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<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
<!-- NewPage -->
<html lang="en">
<head>
<!-- Generated by javadoc (version 1.7.0_79) on Thu Mar 10 15:47:53 PST 2016 -->
<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
<title>All Classes (biojava 4.2.0 API)</title>
<meta name="date" content="2016-03-10">
<link rel="stylesheet" type="text/css" href="stylesheet.css" title="Style">
</head>
<body>
<h1 class="bar">All Classes</h1>
<div class="indexContainer">
<ul>
<li><a href="org/biojava/nbio/core/alignment/matrices/AAindexFactory.html" title="class in org.biojava.nbio.core.alignment.matrices" target="classFrame">AAindexFactory</a></li>
<li><a href="org/biojava/nbio/core/alignment/matrices/AAIndexFileParser.html" title="class in org.biojava.nbio.core.alignment.matrices" target="classFrame">AAIndexFileParser</a></li>
<li><a href="org/biojava/nbio/core/alignment/matrices/AAIndexProvider.html" title="interface in org.biojava.nbio.core.alignment.matrices" target="classFrame"><i>AAIndexProvider</i></a></li>
<li><a href="org/biojava/nbio/structure/align/gui/AboutDialog.html" title="class in org.biojava.nbio.structure.align.gui" target="classFrame">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" target="classFrame">AbstractAlignmentJmol</a></li>
<li><a href="org/biojava/nbio/ontology/utils/AbstractAnnotation.html" title="class in org.biojava.nbio.ontology.utils" target="classFrame">AbstractAnnotation</a></li>
<li><a href="org/biojava/nbio/structure/io/mmcif/model/AbstractBean.html" title="class in org.biojava.nbio.structure.io.mmcif.model" target="classFrame">AbstractBean</a></li>
<li><a href="org/biojava/nbio/core/sequence/template/AbstractCompound.html" title="class in org.biojava.nbio.core.sequence.template" target="classFrame">AbstractCompound</a></li>
<li><a href="org/biojava/nbio/core/sequence/template/AbstractCompoundSet.html" title="class in org.biojava.nbio.core.sequence.template" target="classFrame">AbstractCompoundSet</a></li>
<li><a href="org/biojava/nbio/core/sequence/template/AbstractCompoundTranslator.html" title="class in org.biojava.nbio.core.sequence.template" target="classFrame">AbstractCompoundTranslator</a></li>
<li><a href="org/biojava/nbio/core/sequence/features/AbstractFeature.html" title="class in org.biojava.nbio.core.sequence.features" target="classFrame">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" target="classFrame">AbstractLocation</a></li>
<li><a href="org/biojava/nbio/alignment/template/AbstractMatrixAligner.html" title="class in org.biojava.nbio.alignment.template" target="classFrame">AbstractMatrixAligner</a></li>
<li><a href="org/biojava/nbio/core/sequence/template/AbstractNucleotideCompoundSet.html" title="class in org.biojava.nbio.core.sequence.template" target="classFrame">AbstractNucleotideCompoundSet</a></li>
<li><a href="org/biojava/nbio/alignment/template/AbstractPairwiseSequenceAligner.html" title="class in org.biojava.nbio.alignment.template" target="classFrame">AbstractPairwiseSequenceAligner</a></li>
<li><a href="org/biojava/nbio/alignment/template/AbstractProfileProfileAligner.html" title="class in org.biojava.nbio.alignment.template" target="classFrame">AbstractProfileProfileAligner</a></li>
<li><a href="org/biojava/nbio/alignment/template/AbstractScorer.html" title="class in org.biojava.nbio.alignment.template" target="classFrame">AbstractScorer</a></li>
<li><a href="org/biojava/nbio/structure/align/multiple/AbstractScoresCache.html" title="class in org.biojava.nbio.structure.align.multiple" target="classFrame">AbstractScoresCache</a></li>
<li><a href="org/biojava/nbio/core/sequence/template/AbstractSequence.html" title="class in org.biojava.nbio.core.sequence.template" target="classFrame">AbstractSequence</a></li>
<li><a href="org/biojava/nbio/core/sequence/template/AbstractSequence.AnnotationType.html" title="enum in org.biojava.nbio.core.sequence.template" target="classFrame">AbstractSequence.AnnotationType</a></li>
<li><a href="org/biojava/nbio/structure/align/AbstractStructureAlignment.html" title="class in org.biojava.nbio.structure.align" target="classFrame">AbstractStructureAlignment</a></li>
<li><a href="org/biojava/nbio/ontology/AbstractTerm.html" title="class in org.biojava.nbio.ontology" target="classFrame">AbstractTerm</a></li>
<li><a href="org/biojava/nbio/structure/align/ce/AbstractUserArgumentProcessor.html" title="class in org.biojava.nbio.structure.align.ce" target="classFrame">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" target="classFrame"><i>AccesionedLocation</i></a></li>
<li><a href="org/biojava/nbio/core/sequence/template/Accessioned.html" title="interface in org.biojava.nbio.core.sequence.template" target="classFrame"><i>Accessioned</i></a></li>
<li><a href="org/biojava/nbio/core/sequence/AccessionID.html" title="class in org.biojava.nbio.core.sequence" target="classFrame">AccessionID</a></li>
<li><a href="org/biojava/nbio/structure/align/model/AFP.html" title="class in org.biojava.nbio.structure.align.model" target="classFrame">AFP</a></li>
<li><a href="org/biojava/nbio/structure/align/util/AFPAlignmentDisplay.html" title="class in org.biojava.nbio.structure.align.util" target="classFrame">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" target="classFrame">AFPCalculator</a></li>
<li><a href="org/biojava/nbio/structure/align/model/AFPChain.html" title="class in org.biojava.nbio.structure.align.model" target="classFrame">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" target="classFrame">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" target="classFrame">AFPChainer</a></li>
<li><a href="org/biojava/nbio/structure/align/xml/AFPChainFlipper.html" title="class in org.biojava.nbio.structure.align.xml" target="classFrame">AFPChainFlipper</a></li>
<li><a href="org/biojava/nbio/structure/align/util/AFPChainScorer.html" title="class in org.biojava.nbio.structure.align.util" target="classFrame">AFPChainScorer</a></li>
<li><a href="org/biojava/nbio/structure/align/model/AfpChainWriter.html" title="class in org.biojava.nbio.structure.align.model" target="classFrame">AfpChainWriter</a></li>
<li><a href="org/biojava/nbio/structure/align/xml/AFPChainXMLConverter.html" title="class in org.biojava.nbio.structure.align.xml" target="classFrame">AFPChainXMLConverter</a></li>
<li><a href="org/biojava/nbio/structure/align/xml/AFPChainXMLParser.html" title="class in org.biojava.nbio.structure.align.xml" target="classFrame">AFPChainXMLParser</a></li>
<li><a href="demo/AFPFromFasta.html" title="class in demo" target="classFrame">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" target="classFrame">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" target="classFrame">AFPPostProcessor</a></li>
<li><a href="org/biojava/nbio/structure/align/AFPTwister.html" title="class in org.biojava.nbio.structure.align" target="classFrame">AFPTwister</a></li>
<li><a href="org/biojava/nbio/survival/cox/stats/AgScore.html" title="class in org.biojava.nbio.survival.cox.stats" target="classFrame">AgScore</a></li>
<li><a href="org/biojava/nbio/structure/align/helper/AligMatEl.html" title="class in org.biojava.nbio.structure.align.helper" target="classFrame">AligMatEl</a></li>
<li><a href="org/biojava/nbio/structure/align/pairwise/Alignable.html" title="interface in org.biojava.nbio.structure.align.pairwise" target="classFrame"><i>Alignable</i></a></li>
<li><a href="org/biojava/nbio/structure/gui/util/AlignedPosition.html" title="class in org.biojava.nbio.structure.gui.util" target="classFrame">AlignedPosition</a></li>
<li><a href="org/biojava/nbio/core/alignment/template/AlignedSequence.html" title="interface in org.biojava.nbio.core.alignment.template" target="classFrame"><i>AlignedSequence</i></a></li>
<li><a href="org/biojava/nbio/core/alignment/template/AlignedSequence.Step.html" title="enum in org.biojava.nbio.core.alignment.template" target="classFrame">AlignedSequence.Step</a></li>
<li><a href="org/biojava/nbio/alignment/template/Aligner.html" title="interface in org.biojava.nbio.alignment.template" target="classFrame"><i>Aligner</i></a></li>
<li><a href="org/biojava/nbio/alignment/routines/AlignerHelper.html" title="class in org.biojava.nbio.alignment.routines" target="classFrame">AlignerHelper</a></li>
<li><a href="org/biojava/nbio/alignment/routines/AlignerHelper.Anchor.html" title="class in org.biojava.nbio.alignment.routines" target="classFrame">AlignerHelper.Anchor</a></li>
<li><a href="org/biojava/nbio/alignment/routines/AlignerHelper.Anchor.QueryIndexComparator.html" title="class in org.biojava.nbio.alignment.routines" target="classFrame">AlignerHelper.Anchor.QueryIndexComparator</a></li>
<li><a href="org/biojava/nbio/alignment/routines/AlignerHelper.Cut.html" title="class in org.biojava.nbio.alignment.routines" target="classFrame">AlignerHelper.Cut</a></li>
<li><a href="org/biojava/nbio/alignment/routines/AlignerHelper.Last.html" title="enum in org.biojava.nbio.alignment.routines" target="classFrame">AlignerHelper.Last</a></li>
<li><a href="org/biojava/nbio/alignment/routines/AlignerHelper.Subproblem.html" title="class in org.biojava.nbio.alignment.routines" target="classFrame">AlignerHelper.Subproblem</a></li>
<li><a href="org/biojava/nbio/structure/align/gui/AlignmentCalc.html" title="class in org.biojava.nbio.structure.align.gui" target="classFrame">AlignmentCalc</a></li>
<li><a href="org/biojava/nbio/structure/gui/util/AlignmentCalc.html" title="class in org.biojava.nbio.structure.gui.util" target="classFrame">AlignmentCalc</a></li>
<li><a href="org/biojava/nbio/structure/align/gui/AlignmentCalcDB.html" title="class in org.biojava.nbio.structure.align.gui" target="classFrame">AlignmentCalcDB</a></li>
<li><a href="org/biojava/nbio/structure/align/gui/AlignmentCalculationRunnable.html" title="interface in org.biojava.nbio.structure.align.gui" target="classFrame"><i>AlignmentCalculationRunnable</i></a></li>
<li><a href="org/biojava/nbio/structure/align/gui/AlignmentGui.html" title="class in org.biojava.nbio.structure.align.gui" target="classFrame">AlignmentGui</a></li>
<li><a href="demo/AlignmentGuiDemo.html" title="class in demo" target="classFrame">AlignmentGuiDemo</a></li>
<li><a href="org/biojava/nbio/structure/gui/events/AlignmentPositionListener.html" title="interface in org.biojava.nbio.structure.gui.events" target="classFrame"><i>AlignmentPositionListener</i></a></li>
<li><a href="org/biojava/nbio/structure/align/events/AlignmentProgressListener.html" title="interface in org.biojava.nbio.structure.align.events" target="classFrame"><i>AlignmentProgressListener</i></a></li>
<li><a href="org/biojava/nbio/structure/align/pairwise/AlignmentProgressListener.html" title="class in org.biojava.nbio.structure.align.pairwise" target="classFrame">AlignmentProgressListener</a></li>
<li><a href="org/biojava/nbio/structure/align/pairwise/AlignmentResult.html" title="class in org.biojava.nbio.structure.align.pairwise" target="classFrame">AlignmentResult</a></li>
<li><a href="org/biojava/nbio/alignment/Alignments.html" title="class in org.biojava.nbio.alignment" target="classFrame">Alignments</a></li>
<li><a href="org/biojava/nbio/alignment/Alignments.PairInProfileScorerType.html" title="enum in org.biojava.nbio.alignment" target="classFrame">Alignments.PairInProfileScorerType</a></li>
<li><a href="org/biojava/nbio/alignment/Alignments.PairwiseSequenceAlignerType.html" title="enum in org.biojava.nbio.alignment" target="classFrame">Alignments.PairwiseSequenceAlignerType</a></li>
<li><a href="org/biojava/nbio/alignment/Alignments.PairwiseSequenceScorerType.html" title="enum in org.biojava.nbio.alignment" target="classFrame">Alignments.PairwiseSequenceScorerType</a></li>
<li><a href="org/biojava/nbio/alignment/Alignments.ProfileProfileAlignerType.html" title="enum in org.biojava.nbio.alignment" target="classFrame">Alignments.ProfileProfileAlignerType</a></li>
<li><a href="org/biojava/nbio/alignment/Alignments.RefinerType.html" title="enum in org.biojava.nbio.alignment" target="classFrame">Alignments.RefinerType</a></li>
<li><a href="org/biojava/nbio/structure/align/gui/AlignmentTextPanel.html" title="class in org.biojava.nbio.structure.align.gui" target="classFrame">AlignmentTextPanel</a></li>
<li><a href="org/biojava/nbio/structure/align/util/AlignmentTools.html" title="class in org.biojava.nbio.structure.align.util" target="classFrame">AlignmentTools</a></li>
<li><a href="org/biojava/nbio/structure/align/util/AlignmentTools.IdentityMap.html" title="class in org.biojava.nbio.structure.align.util" target="classFrame">AlignmentTools.IdentityMap</a></li>
<li><a href="org/biojava/nbio/structure/align/pairwise/AligNPE.html" title="class in org.biojava.nbio.structure.align.pairwise" target="classFrame">AligNPE</a></li>
<li><a href="org/biojava/nbio/structure/align/helper/AlignTools.html" title="class in org.biojava.nbio.structure.align.helper" target="classFrame">AlignTools</a></li>
<li><a href="org/biojava/nbio/structure/align/gui/aligpanel/AligPanel.html" title="class in org.biojava.nbio.structure.align.gui.aligpanel" target="classFrame">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" target="classFrame">AligPanelMouseMotionListener</a></li>
<li><a href="org/biojava/nbio/structure/align/webstart/AligUIManager.html" title="class in org.biojava.nbio.structure.align.webstart" target="classFrame">AligUIManager</a></li>
<li><a href="org/biojava/nbio/structure/io/mmcif/AllChemCompProvider.html" title="class in org.biojava.nbio.structure.io.mmcif" target="classFrame">AllChemCompProvider</a></li>
<li><a href="org/biojava/nbio/ontology/AlreadyExistsException.html" title="class in org.biojava.nbio.ontology" target="classFrame">AlreadyExistsException</a></li>
<li><a href="org/biojava/nbio/structure/align/pairwise/AltAligComparator.html" title="class in org.biojava.nbio.structure.align.pairwise" target="classFrame">AltAligComparator</a></li>
<li><a href="org/biojava/nbio/structure/align/pairwise/AlternativeAlignment.html" title="class in org.biojava.nbio.structure.align.pairwise" target="classFrame">AlternativeAlignment</a></li>
<li><a href="org/biojava/nbio/structure/gui/util/AlternativeAlignmentFrame.html" title="class in org.biojava.nbio.structure.gui.util" target="classFrame">AlternativeAlignmentFrame</a></li>
<li><a href="org/biojava/nbio/core/sequence/compound/AmbiguityDNACompoundSet.html" title="class in org.biojava.nbio.core.sequence.compound" target="classFrame">AmbiguityDNACompoundSet</a></li>
<li><a href="org/biojava/nbio/core/sequence/compound/AmbiguityDNARNAHybridCompoundSet.html" title="class in org.biojava.nbio.core.sequence.compound" target="classFrame">AmbiguityDNARNAHybridCompoundSet</a></li>
<li><a href="org/biojava/nbio/core/sequence/compound/AmbiguityRNACompoundSet.html" title="class in org.biojava.nbio.core.sequence.compound" target="classFrame">AmbiguityRNACompoundSet</a></li>
<li><a href="org/biojava/nbio/structure/AminoAcid.html" title="interface in org.biojava.nbio.structure" target="classFrame"><i>AminoAcid</i></a></li>
<li><a href="org/biojava/nbio/aaproperties/xml/AminoAcidComposition.html" title="class in org.biojava.nbio.aaproperties.xml" target="classFrame">AminoAcidComposition</a></li>
<li><a href="org/biojava/nbio/aaproperties/xml/AminoAcidCompositionTable.html" title="class in org.biojava.nbio.aaproperties.xml" target="classFrame">AminoAcidCompositionTable</a></li>
<li><a href="org/biojava/nbio/core/sequence/compound/AminoAcidCompound.html" title="class in org.biojava.nbio.core.sequence.compound" target="classFrame">AminoAcidCompound</a></li>
<li><a href="org/biojava/nbio/core/sequence/compound/AminoAcidCompoundSet.html" title="class in org.biojava.nbio.core.sequence.compound" target="classFrame">AminoAcidCompoundSet</a></li>
<li><a href="org/biojava/nbio/structure/AminoAcidImpl.html" title="class in org.biojava.nbio.structure" target="classFrame">AminoAcidImpl</a></li>
<li><a href="org/biojava/nbio/alignment/routines/AnchoredPairwiseSequenceAligner.html" title="class in org.biojava.nbio.alignment.routines" target="classFrame">AnchoredPairwiseSequenceAligner</a></li>
<li><a href="org/biojava/nbio/structure/symmetry/internal/AngleOrderDetectorPlus.html" title="class in org.biojava.nbio.structure.symmetry.internal" target="classFrame">AngleOrderDetectorPlus</a></li>
<li><a href="org/biojava/nbio/structure/validation/AngleOutlier.html" title="class in org.biojava.nbio.structure.validation" target="classFrame">AngleOutlier</a></li>
<li><a href="org/biojava/nbio/ontology/utils/Annotatable.html" title="interface in org.biojava.nbio.ontology.utils" target="classFrame"><i>Annotatable</i></a></li>
<li><a href="org/biojava/nbio/ontology/utils/Annotation.html" title="interface in org.biojava.nbio.ontology.utils" target="classFrame"><i>Annotation</i></a></li>
<li><a href="org/biojava/nbio/genome/App.html" title="class in org.biojava.nbio.genome" target="classFrame">App</a></li>
<li><a href="org/biojava/nbio/ontology/App.html" title="class in org.biojava.nbio.ontology" target="classFrame">App</a></li>
<li><a href="org/biojava/nbio/core/sequence/loader/ArrayListProxySequenceReader.html" title="class in org.biojava.nbio.core.sequence.loader" target="classFrame">ArrayListProxySequenceReader</a></li>
<li><a href="org/biojava/nbio/core/sequence/storage/ArrayListSequenceReader.html" title="class in org.biojava.nbio.core.sequence.storage" target="classFrame">ArrayListSequenceReader</a></li>
<li><a href="org/biojava/nbio/structure/asa/AsaCalculator.html" title="class in org.biojava.nbio.structure.asa" target="classFrame">AsaCalculator</a></li>
<li><a href="org/biojava/nbio/ontology/utils/AssertionFailure.html" title="class in org.biojava.nbio.ontology.utils" target="classFrame">AssertionFailure</a></li>
<li><a href="org/biojava/nbio/structure/domain/AssignmentXMLSerializer.html" title="class in org.biojava.nbio.structure.domain" target="classFrame">AssignmentXMLSerializer</a></li>
<li><a href="org/biojava/nbio/structure/scop/Astral.html" title="class in org.biojava.nbio.structure.scop" target="classFrame">Astral</a></li>
<li><a href="org/biojava/nbio/structure/scop/Astral.AstralSet.html" title="enum in org.biojava.nbio.structure.scop" target="classFrame">Astral.AstralSet</a></li>
<li><a href="org/biojava/nbio/structure/Atom.html" title="interface in org.biojava.nbio.structure" target="classFrame"><i>Atom</i></a></li>
<li><a href="org/biojava/nbio/structure/align/util/AtomCache.html" title="class in org.biojava.nbio.structure.align.util" target="classFrame">AtomCache</a></li>
<li><a href="org/biojava/nbio/structure/contact/AtomContact.html" title="class in org.biojava.nbio.structure.contact" target="classFrame">AtomContact</a></li>
<li><a href="org/biojava/nbio/structure/contact/AtomContactSet.html" title="class in org.biojava.nbio.structure.contact" target="classFrame">AtomContactSet</a></li>
<li><a href="org/biojava/nbio/structure/contact/AtomIdentifier.html" title="class in org.biojava.nbio.structure.contact" target="classFrame">AtomIdentifier</a></li>
<li><a href="org/biojava/nbio/structure/AtomImpl.html" title="class in org.biojava.nbio.structure" target="classFrame">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" target="classFrame">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" target="classFrame">AtomInfoParser</a></li>
<li><a href="org/biojava/nbio/structure/AtomIterator.html" title="class in org.biojava.nbio.structure" target="classFrame">AtomIterator</a></li>
<li><a href="org/biojava/nbio/structure/AtomPositionMap.html" title="class in org.biojava.nbio.structure" target="classFrame">AtomPositionMap</a></li>
<li><a href="org/biojava/nbio/structure/AtomPositionMap.GroupMatcher.html" title="interface in org.biojava.nbio.structure" target="classFrame"><i>AtomPositionMap.GroupMatcher</i></a></li>
<li><a href="org/biojava/nbio/structure/io/mmcif/model/AtomSite.html" title="class in org.biojava.nbio.structure.io.mmcif.model" target="classFrame">AtomSite</a></li>
<li><a href="org/biojava/nbio/structure/io/mmcif/model/AuditAuthor.html" title="class in org.biojava.nbio.structure.io.mmcif.model" target="classFrame">AuditAuthor</a></li>
<li><a href="org/biojava/nbio/structure/AugmentedResidueRange.html" title="class in org.biojava.nbio.structure" target="classFrame">AugmentedResidueRange</a></li>
<li><a href="org/biojava/nbio/structure/Author.html" title="class in org.biojava.nbio.structure" target="classFrame">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" target="classFrame"><i>AutoSuggestProvider</i></a></li>
<li><a href="org/biojava/nbio/structure/symmetry/core/AxisAligner.html" title="class in org.biojava.nbio.structure.symmetry.core" target="classFrame">AxisAligner</a></li>
<li><a href="org/biojava/nbio/core/sequence/BasicSequence.html" title="class in org.biojava.nbio.core.sequence" target="classFrame">BasicSequence</a></li>
<li><a href="org/biojava/nbio/structure/scop/BerkeleyScopInstallation.html" title="class in org.biojava.nbio.structure.scop" target="classFrame">BerkeleyScopInstallation</a></li>
<li><a href="org/biojava/nbio/structure/secstruc/BetaBridge.html" title="class in org.biojava.nbio.structure.secstruc" target="classFrame">BetaBridge</a></li>
<li><a href="org/biojava/nbio/structure/BioAssemblyIdentifier.html" title="class in org.biojava.nbio.structure" target="classFrame">BioAssemblyIdentifier</a></li>
<li><a href="org/biojava/nbio/structure/quaternary/BioAssemblyInfo.html" title="class in org.biojava.nbio.structure.quaternary" target="classFrame">BioAssemblyInfo</a></li>
<li><a href="org/biojava/nbio/structure/quaternary/BioAssemblyTools.html" title="class in org.biojava.nbio.structure.quaternary" target="classFrame">BioAssemblyTools</a></li>
<li><a href="demo/BioJavaAADemo.html" title="class in demo" target="classFrame">BioJavaAADemo</a></li>
<li><a href="org/biojava/nbio/structure/gui/BiojavaJmol.html" title="class in org.biojava.nbio.structure.gui" target="classFrame">BiojavaJmol</a></li>
<li><a href="org/biojava/nbio/structure/align/BioJavaStructureAlignment.html" title="class in org.biojava.nbio.structure.align" target="classFrame">BioJavaStructureAlignment</a></li>
<li><a href="org/biojava/nbio/structure/quaternary/BiologicalAssemblyBuilder.html" title="class in org.biojava.nbio.structure.quaternary" target="classFrame">BiologicalAssemblyBuilder</a></li>
<li><a href="org/biojava/nbio/structure/quaternary/BiologicalAssemblyTransformation.html" title="class in org.biojava.nbio.structure.quaternary" target="classFrame">BiologicalAssemblyTransformation</a></li>
<li><a href="org/biojava/nbio/structure/quaternary/io/BioUnitDataProvider.html" title="interface in org.biojava.nbio.structure.quaternary.io" target="classFrame"><i>BioUnitDataProvider</i></a></li>
<li><a href="org/biojava/nbio/structure/quaternary/io/BioUnitDataProviderFactory.html" title="class in org.biojava.nbio.structure.quaternary.io" target="classFrame">BioUnitDataProviderFactory</a></li>
<li><a href="org/biojava/nbio/core/sequence/storage/BitSequenceReader.html" title="class in org.biojava.nbio.core.sequence.storage" target="classFrame">BitSequenceReader</a></li>
<li><a href="org/biojava/nbio/core/sequence/storage/BitSequenceReader.BitArrayWorker.html" title="class in org.biojava.nbio.core.sequence.storage" target="classFrame">BitSequenceReader.BitArrayWorker</a></li>
<li><a href="org/biojava/nbio/ws/alignment/qblast/BlastAlignmentParameterEnum.html" title="enum in org.biojava.nbio.ws.alignment.qblast" target="classFrame">BlastAlignmentParameterEnum</a></li>
<li><a href="org/biojava/nbio/structure/symmetry/utils/BlastClustReader.html" title="class in org.biojava.nbio.structure.symmetry.utils" target="classFrame">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" target="classFrame">BlastHitBuilder</a></li>
<li><a href="org/biojava/nbio/genome/homology/BlastHomologyHits.html" title="class in org.biojava.nbio.genome.homology" target="classFrame">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" target="classFrame">BlastHspBuilder</a></li>
<li><a href="org/biojava/nbio/ws/alignment/qblast/BlastJob.html" title="class in org.biojava.nbio.ws.alignment.qblast" target="classFrame">BlastJob</a></li>
<li><a href="org/biojava/nbio/ws/alignment/qblast/BlastMatrixEnum.html" title="enum in org.biojava.nbio.ws.alignment.qblast" target="classFrame">BlastMatrixEnum</a></li>
<li><a href="org/biojava/nbio/ws/alignment/qblast/BlastOutputAlignmentFormatEnum.html" title="enum in org.biojava.nbio.ws.alignment.qblast" target="classFrame">BlastOutputAlignmentFormatEnum</a></li>
<li><a href="org/biojava/nbio/ws/alignment/qblast/BlastOutputFormatEnum.html" title="enum in org.biojava.nbio.ws.alignment.qblast" target="classFrame">BlastOutputFormatEnum</a></li>
<li><a href="org/biojava/nbio/ws/alignment/qblast/BlastOutputParameterEnum.html" title="enum in org.biojava.nbio.ws.alignment.qblast" target="classFrame">BlastOutputParameterEnum</a></li>
<li><a href="org/biojava/nbio/ws/alignment/qblast/BlastProgramEnum.html" title="enum in org.biojava.nbio.ws.alignment.qblast" target="classFrame">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" target="classFrame">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" target="classFrame">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" target="classFrame">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" target="classFrame">BlastXMLParser</a></li>
<li><a href="org/biojava/nbio/genome/query/BlastXMLQuery.html" title="class in org.biojava.nbio.genome.query" target="classFrame">BlastXMLQuery</a></li>
<li><a href="org/biojava/nbio/structure/align/multiple/Block.html" title="interface in org.biojava.nbio.structure.align.multiple" target="classFrame"><i>Block</i></a></li>
<li><a href="org/biojava/nbio/structure/align/multiple/BlockImpl.html" title="class in org.biojava.nbio.structure.align.multiple" target="classFrame">BlockImpl</a></li>
<li><a href="org/biojava/nbio/structure/align/multiple/BlockSet.html" title="interface in org.biojava.nbio.structure.align.multiple" target="classFrame"><i>BlockSet</i></a></li>
<li><a href="org/biojava/nbio/structure/align/multiple/BlockSetImpl.html" title="class in org.biojava.nbio.structure.align.multiple" target="classFrame">BlockSetImpl</a></li>
<li><a href="org/biojava/nbio/structure/Bond.html" title="interface in org.biojava.nbio.structure" target="classFrame"><i>Bond</i></a></li>
<li><a href="org/biojava/nbio/structure/BondImpl.html" title="class in org.biojava.nbio.structure" target="classFrame">BondImpl</a></li>
<li><a href="org/biojava/nbio/structure/io/BondMaker.html" title="class in org.biojava.nbio.structure.io" target="classFrame">BondMaker</a></li>
<li><a href="org/biojava/nbio/structure/validation/BondOutlier.html" title="class in org.biojava.nbio.structure.validation" target="classFrame">BondOutlier</a></li>
<li><a href="org/biojava/nbio/structure/BondType.html" title="enum in org.biojava.nbio.structure" target="classFrame">BondType</a></li>
<li><a href="org/biojava/nbio/structure/contact/BoundingBox.html" title="class in org.biojava.nbio.structure.contact" target="classFrame">BoundingBox</a></li>
<li><a href="org/biojava/nbio/structure/xtal/BravaisLattice.html" title="enum in org.biojava.nbio.structure.xtal" target="classFrame">BravaisLattice</a></li>
<li><a href="org/biojava/nbio/structure/secstruc/BridgeType.html" title="enum in org.biojava.nbio.structure.secstruc" target="classFrame">BridgeType</a></li>
<li><a href="org/biojava/nbio/structure/align/webstart/BrowserOpener.html" title="class in org.biojava.nbio.structure.align.webstart" target="classFrame">BrowserOpener</a></li>
<li><a href="org/biojava/nbio/core/sequence/io/BufferedReaderBytesRead.html" title="class in org.biojava.nbio.core.sequence.io" target="classFrame">BufferedReaderBytesRead</a></li>
<li><a href="org/biojava/nbio/structure/symmetry/core/C2RotationSolver.html" title="class in org.biojava.nbio.structure.symmetry.core" target="classFrame">C2RotationSolver</a></li>
<li><a href="org/biojava/nbio/structure/scop/CachedRemoteScopInstallation.html" title="class in org.biojava.nbio.structure.scop" target="classFrame">CachedRemoteScopInstallation</a></li>
<li><a href="org/biojava/nbio/structure/align/util/CacheFactory.html" title="class in org.biojava.nbio.structure.align.util" target="classFrame">CacheFactory</a></li>
<li><a href="org/biojava/nbio/structure/io/CAConverter.html" title="class in org.biojava.nbio.structure.io" target="classFrame">CAConverter</a></li>
<li><a href="org/biojava/nbio/structure/Calc.html" title="class in org.biojava.nbio.structure" target="classFrame">Calc</a></li>
<li><a href="org/biojava/nbio/structure/symmetry/analysis/CalcBioAssemblySymmetry.html" title="class in org.biojava.nbio.structure.symmetry.analysis" target="classFrame">CalcBioAssemblySymmetry</a></li>
<li><a href="org/biojava/nbio/alignment/template/CallablePairwiseSequenceAligner.html" title="class in org.biojava.nbio.alignment.template" target="classFrame">CallablePairwiseSequenceAligner</a></li>
<li><a href="org/biojava/nbio/alignment/template/CallablePairwiseSequenceScorer.html" title="class in org.biojava.nbio.alignment.template" target="classFrame">CallablePairwiseSequenceScorer</a></li>
<li><a href="org/biojava/nbio/alignment/template/CallableProfileProfileAligner.html" title="class in org.biojava.nbio.alignment.template" target="classFrame">CallableProfileProfileAligner</a></li>
<li><a href="org/biojava/nbio/structure/align/CallableStructureAlignment.html" title="class in org.biojava.nbio.structure.align" target="classFrame">CallableStructureAlignment</a></li>
<li><a href="org/biojava/nbio/structure/quaternary/CartesianProduct.html" title="class in org.biojava.nbio.structure.quaternary" target="classFrame">CartesianProduct</a></li>
<li><a href="org/biojava/nbio/aaproperties/xml/CaseFreeAminoAcidCompoundSet.html" title="class in org.biojava.nbio.aaproperties.xml" target="classFrame">CaseFreeAminoAcidCompoundSet</a></li>
<li><a href="org/biojava/nbio/core/sequence/transcription/CaseInsensitiveCompound.html" title="class in org.biojava.nbio.core.sequence.transcription" target="classFrame">CaseInsensitiveCompound</a></li>
<li><a href="org/biojava/nbio/core/sequence/io/CasePreservingProteinSequenceCreator.html" title="class in org.biojava.nbio.core.sequence.io" target="classFrame">CasePreservingProteinSequenceCreator</a></li>
<li><a href="org/biojava/nbio/structure/cath/CathCategory.html" title="enum in org.biojava.nbio.structure.cath" target="classFrame">CathCategory</a></li>
<li><a href="org/biojava/nbio/structure/cath/CathDatabase.html" title="interface in org.biojava.nbio.structure.cath" target="classFrame"><i>CathDatabase</i></a></li>
<li><a href="org/biojava/nbio/structure/cath/CathDomain.html" title="class in org.biojava.nbio.structure.cath" target="classFrame">CathDomain</a></li>
<li><a href="org/biojava/nbio/structure/cath/CathFactory.html" title="class in org.biojava.nbio.structure.cath" target="classFrame">CathFactory</a></li>
<li><a href="org/biojava/nbio/structure/cath/CathFragment.html" title="class in org.biojava.nbio.structure.cath" target="classFrame">CathFragment</a></li>
<li><a href="org/biojava/nbio/structure/cath/CathInstallation.html" title="class in org.biojava.nbio.structure.cath" target="classFrame">CathInstallation</a></li>
<li><a href="org/biojava/nbio/structure/cath/CathNode.html" title="class in org.biojava.nbio.structure.cath" target="classFrame">CathNode</a></li>
<li><a href="org/biojava/nbio/structure/cath/CathSegment.html" title="class in org.biojava.nbio.structure.cath" target="classFrame">CathSegment</a></li>
<li><a href="org/biojava/nbio/core/sequence/CDSComparator.html" title="class in org.biojava.nbio.core.sequence" target="classFrame">CDSComparator</a></li>
<li><a href="org/biojava/nbio/core/sequence/CDSSequence.html" title="class in org.biojava.nbio.core.sequence" target="classFrame">CDSSequence</a></li>
<li><a href="org/biojava/nbio/structure/align/ce/CECalculator.html" title="class in org.biojava.nbio.structure.align.ce" target="classFrame">CECalculator</a></li>
<li><a href="org/biojava/nbio/structure/align/ce/CeCalculatorEnhanced.html" title="class in org.biojava.nbio.structure.align.ce" target="classFrame">CeCalculatorEnhanced</a></li>
<li><a href="org/biojava/nbio/structure/align/ce/CeCPMain.html" title="class in org.biojava.nbio.structure.align.ce" target="classFrame">CeCPMain</a></li>
<li><a href="org/biojava/nbio/structure/align/ce/CeCPMain.CPRange.html" title="class in org.biojava.nbio.structure.align.ce" target="classFrame">CeCPMain.CPRange</a></li>
<li><a href="org/biojava/nbio/structure/align/ce/CECPParameters.html" title="class in org.biojava.nbio.structure.align.ce" target="classFrame">CECPParameters</a></li>
<li><a href="org/biojava/nbio/structure/align/ce/CECPParameters.DuplicationHint.html" title="enum in org.biojava.nbio.structure.align.ce" target="classFrame">CECPParameters.DuplicationHint</a></li>
<li><a href="org/biojava/nbio/structure/align/ce/CeCPUserArgumentProcessor.html" title="class in org.biojava.nbio.structure.align.ce" target="classFrame">CeCPUserArgumentProcessor</a></li>
<li><a href="org/biojava/nbio/structure/io/mmcif/model/Cell.html" title="class in org.biojava.nbio.structure.io.mmcif.model" target="classFrame">Cell</a></li>
<li><a href="org/biojava/nbio/structure/align/ce/CeMain.html" title="class in org.biojava.nbio.structure.align.ce" target="classFrame">CeMain</a></li>
<li><a href="org/biojava/nbio/survival/kaplanmeier/figure/CensorStatus.html" title="class in org.biojava.nbio.survival.kaplanmeier.figure" target="classFrame">CensorStatus</a></li>
<li><a href="org/biojava/nbio/survival/kaplanmeier/figure/CensorStatusSelect.html" title="interface in org.biojava.nbio.survival.kaplanmeier.figure" target="classFrame"><i>CensorStatusSelect</i></a></li>
<li><a href="org/biojava/nbio/structure/align/ce/CeParameters.html" title="class in org.biojava.nbio.structure.align.ce" target="classFrame">CeParameters</a></li>
<li><a href="org/biojava/nbio/structure/align/ce/CeParameters.ScoringStrategy.html" title="enum in org.biojava.nbio.structure.align.ce" target="classFrame">CeParameters.ScoringStrategy</a></li>
<li><a href="org/biojava/nbio/structure/align/ce/CeSideChainMain.html" title="class in org.biojava.nbio.structure.align.ce" target="classFrame">CeSideChainMain</a></li>
<li><a href="org/biojava/nbio/structure/align/ce/CeSideChainUserArgumentProcessor.html" title="class in org.biojava.nbio.structure.align.ce" target="classFrame">CeSideChainUserArgumentProcessor</a></li>
<li><a href="org/biojava/nbio/structure/symmetry/internal/CeSymm.html" title="class in org.biojava.nbio.structure.symmetry.internal" target="classFrame">CeSymm</a></li>
<li><a href="org/biojava/nbio/structure/symmetry/internal/CeSymmIterative.html" title="class in org.biojava.nbio.structure.symmetry.internal" target="classFrame">CeSymmIterative</a></li>
<li><a href="org/biojava/nbio/structure/symmetry/internal/CESymmParameters.html" title="class in org.biojava.nbio.structure.symmetry.internal" target="classFrame">CESymmParameters</a></li>
<li><a href="org/biojava/nbio/structure/symmetry/internal/CESymmParameters.OrderDetectorMethod.html" title="enum in org.biojava.nbio.structure.symmetry.internal" target="classFrame">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" target="classFrame">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" target="classFrame">CESymmParameters.SymmetryType</a></li>
<li><a href="org/biojava/nbio/structure/symmetry/internal/CeSymmResult.html" title="class in org.biojava.nbio.structure.symmetry.internal" target="classFrame">CeSymmResult</a></li>
<li><a href="org/biojava/nbio/structure/align/ce/CeUserArgumentProcessor.html" title="class in org.biojava.nbio.structure.align.ce" target="classFrame">CeUserArgumentProcessor</a></li>
<li><a href="org/biojava/nbio/structure/align/ce/CeUserArgumentProcessor.CeStartupParams.html" title="class in org.biojava.nbio.structure.align.ce" target="classFrame">CeUserArgumentProcessor.CeStartupParams</a></li>
<li><a href="org/biojava/nbio/structure/Chain.html" title="interface in org.biojava.nbio.structure" target="classFrame"><i>Chain</i></a></li>
<li><a href="org/biojava/nbio/structure/symmetry/core/ChainClusterer.html" title="class in org.biojava.nbio.structure.symmetry.core" target="classFrame">ChainClusterer</a></li>
<li><a href="org/biojava/nbio/structure/ChainImpl.html" title="class in org.biojava.nbio.structure" target="classFrame">ChainImpl</a></li>
<li><a href="org/biojava/nbio/structure/symmetry/misc/ChainSignature.html" title="class in org.biojava.nbio.structure.symmetry.misc" target="classFrame">ChainSignature</a></li>
<li><a href="org/biojava/nbio/survival/data/ChangeValue.html" title="interface in org.biojava.nbio.survival.data" target="classFrame"><i>ChangeValue</i></a></li>
<li><a href="org/biojava/nbio/structure/io/ChargeAdder.html" title="class in org.biojava.nbio.structure.io" target="classFrame">ChargeAdder</a></li>
<li><a href="org/biojava/nbio/structure/io/mmcif/model/ChemComp.html" title="class in org.biojava.nbio.structure.io.mmcif.model" target="classFrame">ChemComp</a></li>
<li><a href="org/biojava/nbio/structure/io/mmcif/model/ChemCompAtom.html" title="class in org.biojava.nbio.structure.io.mmcif.model" target="classFrame">ChemCompAtom</a></li>
<li><a href="org/biojava/nbio/structure/io/mmcif/model/ChemCompBond.html" title="class in org.biojava.nbio.structure.io.mmcif.model" target="classFrame">ChemCompBond</a></li>
<li><a href="org/biojava/nbio/structure/io/mmcif/ChemCompConsumer.html" title="class in org.biojava.nbio.structure.io.mmcif" target="classFrame">ChemCompConsumer</a></li>
<li><a href="org/biojava/nbio/structure/io/mmcif/model/ChemCompDescriptor.html" title="class in org.biojava.nbio.structure.io.mmcif.model" target="classFrame">ChemCompDescriptor</a></li>
<li><a href="demo/ChemCompDistribution.html" title="class in demo" target="classFrame">ChemCompDistribution</a></li>
<li><a href="org/biojava/nbio/structure/io/mmcif/ChemCompGroupFactory.html" title="class in org.biojava.nbio.structure.io.mmcif" target="classFrame">ChemCompGroupFactory</a></li>
<li><a href="org/biojava/nbio/structure/io/mmcif/ChemCompProvider.html" title="interface in org.biojava.nbio.structure.io.mmcif" target="classFrame"><i>ChemCompProvider</i></a></li>
<li><a href="org/biojava/nbio/structure/io/mmcif/chem/ChemCompTools.html" title="class in org.biojava.nbio.structure.io.mmcif.chem" target="classFrame">ChemCompTools</a></li>
<li><a href="org/biojava/nbio/structure/io/mmcif/ChemicalComponentDictionary.html" title="class in org.biojava.nbio.structure.io.mmcif" target="classFrame">ChemicalComponentDictionary</a></li>
<li><a href="org/biojava/nbio/survival/cox/stats/ChiSq.html" title="class in org.biojava.nbio.survival.cox.stats" target="classFrame">ChiSq</a></li>
<li><a href="org/biojava/nbio/survival/cox/stats/Cholesky2.html" title="class in org.biojava.nbio.survival.cox.stats" target="classFrame">Cholesky2</a></li>
<li><a href="org/biojava/nbio/structure/jama/CholeskyDecomposition.html" title="class in org.biojava.nbio.structure.jama" target="classFrame">CholeskyDecomposition</a></li>
<li><a href="org/biojava/nbio/structure/align/gui/ChooseDirAction.html" title="class in org.biojava.nbio.structure.align.gui" target="classFrame">ChooseDirAction</a></li>
<li><a href="org/biojava/nbio/core/sequence/ChromosomeSequence.html" title="class in org.biojava.nbio.core.sequence" target="classFrame">ChromosomeSequence</a></li>
<li><a href="org/biojava/nbio/survival/cox/stats/Chsolve2.html" title="class in org.biojava.nbio.survival.cox.stats" target="classFrame">Chsolve2</a></li>
<li><a href="org/biojava/nbio/structure/validation/Clash.html" title="class in org.biojava.nbio.structure.validation" target="classFrame">Clash</a></li>
<li><a href="org/biojava/nbio/core/sequence/io/util/ClasspathResource.html" title="class in org.biojava.nbio.core.sequence.io.util" target="classFrame">ClasspathResource</a></li>
<li><a href="org/biojava/nbio/survival/kaplanmeier/metadata/ClinicalMetaDataOutcome.html" title="class in org.biojava.nbio.survival.kaplanmeier.metadata" target="classFrame">ClinicalMetaDataOutcome</a></li>
<li><a href="org/biojava/nbio/structure/align/util/CliTools.html" title="class in org.biojava.nbio.structure.align.util" target="classFrame">CliTools</a></li>
<li><a href="org/biojava/nbio/structure/align/ClusterAltAligs.html" title="class in org.biojava.nbio.structure.align" target="classFrame">ClusterAltAligs</a></li>
<li><a href="org/biojava/nbio/structure/domain/pdp/ClusterDomains.html" title="class in org.biojava.nbio.structure.domain.pdp" target="classFrame">ClusterDomains</a></li>
<li><a href="org/biojava/nbio/structure/symmetry/core/ClusterMerger.html" title="class in org.biojava.nbio.structure.symmetry.core" target="classFrame">ClusterMerger</a></li>
<li><a href="org/biojava/nbio/structure/symmetry/core/ClusterProteinChains.html" title="class in org.biojava.nbio.structure.symmetry.core" target="classFrame">ClusterProteinChains</a></li>
<li><a href="org/biojava/nbio/core/sequence/compound/CodonCompound.html" title="class in org.biojava.nbio.core.sequence.compound" target="classFrame">CodonCompound</a></li>
<li><a href="org/biojava/nbio/structure/align/util/CollectionTools.html" title="class in org.biojava.nbio.structure.align.util" target="classFrame">CollectionTools</a></li>
<li><a href="org/biojava/nbio/structure/symmetry/jmolScript/ColorConverter.html" title="class in org.biojava.nbio.structure.symmetry.jmolScript" target="classFrame">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" target="classFrame"><i>ColorInterpolator</i></a></li>
<li><a href="org/biojava/nbio/structure/gui/util/color/ColorUtils.html" title="class in org.biojava.nbio.structure.gui.util.color" target="classFrame">ColorUtils</a></li>
<li><a href="org/biojava/nbio/structure/symmetry/utils/CombinationGenerator.html" title="class in org.biojava.nbio.structure.symmetry.utils" target="classFrame">CombinationGenerator</a></li>
<li><a href="org/biojava/nbio/aaproperties/CommandPrompt.html" title="class in org.biojava.nbio.aaproperties" target="classFrame">CommandPrompt</a></li>
<li><a href="org/biojava/nbio/aaproperties/CommandPrompt.PropertyName.html" title="enum in org.biojava.nbio.aaproperties" target="classFrame">CommandPrompt.PropertyName</a></li>
<li><a href="org/biojava/nbio/survival/data/CompactCharSequence.html" title="class in org.biojava.nbio.survival.data" target="classFrame">CompactCharSequence</a></li>
<li><a href="org/biojava/nbio/phylo/Comparison.html" title="class in org.biojava.nbio.phylo" target="classFrame">Comparison</a></li>
<li><a href="org/biojava/nbio/core/sequence/template/ComplementCompound.html" title="interface in org.biojava.nbio.core.sequence.template" target="classFrame"><i>ComplementCompound</i></a></li>
<li><a href="org/biojava/nbio/core/sequence/views/ComplementSequenceView.html" title="class in org.biojava.nbio.core.sequence.views" target="classFrame">ComplementSequenceView</a></li>
<li><a href="org/biojava/nbio/protmod/Component.html" title="class in org.biojava.nbio.protmod" target="classFrame">Component</a></li>
<li><a href="org/biojava/nbio/protmod/io/ComponentXMLConverter.html" title="class in org.biojava.nbio.protmod.io" target="classFrame">ComponentXMLConverter</a></li>
<li><a href="org/biojava/nbio/core/sequence/template/Compound.html" title="interface in org.biojava.nbio.core.sequence.template" target="classFrame"><i>Compound</i></a></li>
<li><a href="org/biojava/nbio/structure/Compound.html" title="class in org.biojava.nbio.structure" target="classFrame">Compound</a></li>
<li><a href="org/biojava/nbio/structure/io/CompoundFinder.html" title="class in org.biojava.nbio.structure.io" target="classFrame">CompoundFinder</a></li>
<li><a href="org/biojava/nbio/core/exceptions/CompoundNotFoundException.html" title="class in org.biojava.nbio.core.exceptions" target="classFrame">CompoundNotFoundException</a></li>
<li><a href="org/biojava/nbio/core/sequence/template/CompoundSet.html" title="interface in org.biojava.nbio.core.sequence.template" target="classFrame"><i>CompoundSet</i></a></li>
<li><a href="org/biojava/nbio/core/sequence/template/CompoundTranslator.html" title="interface in org.biojava.nbio.core.sequence.template" target="classFrame"><i>CompoundTranslator</i></a></li>
<li><a href="org/biojava/nbio/core/util/ConcurrencyTools.html" title="class in org.biojava.nbio.core.util" target="classFrame">ConcurrencyTools</a></li>
<li><a href="org/biojava/nbio/structure/align/gui/ConfigPDBInstallPanel.html" title="class in org.biojava.nbio.structure.align.gui" target="classFrame">ConfigPDBInstallPanel</a></li>
<li><a href="org/biojava/nbio/structure/align/ce/ConfigStrucAligParams.html" title="interface in org.biojava.nbio.structure.align.ce" target="classFrame"><i>ConfigStrucAligParams</i></a></li>
<li><a href="org/biojava/nbio/structure/align/util/ConfigurationException.html" title="class in org.biojava.nbio.structure.align.util" target="classFrame">ConfigurationException</a></li>
<li><a href="org/biojava/nbio/structure/align/webstart/ConfigXMLHandler.html" title="class in org.biojava.nbio.structure.align.webstart" target="classFrame">ConfigXMLHandler</a></li>
<li><a href="org/biojava/nbio/aaproperties/Constraints.html" title="class in org.biojava.nbio.aaproperties" target="classFrame">Constraints</a></li>
<li><a href="org/biojava/nbio/structure/gui/util/color/ContinuousColorMapper.html" title="interface in org.biojava.nbio.structure.gui.util.color" target="classFrame"><i>ContinuousColorMapper</i></a></li>
<li><a href="org/biojava/nbio/structure/gui/util/color/ContinuousColorMapperTransform.html" title="class in org.biojava.nbio.structure.gui.util.color" target="classFrame">ContinuousColorMapperTransform</a></li>
<li><a href="org/biojava/nbio/aaproperties/profeat/convertor/Convert2Charge.html" title="class in org.biojava.nbio.aaproperties.profeat.convertor" target="classFrame">Convert2Charge</a></li>
<li><a href="org/biojava/nbio/aaproperties/profeat/convertor/Convert2Hydrophobicity.html" title="class in org.biojava.nbio.aaproperties.profeat.convertor" target="classFrame">Convert2Hydrophobicity</a></li>
<li><a href="org/biojava/nbio/aaproperties/profeat/convertor/Convert2NormalizedVanDerWaalsVolume.html" title="class in org.biojava.nbio.aaproperties.profeat.convertor" target="classFrame">Convert2NormalizedVanDerWaalsVolume</a></li>
<li><a href="org/biojava/nbio/aaproperties/profeat/convertor/Convert2Polarity.html" title="class in org.biojava.nbio.aaproperties.profeat.convertor" target="classFrame">Convert2Polarity</a></li>
<li><a href="org/biojava/nbio/aaproperties/profeat/convertor/Convert2Polarizability.html" title="class in org.biojava.nbio.aaproperties.profeat.convertor" target="classFrame">Convert2Polarizability</a></li>
<li><a href="org/biojava/nbio/aaproperties/profeat/convertor/Convert2SecondaryStructure.html" title="class in org.biojava.nbio.aaproperties.profeat.convertor" target="classFrame">Convert2SecondaryStructure</a></li>
<li><a href="org/biojava/nbio/aaproperties/profeat/convertor/Convert2SolventAccessibility.html" title="class in org.biojava.nbio.aaproperties.profeat.convertor" target="classFrame">Convert2SolventAccessibility</a></li>
<li><a href="org/biojava/nbio/aaproperties/profeat/convertor/Convertor.html" title="class in org.biojava.nbio.aaproperties.profeat.convertor" target="classFrame">Convertor</a></li>
<li><a href="demo/CookBook.html" title="class in demo" target="classFrame">CookBook</a></li>
<li><a href="demo/CookbookMSA.html" title="class in demo" target="classFrame">CookbookMSA</a></li>
<li><a href="org/biojava/nbio/structure/gui/util/CoordManager.html" title="class in org.biojava.nbio.structure.gui.util" target="classFrame">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" target="classFrame">CoreSuperimposer</a></li>
<li><a href="org/biojava/nbio/structure/align/client/CountProgressListener.html" title="class in org.biojava.nbio.structure.align.client" target="classFrame">CountProgressListener</a></li>
<li><a href="org/biojava/nbio/survival/cox/CoxCC.html" title="class in org.biojava.nbio.survival.cox" target="classFrame">CoxCC</a></li>
<li><a href="org/biojava/nbio/survival/cox/CoxCoefficient.html" title="class in org.biojava.nbio.survival.cox" target="classFrame">CoxCoefficient</a></li>
<li><a href="org/biojava/nbio/survival/cox/comparators/CoxComparatorInterface.html" title="interface in org.biojava.nbio.survival.cox.comparators" target="classFrame"><i>CoxComparatorInterface</i></a></li>
<li><a href="org/biojava/nbio/survival/cox/CoxHelper.html" title="class in org.biojava.nbio.survival.cox" target="classFrame">CoxHelper</a></li>
<li><a href="org/biojava/nbio/survival/cox/CoxInfo.html" title="class in org.biojava.nbio.survival.cox" target="classFrame">CoxInfo</a></li>
<li><a href="org/biojava/nbio/survival/cox/CoxMart.html" title="class in org.biojava.nbio.survival.cox" target="classFrame">CoxMart</a></li>
<li><a href="org/biojava/nbio/survival/cox/CoxMethod.html" title="enum in org.biojava.nbio.survival.cox" target="classFrame">CoxMethod</a></li>
<li><a href="org/biojava/nbio/survival/cox/CoxR.html" title="class in org.biojava.nbio.survival.cox" target="classFrame">CoxR</a></li>
<li><a href="org/biojava/nbio/survival/cox/CoxScore.html" title="class in org.biojava.nbio.survival.cox" target="classFrame">CoxScore</a></li>
<li><a href="org/biojava/nbio/survival/cox/CoxVariables.html" title="class in org.biojava.nbio.survival.cox" target="classFrame">CoxVariables</a></li>
<li><a href="org/biojava/nbio/survival/cox/comparators/CoxVariablesOverallModelFitComparator.html" title="class in org.biojava.nbio.survival.cox.comparators" target="classFrame">CoxVariablesOverallModelFitComparator</a></li>
<li><a href="org/biojava/nbio/survival/cox/comparators/CoxVariablesVariableComparator.html" title="class in org.biojava.nbio.survival.cox.comparators" target="classFrame">CoxVariablesVariableComparator</a></li>
<li><a href="org/biojava/nbio/core/util/CRC64Checksum.html" title="class in org.biojava.nbio.core.util" target="classFrame">CRC64Checksum</a></li>
<li><a href="org/biojava/nbio/structure/xtal/CrystalBuilder.html" title="class in org.biojava.nbio.structure.xtal" target="classFrame">CrystalBuilder</a></li>
<li><a href="org/biojava/nbio/structure/xtal/CrystalCell.html" title="class in org.biojava.nbio.structure.xtal" target="classFrame">CrystalCell</a></li>
<li><a href="org/biojava/nbio/structure/xtal/CrystalTransform.html" title="class in org.biojava.nbio.structure.xtal" target="classFrame">CrystalTransform</a></li>
<li><a href="org/biojava/nbio/structure/domain/pdp/Cut.html" title="class in org.biojava.nbio.structure.domain.pdp" target="classFrame">Cut</a></li>
<li><a href="org/biojava/nbio/structure/domain/pdp/CutDomain.html" title="class in org.biojava.nbio.structure.domain.pdp" target="classFrame">CutDomain</a></li>
<li><a href="org/biojava/nbio/structure/domain/pdp/CutSites.html" title="class in org.biojava.nbio.structure.domain.pdp" target="classFrame">CutSites</a></li>
<li><a href="org/biojava/nbio/structure/domain/pdp/CutValues.html" title="class in org.biojava.nbio.structure.domain.pdp" target="classFrame">CutValues</a></li>
<li><a href="org/biojava/nbio/genome/parsers/cytoband/Cytoband.html" title="class in org.biojava.nbio.genome.parsers.cytoband" target="classFrame">Cytoband</a></li>
<li><a href="org/biojava/nbio/genome/parsers/cytoband/CytobandParser.html" title="class in org.biojava.nbio.genome.parsers.cytoband" target="classFrame">CytobandParser</a></li>
<li><a href="org/biojava/nbio/structure/io/mmcif/model/DatabasePDBremark.html" title="class in org.biojava.nbio.structure.io.mmcif.model" target="classFrame">DatabasePDBremark</a></li>
<li><a href="org/biojava/nbio/structure/io/mmcif/model/DatabasePDBrev.html" title="class in org.biojava.nbio.structure.io.mmcif.model" target="classFrame">DatabasePDBrev</a></li>
<li><a href="org/biojava/nbio/structure/io/mmcif/model/DatabasePdbrevRecord.html" title="class in org.biojava.nbio.structure.io.mmcif.model" target="classFrame">DatabasePdbrevRecord</a></li>
<li><a href="org/biojava/nbio/core/sequence/features/DatabaseReferenceInterface.html" title="interface in org.biojava.nbio.core.sequence.features" target="classFrame"><i>DatabaseReferenceInterface</i></a></li>
<li><a href="org/biojava/nbio/phosphosite/Dataset.html" title="class in org.biojava.nbio.phosphosite" target="classFrame">Dataset</a></li>
<li><a href="org/biojava/nbio/core/sequence/DataSource.html" title="enum in org.biojava.nbio.core.sequence" target="classFrame">DataSource</a></li>
<li><a href="org/biojava/nbio/structure/DBRef.html" title="class in org.biojava.nbio.structure" target="classFrame">DBRef</a></li>
<li><a href="org/biojava/nbio/core/sequence/features/DBReferenceInfo.html" title="class in org.biojava.nbio.core.sequence.features" target="classFrame">DBReferenceInfo</a></li>
<li><a href="org/biojava/nbio/structure/align/gui/DBResultTable.html" title="class in org.biojava.nbio.structure.align.gui" target="classFrame">DBResultTable</a></li>
<li><a href="org/biojava/nbio/structure/align/gui/DBSearchGUI.html" title="class in org.biojava.nbio.structure.align.gui" target="classFrame">DBSearchGUI</a></li>
<li><a href="org/biojava/nbio/core/alignment/matrices/DefaultAAIndexProvider.html" title="class in org.biojava.nbio.core.alignment.matrices" target="classFrame">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" target="classFrame">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" target="classFrame">DefaultMatrixMapper</a></li>
<li><a href="org/biojava/nbio/ontology/DefaultOps.html" title="class in org.biojava.nbio.ontology" target="classFrame">DefaultOps</a></li>
<li><a href="demo/DemoAlignmentFromFasta.html" title="class in demo" target="classFrame">DemoAlignmentFromFasta</a></li>
<li><a href="demo/DemoAlignProteins.html" title="class in demo" target="classFrame">DemoAlignProteins</a></li>
<li><a href="demo/DemoAsa.html" title="class in demo" target="classFrame">DemoAsa</a></li>
<li><a href="demo/DemoAtomCache.html" title="class in demo" target="classFrame">DemoAtomCache</a></li>
<li><a href="demo/DemoBerkeleyScop.html" title="class in demo" target="classFrame">DemoBerkeleyScop</a></li>
<li><a href="demo/DemoCATH.html" title="class in demo" target="classFrame">DemoCATH</a></li>
<li><a href="demo/DemoCE.html" title="class in demo" target="classFrame">DemoCE</a></li>
<li><a href="demo/DemoCeSymm.html" title="class in demo" target="classFrame">DemoCeSymm</a></li>
<li><a href="demo/DemoChangeChemCompProvider.html" title="class in demo" target="classFrame">DemoChangeChemCompProvider</a></li>
<li><a href="demo/DemoCommandLineStartup.html" title="class in demo" target="classFrame">DemoCommandLineStartup</a></li>
<li><a href="demo/DemoContacts.html" title="class in demo" target="classFrame">DemoContacts</a></li>
<li><a href="demo/DemoCrystalInterfaces.html" title="class in demo" target="classFrame">DemoCrystalInterfaces</a></li>
<li><a href="demo/DemoDistanceTree.html" title="class in demo" target="classFrame">DemoDistanceTree</a></li>
<li><a href="demo/DemoDomainsplit.html" title="class in demo" target="classFrame">DemoDomainsplit</a></li>
<li><a href="demo/DemoFATCAT.html" title="class in demo" target="classFrame">DemoFATCAT</a></li>
<li><a href="demo/DemoLoadSecStruc.html" title="class in demo" target="classFrame">DemoLoadSecStruc</a></li>
<li><a href="demo/DemoLoadStructure.html" title="class in demo" target="classFrame">DemoLoadStructure</a></li>
<li><a href="demo/DemoLoadSubstMax.html" title="class in demo" target="classFrame">DemoLoadSubstMax</a></li>
<li><a href="demo/DemoMMCIFReader.html" title="class in demo" target="classFrame">DemoMMCIFReader</a></li>
<li><a href="demo/DemoMultipleMC.html" title="class in demo" target="classFrame">DemoMultipleMC</a></li>
<li><a href="demo/DemoNWALignment.html" title="class in demo" target="classFrame">DemoNWALignment</a></li>
<li><a href="demo/DemoOrientBioAssembly.html" title="class in demo" target="classFrame">DemoOrientBioAssembly</a></li>
<li><a href="demo/DemoRotationAxis.html" title="class in demo" target="classFrame">DemoRotationAxis</a></li>
<li><a href="demo/DemoSCOP.html" title="class in demo" target="classFrame">DemoSCOP</a></li>
<li><a href="demo/DemoSecStrucCalc.html" title="class in demo" target="classFrame">DemoSecStrucCalc</a></li>
<li><a href="demo/DemoShowBiolAssembly.html" title="class in demo" target="classFrame">DemoShowBiolAssembly</a></li>
<li><a href="demo/DemoShowCATHDomain.html" title="class in demo" target="classFrame">DemoShowCATHDomain</a></li>
<li><a href="demo/DemoShowLargeAssembly.html" title="class in demo" target="classFrame">DemoShowLargeAssembly</a></li>
<li><a href="demo/DemoShowValidationResults.html" title="class in demo" target="classFrame">DemoShowValidationResults</a></li>
<li><a href="demo/DemoSixFrameTranslation.html" title="class in demo" target="classFrame">DemoSixFrameTranslation</a></li>
<li><a href="demo/DemoStructureFromFasta.html" title="class in demo" target="classFrame">DemoStructureFromFasta</a></li>
<li><a href="demo/DemoSW3DAligner.html" title="class in demo" target="classFrame">DemoSW3DAligner</a></li>
<li><a href="org/biojava/nbio/survival/kaplanmeier/metadata/DiscreteQuantizerInterface.html" title="interface in org.biojava.nbio.survival.kaplanmeier.metadata" target="classFrame"><i>DiscreteQuantizerInterface</i></a></li>
<li><a href="org/biojava/nbio/structure/align/gui/DisplayAFP.html" title="class in org.biojava.nbio.structure.align.gui" target="classFrame">DisplayAFP</a></li>
<li><a href="org/biojava/nbio/structure/symmetry/geometry/DistanceBox.html" title="class in org.biojava.nbio.structure.symmetry.geometry" target="classFrame">DistanceBox</a></li>
<li><a href="org/biojava/nbio/phylo/DistanceMatrixCalculator.html" title="class in org.biojava.nbio.phylo" target="classFrame">DistanceMatrixCalculator</a></li>
<li><a href="org/biojava/nbio/phylo/DistanceTreeEvaluator.html" title="class in org.biojava.nbio.phylo" target="classFrame">DistanceTreeEvaluator</a></li>
<li><a href="org/biojava/nbio/core/sequence/compound/DNACompoundSet.html" title="class in org.biojava.nbio.core.sequence.compound" target="classFrame">DNACompoundSet</a></li>
<li><a href="org/biojava/nbio/core/sequence/DNASequence.html" title="class in org.biojava.nbio.core.sequence" target="classFrame">DNASequence</a></li>
<li><a href="org/biojava/nbio/core/sequence/DNASequence.DNAType.html" title="enum in org.biojava.nbio.core.sequence" target="classFrame">DNASequence.DNAType</a></li>
<li><a href="org/biojava/nbio/core/sequence/io/DNASequenceCreator.html" title="class in org.biojava.nbio.core.sequence.io" target="classFrame">DNASequenceCreator</a></li>
<li><a href="org/biojava/nbio/core/sequence/transcription/DNAToRNATranslator.html" title="class in org.biojava.nbio.core.sequence.transcription" target="classFrame">DNAToRNATranslator</a></li>
<li><a href="org/biojava/nbio/structure/domain/pdp/Domain.html" title="class in org.biojava.nbio.structure.domain.pdp" target="classFrame">Domain</a></li>
<li><a href="org/biojava/nbio/structure/domain/DomainProvider.html" title="interface in org.biojava.nbio.structure.domain" target="classFrame"><i>DomainProvider</i></a></li>
<li><a href="org/biojava/nbio/structure/domain/DomainProviderFactory.html" title="class in org.biojava.nbio.structure.domain" target="classFrame">DomainProviderFactory</a></li>
<li><a href="org/biojava/nbio/structure/align/gui/DotPlotPanel.html" title="class in org.biojava.nbio.structure.align.gui" target="classFrame">DotPlotPanel</a></li>
<li><a href="org/biojava/nbio/structure/io/mmcif/DownloadChemCompProvider.html" title="class in org.biojava.nbio.structure.io.mmcif" target="classFrame">DownloadChemCompProvider</a></li>
<li><a href="org/biojava/nbio/structure/secstruc/DSSPParser.html" title="class in org.biojava.nbio.structure.secstruc" target="classFrame">DSSPParser</a></li>
<li><a href="org/biojava/nbio/structure/ecod/EcodDatabase.html" title="interface in org.biojava.nbio.structure.ecod" target="classFrame"><i>EcodDatabase</i></a></li>
<li><a href="org/biojava/nbio/structure/ecod/EcodDomain.html" title="class in org.biojava.nbio.structure.ecod" target="classFrame">EcodDomain</a></li>
<li><a href="org/biojava/nbio/structure/ecod/EcodFactory.html" title="class in org.biojava.nbio.structure.ecod" target="classFrame">EcodFactory</a></li>
<li><a href="org/biojava/nbio/structure/ecod/EcodInstallation.html" title="class in org.biojava.nbio.structure.ecod" target="classFrame">EcodInstallation</a></li>
<li><a href="org/biojava/nbio/structure/ecod/EcodInstallation.EcodParser.html" title="class in org.biojava.nbio.structure.ecod" target="classFrame">EcodInstallation.EcodParser</a></li>
<li><a href="org/biojava/nbio/core/sequence/edits/Edit.html" title="interface in org.biojava.nbio.core.sequence.edits" target="classFrame"><i>Edit</i></a></li>
<li><a href="org/biojava/nbio/core/sequence/edits/Edit.AbstractEdit.html" title="class in org.biojava.nbio.core.sequence.edits" target="classFrame">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" target="classFrame">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" target="classFrame">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" target="classFrame">Edit.Substitute</a></li>
<li><a href="org/biojava/nbio/structure/jama/EigenvalueDecomposition.html" title="class in org.biojava.nbio.structure.jama" target="classFrame">EigenvalueDecomposition</a></li>
<li><a href="org/biojava/nbio/aaproperties/xml/Element.html" title="class in org.biojava.nbio.aaproperties.xml" target="classFrame">Element</a></li>
<li><a href="org/biojava/nbio/structure/Element.html" title="enum in org.biojava.nbio.structure" target="classFrame">Element</a></li>
<li><a href="org/biojava/nbio/aaproperties/xml/ElementTable.html" title="class in org.biojava.nbio.aaproperties.xml" target="classFrame">ElementTable</a></li>
<li><a href="org/biojava/nbio/structure/ElementType.html" title="enum in org.biojava.nbio.structure" target="classFrame">ElementType</a></li>
<li><a href="org/biojava/nbio/structure/io/mmcif/model/Entity.html" title="class in org.biojava.nbio.structure.io.mmcif.model" target="classFrame">Entity</a></li>
<li><a href="org/biojava/nbio/structure/io/mmcif/model/EntityPolySeq.html" title="class in org.biojava.nbio.structure.io.mmcif.model" target="classFrame">EntityPolySeq</a></li>
<li><a href="org/biojava/nbio/structure/io/mmcif/model/EntitySrcGen.html" title="class in org.biojava.nbio.structure.io.mmcif.model" target="classFrame">EntitySrcGen</a></li>
<li><a href="org/biojava/nbio/structure/io/mmcif/model/EntitySrcNat.html" title="class in org.biojava.nbio.structure.io.mmcif.model" target="classFrame">EntitySrcNat</a></li>
<li><a href="org/biojava/nbio/structure/io/mmcif/model/EntitySrcSyn.html" title="class in org.biojava.nbio.structure.io.mmcif.model" target="classFrame">EntitySrcSyn</a></li>
<li><a href="org/biojava/nbio/structure/validation/Entry.html" title="class in org.biojava.nbio.structure.validation" target="classFrame">Entry</a></li>
<li><a href="org/biojava/nbio/core/util/Equals.html" title="class in org.biojava.nbio.core.util" target="classFrame">Equals</a></li>
<li><a href="org/biojava/nbio/core/sequence/ExonComparator.html" title="class in org.biojava.nbio.core.sequence" target="classFrame">ExonComparator</a></li>
<li><a href="org/biojava/nbio/core/sequence/ExonSequence.html" title="class in org.biojava.nbio.core.sequence" target="classFrame">ExonSequence</a></li>
<li><a href="org/biojava/nbio/structure/ExperimentalTechnique.html" title="enum in org.biojava.nbio.structure" target="classFrame">ExperimentalTechnique</a></li>
<li><a href="org/biojava/nbio/survival/kaplanmeier/figure/ExpressionFigure.html" title="class in org.biojava.nbio.survival.kaplanmeier.figure" target="classFrame">ExpressionFigure</a></li>
<li><a href="org/biojava/nbio/structure/io/mmcif/model/Exptl.html" title="class in org.biojava.nbio.structure.io.mmcif.model" target="classFrame">Exptl</a></li>
<li><a href="org/biojava/nbio/structure/align/FarmJob.html" title="class in org.biojava.nbio.structure.align" target="classFrame">FarmJob</a></li>
<li><a href="org/biojava/nbio/structure/align/client/FarmJobParameters.html" title="class in org.biojava.nbio.structure.align.client" target="classFrame">FarmJobParameters</a></li>
<li><a href="org/biojava/nbio/structure/align/client/FarmJobRunnable.html" title="class in org.biojava.nbio.structure.align.client" target="classFrame">FarmJobRunnable</a></li>
<li><a href="org/biojava/nbio/structure/io/FastaAFPChainConverter.html" title="class in org.biojava.nbio.structure.io" target="classFrame">FastaAFPChainConverter</a></li>
<li><a href="org/biojava/nbio/core/sequence/io/FastaGeneWriter.html" title="class in org.biojava.nbio.core.sequence.io" target="classFrame">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" target="classFrame"><i>FastaHeaderFormatInterface</i></a></li>
<li><a href="org/biojava/nbio/core/sequence/io/FastaReader.html" title="class in org.biojava.nbio.core.sequence.io" target="classFrame">FastaReader</a></li>
<li><a href="org/biojava/nbio/core/sequence/io/FastaReaderHelper.html" title="class in org.biojava.nbio.core.sequence.io" target="classFrame">FastaReaderHelper</a></li>
<li><a href="org/biojava/nbio/data/sequence/FastaSequence.html" title="class in org.biojava.nbio.data.sequence" target="classFrame">FastaSequence</a></li>
<li><a href="org/biojava/nbio/core/sequence/io/FastaSequenceParser.html" title="class in org.biojava.nbio.core.sequence.io" target="classFrame">FastaSequenceParser</a></li>
<li><a href="org/biojava/nbio/structure/io/FastaStructureParser.html" title="class in org.biojava.nbio.structure.io" target="classFrame">FastaStructureParser</a></li>
<li><a href="org/biojava/nbio/core/sequence/io/FastaWriter.html" title="class in org.biojava.nbio.core.sequence.io" target="classFrame">FastaWriter</a></li>
<li><a href="org/biojava/nbio/core/sequence/io/FastaWriterHelper.html" title="class in org.biojava.nbio.core.sequence.io" target="classFrame">FastaWriterHelper</a></li>
<li><a href="org/biojava/nbio/sequencing/io/fastq/Fastq.html" title="class in org.biojava.nbio.sequencing.io.fastq" target="classFrame">Fastq</a></li>
<li><a href="org/biojava/nbio/sequencing/io/fastq/FastqBuilder.html" title="class in org.biojava.nbio.sequencing.io.fastq" target="classFrame">FastqBuilder</a></li>
<li><a href="org/biojava/nbio/sequencing/io/fastq/FastqReader.html" title="interface in org.biojava.nbio.sequencing.io.fastq" target="classFrame"><i>FastqReader</i></a></li>
<li><a href="org/biojava/nbio/sequencing/io/fastq/FastqTools.html" title="class in org.biojava.nbio.sequencing.io.fastq" target="classFrame">FastqTools</a></li>
<li><a href="org/biojava/nbio/sequencing/io/fastq/FastqVariant.html" title="enum in org.biojava.nbio.sequencing.io.fastq" target="classFrame">FastqVariant</a></li>
<li><a href="org/biojava/nbio/sequencing/io/fastq/FastqWriter.html" title="interface in org.biojava.nbio.sequencing.io.fastq" target="classFrame"><i>FastqWriter</i></a></li>
<li><a href="org/biojava/nbio/structure/align/fatcat/FatCat.html" title="class in org.biojava.nbio.structure.align.fatcat" target="classFrame">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" target="classFrame">FatCatAligner</a></li>
<li><a href="org/biojava/nbio/structure/align/fatcat/FatCatFlexible.html" title="class in org.biojava.nbio.structure.align.fatcat" target="classFrame">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" target="classFrame">FatCatParameters</a></li>
<li><a href="org/biojava/nbio/structure/align/fatcat/FatCatRigid.html" title="class in org.biojava.nbio.structure.align.fatcat" target="classFrame">FatCatRigid</a></li>
<li><a href="org/biojava/nbio/structure/align/fatcat/FatCatUserArgumentProcessor.html" title="class in org.biojava.nbio.structure.align.fatcat" target="classFrame">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" target="classFrame">FCAlignHelper</a></li>
<li><a href="org/biojava/nbio/genome/parsers/gff/Feature.html" title="class in org.biojava.nbio.genome.parsers.gff" target="classFrame">Feature</a></li>
<li><a href="org/biojava/nbio/core/sequence/features/FeatureDbReferenceInfo.html" title="class in org.biojava.nbio.core.sequence.features" target="classFrame">FeatureDbReferenceInfo</a></li>
<li><a href="org/biojava/nbio/genome/parsers/gff/FeatureHelper.html" title="class in org.biojava.nbio.genome.parsers.gff" target="classFrame">FeatureHelper</a></li>
<li><a href="org/biojava/nbio/genome/parsers/gff/FeatureI.html" title="interface in org.biojava.nbio.genome.parsers.gff" target="classFrame"><i>FeatureI</i></a></li>
<li><a href="org/biojava/nbio/core/sequence/features/FeatureInterface.html" title="interface in org.biojava.nbio.core.sequence.features" target="classFrame"><i>FeatureInterface</i></a></li>
<li><a href="org/biojava/nbio/genome/parsers/gff/FeatureList.html" title="class in org.biojava.nbio.genome.parsers.gff" target="classFrame">FeatureList</a></li>
<li><a href="org/biojava/nbio/core/sequence/features/FeatureRetriever.html" title="interface in org.biojava.nbio.core.sequence.features" target="classFrame"><i>FeatureRetriever</i></a></li>
<li><a href="org/biojava/nbio/core/sequence/features/FeaturesKeyWordInterface.html" title="interface in org.biojava.nbio.core.sequence.features" target="classFrame"><i>FeaturesKeyWordInterface</i></a></li>
<li><a href="org/biojava/nbio/structure/io/FileConvert.html" title="class in org.biojava.nbio.structure.io" target="classFrame">FileConvert</a></li>
<li><a href="org/biojava/nbio/structure/io/util/FileDownloadUtils.html" title="class in org.biojava.nbio.structure.io.util" target="classFrame">FileDownloadUtils</a></li>
<li><a href="org/biojava/nbio/structure/io/FileParsingParameters.html" title="class in org.biojava.nbio.structure.io" target="classFrame">FileParsingParameters</a></li>
<li><a href="org/biojava/nbio/core/sequence/io/FileProxyDNASequenceCreator.html" title="class in org.biojava.nbio.core.sequence.io" target="classFrame">FileProxyDNASequenceCreator</a></li>
<li><a href="org/biojava/nbio/core/sequence/io/FileProxyProteinSequenceCreator.html" title="class in org.biojava.nbio.core.sequence.io" target="classFrame">FileProxyProteinSequenceCreator</a></li>
<li><a href="org/biojava/nbio/core/util/FlatFileCache.html" title="class in org.biojava.nbio.core.util" target="classFrame">FlatFileCache</a></li>
<li><a href="org/biojava/nbio/phylo/ForesterWrapper.html" title="class in org.biojava.nbio.phylo" target="classFrame">ForesterWrapper</a></li>
<li><a href="org/biojava/nbio/core/sequence/storage/FourBitSequenceReader.html" title="class in org.biojava.nbio.core.sequence.storage" target="classFrame">FourBitSequenceReader</a></li>
<li><a href="org/biojava/nbio/core/sequence/storage/FourBitSequenceReader.FourBitArrayWorker.html" title="class in org.biojava.nbio.core.sequence.storage" target="classFrame">FourBitSequenceReader.FourBitArrayWorker</a></li>
<li><a href="org/biojava/nbio/alignment/FractionalIdentityInProfileScorer.html" title="class in org.biojava.nbio.alignment" target="classFrame">FractionalIdentityInProfileScorer</a></li>
<li><a href="org/biojava/nbio/alignment/FractionalIdentityScorer.html" title="class in org.biojava.nbio.alignment" target="classFrame">FractionalIdentityScorer</a></li>
<li><a href="org/biojava/nbio/alignment/FractionalSimilarityInProfileScorer.html" title="class in org.biojava.nbio.alignment" target="classFrame">FractionalSimilarityInProfileScorer</a></li>
<li><a href="org/biojava/nbio/alignment/FractionalSimilarityScorer.html" title="class in org.biojava.nbio.alignment" target="classFrame">FractionalSimilarityScorer</a></li>
<li><a href="org/biojava/nbio/structure/align/pairwise/FragmentJoiner.html" title="class in org.biojava.nbio.structure.align.pairwise" target="classFrame">FragmentJoiner</a></li>
<li><a href="org/biojava/nbio/structure/align/pairwise/FragmentPair.html" title="class in org.biojava.nbio.structure.align.pairwise" target="classFrame">FragmentPair</a></li>
<li><a href="org/biojava/nbio/core/sequence/transcription/Frame.html" title="enum in org.biojava.nbio.core.sequence.transcription" target="classFrame">Frame</a></li>
<li><a href="org/biojava/nbio/core/sequence/location/FuzzyPoint.html" title="class in org.biojava.nbio.core.sequence.location" target="classFrame">FuzzyPoint</a></li>
<li><a href="org/biojava/nbio/structure/align/helper/GapArray.html" title="class in org.biojava.nbio.structure.align.helper" target="classFrame">GapArray</a></li>
<li><a href="org/biojava/nbio/alignment/template/GapPenalty.html" title="interface in org.biojava.nbio.alignment.template" target="classFrame"><i>GapPenalty</i></a></li>
<li><a href="org/biojava/nbio/alignment/template/GapPenalty.Type.html" title="enum in org.biojava.nbio.alignment.template" target="classFrame">GapPenalty.Type</a></li>
<li><a href="org/biojava/nbio/genome/parsers/gff/GCStats.html" title="class in org.biojava.nbio.genome.parsers.gff" target="classFrame">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" target="classFrame"><i>GenbankHeaderFormatInterface</i></a></li>
<li><a href="org/biojava/nbio/core/sequence/loader/GenbankProxySequenceReader.html" title="class in org.biojava.nbio.core.sequence.loader" target="classFrame">GenbankProxySequenceReader</a></li>
<li><a href="org/biojava/nbio/core/sequence/io/GenbankReader.html" title="class in org.biojava.nbio.core.sequence.io" target="classFrame">GenbankReader</a></li>
<li><a href="org/biojava/nbio/core/sequence/io/GenbankReaderHelper.html" title="class in org.biojava.nbio.core.sequence.io" target="classFrame">GenbankReaderHelper</a></li>
<li><a href="org/biojava/nbio/core/sequence/io/GenbankSequenceParser.html" title="class in org.biojava.nbio.core.sequence.io" target="classFrame">GenbankSequenceParser</a></li>
<li><a href="org/biojava/nbio/core/sequence/io/GenbankWriter.html" title="class in org.biojava.nbio.core.sequence.io" target="classFrame">GenbankWriter</a></li>
<li><a href="org/biojava/nbio/core/sequence/io/GenbankWriterHelper.html" title="class in org.biojava.nbio.core.sequence.io" target="classFrame">GenbankWriterHelper</a></li>
<li><a href="org/biojava/nbio/genome/parsers/genename/GeneChromosomePosition.html" title="class in org.biojava.nbio.genome.parsers.genename" target="classFrame">GeneChromosomePosition</a></li>
<li><a href="org/biojava/nbio/genome/parsers/genename/GeneChromosomePositionParser.html" title="class in org.biojava.nbio.genome.parsers.genename" target="classFrame">GeneChromosomePositionParser</a></li>
<li><a href="org/biojava/nbio/genome/GeneFeatureHelper.html" title="class in org.biojava.nbio.genome" target="classFrame">GeneFeatureHelper</a></li>
<li><a href="org/biojava/nbio/genome/parsers/gff/GeneIDGFF2Reader.html" title="class in org.biojava.nbio.genome.parsers.gff" target="classFrame">GeneIDGFF2Reader</a></li>
<li><a href="org/biojava/nbio/genome/parsers/geneid/GeneIDXMLReader.html" title="class in org.biojava.nbio.genome.parsers.geneid" target="classFrame">GeneIDXMLReader</a></li>
<li><a href="org/biojava/nbio/genome/parsers/gff/GeneMarkGTFReader.html" title="class in org.biojava.nbio.genome.parsers.gff" target="classFrame">GeneMarkGTFReader</a></li>
<li><a href="org/biojava/nbio/genome/parsers/genename/GeneName.html" title="class in org.biojava.nbio.genome.parsers.genename" target="classFrame">GeneName</a></li>
<li><a href="org/biojava/nbio/genome/parsers/genename/GeneNamesParser.html" title="class in org.biojava.nbio.genome.parsers.genename" target="classFrame">GeneNamesParser</a></li>
<li><a href="org/biojava/nbio/core/sequence/io/GenericFastaHeaderFormat.html" title="class in org.biojava.nbio.core.sequence.io" target="classFrame">GenericFastaHeaderFormat</a></li>
<li><a href="org/biojava/nbio/core/sequence/io/GenericFastaHeaderParser.html" title="class in org.biojava.nbio.core.sequence.io" target="classFrame">GenericFastaHeaderParser</a></li>
<li><a href="org/biojava/nbio/core/sequence/io/GenericGenbankHeaderFormat.html" title="class in org.biojava.nbio.core.sequence.io" target="classFrame">GenericGenbankHeaderFormat</a></li>
<li><a href="org/biojava/nbio/core/sequence/io/GenericGenbankHeaderParser.html" title="class in org.biojava.nbio.core.sequence.io" target="classFrame">GenericGenbankHeaderParser</a></li>
<li><a href="org/biojava/nbio/core/sequence/io/GenericInsdcHeaderFormat.html" title="class in org.biojava.nbio.core.sequence.io" target="classFrame">GenericInsdcHeaderFormat</a></li>
<li><a href="org/biojava/nbio/core/sequence/GeneSequence.html" title="class in org.biojava.nbio.core.sequence" target="classFrame">GeneSequence</a></li>
<li><a href="org/biojava/nbio/structure/domain/pdp/GetDistanceMatrix.html" title="class in org.biojava.nbio.structure.domain.pdp" target="classFrame">GetDistanceMatrix</a></li>
<li><a href="org/biojava/nbio/structure/rcsb/GetRepresentatives.html" title="class in org.biojava.nbio.structure.rcsb" target="classFrame">GetRepresentatives</a></li>
<li><a href="org/biojava/nbio/genome/homology/GFF3FromUniprotBlastHits.html" title="class in org.biojava.nbio.genome.homology" target="classFrame">GFF3FromUniprotBlastHits</a></li>
<li><a href="org/biojava/nbio/genome/parsers/gff/GFF3Reader.html" title="class in org.biojava.nbio.genome.parsers.gff" target="classFrame">GFF3Reader</a></li>
<li><a href="org/biojava/nbio/genome/parsers/gff/GFF3Writer.html" title="class in org.biojava.nbio.genome.parsers.gff" target="classFrame">GFF3Writer</a></li>
<li><a href="org/biojava/nbio/ontology/io/GOParser.html" title="class in org.biojava.nbio.ontology.io" target="classFrame">GOParser</a></li>
<li><a href="org/biojava/nbio/structure/align/pairwise/Gotoh.html" title="class in org.biojava.nbio.structure.align.pairwise" target="classFrame">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" target="classFrame">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" target="classFrame">GradientPanel</a></li>
<li><a href="org/biojava/nbio/structure/symmetry/internal/GraphComponentOrderDetector.html" title="class in org.biojava.nbio.structure.symmetry.internal" target="classFrame">GraphComponentOrderDetector</a></li>
<li><a href="org/biojava/nbio/structure/symmetry/internal/GraphComponentRefiner.html" title="class in org.biojava.nbio.structure.symmetry.internal" target="classFrame">GraphComponentRefiner</a></li>
<li><a href="org/biojava/nbio/structure/contact/Grid.html" title="class in org.biojava.nbio.structure.contact" target="classFrame">Grid</a></li>
<li><a href="org/biojava/nbio/structure/contact/GridCell.html" title="class in org.biojava.nbio.structure.contact" target="classFrame">GridCell</a></li>
<li><a href="org/biojava/nbio/structure/Group.html" title="interface in org.biojava.nbio.structure" target="classFrame"><i>Group</i></a></li>
<li><a href="org/biojava/nbio/structure/asa/GroupAsa.html" title="class in org.biojava.nbio.structure.asa" target="classFrame">GroupAsa</a></li>
<li><a href="org/biojava/nbio/structure/contact/GroupContact.html" title="class in org.biojava.nbio.structure.contact" target="classFrame">GroupContact</a></li>
<li><a href="org/biojava/nbio/structure/contact/GroupContactSet.html" title="class in org.biojava.nbio.structure.contact" target="classFrame">GroupContactSet</a></li>
<li><a href="org/biojava/nbio/structure/GroupIterator.html" title="class in org.biojava.nbio.structure" target="classFrame">GroupIterator</a></li>
<li><a href="org/biojava/nbio/survival/kaplanmeier/figure/GroupResults.html" title="class in org.biojava.nbio.survival.kaplanmeier.figure" target="classFrame">GroupResults</a></li>
<li><a href="org/biojava/nbio/structure/io/GroupToSDF.html" title="class in org.biojava.nbio.structure.io" target="classFrame">GroupToSDF</a></li>
<li><a href="org/biojava/nbio/structure/GroupType.html" title="enum in org.biojava.nbio.structure" target="classFrame">GroupType</a></li>
<li><a href="org/biojava/nbio/alignment/routines/GuanUberbacher.html" title="class in org.biojava.nbio.alignment.routines" target="classFrame">GuanUberbacher</a></li>
<li><a href="org/biojava/nbio/structure/align/gui/GUIAlignmentProgressListener.html" title="class in org.biojava.nbio.structure.align.gui" target="classFrame">GUIAlignmentProgressListener</a></li>
<li><a href="org/biojava/nbio/alignment/GuideTree.html" title="class in org.biojava.nbio.alignment" target="classFrame">GuideTree</a></li>
<li><a href="org/biojava/nbio/alignment/template/GuideTreeNode.html" title="interface in org.biojava.nbio.alignment.template" target="classFrame"><i>GuideTreeNode</i></a></li>
<li><a href="org/biojava/nbio/structure/align/gui/GUIFarmJobRunnable.html" title="class in org.biojava.nbio.structure.align.gui" target="classFrame">GUIFarmJobRunnable</a></li>
<li><a href="org/biojava/nbio/structure/align/ce/GuiWrapper.html" title="class in org.biojava.nbio.structure.align.ce" target="classFrame">GuiWrapper</a></li>
<li><a href="org/biojava/nbio/core/util/Hashcoder.html" title="class in org.biojava.nbio.core.util" target="classFrame">Hashcoder</a></li>
<li><a href="org/biojava/nbio/structure/align/xml/HasResultXMLConverter.html" title="class in org.biojava.nbio.structure.align.xml" target="classFrame">HasResultXMLConverter</a></li>
<li><a href="org/biojava/nbio/structure/secstruc/HBond.html" title="class in org.biojava.nbio.structure.secstruc" target="classFrame">HBond</a></li>
<li><a href="org/biojava/nbio/survival/data/HeaderInfo.html" title="class in org.biojava.nbio.survival.data" target="classFrame">HeaderInfo</a></li>
<li><a href="org/biojava/nbio/structure/symmetry/core/HelicalRepeatUnit.html" title="class in org.biojava.nbio.structure.symmetry.core" target="classFrame">HelicalRepeatUnit</a></li>
<li><a href="org/biojava/nbio/structure/symmetry/core/Helix.html" title="class in org.biojava.nbio.structure.symmetry.core" target="classFrame">Helix</a></li>
<li><a href="org/biojava/nbio/structure/symmetry/core/HelixAxisAligner.html" title="class in org.biojava.nbio.structure.symmetry.core" target="classFrame">HelixAxisAligner</a></li>
<li><a href="org/biojava/nbio/structure/symmetry/core/HelixExtender.html" title="class in org.biojava.nbio.structure.symmetry.core" target="classFrame">HelixExtender</a></li>
<li><a href="org/biojava/nbio/structure/symmetry/core/HelixLayers.html" title="class in org.biojava.nbio.structure.symmetry.core" target="classFrame">HelixLayers</a></li>
<li><a href="org/biojava/nbio/structure/symmetry/core/HelixSolver.html" title="class in org.biojava.nbio.structure.symmetry.core" target="classFrame">HelixSolver</a></li>
<li><a href="org/biojava/nbio/structure/align/gui/HelpDialog.html" title="class in org.biojava.nbio.structure.align.gui" target="classFrame">HelpDialog</a></li>
<li><a href="org/biojava/nbio/structure/HetatomImpl.html" title="class in org.biojava.nbio.structure" target="classFrame">HetatomImpl</a></li>
<li><a href="org/biojava/nbio/structure/HetatomImpl.PerformanceBehavior.html" title="enum in org.biojava.nbio.structure" target="classFrame">HetatomImpl.PerformanceBehavior</a></li>
<li><a href="org/biojava/nbio/alignment/template/HierarchicalClusterer.html" title="interface in org.biojava.nbio.alignment.template" target="classFrame"><i>HierarchicalClusterer</i></a></li>
<li><a href="org/biojava/nbio/core/search/io/Hit.html" title="class in org.biojava.nbio.core.search.io" target="classFrame">Hit</a></li>
<li><a href="demo/HmmerDemo.html" title="class in demo" target="classFrame">HmmerDemo</a></li>
<li><a href="org/biojava/nbio/ws/hmmer/HmmerDomain.html" title="class in org.biojava.nbio.ws.hmmer" target="classFrame">HmmerDomain</a></li>
<li><a href="org/biojava/nbio/ws/hmmer/HmmerResult.html" title="class in org.biojava.nbio.ws.hmmer" target="classFrame">HmmerResult</a></li>
<li><a href="org/biojava/nbio/ws/hmmer/HmmerScan.html" title="interface in org.biojava.nbio.ws.hmmer" target="classFrame"><i>HmmerScan</i></a></li>
<li><a href="org/biojava/nbio/core/search/io/Hsp.html" title="class in org.biojava.nbio.core.search.io" target="classFrame">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" target="classFrame">HSVColorSpace</a></li>
<li><a href="org/biojava/nbio/structure/align/util/HTTPConnectionTools.html" title="class in org.biojava.nbio.structure.align.util" target="classFrame">HTTPConnectionTools</a></li>
<li><a href="org/biojava/nbio/structure/symmetry/geometry/IcosahedralSampler.html" title="class in org.biojava.nbio.structure.symmetry.geometry" target="classFrame">IcosahedralSampler</a></li>
<li><a href="org/biojava/nbio/structure/symmetry/geometry/Icosahedron.html" title="class in org.biojava.nbio.structure.symmetry.geometry" target="classFrame">Icosahedron</a></li>
<li><a href="org/biojava/nbio/structure/Identifier.html" title="class in org.biojava.nbio.structure" target="classFrame">Identifier</a></li>
<li><a href="org/biojava/nbio/structure/align/helper/IdxComparator.html" title="class in org.biojava.nbio.structure.align.helper" target="classFrame">IdxComparator</a></li>
<li><a href="org/biojava/nbio/sequencing/io/fastq/IlluminaFastqReader.html" title="class in org.biojava.nbio.sequencing.io.fastq" target="classFrame">IlluminaFastqReader</a></li>
<li><a href="org/biojava/nbio/sequencing/io/fastq/IlluminaFastqWriter.html" title="class in org.biojava.nbio.sequencing.io.fastq" target="classFrame">IlluminaFastqWriter</a></li>
<li><a href="org/biojava/nbio/structure/align/helper/IndexPair.html" title="class in org.biojava.nbio.structure.align.helper" target="classFrame">IndexPair</a></li>
<li><a href="org/biojava/nbio/core/util/InputStreamProvider.html" title="class in org.biojava.nbio.core.util" target="classFrame">InputStreamProvider</a></li>
<li><a href="org/biojava/nbio/core/sequence/location/InsdcLocations.html" title="class in org.biojava.nbio.core.sequence.location" target="classFrame">InsdcLocations</a></li>
<li><a href="org/biojava/nbio/core/sequence/location/InsdcLocations.BondLocation.html" title="class in org.biojava.nbio.core.sequence.location" target="classFrame">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" target="classFrame">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" target="classFrame">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" target="classFrame">InsdcLocations.OrderLocation</a></li>
<li><a href="org/biojava/nbio/core/sequence/location/InsdcParser.html" title="class in org.biojava.nbio.core.sequence.location" target="classFrame">InsdcParser</a></li>
<li><a href="org/biojava/nbio/ontology/IntegerOntology.html" title="class in org.biojava.nbio.ontology" target="classFrame">IntegerOntology</a></li>
<li><a href="org/biojava/nbio/core/sequence/IntronSequence.html" title="class in org.biojava.nbio.core.sequence" target="classFrame">IntronSequence</a></li>
<li><a href="org/biojava/nbio/ontology/InvalidTermException.html" title="class in org.biojava.nbio.ontology" target="classFrame">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" target="classFrame">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" target="classFrame"><i>IOUtils.ReaderProcessor</i></a></li>
<li><a href="org/biojava/nbio/aaproperties/IPeptideProperties.html" title="interface in org.biojava.nbio.aaproperties" target="classFrame"><i>IPeptideProperties</i></a></li>
<li><a href="org/biojava/nbio/aaproperties/profeat/IProfeatProperties.html" title="interface in org.biojava.nbio.aaproperties.profeat" target="classFrame"><i>IProfeatProperties</i></a></li>
<li><a href="org/biojava/nbio/aaproperties/profeat/IProfeatProperties.ATTRIBUTE.html" title="enum in org.biojava.nbio.aaproperties.profeat" target="classFrame">IProfeatProperties.ATTRIBUTE</a></li>
<li><a href="org/biojava/nbio/aaproperties/profeat/IProfeatProperties.DISTRIBUTION.html" title="enum in org.biojava.nbio.aaproperties.profeat" target="classFrame">IProfeatProperties.DISTRIBUTION</a></li>
<li><a href="org/biojava/nbio/aaproperties/profeat/IProfeatProperties.GROUPING.html" title="enum in org.biojava.nbio.aaproperties.profeat" target="classFrame">IProfeatProperties.GROUPING</a></li>
<li><a href="org/biojava/nbio/aaproperties/profeat/IProfeatProperties.TRANSITION.html" title="enum in org.biojava.nbio.aaproperties.profeat" target="classFrame">IProfeatProperties.TRANSITION</a></li>
<li><a href="org/biojava/nbio/aaproperties/xml/Isotope.html" title="class in org.biojava.nbio.aaproperties.xml" target="classFrame">Isotope</a></li>
<li><a href="org/biojava/nbio/core/sequence/io/IUPACParser.html" title="class in org.biojava.nbio.core.sequence.io" target="classFrame">IUPACParser</a></li>
<li><a href="org/biojava/nbio/core/sequence/io/IUPACParser.IUPACTable.html" title="class in org.biojava.nbio.core.sequence.io" target="classFrame">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" target="classFrame">JAutoSuggest</a></li>
<li><a href="org/biojava/nbio/structure/align/client/JFatCatClient.html" title="class in org.biojava.nbio.structure.align.client" target="classFrame">JFatCatClient</a></li>
<li><a href="org/biojava/nbio/structure/gui/JMatrixPanel.html" title="class in org.biojava.nbio.structure.gui" target="classFrame">JMatrixPanel</a></li>
<li><a href="org/biojava/nbio/structure/gui/events/JmolAlignedPositionListener.html" title="class in org.biojava.nbio.structure.gui.events" target="classFrame">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" target="classFrame">JmolPanel</a></li>
<li><a href="org/biojava/nbio/structure/symmetry/jmolScript/JmolSymmetryScriptGenerator.html" title="class in org.biojava.nbio.structure.symmetry.jmolScript" target="classFrame">JmolSymmetryScriptGenerator</a></li>
<li><a href="org/biojava/nbio/structure/symmetry/jmolScript/JmolSymmetryScriptGeneratorC1.html" title="class in org.biojava.nbio.structure.symmetry.jmolScript" target="classFrame">JmolSymmetryScriptGeneratorC1</a></li>
<li><a href="org/biojava/nbio/structure/symmetry/jmolScript/JmolSymmetryScriptGeneratorCn.html" title="class in org.biojava.nbio.structure.symmetry.jmolScript" target="classFrame">JmolSymmetryScriptGeneratorCn</a></li>
<li><a href="org/biojava/nbio/structure/symmetry/jmolScript/JmolSymmetryScriptGeneratorDn.html" title="class in org.biojava.nbio.structure.symmetry.jmolScript" target="classFrame">JmolSymmetryScriptGeneratorDn</a></li>
<li><a href="org/biojava/nbio/structure/symmetry/jmolScript/JmolSymmetryScriptGeneratorH.html" title="class in org.biojava.nbio.structure.symmetry.jmolScript" target="classFrame">JmolSymmetryScriptGeneratorH</a></li>
<li><a href="org/biojava/nbio/structure/symmetry/jmolScript/JmolSymmetryScriptGeneratorI.html" title="class in org.biojava.nbio.structure.symmetry.jmolScript" target="classFrame">JmolSymmetryScriptGeneratorI</a></li>
<li><a href="org/biojava/nbio/structure/symmetry/jmolScript/JmolSymmetryScriptGeneratorO.html" title="class in org.biojava.nbio.structure.symmetry.jmolScript" target="classFrame">JmolSymmetryScriptGeneratorO</a></li>
<li><a href="org/biojava/nbio/structure/symmetry/jmolScript/JmolSymmetryScriptGeneratorPointGroup.html" title="class in org.biojava.nbio.structure.symmetry.jmolScript" target="classFrame">JmolSymmetryScriptGeneratorPointGroup</a></li>
<li><a href="org/biojava/nbio/structure/symmetry/jmolScript/JmolSymmetryScriptGeneratorT.html" title="class in org.biojava.nbio.structure.symmetry.jmolScript" target="classFrame">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" target="classFrame">JmolTools</a></li>
<li><a href="org/biojava/nbio/structure/gui/JmolViewerImpl.html" title="class in org.biojava.nbio.structure.gui" target="classFrame">JmolViewerImpl</a></li>
<li><a href="org/biojava/nbio/structure/align/webstart/JNLPProxy.html" title="class in org.biojava.nbio.structure.align.webstart" target="classFrame">JNLPProxy</a></li>
<li><a href="org/biojava/nbio/structure/align/client/JobKillException.html" title="class in org.biojava.nbio.structure.align.client" target="classFrame">JobKillException</a></li>
<li><a href="org/biojava/nbio/core/sequence/storage/JoiningSequenceReader.html" title="class in org.biojava.nbio.core.sequence.storage" target="classFrame">JoiningSequenceReader</a></li>
<li><a href="org/biojava/nbio/structure/align/helper/JointFragments.html" title="class in org.biojava.nbio.structure.align.helper" target="classFrame">JointFragments</a></li>
<li><a href="org/biojava/nbio/structure/JournalArticle.html" title="class in org.biojava.nbio.structure" target="classFrame">JournalArticle</a></li>
<li><a href="org/biojava/nbio/structure/align/gui/JPrintPanel.html" title="class in org.biojava.nbio.structure.align.gui" target="classFrame">JPrintPanel</a></li>
<li><a href="org/biojava/nbio/ronn/Jronn.html" title="class in org.biojava.nbio.ronn" target="classFrame">Jronn</a></li>
<li><a href="org/biojava/nbio/ronn/Jronn.Range.html" title="class in org.biojava.nbio.ronn" target="classFrame">Jronn.Range</a></li>
<li><a href="org/biojava/nbio/survival/kaplanmeier/figure/KaplanMeierFigure.html" title="class in org.biojava.nbio.survival.kaplanmeier.figure" target="classFrame">KaplanMeierFigure</a></li>
<li><a href="org/biojava/nbio/ontology/utils/KeyedWeakReference.html" title="class in org.biojava.nbio.ontology.utils" target="classFrame">KeyedWeakReference</a></li>
<li><a href="org/biojava/nbio/survival/kaplanmeier/figure/KMFigureInfo.html" title="class in org.biojava.nbio.survival.kaplanmeier.figure" target="classFrame">KMFigureInfo</a></li>
<li><a href="org/biojava/nbio/structure/secstruc/Ladder.html" title="class in org.biojava.nbio.structure.secstruc" target="classFrame">Ladder</a></li>
<li><a href="org/biojava/nbio/core/sequence/template/LightweightProfile.html" title="interface in org.biojava.nbio.core.sequence.template" target="classFrame"><i>LightweightProfile</i></a></li>
<li><a href="org/biojava/nbio/core/sequence/template/LightweightProfile.StringFormat.html" title="enum in org.biojava.nbio.core.sequence.template" target="classFrame">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" target="classFrame">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" target="classFrame">LinearColorInterpolator.InterpolationDirection</a></li>
<li><a href="org/biojava/nbio/structure/scop/server/ListStringWrapper.html" title="class in org.biojava.nbio.structure.scop.server" target="classFrame">ListStringWrapper</a></li>
<li><a href="org/biojava/nbio/structure/io/LocalPDBDirectory.html" title="class in org.biojava.nbio.structure.io" target="classFrame">LocalPDBDirectory</a></li>
<li><a href="org/biojava/nbio/structure/io/LocalPDBDirectory.FetchBehavior.html" title="enum in org.biojava.nbio.structure.io" target="classFrame">LocalPDBDirectory.FetchBehavior</a></li>
<li><a href="org/biojava/nbio/structure/io/LocalPDBDirectory.ObsoleteBehavior.html" title="enum in org.biojava.nbio.structure.io" target="classFrame">LocalPDBDirectory.ObsoleteBehavior</a></li>
<li><a href="org/biojava/nbio/structure/domain/LocalProteinDomainParser.html" title="class in org.biojava.nbio.structure.domain" target="classFrame">LocalProteinDomainParser</a></li>
<li><a href="org/biojava/nbio/structure/scop/LocalScopDatabase.html" title="interface in org.biojava.nbio.structure.scop" target="classFrame"><i>LocalScopDatabase</i></a></li>
<li><a href="org/biojava/nbio/core/sequence/location/template/Location.html" title="interface in org.biojava.nbio.core.sequence.location.template" target="classFrame"><i>Location</i></a></li>
<li><a href="org/biojava/nbio/genome/parsers/gff/Location.html" title="class in org.biojava.nbio.genome.parsers.gff" target="classFrame">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" target="classFrame">Location.Tools</a></li>
<li><a href="org/biojava/nbio/core/sequence/location/LocationHelper.html" title="class in org.biojava.nbio.core.sequence.location" target="classFrame">LocationHelper</a></li>
<li><a href="org/biojava/nbio/genome/parsers/gff/LocIterator.html" title="class in org.biojava.nbio.genome.parsers.gff" target="classFrame">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" target="classFrame">LogColorMapper</a></li>
<li><a href="org/biojava/nbio/structure/jama/LUDecomposition.html" title="class in org.biojava.nbio.structure.jama" target="classFrame">LUDecomposition</a></li>
<li><a href="org/biojava/nbio/ws/alignment/qblast/MapToStringTransformer.html" title="class in org.biojava.nbio.ws.alignment.qblast" target="classFrame">MapToStringTransformer</a></li>
<li><a href="org/biojava/nbio/structure/jama/Maths.html" title="class in org.biojava.nbio.structure.jama" target="classFrame">Maths</a></li>
<li><a href="org/biojava/nbio/structure/jama/Matrix.html" title="class in org.biojava.nbio.structure.jama" target="classFrame">Matrix</a></li>
<li><a href="org/biojava/nbio/survival/cox/matrix/Matrix.html" title="class in org.biojava.nbio.survival.cox.matrix" target="classFrame">Matrix</a></li>
<li><a href="org/biojava/nbio/alignment/template/MatrixAligner.html" title="interface in org.biojava.nbio.alignment.template" target="classFrame"><i>MatrixAligner</i></a></li>
<li><a href="org/biojava/nbio/structure/align/ce/MatrixListener.html" title="interface in org.biojava.nbio.structure.align.ce" target="classFrame"><i>MatrixListener</i></a></li>
<li><a href="org/biojava/nbio/survival/cox/comparators/MeanModelComparator.html" title="class in org.biojava.nbio.survival.cox.comparators" target="classFrame">MeanModelComparator</a></li>
<li><a href="org/biojava/nbio/survival/kaplanmeier/metadata/MeanQuantizer.html" title="class in org.biojava.nbio.survival.kaplanmeier.metadata" target="classFrame">MeanQuantizer</a></li>
<li><a href="org/biojava/nbio/structure/align/gui/MemoryMonitor.html" title="class in org.biojava.nbio.structure.align.gui" target="classFrame">MemoryMonitor</a></li>
<li><a href="org/biojava/nbio/structure/align/gui/MenuCreator.html" title="class in org.biojava.nbio.structure.align.gui" target="classFrame">MenuCreator</a></li>
<li><a href="org/biojava/nbio/structure/gui/util/MenuCreator.html" title="class in org.biojava.nbio.structure.gui.util" target="classFrame">MenuCreator</a></li>
<li><a href="org/biojava/nbio/structure/align/gui/MenuCreator.DotPlotListener.html" title="class in org.biojava.nbio.structure.align.gui" target="classFrame">MenuCreator.DotPlotListener</a></li>
<li><a href="org/biojava/nbio/core/exceptions/Messages.html" title="class in org.biojava.nbio.core.exceptions" target="classFrame">Messages</a></li>
<li><a href="org/biojava/nbio/survival/kaplanmeier/metadata/MetaDataInfo.html" title="class in org.biojava.nbio.survival.kaplanmeier.metadata" target="classFrame">MetaDataInfo</a></li>
<li><a href="org/biojava/nbio/structure/quaternary/io/MmCifBiolAssemblyProvider.html" title="class in org.biojava.nbio.structure.quaternary.io" target="classFrame">MmCifBiolAssemblyProvider</a></li>
<li><a href="org/biojava/nbio/structure/io/mmcif/MMcifConsumer.html" title="interface in org.biojava.nbio.structure.io.mmcif" target="classFrame"><i>MMcifConsumer</i></a></li>
<li><a href="org/biojava/nbio/structure/io/MMCIFFileReader.html" title="class in org.biojava.nbio.structure.io" target="classFrame">MMCIFFileReader</a></li>
<li><a href="org/biojava/nbio/structure/io/mmcif/MMCIFFileTools.html" title="class in org.biojava.nbio.structure.io.mmcif" target="classFrame">MMCIFFileTools</a></li>
<li><a href="org/biojava/nbio/structure/io/mmcif/MMcifParser.html" title="interface in org.biojava.nbio.structure.io.mmcif" target="classFrame"><i>MMcifParser</i></a></li>
<li><a href="org/biojava/nbio/structure/quaternary/io/MmCifPDBBiolAssemblyProvider.html" title="class in org.biojava.nbio.structure.quaternary.io" target="classFrame">MmCifPDBBiolAssemblyProvider</a></li>
<li><a href="org/biojava/nbio/structure/validation/ModelledSubgroup.html" title="class in org.biojava.nbio.structure.validation" target="classFrame">ModelledSubgroup</a></li>
<li><a href="org/biojava/nbio/ronn/ModelLoader.html" title="class in org.biojava.nbio.ronn" target="classFrame">ModelLoader</a></li>
<li><a href="org/biojava/nbio/ronn/ModelLoader.Model.html" title="class in org.biojava.nbio.ronn" target="classFrame">ModelLoader.Model</a></li>
<li><a href="org/biojava/nbio/ronn/ModelLoader.Threshold.html" title="class in org.biojava.nbio.ronn" target="classFrame">ModelLoader.Threshold</a></li>
<li><a href="org/biojava/nbio/protmod/ModificationCategory.html" title="enum in org.biojava.nbio.protmod" target="classFrame">ModificationCategory</a></li>
<li><a href="org/biojava/nbio/protmod/ModificationCondition.html" title="interface in org.biojava.nbio.protmod" target="classFrame"><i>ModificationCondition</i></a></li>
<li><a href="org/biojava/nbio/protmod/ModificationConditionImpl.html" title="class in org.biojava.nbio.protmod" target="classFrame">ModificationConditionImpl</a></li>
<li><a href="org/biojava/nbio/protmod/ModificationLinkage.html" title="class in org.biojava.nbio.protmod" target="classFrame">ModificationLinkage</a></li>
<li><a href="org/biojava/nbio/protmod/ModificationOccurrenceType.html" title="enum in org.biojava.nbio.protmod" target="classFrame">ModificationOccurrenceType</a></li>
<li><a href="org/biojava/nbio/aaproperties/xml/ModifiedAminoAcidCompoundSet.html" title="class in org.biojava.nbio.aaproperties.xml" target="classFrame">ModifiedAminoAcidCompoundSet</a></li>
<li><a href="org/biojava/nbio/protmod/structure/ModifiedCompound.html" title="interface in org.biojava.nbio.protmod.structure" target="classFrame"><i>ModifiedCompound</i></a></li>
<li><a href="org/biojava/nbio/protmod/structure/ModifiedCompoundImpl.html" title="class in org.biojava.nbio.protmod.structure" target="classFrame">ModifiedCompoundImpl</a></li>
<li><a href="org/biojava/nbio/protmod/io/ModifiedCompoundXMLConverter.html" title="class in org.biojava.nbio.protmod.io" target="classFrame">ModifiedCompoundXMLConverter</a></li>
<li><a href="org/biojava/nbio/structure/validation/MogAngleOutlier.html" title="class in org.biojava.nbio.structure.validation" target="classFrame">MogAngleOutlier</a></li>
<li><a href="org/biojava/nbio/structure/validation/MogBondOutlier.html" title="class in org.biojava.nbio.structure.validation" target="classFrame">MogBondOutlier</a></li>
<li><a href="org/biojava/nbio/structure/symmetry/geometry/MomentsOfInertia.html" title="class in org.biojava.nbio.structure.symmetry.geometry" target="classFrame">MomentsOfInertia</a></li>
<li><a href="org/biojava/nbio/structure/symmetry/geometry/MomentsOfInertia.SymmetryClass.html" title="enum in org.biojava.nbio.structure.symmetry.geometry" target="classFrame">MomentsOfInertia.SymmetryClass</a></li>
<li><a href="org/biojava/nbio/structure/align/multiple/MultipleAlignment.html" title="interface in org.biojava.nbio.structure.align.multiple" target="classFrame"><i>MultipleAlignment</i></a></li>
<li><a href="org/biojava/nbio/structure/align/gui/MultipleAlignmentCalc.html" title="class in org.biojava.nbio.structure.align.gui" target="classFrame">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" target="classFrame">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" target="classFrame">MultipleAlignmentDisplay</a></li>
<li><a href="org/biojava/nbio/structure/align/multiple/MultipleAlignmentEnsemble.html" title="interface in org.biojava.nbio.structure.align.multiple" target="classFrame"><i>MultipleAlignmentEnsemble</i></a></li>
<li><a href="org/biojava/nbio/structure/align/multiple/MultipleAlignmentEnsembleImpl.html" title="class in org.biojava.nbio.structure.align.multiple" target="classFrame">MultipleAlignmentEnsembleImpl</a></li>
<li><a href="org/biojava/nbio/structure/align/gui/MultipleAlignmentGUI.html" title="class in org.biojava.nbio.structure.align.gui" target="classFrame">MultipleAlignmentGUI</a></li>
<li><a href="org/biojava/nbio/structure/align/multiple/MultipleAlignmentImpl.html" title="class in org.biojava.nbio.structure.align.multiple" target="classFrame">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" target="classFrame">MultipleAlignmentJmol</a></li>
<li><a href="org/biojava/nbio/structure/align/gui/MultipleAlignmentJmolDisplay.html" title="class in org.biojava.nbio.structure.align.gui" target="classFrame">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" target="classFrame">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" target="classFrame">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" target="classFrame">MultipleAlignmentWriter</a></li>
<li><a href="org/biojava/nbio/structure/align/xml/MultipleAlignmentXMLConverter.html" title="class in org.biojava.nbio.structure.align.xml" target="classFrame">MultipleAlignmentXMLConverter</a></li>
<li><a href="org/biojava/nbio/structure/align/xml/MultipleAlignmentXMLParser.html" title="class in org.biojava.nbio.structure.align.xml" target="classFrame">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" target="classFrame">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" target="classFrame">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" target="classFrame">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" target="classFrame">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" target="classFrame">MultipleMcParameters</a></li>
<li><a href="org/biojava/nbio/core/sequence/MultipleSequenceAlignment.html" title="class in org.biojava.nbio.core.sequence" target="classFrame">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" target="classFrame">MultipleStatusDisplay</a></li>
<li><a href="org/biojava/nbio/structure/align/MultipleStructureAligner.html" title="interface in org.biojava.nbio.structure.align" target="classFrame"><i>MultipleStructureAligner</i></a></li>
<li><a href="org/biojava/nbio/structure/align/multiple/util/MultipleSuperimposer.html" title="interface in org.biojava.nbio.structure.align.multiple.util" target="classFrame"><i>MultipleSuperimposer</i></a></li>
<li><a href="org/biojava/nbio/structure/align/MultiThreadedDBSearch.html" title="class in org.biojava.nbio.structure.align" target="classFrame">MultiThreadedDBSearch</a></li>
<li><a href="org/biojava/nbio/core/alignment/template/MutableAlignedSequence.html" title="interface in org.biojava.nbio.core.alignment.template" target="classFrame"><i>MutableAlignedSequence</i></a></li>
<li><a href="org/biojava/nbio/core/alignment/template/MutableProfile.html" title="interface in org.biojava.nbio.core.alignment.template" target="classFrame"><i>MutableProfile</i></a></li>
<li><a href="org/biojava/nbio/core/alignment/template/MutableProfilePair.html" title="interface in org.biojava.nbio.core.alignment.template" target="classFrame"><i>MutableProfilePair</i></a></li>
<li><a href="org/biojava/nbio/core/alignment/template/MutableSequencePair.html" title="interface in org.biojava.nbio.core.alignment.template" target="classFrame"><i>MutableSequencePair</i></a></li>
<li><a href="org/biojava/nbio/structure/Mutator.html" title="class in org.biojava.nbio.structure" target="classFrame">Mutator</a></li>
<li><a href="org/biojava/nbio/structure/align/gui/MyAlignmentLoadListener.html" title="class in org.biojava.nbio.structure.align.gui" target="classFrame">MyAlignmentLoadListener</a></li>
<li><a href="org/biojava/nbio/structure/align/gui/MyDistMaxListener.html" title="class in org.biojava.nbio.structure.align.gui" target="classFrame">MyDistMaxListener</a></li>
<li><a href="org/biojava/nbio/structure/align/gui/MyExportListener.html" title="class in org.biojava.nbio.structure.align.gui" target="classFrame">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" target="classFrame">MyJmolStatusListener</a></li>
<li><a href="org/biojava/nbio/structure/align/gui/MyOpenPdbFileListener.html" title="class in org.biojava.nbio.structure.align.gui" target="classFrame">MyOpenPdbFileListener</a></li>
<li><a href="org/biojava/nbio/structure/align/gui/MySaveFileListener.html" title="class in org.biojava.nbio.structure.align.gui" target="classFrame">MySaveFileListener</a></li>
<li><a href="org/biojava/nbio/structure/align/gui/MyTableRowSorter.html" title="class in org.biojava.nbio.structure.align.gui" target="classFrame">MyTableRowSorter</a></li>
<li><a href="org/biojava/nbio/aaproperties/xml/MyValidationEventHandler.html" title="class in org.biojava.nbio.aaproperties.xml" target="classFrame">MyValidationEventHandler</a></li>
<li><a href="org/biojava/nbio/aaproperties/xml/Name2Count.html" title="class in org.biojava.nbio.aaproperties.xml" target="classFrame">Name2Count</a></li>
<li><a href="org/biojava/nbio/ws/alignment/qblast/NCBIQBlastAlignmentProperties.html" title="class in org.biojava.nbio.ws.alignment.qblast" target="classFrame">NCBIQBlastAlignmentProperties</a></li>
<li><a href="org/biojava/nbio/ws/alignment/qblast/NCBIQBlastOutputProperties.html" title="class in org.biojava.nbio.ws.alignment.qblast" target="classFrame">NCBIQBlastOutputProperties</a></li>
<li><a href="org/biojava/nbio/ws/alignment/qblast/NCBIQBlastService.html" title="class in org.biojava.nbio.ws.alignment.qblast" target="classFrame">NCBIQBlastService</a></li>
<li><a href="demo/NCBIQBlastServiceDemo.html" title="class in demo" target="classFrame">NCBIQBlastServiceDemo</a></li>
<li><a href="org/biojava/nbio/alignment/NeedlemanWunsch.html" title="class in org.biojava.nbio.alignment" target="classFrame">NeedlemanWunsch</a></li>
<li><a href="org/biojava/nbio/core/sequence/compound/NucleotideCompound.html" title="class in org.biojava.nbio.core.sequence.compound" target="classFrame">NucleotideCompound</a></li>
<li><a href="org/biojava/nbio/structure/NucleotideImpl.html" title="class in org.biojava.nbio.structure" target="classFrame">NucleotideImpl</a></li>
<li><a href="org/biojava/nbio/ronn/NullOutputStream.html" title="class in org.biojava.nbio.ronn" target="classFrame">NullOutputStream</a></li>
<li><a href="org/biojava/nbio/survival/kaplanmeier/figure/NumbersAtRiskPanel.html" title="class in org.biojava.nbio.survival.kaplanmeier.figure" target="classFrame">NumbersAtRiskPanel</a></li>
<li><a href="org/biojava/nbio/structure/validation/ObjectFactory.html" title="class in org.biojava.nbio.structure.validation" target="classFrame">ObjectFactory</a></li>
<li><a href="org/biojava/nbio/ontology/obo/OboFileEventListener.html" title="interface in org.biojava.nbio.ontology.obo" target="classFrame"><i>OboFileEventListener</i></a></li>
<li><a href="org/biojava/nbio/ontology/obo/OboFileHandler.html" title="class in org.biojava.nbio.ontology.obo" target="classFrame">OboFileHandler</a></li>
<li><a href="org/biojava/nbio/ontology/obo/OboFileParser.html" title="class in org.biojava.nbio.ontology.obo" target="classFrame">OboFileParser</a></li>
<li><a href="org/biojava/nbio/ontology/obo/OboFileParser.SOPair.html" title="class in org.biojava.nbio.ontology.obo" target="classFrame">OboFileParser.SOPair</a></li>
<li><a href="org/biojava/nbio/ontology/io/OboParser.html" title="class in org.biojava.nbio.ontology.io" target="classFrame">OboParser</a></li>
<li><a href="org/biojava/nbio/structure/symmetry/geometry/Octahedron.html" title="class in org.biojava.nbio.structure.symmetry.geometry" target="classFrame">Octahedron</a></li>
<li><a href="org/biojava/nbio/ontology/Ontology.html" title="interface in org.biojava.nbio.ontology" target="classFrame"><i>Ontology</i></a></li>
<li><a href="org/biojava/nbio/ontology/Ontology.Impl.html" title="class in org.biojava.nbio.ontology" target="classFrame">Ontology.Impl</a></li>
<li><a href="org/biojava/nbio/ontology/OntologyException.html" title="class in org.biojava.nbio.ontology" target="classFrame">OntologyException</a></li>
<li><a href="org/biojava/nbio/ontology/OntologyFactory.html" title="interface in org.biojava.nbio.ontology" target="classFrame"><i>OntologyFactory</i></a></li>
<li><a href="org/biojava/nbio/ontology/OntologyOps.html" title="interface in org.biojava.nbio.ontology" target="classFrame"><i>OntologyOps</i></a></li>
<li><a href="org/biojava/nbio/ontology/OntologyTerm.html" title="interface in org.biojava.nbio.ontology" target="classFrame"><i>OntologyTerm</i></a></li>
<li><a href="org/biojava/nbio/ontology/OntologyTerm.Impl.html" title="class in org.biojava.nbio.ontology" target="classFrame">OntologyTerm.Impl</a></li>
<li><a href="org/biojava/nbio/ontology/OntoTools.html" title="class in org.biojava.nbio.ontology" target="classFrame">OntoTools</a></li>
<li><a href="org/biojava/nbio/structure/quaternary/OperatorResolver.html" title="class in org.biojava.nbio.structure.quaternary" target="classFrame">OperatorResolver</a></li>
<li><a href="org/biojava/nbio/structure/align/ce/OptimalCECPMain.html" title="class in org.biojava.nbio.structure.align.ce" target="classFrame">OptimalCECPMain</a></li>
<li><a href="org/biojava/nbio/structure/align/ce/OptimalCECPParameters.html" title="class in org.biojava.nbio.structure.align.ce" target="classFrame">OptimalCECPParameters</a></li>
<li><a href="org/biojava/nbio/structure/symmetry/internal/OrderDetector.html" title="interface in org.biojava.nbio.structure.symmetry.internal" target="classFrame"><i>OrderDetector</i></a></li>
<li><a href="org/biojava/nbio/structure/quaternary/OrderedPair.html" title="class in org.biojava.nbio.structure.quaternary" target="classFrame">OrderedPair</a></li>
<li><a href="org/biojava/nbio/ronn/ORonn.html" title="class in org.biojava.nbio.ronn" target="classFrame">ORonn</a></li>
<li><a href="org/biojava/nbio/ronn/ORonnModel.html" title="class in org.biojava.nbio.ronn" target="classFrame">ORonnModel</a></li>
<li><a href="org/biojava/nbio/genome/query/OutputHitsGFF.html" title="class in org.biojava.nbio.genome.query" target="classFrame">OutputHitsGFF</a></li>
<li><a href="org/biojava/nbio/structure/contact/Pair.html" title="class in org.biojava.nbio.structure.contact" target="classFrame">Pair</a></li>
<li><a href="org/biojava/nbio/alignment/template/PairInProfileScorer.html" title="interface in org.biojava.nbio.alignment.template" target="classFrame"><i>PairInProfileScorer</i></a></li>
<li><a href="org/biojava/nbio/structure/symmetry/core/PairwiseAlignment.html" title="class in org.biojava.nbio.structure.symmetry.core" target="classFrame">PairwiseAlignment</a></li>
<li><a href="org/biojava/nbio/alignment/template/PairwiseSequenceAligner.html" title="interface in org.biojava.nbio.alignment.template" target="classFrame"><i>PairwiseSequenceAligner</i></a></li>
<li><a href="org/biojava/nbio/alignment/template/PairwiseSequenceScorer.html" title="interface in org.biojava.nbio.alignment.template" target="classFrame"><i>PairwiseSequenceScorer</i></a></li>
<li><a href="org/biojava/nbio/structure/align/gui/ParameterGUI.html" title="class in org.biojava.nbio.structure.align.gui" target="classFrame">ParameterGUI</a></li>
<li><a href="demo/ParseFastaFileDemo.html" title="class in demo" target="classFrame">ParseFastaFileDemo</a></li>
<li><a href="demo/ParseGO.html" title="class in demo" target="classFrame">ParseGO</a></li>
<li><a href="org/biojava/nbio/sequencing/io/fastq/ParseListener.html" title="interface in org.biojava.nbio.sequencing.io.fastq" target="classFrame"><i>ParseListener</i></a></li>
<li><a href="org/biojava/nbio/core/exceptions/ParserException.html" title="class in org.biojava.nbio.core.exceptions" target="classFrame">ParserException</a></li>
<li><a href="org/biojava/nbio/alignment/template/PartitionRefiner.html" title="interface in org.biojava.nbio.alignment.template" target="classFrame"><i>PartitionRefiner</i></a></li>
<li><a href="org/biojava/nbio/structure/PassthroughIdentifier.html" title="class in org.biojava.nbio.structure" target="classFrame">PassthroughIdentifier</a></li>
<li><a href="org/biojava/nbio/structure/io/PDBBioAssemblyParser.html" title="class in org.biojava.nbio.structure.io" target="classFrame">PDBBioAssemblyParser</a></li>
<li><a href="org/biojava/nbio/structure/quaternary/io/PDBBioUnitDataProvider.html" title="class in org.biojava.nbio.structure.quaternary.io" target="classFrame">PDBBioUnitDataProvider</a></li>
<li><a href="org/biojava/nbio/structure/PDBCrystallographicInfo.html" title="class in org.biojava.nbio.structure" target="classFrame">PDBCrystallographicInfo</a></li>
<li><a href="org/biojava/nbio/structure/gui/util/PDBDirPanel.html" title="class in org.biojava.nbio.structure.gui.util" target="classFrame">PDBDirPanel</a></li>
<li><a href="org/biojava/nbio/structure/domain/PDBDomainProvider.html" title="class in org.biojava.nbio.structure.domain" target="classFrame">PDBDomainProvider</a></li>
<li><a href="org/biojava/nbio/structure/io/PDBFileParser.html" title="class in org.biojava.nbio.structure.io" target="classFrame">PDBFileParser</a></li>
<li><a href="org/biojava/nbio/structure/io/PDBFileReader.html" title="class in org.biojava.nbio.structure.io" target="classFrame">PDBFileReader</a></li>
<li><a href="org/biojava/nbio/structure/PDBHeader.html" title="class in org.biojava.nbio.structure" target="classFrame">PDBHeader</a></li>
<li><a href="org/biojava/nbio/structure/rcsb/PdbIdLists.html" title="class in org.biojava.nbio.structure.rcsb" target="classFrame">PdbIdLists</a></li>
<li><a href="org/biojava/nbio/structure/align/client/PdbPair.html" title="class in org.biojava.nbio.structure.align.client" target="classFrame">PdbPair</a></li>
<li><a href="org/biojava/nbio/structure/align/xml/PdbPairsMessage.html" title="class in org.biojava.nbio.structure.align.xml" target="classFrame">PdbPairsMessage</a></li>
<li><a href="org/biojava/nbio/structure/align/xml/PdbPairXMLConverter.html" title="class in org.biojava.nbio.structure.align.xml" target="classFrame">PdbPairXMLConverter</a></li>
<li><a href="org/biojava/nbio/structure/io/PDBParseException.html" title="class in org.biojava.nbio.structure.io" target="classFrame">PDBParseException</a></li>
<li><a href="org/biojava/nbio/structure/PDBRecord.html" title="interface in org.biojava.nbio.structure" target="classFrame"><i>PDBRecord</i></a></li>
<li><a href="org/biojava/nbio/structure/gui/util/PDBServerPanel.html" title="class in org.biojava.nbio.structure.gui.util" target="classFrame">PDBServerPanel</a></li>
<li><a href="org/biojava/nbio/structure/PDBStatus.html" title="class in org.biojava.nbio.structure" target="classFrame">PDBStatus</a></li>
<li><a href="org/biojava/nbio/structure/PDBStatus.Status.html" title="enum in org.biojava.nbio.structure" target="classFrame">PDBStatus.Status</a></li>
<li><a href="org/biojava/nbio/structure/io/util/PDBTemporaryStorageUtils.html" title="class in org.biojava.nbio.structure.io.util" target="classFrame">PDBTemporaryStorageUtils</a></li>
<li><a href="org/biojava/nbio/structure/io/util/PDBTemporaryStorageUtils.LinkRecord.html" title="class in org.biojava.nbio.structure.io.util" target="classFrame">PDBTemporaryStorageUtils.LinkRecord</a></li>
<li><a href="org/biojava/nbio/structure/gui/util/PDBUploadPanel.html" title="class in org.biojava.nbio.structure.gui.util" target="classFrame">PDBUploadPanel</a></li>
<li><a href="org/biojava/nbio/structure/io/mmcif/model/PdbxChemCompDescriptor.html" title="class in org.biojava.nbio.structure.io.mmcif.model" target="classFrame">PdbxChemCompDescriptor</a></li>
<li><a href="org/biojava/nbio/structure/io/mmcif/model/PdbxChemCompIdentifier.html" title="class in org.biojava.nbio.structure.io.mmcif.model" target="classFrame">PdbxChemCompIdentifier</a></li>
<li><a href="org/biojava/nbio/structure/io/mmcif/model/PdbxEntityNonPoly.html" title="class in org.biojava.nbio.structure.io.mmcif.model" target="classFrame">PdbxEntityNonPoly</a></li>
<li><a href="org/biojava/nbio/structure/io/mmcif/model/PdbxNonPolyScheme.html" title="class in org.biojava.nbio.structure.io.mmcif.model" target="classFrame">PdbxNonPolyScheme</a></li>
<li><a href="org/biojava/nbio/structure/io/mmcif/model/PdbxPolySeqScheme.html" title="class in org.biojava.nbio.structure.io.mmcif.model" target="classFrame">PdbxPolySeqScheme</a></li>
<li><a href="org/biojava/nbio/structure/io/mmcif/model/PdbxStructAssembly.html" title="class in org.biojava.nbio.structure.io.mmcif.model" target="classFrame">PdbxStructAssembly</a></li>
<li><a href="org/biojava/nbio/structure/io/mmcif/model/PdbxStructAssemblyGen.html" title="class in org.biojava.nbio.structure.io.mmcif.model" target="classFrame">PdbxStructAssemblyGen</a></li>
<li><a href="org/biojava/nbio/structure/io/mmcif/model/PdbxStructAssemblyGenXMLContainer.html" title="class in org.biojava.nbio.structure.io.mmcif.model" target="classFrame">PdbxStructAssemblyGenXMLContainer</a></li>
<li><a href="org/biojava/nbio/structure/io/mmcif/model/PdbxStructAssemblyXMLContainer.html" title="class in org.biojava.nbio.structure.io.mmcif.model" target="classFrame">PdbxStructAssemblyXMLContainer</a></li>
<li><a href="org/biojava/nbio/structure/io/mmcif/model/PdbxStructOperList.html" title="class in org.biojava.nbio.structure.io.mmcif.model" target="classFrame">PdbxStructOperList</a></li>
<li><a href="org/biojava/nbio/structure/io/mmcif/model/PdbxStructOperListXMLContainer.html" title="class in org.biojava.nbio.structure.io.mmcif.model" target="classFrame">PdbxStructOperListXMLContainer</a></li>
<li><a href="org/biojava/nbio/structure/domain/pdp/PDPDistanceMatrix.html" title="class in org.biojava.nbio.structure.domain.pdp" target="classFrame">PDPDistanceMatrix</a></li>
<li><a href="org/biojava/nbio/structure/domain/PDPDomain.html" title="class in org.biojava.nbio.structure.domain" target="classFrame">PDPDomain</a></li>
<li><a href="org/biojava/nbio/structure/domain/pdp/PDPParameters.html" title="class in org.biojava.nbio.structure.domain.pdp" target="classFrame">PDPParameters</a></li>
<li><a href="org/biojava/nbio/structure/domain/PDPProvider.html" title="interface in org.biojava.nbio.structure.domain" target="classFrame"><i>PDPProvider</i></a></li>
<li><a href="org/biojava/nbio/aaproperties/PeptideProperties.html" title="class in org.biojava.nbio.aaproperties" target="classFrame">PeptideProperties</a></li>
<li><a href="org/biojava/nbio/aaproperties/PeptideProperties.SingleLetterAACode.html" title="enum in org.biojava.nbio.aaproperties" target="classFrame">PeptideProperties.SingleLetterAACode</a></li>
<li><a href="org/biojava/nbio/aaproperties/PeptidePropertiesImpl.html" title="class in org.biojava.nbio.aaproperties" target="classFrame">PeptidePropertiesImpl</a></li>
<li><a href="org/biojava/nbio/structure/symmetry/utils/PermutationGenerator.html" title="class in org.biojava.nbio.structure.symmetry.utils" target="classFrame">PermutationGenerator</a></li>
<li><a href="org/biojava/nbio/structure/symmetry/core/PermutationGroup.html" title="class in org.biojava.nbio.structure.symmetry.core" target="classFrame">PermutationGroup</a></li>
<li><a href="org/biojava/nbio/structure/align/webstart/PersistentConfig.html" title="class in org.biojava.nbio.structure.align.webstart" target="classFrame">PersistentConfig</a></li>
<li><a href="org/biojava/nbio/core/sequence/io/PlainFastaHeaderParser.html" title="class in org.biojava.nbio.core.sequence.io" target="classFrame">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" target="classFrame"><i>Point</i></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" target="classFrame"><i>Point.Resolver</i></a></li>
<li><a href="org/biojava/nbio/structure/symmetry/geometry/Polyhedron.html" title="interface in org.biojava.nbio.structure.symmetry.geometry" target="classFrame"><i>Polyhedron</i></a></li>
<li><a href="org/biojava/nbio/structure/io/mmcif/chem/PolymerType.html" title="enum in org.biojava.nbio.structure.io.mmcif.chem" target="classFrame">PolymerType</a></li>
<li><a href="org/biojava/nbio/structure/align/xml/PositionInQueueXMLConverter.html" title="class in org.biojava.nbio.structure.align.xml" target="classFrame">PositionInQueueXMLConverter</a></li>
<li><a href="demo/PredictDisorder.html" title="class in demo" target="classFrame">PredictDisorder</a></li>
<li><a href="org/biojava/nbio/core/util/PrettyXMLWriter.html" title="class in org.biojava.nbio.core.util" target="classFrame">PrettyXMLWriter</a></li>
<li><a href="org/biojava/nbio/structure/symmetry/geometry/Prism.html" title="class in org.biojava.nbio.structure.symmetry.geometry" target="classFrame">Prism</a></li>
<li><a href="org/biojava/nbio/aaproperties/profeat/ProfeatProperties.html" title="class in org.biojava.nbio.aaproperties.profeat" target="classFrame">ProfeatProperties</a></li>
<li><a href="org/biojava/nbio/aaproperties/profeat/ProfeatPropertiesImpl.html" title="class in org.biojava.nbio.aaproperties.profeat" target="classFrame">ProfeatPropertiesImpl</a></li>
<li><a href="org/biojava/nbio/core/alignment/template/Profile.html" title="interface in org.biojava.nbio.core.alignment.template" target="classFrame"><i>Profile</i></a></li>
<li><a href="org/biojava/nbio/core/alignment/template/Profile.StringFormat.html" title="enum in org.biojava.nbio.core.alignment.template" target="classFrame">Profile.StringFormat</a></li>
<li><a href="org/biojava/nbio/core/alignment/template/ProfilePair.html" title="interface in org.biojava.nbio.core.alignment.template" target="classFrame"><i>ProfilePair</i></a></li>
<li><a href="org/biojava/nbio/alignment/template/ProfileProfileAligner.html" title="interface in org.biojava.nbio.alignment.template" target="classFrame"><i>ProfileProfileAligner</i></a></li>
<li><a href="org/biojava/nbio/alignment/template/ProfileProfileScorer.html" title="interface in org.biojava.nbio.alignment.template" target="classFrame"><i>ProfileProfileScorer</i></a></li>
<li><a href="org/biojava/nbio/core/alignment/template/ProfileView.html" title="interface in org.biojava.nbio.core.alignment.template" target="classFrame"><i>ProfileView</i></a></li>
<li><a href="org/biojava/nbio/structure/validation/Program.html" title="class in org.biojava.nbio.structure.validation" target="classFrame">Program</a></li>
<li><a href="org/biojava/nbio/structure/validation/Programs.html" title="class in org.biojava.nbio.structure.validation" target="classFrame">Programs</a></li>
<li><a href="org/biojava/nbio/structure/symmetry/core/ProteinChainExtractor.html" title="class in org.biojava.nbio.structure.symmetry.core" target="classFrame">ProteinChainExtractor</a></li>
<li><a href="org/biojava/nbio/structure/symmetry/misc/ProteinComplexSignature.html" title="class in org.biojava.nbio.structure.symmetry.misc" target="classFrame">ProteinComplexSignature</a></li>
<li><a href="org/biojava/nbio/protmod/ProteinModification.html" title="interface in org.biojava.nbio.protmod" target="classFrame"><i>ProteinModification</i></a></li>
<li><a href="org/biojava/nbio/protmod/structure/ProteinModificationIdentifier.html" title="class in org.biojava.nbio.protmod.structure" target="classFrame">ProteinModificationIdentifier</a></li>
<li><a href="org/biojava/nbio/protmod/ProteinModificationImpl.html" title="class in org.biojava.nbio.protmod" target="classFrame">ProteinModificationImpl</a></li>
<li><a href="org/biojava/nbio/protmod/ProteinModificationImpl.Builder.html" title="class in org.biojava.nbio.protmod" target="classFrame">ProteinModificationImpl.Builder</a></li>
<li><a href="org/biojava/nbio/protmod/ProteinModificationRegistry.html" title="class in org.biojava.nbio.protmod" target="classFrame">ProteinModificationRegistry</a></li>
<li><a href="org/biojava/nbio/protmod/io/ProteinModificationXmlReader.html" title="class in org.biojava.nbio.protmod.io" target="classFrame">ProteinModificationXmlReader</a></li>
<li><a href="org/biojava/nbio/core/sequence/ProteinSequence.html" title="class in org.biojava.nbio.core.sequence" target="classFrame">ProteinSequence</a></li>
<li><a href="org/biojava/nbio/structure/symmetry/core/ProteinSequenceClusterer.html" title="class in org.biojava.nbio.structure.symmetry.core" target="classFrame">ProteinSequenceClusterer</a></li>
<li><a href="org/biojava/nbio/core/sequence/io/ProteinSequenceCreator.html" title="class in org.biojava.nbio.core.sequence.io" target="classFrame">ProteinSequenceCreator</a></li>
<li><a href="org/biojava/nbio/core/sequence/template/ProxySequenceReader.html" title="interface in org.biojava.nbio.core.sequence.template" target="classFrame"><i>ProxySequenceReader</i></a></li>
<li><a href="org/biojava/nbio/structure/jama/QRDecomposition.html" title="class in org.biojava.nbio.structure.jama" target="classFrame">QRDecomposition</a></li>
<li><a href="org/biojava/nbio/core/sequence/features/Qualifier.html" title="class in org.biojava.nbio.core.sequence.features" target="classFrame">Qualifier</a></li>
<li><a href="org/biojava/nbio/core/sequence/features/QualityFeature.html" title="class in org.biojava.nbio.core.sequence.features" target="classFrame">QualityFeature</a></li>
<li><a href="org/biojava/nbio/core/sequence/features/QuantityFeature.html" title="class in org.biojava.nbio.core.sequence.features" target="classFrame">QuantityFeature</a></li>
<li><a href="org/biojava/nbio/structure/symmetry/core/QuatSuperpositionScorer.html" title="class in org.biojava.nbio.structure.symmetry.core" target="classFrame">QuatSuperpositionScorer</a></li>
<li><a href="org/biojava/nbio/structure/symmetry/core/QuatSymmetryDetector.html" title="class in org.biojava.nbio.structure.symmetry.core" target="classFrame">QuatSymmetryDetector</a></li>
<li><a href="org/biojava/nbio/structure/symmetry/core/QuatSymmetryParameters.html" title="class in org.biojava.nbio.structure.symmetry.core" target="classFrame">QuatSymmetryParameters</a></li>
<li><a href="org/biojava/nbio/structure/symmetry/core/QuatSymmetryResults.html" title="class in org.biojava.nbio.structure.symmetry.core" target="classFrame">QuatSymmetryResults</a></li>
<li><a href="org/biojava/nbio/structure/symmetry/core/QuatSymmetryScores.html" title="class in org.biojava.nbio.structure.symmetry.core" target="classFrame">QuatSymmetryScores</a></li>
<li><a href="org/biojava/nbio/structure/symmetry/core/QuatSymmetrySolver.html" title="interface in org.biojava.nbio.structure.symmetry.core" target="classFrame"><i>QuatSymmetrySolver</i></a></li>
<li><a href="org/biojava/nbio/structure/align/gui/jmol/RasmolCommandListener.html" title="class in org.biojava.nbio.structure.align.gui.jmol" target="classFrame">RasmolCommandListener</a></li>
<li><a href="org/biojava/nbio/structure/gui/RasmolCommandListener.html" title="class in org.biojava.nbio.structure.gui" target="classFrame">RasmolCommandListener</a></li>
<li><a href="org/biojava/nbio/structure/quaternary/io/RawBioUnitDataProvider.html" title="interface in org.biojava.nbio.structure.quaternary.io" target="classFrame"><i>RawBioUnitDataProvider</i></a></li>
<li><a href="org/biojava/nbio/structure/rcsb/RCSBDescription.html" title="class in org.biojava.nbio.structure.rcsb" target="classFrame">RCSBDescription</a></li>
<li><a href="org/biojava/nbio/structure/rcsb/RCSBDescriptionFactory.html" title="class in org.biojava.nbio.structure.rcsb" target="classFrame">RCSBDescriptionFactory</a></li>
<li><a href="org/biojava/nbio/structure/rcsb/RCSBLigand.html" title="class in org.biojava.nbio.structure.rcsb" target="classFrame">RCSBLigand</a></li>
<li><a href="org/biojava/nbio/structure/rcsb/RCSBLigands.html" title="class in org.biojava.nbio.structure.rcsb" target="classFrame">RCSBLigands</a></li>
<li><a href="org/biojava/nbio/structure/rcsb/RCSBLigandsFactory.html" title="class in org.biojava.nbio.structure.rcsb" target="classFrame">RCSBLigandsFactory</a></li>
<li><a href="org/biojava/nbio/structure/rcsb/RCSBMacromolecule.html" title="class in org.biojava.nbio.structure.rcsb" target="classFrame">RCSBMacromolecule</a></li>
<li><a href="org/biojava/nbio/structure/rcsb/RCSBPolymer.html" title="class in org.biojava.nbio.structure.rcsb" target="classFrame">RCSBPolymer</a></li>
<li><a href="org/biojava/nbio/structure/rcsb/RCSBTaxonomy.html" title="class in org.biojava.nbio.structure.rcsb" target="classFrame">RCSBTaxonomy</a></li>
<li><a href="org/biojava/nbio/structure/rcsb/RCSBUpdates.html" title="class in org.biojava.nbio.structure.rcsb" target="classFrame">RCSBUpdates</a></li>
<li><a href="org/biojava/nbio/structure/rcsb/ReadUtils.html" title="class in org.biojava.nbio.structure.rcsb" target="classFrame">ReadUtils</a></li>
<li><a href="org/biojava/nbio/structure/symmetry/geometry/RectangularPrism.html" title="class in org.biojava.nbio.structure.symmetry.geometry" target="classFrame">RectangularPrism</a></li>
<li><a href="org/biojava/nbio/structure/io/mmcif/ReducedChemCompProvider.html" title="class in org.biojava.nbio.structure.io.mmcif" target="classFrame">ReducedChemCompProvider</a></li>
<li><a href="org/biojava/nbio/structure/align/multiple/util/ReferenceSuperimposer.html" title="class in org.biojava.nbio.structure.align.multiple.util" target="classFrame">ReferenceSuperimposer</a></li>
<li><a href="org/biojava/nbio/structure/io/mmcif/model/Refine.html" title="class in org.biojava.nbio.structure.io.mmcif.model" target="classFrame">Refine</a></li>
<li><a href="org/biojava/nbio/structure/symmetry/internal/RefinerFailedException.html" title="class in org.biojava.nbio.structure.symmetry.internal" target="classFrame">RefinerFailedException</a></li>
<li><a href="org/biojava/nbio/structure/quaternary/io/RemoteBioUnitDataProvider.html" title="class in org.biojava.nbio.structure.quaternary.io" target="classFrame">RemoteBioUnitDataProvider</a></li>
<li><a href="org/biojava/nbio/structure/domain/RemoteDomainProvider.html" title="class in org.biojava.nbio.structure.domain" target="classFrame">RemoteDomainProvider</a></li>
<li><a href="org/biojava/nbio/ws/hmmer/RemoteHmmerScan.html" title="class in org.biojava.nbio.ws.hmmer" target="classFrame">RemoteHmmerScan</a></li>
<li><a href="org/biojava/nbio/ws/alignment/RemotePairwiseAlignmentOutputProperties.html" title="interface in org.biojava.nbio.ws.alignment" target="classFrame"><i>RemotePairwiseAlignmentOutputProperties</i></a></li>
<li><a href="org/biojava/nbio/ws/alignment/RemotePairwiseAlignmentProperties.html" title="interface in org.biojava.nbio.ws.alignment" target="classFrame"><i>RemotePairwiseAlignmentProperties</i></a></li>
<li><a href="org/biojava/nbio/ws/alignment/RemotePairwiseAlignmentService.html" title="interface in org.biojava.nbio.ws.alignment" target="classFrame"><i>RemotePairwiseAlignmentService</i></a></li>
<li><a href="org/biojava/nbio/structure/domain/RemotePDPProvider.html" title="class in org.biojava.nbio.structure.domain" target="classFrame">RemotePDPProvider</a></li>
<li><a href="org/biojava/nbio/structure/quaternary/io/RemoteRawBioUnitDataProvider.html" title="class in org.biojava.nbio.structure.quaternary.io" target="classFrame">RemoteRawBioUnitDataProvider</a></li>
<li><a href="org/biojava/nbio/structure/scop/RemoteScopInstallation.html" title="class in org.biojava.nbio.structure.scop" target="classFrame">RemoteScopInstallation</a></li>
<li><a href="org/biojava/nbio/ontology/RemoteTerm.html" title="interface in org.biojava.nbio.ontology" target="classFrame"><i>RemoteTerm</i></a></li>
<li><a href="org/biojava/nbio/ontology/RemoteTerm.Impl.html" title="class in org.biojava.nbio.ontology" target="classFrame">RemoteTerm.Impl</a></li>
<li><a href="org/biojava/nbio/structure/gui/RenderStyle.html" title="enum in org.biojava.nbio.structure.gui" target="classFrame">RenderStyle</a></li>
<li><a href="org/biojava/nbio/structure/align/xml/RepresentativeXMLConverter.html" title="class in org.biojava.nbio.structure.align.xml" target="classFrame">RepresentativeXMLConverter</a></li>
<li><a href="org/biojava/nbio/alignment/template/RescoreRefiner.html" title="interface in org.biojava.nbio.alignment.template" target="classFrame"><i>RescoreRefiner</i></a></li>
<li><a href="org/biojava/nbio/survival/cox/ResidualsCoxph.html" title="class in org.biojava.nbio.survival.cox" target="classFrame">ResidualsCoxph</a></li>
<li><a href="org/biojava/nbio/survival/cox/ResidualsCoxph.Type.html" title="enum in org.biojava.nbio.survival.cox" target="classFrame">ResidualsCoxph.Type</a></li>
<li><a href="org/biojava/nbio/structure/symmetry/internal/ResidueGroup.html" title="class in org.biojava.nbio.structure.symmetry.internal" target="classFrame">ResidueGroup</a></li>
<li><a href="org/biojava/nbio/structure/ResidueNumber.html" title="class in org.biojava.nbio.structure" target="classFrame">ResidueNumber</a></li>
<li><a href="org/biojava/nbio/structure/ResidueRange.html" title="class in org.biojava.nbio.structure" target="classFrame">ResidueRange</a></li>
<li><a href="org/biojava/nbio/structure/ResidueRangeAndLength.html" title="class in org.biojava.nbio.structure" target="classFrame">ResidueRangeAndLength</a></li>
<li><a href="org/biojava/nbio/structure/io/mmcif/chem/ResidueType.html" title="enum in org.biojava.nbio.structure.io.mmcif.chem" target="classFrame">ResidueType</a></li>
<li><a href="org/biojava/nbio/structure/align/util/ResourceManager.html" title="class in org.biojava.nbio.structure.align.util" target="classFrame">ResourceManager</a></li>
<li><a href="org/biojava/nbio/core/search/io/Result.html" title="class in org.biojava.nbio.core.search.io" target="classFrame">Result</a></li>
<li><a href="org/biojava/nbio/core/search/io/ResultFactory.html" title="interface in org.biojava.nbio.core.search.io" target="classFrame"><i>ResultFactory</i></a></li>
<li><a href="org/biojava/nbio/core/sequence/views/ReversedSequenceView.html" title="class in org.biojava.nbio.core.sequence.views" target="classFrame">ReversedSequenceView</a></li>
<li><a href="org/biojava/nbio/survival/cox/RiskInfo.html" title="class in org.biojava.nbio.survival.cox" target="classFrame">RiskInfo</a></li>
<li><a href="org/biojava/nbio/core/sequence/compound/RNACompoundSet.html" title="class in org.biojava.nbio.core.sequence.compound" target="classFrame">RNACompoundSet</a></li>
<li><a href="org/biojava/nbio/core/sequence/RNASequence.html" title="class in org.biojava.nbio.core.sequence" target="classFrame">RNASequence</a></li>
<li><a href="org/biojava/nbio/core/sequence/io/RNASequenceCreator.html" title="class in org.biojava.nbio.core.sequence.io" target="classFrame">RNASequenceCreator</a></li>
<li><a href="org/biojava/nbio/core/sequence/views/RnaSequenceView.html" title="class in org.biojava.nbio.core.sequence.views" target="classFrame">RnaSequenceView</a></li>
<li><a href="org/biojava/nbio/core/sequence/transcription/RNAToAminoAcidTranslator.html" title="class in org.biojava.nbio.core.sequence.transcription" target="classFrame">RNAToAminoAcidTranslator</a></li>
<li><a href="org/biojava/nbio/ronn/RonnConstraint.html" title="class in org.biojava.nbio.ronn" target="classFrame">RonnConstraint</a></li>
<li><a href="org/biojava/nbio/ronn/RonnConstraint.Threshold.html" title="enum in org.biojava.nbio.ronn" target="classFrame">RonnConstraint.Threshold</a></li>
<li><a href="org/biojava/nbio/structure/symmetry/core/Rotation.html" title="class in org.biojava.nbio.structure.symmetry.core" target="classFrame">Rotation</a></li>
<li><a href="org/biojava/nbio/structure/align/util/RotationAxis.html" title="class in org.biojava.nbio.structure.align.util" target="classFrame">RotationAxis</a></li>
<li><a href="org/biojava/nbio/structure/symmetry/core/RotationAxisAligner.html" title="class in org.biojava.nbio.structure.symmetry.core" target="classFrame">RotationAxisAligner</a></li>
<li><a href="org/biojava/nbio/structure/symmetry/core/RotationGroup.html" title="class in org.biojava.nbio.structure.symmetry.core" target="classFrame">RotationGroup</a></li>
<li><a href="org/biojava/nbio/structure/symmetry/core/RotationSolver.html" title="class in org.biojava.nbio.structure.symmetry.core" target="classFrame">RotationSolver</a></li>
<li><a href="org/biojava/nbio/structure/io/SandboxStyleStructureProvider.html" title="class in org.biojava.nbio.structure.io" target="classFrame">SandboxStyleStructureProvider</a></li>
<li><a href="org/biojava/nbio/sequencing/io/fastq/SangerFastqReader.html" title="class in org.biojava.nbio.sequencing.io.fastq" target="classFrame">SangerFastqReader</a></li>
<li><a href="org/biojava/nbio/sequencing/io/fastq/SangerFastqWriter.html" title="class in org.biojava.nbio.sequencing.io.fastq" target="classFrame">SangerFastqWriter</a></li>
<li><a href="org/biojava/nbio/structure/gui/ScaleableMatrixPanel.html" title="class in org.biojava.nbio.structure.gui" target="classFrame">ScaleableMatrixPanel</a></li>
<li><a href="org/biojava/nbio/core/alignment/matrices/ScaledSubstitutionMatrix.html" title="class in org.biojava.nbio.core.alignment.matrices" target="classFrame">ScaledSubstitutionMatrix</a></li>
<li><a href="org/biojava/nbio/structure/symmetry/analysis/ScanSymmetry.html" title="class in org.biojava.nbio.structure.symmetry.analysis" target="classFrame">ScanSymmetry</a></li>
<li><a href="org/biojava/nbio/aaproperties/xml/SchemaGenerator.html" title="class in org.biojava.nbio.aaproperties.xml" target="classFrame">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" target="classFrame">SCOPAutoSuggestProvider</a></li>
<li><a href="org/biojava/nbio/structure/scop/ScopCategory.html" title="enum in org.biojava.nbio.structure.scop" target="classFrame">ScopCategory</a></li>
<li><a href="org/biojava/nbio/structure/scop/ScopDatabase.html" title="interface in org.biojava.nbio.structure.scop" target="classFrame"><i>ScopDatabase</i></a></li>
<li><a href="org/biojava/nbio/structure/scop/ScopDescription.html" title="class in org.biojava.nbio.structure.scop" target="classFrame">ScopDescription</a></li>
<li><a href="org/biojava/nbio/structure/scop/server/ScopDescriptions.html" title="class in org.biojava.nbio.structure.scop.server" target="classFrame">ScopDescriptions</a></li>
<li><a href="org/biojava/nbio/structure/scop/ScopDomain.html" title="class in org.biojava.nbio.structure.scop" target="classFrame">ScopDomain</a></li>
<li><a href="org/biojava/nbio/structure/scop/server/ScopDomains.html" title="class in org.biojava.nbio.structure.scop.server" target="classFrame">ScopDomains</a></li>
<li><a href="org/biojava/nbio/structure/scop/ScopFactory.html" title="class in org.biojava.nbio.structure.scop" target="classFrame">ScopFactory</a></li>
<li><a href="org/biojava/nbio/structure/scop/ScopInstallation.html" title="class in org.biojava.nbio.structure.scop" target="classFrame">ScopInstallation</a></li>
<li><a href="org/biojava/nbio/structure/gui/util/ScopInstallationInstance.html" title="class in org.biojava.nbio.structure.gui.util" target="classFrame">ScopInstallationInstance</a></li>
<li><a href="org/biojava/nbio/structure/scop/ScopIOException.html" title="class in org.biojava.nbio.structure.scop" target="classFrame">ScopIOException</a></li>
<li><a href="org/biojava/nbio/structure/scop/ScopMirror.html" title="class in org.biojava.nbio.structure.scop" target="classFrame">ScopMirror</a></li>
<li><a href="org/biojava/nbio/structure/scop/ScopNode.html" title="class in org.biojava.nbio.structure.scop" target="classFrame">ScopNode</a></li>
<li><a href="org/biojava/nbio/structure/scop/server/ScopNodes.html" title="class in org.biojava.nbio.structure.scop.server" target="classFrame">ScopNodes</a></li>
<li><a href="org/biojava/nbio/structure/gui/util/ScopSelectPanel.html" title="class in org.biojava.nbio.structure.gui.util" target="classFrame">ScopSelectPanel</a></li>
<li><a href="org/biojava/nbio/alignment/template/Scorer.html" title="interface in org.biojava.nbio.alignment.template" target="classFrame"><i>Scorer</i></a></li>
<li><a href="org/biojava/nbio/structure/align/multiple/ScoresCache.html" title="interface in org.biojava.nbio.structure.align.multiple" target="classFrame"><i>ScoresCache</i></a></li>
<li><a href="org/biojava/nbio/core/search/io/SearchIO.html" title="class in org.biojava.nbio.core.search.io" target="classFrame">SearchIO</a></li>
<li><a href="org/biojava/nbio/structure/secstruc/SecStrucCalc.html" title="class in org.biojava.nbio.structure.secstruc" target="classFrame">SecStrucCalc</a></li>
<li><a href="org/biojava/nbio/structure/secstruc/SecStrucElement.html" title="class in org.biojava.nbio.structure.secstruc" target="classFrame">SecStrucElement</a></li>
<li><a href="org/biojava/nbio/structure/secstruc/SecStrucInfo.html" title="class in org.biojava.nbio.structure.secstruc" target="classFrame">SecStrucInfo</a></li>
<li><a href="org/biojava/nbio/structure/secstruc/SecStrucState.html" title="class in org.biojava.nbio.structure.secstruc" target="classFrame">SecStrucState</a></li>
<li><a href="org/biojava/nbio/structure/secstruc/SecStrucTools.html" title="class in org.biojava.nbio.structure.secstruc" target="classFrame">SecStrucTools</a></li>
<li><a href="org/biojava/nbio/structure/secstruc/SecStrucType.html" title="enum in org.biojava.nbio.structure.secstruc" target="classFrame">SecStrucType</a></li>
<li><a href="org/biojava/nbio/structure/domain/pdp/Segment.html" title="class in org.biojava.nbio.structure.domain.pdp" target="classFrame">Segment</a></li>
<li><a href="org/biojava/nbio/structure/domain/pdp/SegmentComparator.html" title="class in org.biojava.nbio.structure.domain.pdp" target="classFrame">SegmentComparator</a></li>
<li><a href="org/biojava/nbio/structure/gui/Selection.html" title="interface in org.biojava.nbio.structure.gui" target="classFrame"><i>Selection</i></a></li>
<li><a href="org/biojava/nbio/structure/gui/SelectionImpl.html" title="class in org.biojava.nbio.structure.gui" target="classFrame">SelectionImpl</a></li>
<li><a href="org/biojava/nbio/structure/gui/util/SelectMultiplePanel.html" title="class in org.biojava.nbio.structure.gui.util" target="classFrame">SelectMultiplePanel</a></li>
<li><a href="org/biojava/nbio/structure/align/gui/SelectPDBPanel.html" title="class in org.biojava.nbio.structure.align.gui" target="classFrame">SelectPDBPanel</a></li>
<li><a href="org/biojava/nbio/structure/SeqMisMatch.html" title="interface in org.biojava.nbio.structure" target="classFrame"><i>SeqMisMatch</i></a></li>
<li><a href="org/biojava/nbio/structure/SeqMisMatchImpl.html" title="class in org.biojava.nbio.structure" target="classFrame">SeqMisMatchImpl</a></li>
<li><a href="org/biojava/nbio/structure/io/SeqRes2AtomAligner.html" title="class in org.biojava.nbio.structure.io" target="classFrame">SeqRes2AtomAligner</a></li>
<li><a href="org/biojava/nbio/core/sequence/template/Sequence.html" title="interface in org.biojava.nbio.core.sequence.template" target="classFrame"><i>Sequence</i></a></li>
<li><a href="org/biojava/nbio/structure/symmetry/core/SequenceAlignmentCluster.html" title="class in org.biojava.nbio.structure.symmetry.core" target="classFrame">SequenceAlignmentCluster</a></li>
<li><a href="org/biojava/nbio/core/sequence/storage/SequenceAsStringHelper.html" title="class in org.biojava.nbio.core.sequence.storage" target="classFrame">SequenceAsStringHelper</a></li>
<li><a href="org/biojava/nbio/core/sequence/SequenceComparator.html" title="class in org.biojava.nbio.core.sequence" target="classFrame">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" target="classFrame"><i>SequenceCreatorInterface</i></a></li>
<li><a href="org/biojava/nbio/structure/gui/SequenceDisplay.html" title="class in org.biojava.nbio.structure.gui" target="classFrame">SequenceDisplay</a></li>
<li><a href="org/biojava/nbio/core/sequence/loader/SequenceFileProxyLoader.html" title="class in org.biojava.nbio.core.sequence.loader" target="classFrame">SequenceFileProxyLoader</a></li>
<li><a href="org/biojava/nbio/structure/symmetry/internal/SequenceFunctionOrderDetector.html" title="class in org.biojava.nbio.structure.symmetry.internal" target="classFrame">SequenceFunctionOrderDetector</a></li>
<li><a href="org/biojava/nbio/structure/symmetry/internal/SequenceFunctionRefiner.html" title="class in org.biojava.nbio.structure.symmetry.internal" target="classFrame">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" target="classFrame"><i>SequenceHeaderParserInterface</i></a></li>
<li><a href="org/biojava/nbio/core/sequence/location/SequenceLocation.html" title="class in org.biojava.nbio.core.sequence.location" target="classFrame">SequenceLocation</a></li>
<li><a href="org/biojava/nbio/core/sequence/template/SequenceMixin.html" title="class in org.biojava.nbio.core.sequence.template" target="classFrame">SequenceMixin</a></li>
<li><a href="org/biojava/nbio/core/sequence/template/SequenceMixin.SequenceIterator.html" title="class in org.biojava.nbio.core.sequence.template" target="classFrame">SequenceMixin.SequenceIterator</a></li>
<li><a href="org/biojava/nbio/structure/gui/util/SequenceMouseListener.html" title="class in org.biojava.nbio.structure.gui.util" target="classFrame">SequenceMouseListener</a></li>
<li><a href="org/biojava/nbio/core/sequence/SequenceOptimizationHints.html" title="class in org.biojava.nbio.core.sequence" target="classFrame">SequenceOptimizationHints</a></li>
<li><a href="org/biojava/nbio/core/sequence/SequenceOptimizationHints.SequenceCollection.html" title="enum in org.biojava.nbio.core.sequence" target="classFrame">SequenceOptimizationHints.SequenceCollection</a></li>
<li><a href="org/biojava/nbio/core/sequence/SequenceOptimizationHints.SequenceUsage.html" title="enum in org.biojava.nbio.core.sequence" target="classFrame">SequenceOptimizationHints.SequenceUsage</a></li>
<li><a href="org/biojava/nbio/core/alignment/template/SequencePair.html" title="interface in org.biojava.nbio.core.alignment.template" target="classFrame"><i>SequencePair</i></a></li>
<li><a href="org/biojava/nbio/core/sequence/io/template/SequenceParserInterface.html" title="interface in org.biojava.nbio.core.sequence.io.template" target="classFrame"><i>SequenceParserInterface</i></a></li>
<li><a href="org/biojava/nbio/core/sequence/template/SequenceProxyView.html" title="class in org.biojava.nbio.core.sequence.template" target="classFrame">SequenceProxyView</a></li>
<li><a href="org/biojava/nbio/core/sequence/template/SequenceReader.html" title="interface in org.biojava.nbio.core.sequence.template" target="classFrame"><i>SequenceReader</i></a></li>
<li><a href="org/biojava/nbio/structure/gui/util/SequenceScalePanel.html" title="class in org.biojava.nbio.structure.gui.util" target="classFrame">SequenceScalePanel</a></li>
<li><a href="org/biojava/nbio/core/util/SequenceTools.html" title="class in org.biojava.nbio.core.util" target="classFrame">SequenceTools</a></li>
<li><a href="org/biojava/nbio/data/sequence/SequenceUtil.html" title="class in org.biojava.nbio.data.sequence" target="classFrame">SequenceUtil</a></li>
<li><a href="org/biojava/nbio/core/sequence/template/SequenceView.html" title="interface in org.biojava.nbio.core.sequence.template" target="classFrame"><i>SequenceView</i></a></li>
<li><a href="org/biojava/nbio/structure/domain/SerializableCache.html" title="class in org.biojava.nbio.structure.domain" target="classFrame">SerializableCache</a></li>
<li><a href="org/biojava/nbio/structure/domain/pdp/ShortSegmentRemover.html" title="class in org.biojava.nbio.structure.domain.pdp" target="classFrame">ShortSegmentRemover</a></li>
<li><a href="org/biojava/nbio/structure/align/gui/ShowPDBIDListener.html" title="class in org.biojava.nbio.structure.align.gui" target="classFrame">ShowPDBIDListener</a></li>
<li><a href="demo/ShowStructureInJmol.html" title="class in demo" target="classFrame">ShowStructureInJmol</a></li>
<li><a href="org/biojava/nbio/structure/io/sifts/SiftsChainEntry.html" title="class in org.biojava.nbio.structure.io.sifts" target="classFrame">SiftsChainEntry</a></li>
<li><a href="org/biojava/nbio/structure/io/sifts/SiftsChainToUniprotMapping.html" title="class in org.biojava.nbio.structure.io.sifts" target="classFrame">SiftsChainToUniprotMapping</a></li>
<li><a href="org/biojava/nbio/structure/io/sifts/SiftsEntity.html" title="class in org.biojava.nbio.structure.io.sifts" target="classFrame">SiftsEntity</a></li>
<li><a href="org/biojava/nbio/structure/io/sifts/SiftsMappingProvider.html" title="class in org.biojava.nbio.structure.io.sifts" target="classFrame">SiftsMappingProvider</a></li>
<li><a href="org/biojava/nbio/structure/io/sifts/SiftsResidue.html" title="class in org.biojava.nbio.structure.io.sifts" target="classFrame">SiftsResidue</a></li>
<li><a href="org/biojava/nbio/structure/io/sifts/SiftsSegment.html" title="class in org.biojava.nbio.structure.io.sifts" target="classFrame">SiftsSegment</a></li>
<li><a href="org/biojava/nbio/structure/io/sifts/SiftsXMLParser.html" title="class in org.biojava.nbio.structure.io.sifts" target="classFrame">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" target="classFrame">SigEva</a></li>
<li><a href="org/biojava/nbio/core/alignment/SimpleAlignedSequence.html" title="class in org.biojava.nbio.core.alignment" target="classFrame">SimpleAlignedSequence</a></li>
<li><a href="org/biojava/nbio/alignment/SimpleGapPenalty.html" title="class in org.biojava.nbio.alignment" target="classFrame">SimpleGapPenalty</a></li>
<li><a href="org/biojava/nbio/core/sequence/location/SimpleLocation.html" title="class in org.biojava.nbio.core.sequence.location" target="classFrame">SimpleLocation</a></li>
<li><a href="org/biojava/nbio/structure/io/mmcif/SimpleMMcifConsumer.html" title="class in org.biojava.nbio.structure.io.mmcif" target="classFrame">SimpleMMcifConsumer</a></li>
<li><a href="org/biojava/nbio/structure/io/mmcif/SimpleMMcifParser.html" title="class in org.biojava.nbio.structure.io.mmcif" target="classFrame">SimpleMMcifParser</a></li>
<li><a href="org/biojava/nbio/core/sequence/location/SimplePoint.html" title="class in org.biojava.nbio.core.sequence.location" target="classFrame">SimplePoint</a></li>
<li><a href="org/biojava/nbio/core/alignment/SimpleProfile.html" title="class in org.biojava.nbio.core.alignment" target="classFrame">SimpleProfile</a></li>
<li><a href="org/biojava/nbio/core/alignment/SimpleProfilePair.html" title="class in org.biojava.nbio.core.alignment" target="classFrame">SimpleProfilePair</a></li>
<li><a href="org/biojava/nbio/alignment/SimpleProfileProfileAligner.html" title="class in org.biojava.nbio.alignment" target="classFrame">SimpleProfileProfileAligner</a></li>
<li><a href="org/biojava/nbio/core/alignment/SimpleSequencePair.html" title="class in org.biojava.nbio.core.alignment" target="classFrame">SimpleSequencePair</a></li>
<li><a href="org/biojava/nbio/core/alignment/matrices/SimpleSubstitutionMatrix.html" title="class in org.biojava.nbio.core.alignment.matrices" target="classFrame">SimpleSubstitutionMatrix</a></li>
<li><a href="org/biojava/nbio/core/sequence/storage/SingleCompoundSequenceReader.html" title="class in org.biojava.nbio.core.sequence.storage" target="classFrame">SingleCompoundSequenceReader</a></li>
<li><a href="org/biojava/nbio/core/util/SingleLinkageClusterer.html" title="class in org.biojava.nbio.core.util" target="classFrame">SingleLinkageClusterer</a></li>
<li><a href="org/biojava/nbio/structure/jama/SingularValueDecomposition.html" title="class in org.biojava.nbio.structure.jama" target="classFrame">SingularValueDecomposition</a></li>
<li><a href="org/biojava/nbio/phosphosite/Site.html" title="class in org.biojava.nbio.phosphosite" target="classFrame">Site</a></li>
<li><a href="org/biojava/nbio/structure/Site.html" title="class in org.biojava.nbio.structure" target="classFrame">Site</a></li>
<li><a href="org/biojava/nbio/ontology/utils/SmallAnnotation.html" title="class in org.biojava.nbio.ontology.utils" target="classFrame">SmallAnnotation</a></li>
<li><a href="org/biojava/nbio/ontology/utils/SmallMap.html" title="class in org.biojava.nbio.ontology.utils" target="classFrame">SmallMap</a></li>
<li><a href="org/biojava/nbio/alignment/SmithWaterman.html" title="class in org.biojava.nbio.alignment" target="classFrame">SmithWaterman</a></li>
<li><a href="org/biojava/nbio/structure/align/seq/SmithWaterman3Daligner.html" title="class in org.biojava.nbio.structure.align.seq" target="classFrame">SmithWaterman3Daligner</a></li>
<li><a href="org/biojava/nbio/structure/align/seq/SmithWaterman3DParameters.html" title="class in org.biojava.nbio.structure.align.seq" target="classFrame">SmithWaterman3DParameters</a></li>
<li><a href="org/biojava/nbio/structure/align/seq/SmithWatermanUserArgumentProcessor.html" title="class in org.biojava.nbio.structure.align.seq" target="classFrame">SmithWatermanUserArgumentProcessor</a></li>
<li><a href="org/biojava/nbio/structure/align/seq/SmithWatermanUserArgumentProcessor.SmithWatermanStartupParams.html" title="class in org.biojava.nbio.structure.align.seq" target="classFrame">SmithWatermanUserArgumentProcessor.SmithWatermanStartupParams</a></li>
<li><a href="org/biojava/nbio/core/util/SoftHashMap.html" title="class in org.biojava.nbio.core.util" target="classFrame">SoftHashMap</a></li>
<li><a href="org/biojava/nbio/sequencing/io/fastq/SolexaFastqReader.html" title="class in org.biojava.nbio.sequencing.io.fastq" target="classFrame">SolexaFastqReader</a></li>
<li><a href="org/biojava/nbio/sequencing/io/fastq/SolexaFastqWriter.html" title="class in org.biojava.nbio.sequencing.io.fastq" target="classFrame">SolexaFastqWriter</a></li>
<li><a href="org/biojava/nbio/structure/xtal/SpaceGroup.html" title="class in org.biojava.nbio.structure.xtal" target="classFrame">SpaceGroup</a></li>
<li><a href="org/biojava/nbio/structure/xtal/io/SpaceGroupMapElements.html" title="class in org.biojava.nbio.structure.xtal.io" target="classFrame">SpaceGroupMapElements</a></li>
<li><a href="org/biojava/nbio/structure/xtal/io/SpaceGroupMapRoot.html" title="class in org.biojava.nbio.structure.xtal.io" target="classFrame">SpaceGroupMapRoot</a></li>
<li><a href="org/biojava/nbio/structure/math/SparseSquareMatrix.html" title="class in org.biojava.nbio.structure.math" target="classFrame">SparseSquareMatrix</a></li>
<li><a href="org/biojava/nbio/structure/math/SparseVector.html" title="class in org.biojava.nbio.structure.math" target="classFrame">SparseVector</a></li>
<li><a href="org/biojava/nbio/structure/symmetry/geometry/SphereSampler.html" title="class in org.biojava.nbio.structure.symmetry.geometry" target="classFrame">SphereSampler</a></li>
<li><a href="org/biojava/nbio/genome/util/SplitFasta.html" title="class in org.biojava.nbio.genome.util" target="classFrame">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" target="classFrame">SqrtColorMapper</a></li>
<li><a href="org/biojava/nbio/structure/io/SSBondImpl.html" title="class in org.biojava.nbio.structure.io" target="classFrame">SSBondImpl</a></li>
<li><a href="org/biojava/nbio/genome/parsers/cytoband/StainType.html" title="enum in org.biojava.nbio.genome.parsers.cytoband" target="classFrame">StainType</a></li>
<li><a href="org/biojava/nbio/structure/StandardAminoAcid.html" title="class in org.biojava.nbio.structure" target="classFrame">StandardAminoAcid</a></li>
<li><a href="org/biojava/nbio/alignment/StandardRescoreRefiner.html" title="class in org.biojava.nbio.alignment" target="classFrame">StandardRescoreRefiner</a></li>
<li><a href="org/biojava/nbio/core/sequence/StartCodonSequence.html" title="class in org.biojava.nbio.core.sequence" target="classFrame">StartCodonSequence</a></li>
<li><a href="org/biojava/nbio/structure/align/ce/StartupParameters.html" title="class in org.biojava.nbio.structure.align.ce" target="classFrame">StartupParameters</a></li>
<li><a href="org/biojava/nbio/ontology/utils/StaticMemberPlaceHolder.html" title="class in org.biojava.nbio.ontology.utils" target="classFrame">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" target="classFrame">StatusDisplay</a></li>
<li><a href="org/biojava/nbio/survival/cox/matrix/StdArrayIO.html" title="class in org.biojava.nbio.survival.cox.matrix" target="classFrame">StdArrayIO</a></li>
<li><a href="org/biojava/nbio/alignment/io/StockholmFileAnnotation.html" title="class in org.biojava.nbio.alignment.io" target="classFrame">StockholmFileAnnotation</a></li>
<li><a href="org/biojava/nbio/alignment/io/StockholmFileAnnotation.StockholmFileAnnotationReference.html" title="class in org.biojava.nbio.alignment.io" target="classFrame">StockholmFileAnnotation.StockholmFileAnnotationReference</a></li>
<li><a href="org/biojava/nbio/alignment/io/StockholmFileParser.html" title="class in org.biojava.nbio.alignment.io" target="classFrame">StockholmFileParser</a></li>
<li><a href="org/biojava/nbio/alignment/io/StockholmStructure.html" title="class in org.biojava.nbio.alignment.io" target="classFrame">StockholmStructure</a></li>
<li><a href="org/biojava/nbio/alignment/io/StockholmStructure.DatabaseReference.html" title="class in org.biojava.nbio.alignment.io" target="classFrame">StockholmStructure.DatabaseReference</a></li>
<li><a href="org/biojava/nbio/core/sequence/StopCodonSequence.html" title="class in org.biojava.nbio.core.sequence" target="classFrame">StopCodonSequence</a></li>
<li><a href="org/biojava/nbio/core/sequence/Strand.html" title="enum in org.biojava.nbio.core.sequence" target="classFrame">Strand</a></li>
<li><a href="org/biojava/nbio/survival/cox/StrataInfo.html" title="class in org.biojava.nbio.survival.cox" target="classFrame">StrataInfo</a></li>
<li><a href="org/biojava/nbio/structure/align/pairwise/StrCompAlignment.html" title="class in org.biojava.nbio.structure.align.pairwise" target="classFrame">StrCompAlignment</a></li>
<li><a href="org/biojava/nbio/sequencing/io/fastq/StreamListener.html" title="interface in org.biojava.nbio.sequencing.io.fastq" target="classFrame"><i>StreamListener</i></a></li>
<li><a href="org/biojava/nbio/core/util/StringManipulationHelper.html" title="class in org.biojava.nbio.core.util" target="classFrame">StringManipulationHelper</a></li>
<li><a href="org/biojava/nbio/core/sequence/loader/StringProxySequenceReader.html" title="class in org.biojava.nbio.core.sequence.loader" target="classFrame">StringProxySequenceReader</a></li>