio/structure/scop/ScopFactory.html" title="class in org.biojava.nbio.structure.scop">ScopFactory</a></li>
<li><a href="org/biojava/nbio/structure/scop/ScopInstallation.html" title="class in org.biojava.nbio.structure.scop">ScopInstallation</a></li>
<li><a href="org/biojava/nbio/structure/gui/util/ScopInstallationInstance.html" title="class in org.biojava.nbio.structure.gui.util">ScopInstallationInstance</a></li>
<li><a href="org/biojava/nbio/structure/scop/ScopIOException.html" title="class in org.biojava.nbio.structure.scop">ScopIOException</a></li>
<li><a href="org/biojava/nbio/structure/scop/ScopMirror.html" title="class in org.biojava.nbio.structure.scop">ScopMirror</a></li>
<li><a href="org/biojava/nbio/structure/scop/ScopNode.html" title="class in org.biojava.nbio.structure.scop">ScopNode</a></li>
<li><a href="org/biojava/nbio/structure/gui/util/ScopSelectPanel.html" title="class in org.biojava.nbio.structure.gui.util">ScopSelectPanel</a></li>
<li><a href="org/biojava/nbio/alignment/template/Scorer.html" title="interface in org.biojava.nbio.alignment.template"><span class="interfaceName">Scorer</span></a></li>
<li><a href="org/biojava/nbio/structure/align/multiple/ScoresCache.html" title="interface in org.biojava.nbio.structure.align.multiple"><span class="interfaceName">ScoresCache</span></a></li>
<li><a href="org/biojava/nbio/core/search/io/SearchIO.html" title="class in org.biojava.nbio.core.search.io">SearchIO</a></li>
<li><a href="org/biojava/nbio/structure/secstruc/SecStrucCalc.html" title="class in org.biojava.nbio.structure.secstruc">SecStrucCalc</a></li>
<li><a href="org/biojava/nbio/structure/secstruc/SecStrucElement.html" title="class in org.biojava.nbio.structure.secstruc">SecStrucElement</a></li>
<li><a href="org/biojava/nbio/structure/secstruc/SecStrucInfo.html" title="class in org.biojava.nbio.structure.secstruc">SecStrucInfo</a></li>
<li><a href="org/biojava/nbio/structure/secstruc/SecStrucState.html" title="class in org.biojava.nbio.structure.secstruc">SecStrucState</a></li>
<li><a href="org/biojava/nbio/structure/secstruc/SecStrucTools.html" title="class in org.biojava.nbio.structure.secstruc">SecStrucTools</a></li>
<li><a href="org/biojava/nbio/structure/secstruc/SecStrucType.html" title="enum in org.biojava.nbio.structure.secstruc">SecStrucType</a></li>
<li><a href="org/biojava/nbio/structure/domain/pdp/Segment.html" title="class in org.biojava.nbio.structure.domain.pdp">Segment</a></li>
<li><a href="org/biojava/nbio/structure/domain/pdp/SegmentComparator.html" title="class in org.biojava.nbio.structure.domain.pdp">SegmentComparator</a></li>
<li><a href="org/biojava/nbio/structure/gui/Selection.html" title="interface in org.biojava.nbio.structure.gui"><span class="interfaceName">Selection</span></a></li>
<li><a href="org/biojava/nbio/structure/gui/SelectionImpl.html" title="class in org.biojava.nbio.structure.gui">SelectionImpl</a></li>
<li><a href="org/biojava/nbio/structure/gui/util/SelectMultiplePanel.html" title="class in org.biojava.nbio.structure.gui.util">SelectMultiplePanel</a></li>
<li><a href="org/biojava/nbio/structure/align/gui/SelectPDBPanel.html" title="class in org.biojava.nbio.structure.align.gui">SelectPDBPanel</a></li>
<li><a href="org/biojava/nbio/structure/SeqMisMatch.html" title="interface in org.biojava.nbio.structure"><span class="interfaceName">SeqMisMatch</span></a></li>
<li><a href="org/biojava/nbio/structure/SeqMisMatchImpl.html" title="class in org.biojava.nbio.structure">SeqMisMatchImpl</a></li>
<li><a href="org/biojava/nbio/structure/io/SeqRes2AtomAligner.html" title="class in org.biojava.nbio.structure.io">SeqRes2AtomAligner</a></li>
<li><a href="org/biojava/nbio/core/sequence/template/Sequence.html" title="interface in org.biojava.nbio.core.sequence.template"><span class="interfaceName">Sequence</span></a></li>
<li><a href="org/biojava/nbio/core/sequence/storage/SequenceAsStringHelper.html" title="class in org.biojava.nbio.core.sequence.storage">SequenceAsStringHelper</a></li>
<li><a href="org/biojava/nbio/core/sequence/SequenceComparator.html" title="class in org.biojava.nbio.core.sequence">SequenceComparator</a></li>
<li><a href="org/biojava/nbio/core/sequence/io/template/SequenceCreatorInterface.html" title="interface in org.biojava.nbio.core.sequence.io.template"><span class="interfaceName">SequenceCreatorInterface</span></a></li>
<li><a href="org/biojava/nbio/structure/gui/SequenceDisplay.html" title="class in org.biojava.nbio.structure.gui">SequenceDisplay</a></li>
<li><a href="org/biojava/nbio/core/sequence/loader/SequenceFileProxyLoader.html" title="class in org.biojava.nbio.core.sequence.loader">SequenceFileProxyLoader</a></li>
<li><a href="org/biojava/nbio/structure/symmetry/internal/SequenceFunctionOrderDetector.html" title="class in org.biojava.nbio.structure.symmetry.internal">SequenceFunctionOrderDetector</a></li>
<li><a href="org/biojava/nbio/structure/symmetry/internal/SequenceFunctionRefiner.html" title="class in org.biojava.nbio.structure.symmetry.internal">SequenceFunctionRefiner</a></li>
<li><a href="org/biojava/nbio/core/sequence/io/template/SequenceHeaderParserInterface.html" title="interface in org.biojava.nbio.core.sequence.io.template"><span class="interfaceName">SequenceHeaderParserInterface</span></a></li>
<li><a href="org/biojava/nbio/core/sequence/location/SequenceLocation.html" title="class in org.biojava.nbio.core.sequence.location">SequenceLocation</a></li>
<li><a href="org/biojava/nbio/core/sequence/template/SequenceMixin.html" title="class in org.biojava.nbio.core.sequence.template">SequenceMixin</a></li>
<li><a href="org/biojava/nbio/core/sequence/template/SequenceMixin.SequenceIterator.html" title="class in org.biojava.nbio.core.sequence.template">SequenceMixin.SequenceIterator</a></li>
<li><a href="org/biojava/nbio/structure/gui/util/SequenceMouseListener.html" title="class in org.biojava.nbio.structure.gui.util">SequenceMouseListener</a></li>
<li><a href="org/biojava/nbio/core/sequence/SequenceOptimizationHints.html" title="class in org.biojava.nbio.core.sequence">SequenceOptimizationHints</a></li>
<li><a href="org/biojava/nbio/core/sequence/SequenceOptimizationHints.SequenceCollection.html" title="enum in org.biojava.nbio.core.sequence">SequenceOptimizationHints.SequenceCollection</a></li>
<li><a href="org/biojava/nbio/core/sequence/SequenceOptimizationHints.SequenceUsage.html" title="enum in org.biojava.nbio.core.sequence">SequenceOptimizationHints.SequenceUsage</a></li>
<li><a href="org/biojava/nbio/core/alignment/template/SequencePair.html" title="interface in org.biojava.nbio.core.alignment.template"><span class="interfaceName">SequencePair</span></a></li>
<li><a href="org/biojava/nbio/core/sequence/io/template/SequenceParserInterface.html" title="interface in org.biojava.nbio.core.sequence.io.template"><span class="interfaceName">SequenceParserInterface</span></a></li>
<li><a href="org/biojava/nbio/core/sequence/template/SequenceProxyView.html" title="class in org.biojava.nbio.core.sequence.template">SequenceProxyView</a></li>
<li><a href="org/biojava/nbio/core/sequence/template/SequenceReader.html" title="interface in org.biojava.nbio.core.sequence.template"><span class="interfaceName">SequenceReader</span></a></li>
<li><a href="org/biojava/nbio/structure/gui/util/SequenceScalePanel.html" title="class in org.biojava.nbio.structure.gui.util">SequenceScalePanel</a></li>
<li><a href="org/biojava/nbio/core/util/SequenceTools.html" title="class in org.biojava.nbio.core.util">SequenceTools</a></li>
<li><a href="org/biojava/nbio/data/sequence/SequenceUtil.html" title="class in org.biojava.nbio.data.sequence">SequenceUtil</a></li>
<li><a href="org/biojava/nbio/core/sequence/template/SequenceView.html" title="interface in org.biojava.nbio.core.sequence.template"><span class="interfaceName">SequenceView</span></a></li>
<li><a href="org/biojava/nbio/structure/domain/SerializableCache.html" title="class in org.biojava.nbio.structure.domain">SerializableCache</a></li>
<li><a href="org/biojava/nbio/structure/domain/pdp/ShortSegmentRemover.html" title="class in org.biojava.nbio.structure.domain.pdp">ShortSegmentRemover</a></li>
<li><a href="org/biojava/nbio/structure/align/gui/ShowPDBIDListener.html" title="class in org.biojava.nbio.structure.align.gui">ShowPDBIDListener</a></li>
<li><a href="demo/ShowStructureInJmol.html" title="class in demo">ShowStructureInJmol</a></li>
<li><a href="org/biojava/nbio/structure/io/sifts/SiftsChainEntry.html" title="class in org.biojava.nbio.structure.io.sifts">SiftsChainEntry</a></li>
<li><a href="org/biojava/nbio/structure/io/sifts/SiftsChainToUniprotMapping.html" title="class in org.biojava.nbio.structure.io.sifts">SiftsChainToUniprotMapping</a></li>
<li><a href="org/biojava/nbio/structure/io/sifts/SiftsEntity.html" title="class in org.biojava.nbio.structure.io.sifts">SiftsEntity</a></li>
<li><a href="org/biojava/nbio/structure/io/sifts/SiftsMappingProvider.html" title="class in org.biojava.nbio.structure.io.sifts">SiftsMappingProvider</a></li>
<li><a href="org/biojava/nbio/structure/io/sifts/SiftsResidue.html" title="class in org.biojava.nbio.structure.io.sifts">SiftsResidue</a></li>
<li><a href="org/biojava/nbio/structure/io/sifts/SiftsSegment.html" title="class in org.biojava.nbio.structure.io.sifts">SiftsSegment</a></li>
<li><a href="org/biojava/nbio/structure/io/sifts/SiftsXMLParser.html" title="class in org.biojava.nbio.structure.io.sifts">SiftsXMLParser</a></li>
<li><a href="org/biojava/nbio/structure/align/fatcat/calc/SigEva.html" title="class in org.biojava.nbio.structure.align.fatcat.calc">SigEva</a></li>
<li><a href="org/biojava/nbio/core/alignment/SimpleAlignedSequence.html" title="class in org.biojava.nbio.core.alignment">SimpleAlignedSequence</a></li>
<li><a href="org/biojava/nbio/alignment/SimpleGapPenalty.html" title="class in org.biojava.nbio.alignment">SimpleGapPenalty</a></li>
<li><a href="org/biojava/nbio/core/sequence/location/SimpleLocation.html" title="class in org.biojava.nbio.core.sequence.location">SimpleLocation</a></li>
<li><a href="org/biojava/nbio/core/sequence/location/SimplePoint.html" title="class in org.biojava.nbio.core.sequence.location">SimplePoint</a></li>
<li><a href="org/biojava/nbio/core/alignment/SimpleProfile.html" title="class in org.biojava.nbio.core.alignment">SimpleProfile</a></li>
<li><a href="org/biojava/nbio/core/alignment/SimpleProfilePair.html" title="class in org.biojava.nbio.core.alignment">SimpleProfilePair</a></li>
<li><a href="org/biojava/nbio/alignment/SimpleProfileProfileAligner.html" title="class in org.biojava.nbio.alignment">SimpleProfileProfileAligner</a></li>
<li><a href="org/biojava/nbio/core/alignment/SimpleSequencePair.html" title="class in org.biojava.nbio.core.alignment">SimpleSequencePair</a></li>
<li><a href="org/biojava/nbio/core/alignment/matrices/SimpleSubstitutionMatrix.html" title="class in org.biojava.nbio.core.alignment.matrices">SimpleSubstitutionMatrix</a></li>
<li><a href="org/biojava/nbio/core/sequence/storage/SingleCompoundSequenceReader.html" title="class in org.biojava.nbio.core.sequence.storage">SingleCompoundSequenceReader</a></li>
<li><a href="org/biojava/nbio/core/util/SingleLinkageClusterer.html" title="class in org.biojava.nbio.core.util">SingleLinkageClusterer</a></li>
<li><a href="org/biojava/nbio/structure/jama/SingularValueDecomposition.html" title="class in org.biojava.nbio.structure.jama">SingularValueDecomposition</a></li>
<li><a href="org/biojava/nbio/phosphosite/Site.html" title="class in org.biojava.nbio.phosphosite">Site</a></li>
<li><a href="org/biojava/nbio/structure/Site.html" title="class in org.biojava.nbio.structure">Site</a></li>
<li><a href="org/biojava/nbio/ontology/utils/SmallAnnotation.html" title="class in org.biojava.nbio.ontology.utils">SmallAnnotation</a></li>
<li><a href="org/biojava/nbio/ontology/utils/SmallMap.html" title="class in org.biojava.nbio.ontology.utils">SmallMap</a></li>
<li><a href="org/biojava/nbio/alignment/SmithWaterman.html" title="class in org.biojava.nbio.alignment">SmithWaterman</a></li>
<li><a href="org/biojava/nbio/structure/align/seq/SmithWaterman3Daligner.html" title="class in org.biojava.nbio.structure.align.seq">SmithWaterman3Daligner</a></li>
<li><a href="org/biojava/nbio/structure/align/seq/SmithWaterman3DParameters.html" title="class in org.biojava.nbio.structure.align.seq">SmithWaterman3DParameters</a></li>
<li><a href="org/biojava/nbio/structure/align/seq/SmithWatermanUserArgumentProcessor.html" title="class in org.biojava.nbio.structure.align.seq">SmithWatermanUserArgumentProcessor</a></li>
<li><a href="org/biojava/nbio/structure/align/seq/SmithWatermanUserArgumentProcessor.SmithWatermanStartupParams.html" title="class in org.biojava.nbio.structure.align.seq">SmithWatermanUserArgumentProcessor.SmithWatermanStartupParams</a></li>
<li><a href="org/biojava/nbio/core/util/SoftHashMap.html" title="class in org.biojava.nbio.core.util">SoftHashMap</a></li>
<li><a href="org/biojava/nbio/genome/io/fastq/SolexaFastqReader.html" title="class in org.biojava.nbio.genome.io.fastq">SolexaFastqReader</a></li>
<li><a href="org/biojava/nbio/genome/io/fastq/SolexaFastqWriter.html" title="class in org.biojava.nbio.genome.io.fastq">SolexaFastqWriter</a></li>
<li><a href="org/biojava/nbio/structure/xtal/SpaceGroup.html" title="class in org.biojava.nbio.structure.xtal">SpaceGroup</a></li>
<li><a href="org/biojava/nbio/structure/xtal/io/SpaceGroupMapElements.html" title="class in org.biojava.nbio.structure.xtal.io">SpaceGroupMapElements</a></li>
<li><a href="org/biojava/nbio/structure/xtal/io/SpaceGroupMapRoot.html" title="class in org.biojava.nbio.structure.xtal.io">SpaceGroupMapRoot</a></li>
<li><a href="org/biojava/nbio/structure/math/SparseSquareMatrix.html" title="class in org.biojava.nbio.structure.math">SparseSquareMatrix</a></li>
<li><a href="org/biojava/nbio/structure/math/SparseVector.html" title="class in org.biojava.nbio.structure.math">SparseVector</a></li>
<li><a href="org/biojava/nbio/structure/symmetry/geometry/SphereSampler.html" title="class in org.biojava.nbio.structure.symmetry.geometry">SphereSampler</a></li>
<li><a href="org/biojava/nbio/genome/util/SplitFasta.html" title="class in org.biojava.nbio.genome.util">SplitFasta</a></li>
<li><a href="org/biojava/nbio/structure/gui/util/color/SqrtColorMapper.html" title="class in org.biojava.nbio.structure.gui.util.color">SqrtColorMapper</a></li>
<li><a href="org/biojava/nbio/structure/io/SSBondImpl.html" title="class in org.biojava.nbio.structure.io">SSBondImpl</a></li>
<li><a href="org/biojava/nbio/genome/parsers/cytoband/StainType.html" title="enum in org.biojava.nbio.genome.parsers.cytoband">StainType</a></li>
<li><a href="org/biojava/nbio/structure/StandardAminoAcid.html" title="class in org.biojava.nbio.structure">StandardAminoAcid</a></li>
<li><a href="org/biojava/nbio/alignment/StandardRescoreRefiner.html" title="class in org.biojava.nbio.alignment">StandardRescoreRefiner</a></li>
<li><a href="org/biojava/nbio/core/sequence/StartCodonSequence.html" title="class in org.biojava.nbio.core.sequence">StartCodonSequence</a></li>
<li><a href="org/biojava/nbio/structure/align/ce/StartupParameters.html" title="class in org.biojava.nbio.structure.align.ce">StartupParameters</a></li>
<li><a href="org/biojava/nbio/ontology/utils/StaticMemberPlaceHolder.html" title="class in org.biojava.nbio.ontology.utils">StaticMemberPlaceHolder</a></li>
<li><a href="org/biojava/nbio/structure/align/gui/aligpanel/StatusDisplay.html" title="class in org.biojava.nbio.structure.align.gui.aligpanel">StatusDisplay</a></li>
<li><a href="org/biojava/nbio/survival/cox/matrix/StdArrayIO.html" title="class in org.biojava.nbio.survival.cox.matrix">StdArrayIO</a></li>
<li><a href="org/biojava/nbio/alignment/io/StockholmFileAnnotation.html" title="class in org.biojava.nbio.alignment.io">StockholmFileAnnotation</a></li>
<li><a href="org/biojava/nbio/alignment/io/StockholmFileAnnotation.StockholmFileAnnotationReference.html" title="class in org.biojava.nbio.alignment.io">StockholmFileAnnotation.StockholmFileAnnotationReference</a></li>
<li><a href="org/biojava/nbio/alignment/io/StockholmFileParser.html" title="class in org.biojava.nbio.alignment.io">StockholmFileParser</a></li>
<li><a href="org/biojava/nbio/alignment/io/StockholmStructure.html" title="class in org.biojava.nbio.alignment.io">StockholmStructure</a></li>
<li><a href="org/biojava/nbio/alignment/io/StockholmStructure.DatabaseReference.html" title="class in org.biojava.nbio.alignment.io">StockholmStructure.DatabaseReference</a></li>
<li><a href="org/biojava/nbio/structure/symmetry/core/Stoichiometry.html" title="class in org.biojava.nbio.structure.symmetry.core">Stoichiometry</a></li>
<li><a href="org/biojava/nbio/structure/symmetry/core/Stoichiometry.StringOverflowStrategy.html" title="enum in org.biojava.nbio.structure.symmetry.core">Stoichiometry.StringOverflowStrategy</a></li>
<li><a href="org/biojava/nbio/core/sequence/StopCodonSequence.html" title="class in org.biojava.nbio.core.sequence">StopCodonSequence</a></li>
<li><a href="org/biojava/nbio/core/sequence/Strand.html" title="enum in org.biojava.nbio.core.sequence">Strand</a></li>
<li><a href="org/biojava/nbio/survival/cox/StrataInfo.html" title="class in org.biojava.nbio.survival.cox">StrataInfo</a></li>
<li><a href="org/biojava/nbio/structure/align/pairwise/StrCompAlignment.html" title="class in org.biojava.nbio.structure.align.pairwise">StrCompAlignment</a></li>
<li><a href="org/biojava/nbio/genome/io/fastq/StreamListener.html" title="interface in org.biojava.nbio.genome.io.fastq"><span class="interfaceName">StreamListener</span></a></li>
<li><a href="org/biojava/nbio/core/util/StringManipulationHelper.html" title="class in org.biojava.nbio.core.util">StringManipulationHelper</a></li>
<li><a href="org/biojava/nbio/core/sequence/loader/StringProxySequenceReader.html" title="class in org.biojava.nbio.core.sequence.loader">StringProxySequenceReader</a></li>
<li><a href="org/biojava/nbio/structure/align/StrucAligParameters.html" title="class in org.biojava.nbio.structure.align">StrucAligParameters</a></li>
<li><a href="org/biojava/nbio/structure/Structure.html" title="interface in org.biojava.nbio.structure"><span class="interfaceName">Structure</span></a></li>
<li><a href="org/biojava/nbio/structure/align/StructureAlignment.html" title="interface in org.biojava.nbio.structure.align"><span class="interfaceName">StructureAlignment</span></a></li>
<li><a href="org/biojava/nbio/structure/align/gui/StructureAlignmentDisplay.html" title="class in org.biojava.nbio.structure.align.gui">StructureAlignmentDisplay</a></li>
<li><a href="org/biojava/nbio/structure/align/StructureAlignmentFactory.html" title="class in org.biojava.nbio.structure.align">StructureAlignmentFactory</a></li>
<li><a href="org/biojava/nbio/structure/align/gui/jmol/StructureAlignmentJmol.html" title="class in org.biojava.nbio.structure.align.gui.jmol">StructureAlignmentJmol</a></li>
<li><a href="org/biojava/nbio/structure/align/fatcat/calc/StructureAlignmentOptimizer.html" title="class in org.biojava.nbio.structure.align.fatcat.calc">StructureAlignmentOptimizer</a></li>
<li><a href="org/biojava/nbio/protmod/structure/StructureAtom.html" title="class in org.biojava.nbio.protmod.structure">StructureAtom</a></li>
<li><a href="org/biojava/nbio/protmod/structure/StructureAtomLinkage.html" title="class in org.biojava.nbio.protmod.structure">StructureAtomLinkage</a></li>
<li><a href="org/biojava/nbio/protmod/io/StructureAtomXMLConverter.html" title="class in org.biojava.nbio.protmod.io">StructureAtomXMLConverter</a></li>
<li><a href="org/biojava/nbio/structure/StructureException.html" title="class in org.biojava.nbio.structure">StructureException</a></li>
<li><a href="org/biojava/nbio/structure/io/StructureFiletype.html" title="enum in org.biojava.nbio.structure.io">StructureFiletype</a></li>
<li><a href="org/biojava/nbio/protmod/structure/StructureGroup.html" title="class in org.biojava.nbio.protmod.structure">StructureGroup</a></li>
<li><a href="org/biojava/nbio/protmod/io/StructureGroupXMLConverter.html" title="class in org.biojava.nbio.protmod.io">StructureGroupXMLConverter</a></li>
<li><a href="org/biojava/nbio/structure/StructureIdentifier.html" title="interface in org.biojava.nbio.structure"><span class="interfaceName">StructureIdentifier</span></a></li>
<li><a href="org/biojava/nbio/structure/StructureImpl.html" title="class in org.biojava.nbio.structure">StructureImpl</a></li>
<li><a href="org/biojava/nbio/structure/contact/StructureInterface.html" title="class in org.biojava.nbio.structure.contact">StructureInterface</a></li>
<li><a href="org/biojava/nbio/structure/contact/StructureInterfaceCluster.html" title="class in org.biojava.nbio.structure.contact">StructureInterfaceCluster</a></li>
<li><a href="org/biojava/nbio/structure/contact/StructureInterfaceList.html" title="class in org.biojava.nbio.structure.contact">StructureInterfaceList</a></li>
<li><a href="org/biojava/nbio/structure/StructureIO.html" title="class in org.biojava.nbio.structure">StructureIO</a></li>
<li><a href="org/biojava/nbio/structure/io/StructureIOFile.html" title="interface in org.biojava.nbio.structure.io"><span class="interfaceName">StructureIOFile</span></a></li>
<li><a href="org/biojava/nbio/structure/align/gui/StructureLoaderThread.html" title="class in org.biojava.nbio.structure.align.gui">StructureLoaderThread</a></li>
<li><a href="org/biojava/nbio/structure/align/client/StructureName.html" title="class in org.biojava.nbio.structure.align.client">StructureName</a></li>
<li><a href="org/biojava/nbio/structure/align/client/StructureName.Source.html" title="enum in org.biojava.nbio.structure.align.client">StructureName.Source</a></li>
<li><a href="org/biojava/nbio/structure/align/StructurePairAligner.html" title="class in org.biojava.nbio.structure.align">StructurePairAligner</a></li>
<li><a href="org/biojava/nbio/structure/gui/util/StructurePairSelector.html" title="interface in org.biojava.nbio.structure.gui.util"><span class="interfaceName">StructurePairSelector</span></a></li>
<li><a href="org/biojava/nbio/structure/io/StructureProvider.html" title="interface in org.biojava.nbio.structure.io"><span class="interfaceName">StructureProvider</span></a></li>
<li><a href="org/biojava/nbio/structure/io/StructureSequenceMatcher.html" title="class in org.biojava.nbio.structure.io">StructureSequenceMatcher</a></li>
<li><a href="org/biojava/nbio/structure/StructureTools.html" title="class in org.biojava.nbio.structure">StructureTools</a></li>
<li><a href="org/biojava/nbio/protmod/structure/StructureUtil.html" title="class in org.biojava.nbio.protmod.structure">StructureUtil</a></li>
<li><a href="org/biojava/nbio/structure/gui/StructureViewer.html" title="interface in org.biojava.nbio.structure.gui"><span class="interfaceName">StructureViewer</span></a></li>
<li><a href="org/biojava/nbio/core/alignment/template/SubstitutionMatrix.html" title="interface in org.biojava.nbio.core.alignment.template"><span class="interfaceName">SubstitutionMatrix</span></a></li>
<li><a href="org/biojava/nbio/core/alignment/matrices/SubstitutionMatrixHelper.html" title="class in org.biojava.nbio.core.alignment.matrices">SubstitutionMatrixHelper</a></li>
<li><a href="org/biojava/nbio/alignment/SubstitutionMatrixScorer.html" title="class in org.biojava.nbio.alignment">SubstitutionMatrixScorer</a></li>
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