# filelist

dirname: /usr/share/javadoc/biojava-1.7.1/org/biojava/bio/gui
filetypes: dddffffffffffffffffff
filenames:
  sequence/glyph/class-use/package-use.html/package-tree.html/package-summary.html/package-frame.html/TextLogoPainter.html/TextBlock.html/SymbolStyle.html/StackedLogoPainter.html/SimpleSymbolStyle.html/PlainStyle.html/PlainBlock.html/LogoPainter.html/LogoContext.html/FeatureTree.html/DistributionLogo.html/DNAStyle.html/BlockPainter.html/BarLogoPainter.html


dirname: /usr/share/javadoc/biojava-1.7.1/org/biojavax/bio/seq
filetypes: ddfffffffffffffffffffffffffffffffffff
filenames:
  io/class-use/package-use.html/package-tree.html/package-summary.html/package-frame.html/ThinRichSequence.html/SimpleRichSequence.html/SimpleRichLocation.html/SimpleRichFeatureRelationship.html/SimpleRichFeature.html/SimplePosition.html/RichSequenceIterator.html/RichSequenceHandler.html/RichSequence.html/RichSequence.Tools.html/RichSequence.Terms.html/RichSequence.IOTools.html/RichSequence.IOTools.SingleRichSeqIterator.html/RichLocation.html/RichLocation.Tools.html/RichLocation.Strand.html/RichFeatureRelationshipHolder.html/RichFeatureRelationship.html/RichFeature.html/RichFeature.Tools.html/RichFeature.Template.html/PositionResolver.html/PositionResolver.MinimalResolver.html/PositionResolver.MaximalResolver.html/PositionResolver.AverageResolver.html/Position.html/MultiSourceCompoundRichLocation.html/InfinitelyAmbiguousSymbolList.html/EmptyRichLocation.html/DummyRichSequenceHandler.html/CompoundRichLocation.html


dirname: /usr/share/javadoc/biojava-1.7.1/org/biojavax/bio/db/ncbi
filetypes: dffffff
filenames:
  class-use/package-use.html/package-tree.html/package-summary.html/package-frame.html/GenpeptRichSequenceDB.html/GenbankRichSequenceDB.html


dirname: /usr/share/javadoc/biojava-1.7.1/org/biojava/bio/program/formats
filetypes: dfffffffffffff
filenames:
  class-use/package-use.html/package-tree.html/package-summary.html/package-frame.html/Swissprot.html/Ligand.html/Ligand.Reaction.html/Ligand.Enzyme.html/Ligand.Compound.html/FormatTools.html/Format.html/Enzyme.html/Embl.html


dirname: /usr/share/javadoc/biojava-1.7.1/org/biojava/utils/walker
filetypes: dfffffff
filenames:
  class-use/package-use.html/package-tree.html/package-summary.html/package-frame.html/WalkerFactory.html/Walker.html/Visitor.html


dirname: /usr/share/javadoc/biojava-1.7.1/org/biojava/bio/structure/io/mmcif/model/class-use
filetypes: fffffffffffffffff
filenames:
  StructRefSeq.html/StructRef.html/StructKeywords.html/StructAsym.html/Struct.html/Refine.html/PdbxPolySeqScheme.html/PdbxNonPolyScheme.html/PdbxEntityNonPoly.html/Exptl.html/EntityPolySeq.html/Entity.html/DatabasePDBrev.html/DatabasePDBremark.html/ChemComp.html/AtomSite.html/AbstractBean.html


dirname: /usr/share/javadoc/biojava-1.7.1/org/biojava/bio/proteomics/aaindex
filetypes: dfffffffff
filenames:
  class-use/package-use.html/package-tree.html/package-summary.html/package-frame.html/SymbolPropertyTableIterator.html/SymbolPropertyTableDB.html/SimpleSymbolPropertyTableDB.html/AAindexStreamReader.html/AAindex.html


dirname: /usr/share/javadoc/biojava-1.7.1/org/biojava/bio/dist
filetypes: dfffffffffffffffffffffffffffff
filenames:
  class-use/package-use.html/package-tree.html/package-summary.html/package-frame.html/XMLDistributionWriter.html/XMLDistributionReader.html/UntrainableDistribution.html/UniformDistribution.html/TranslatedDistribution.html/SimpleDistributionTrainerContext.html/SimpleDistributionTrainer.html/SimpleDistribution.html/SimpleDistribution.Trainer.html/PairDistribution.html/OrderNDistributionFactory.html/OrderNDistribution.html/IndexedCount.html/IgnoreCountsTrainer.html/GapDistribution.html/DistributionTrainerContext.html/DistributionTrainer.html/DistributionTools.html/DistributionFactory.html/DistributionFactory.DefaultDistributionFactory.html/Distribution.html/Distribution.NullModelForwarder.html/Count.html/AbstractOrderNDistribution.html/AbstractDistribution.html


dirname: /usr/share/javadoc/biojava-1.7.1/org/biojava/bio/program/xff
filetypes: dffffffffffffffffffff
filenames:
  class-use/package-use.html/package-tree.html/package-summary.html/package-frame.html/XFFWriter.html/XFFTools.html/XFFPartHandlerFactory.html/XFFHelper.html/XFFFeatureSetHandler.html/StrandedFeatureHandler.html/PropertyWriter.html/PropDetailHandler.html/LocationHandlerBase.html/FeatureHandler.html/ElementRecognizer.html/ElementRecognizer.HasAttribute.html/ElementRecognizer.ByNSName.html/ElementRecognizer.ByLocalName.html/ElementRecognizer.AllElementRecognizer.html/BasicXFFHelper.html


dirname: /usr/share/javadoc/biojava-1.7.1/org/biojava/bio/structure/jama/class-use
filetypes: fffffff
filenames:
  SingularValueDecomposition.html/QRDecomposition.html/Matrix.html/Maths.html/LUDecomposition.html/EigenvalueDecomposition.html/CholeskyDecomposition.html


dirname: /usr/share/javadoc/biojava-1.7.1/org/biojava/bio/program/blast2html/class-use
filetypes: fffffffffff
filenames:
  URLGeneratorFactory.html/SimpleAlignmentStyler.html/NcbiDatabaseURLGenerator.html/HTMLRenderer.html/EbiDatabaseURLGenerator.html/DefaultURLGeneratorFactory.html/DatabaseURLGenerator.html/ColourCommand.html/Blast2HTMLHandler.html/AlignmentMarker.html/AbstractAlignmentStyler.html


dirname: /usr/share/javadoc/biojava-1.7.1/org/biojava/bio/seq/io/filterxml
filetypes: dfffffffffffffffff
filenames:
  class-use/package-use.html/package-tree.html/package-summary.html/package-frame.html/XMLFilterWriter.html/XMLFilterWriter.FilterWriter.html/XMLFilterHandler.html/XMLFilterHandler.FilterHandlerFactory.html/XMLFilterHandler.FilterHandler.html/XMLAnnotationTypeWriter.html/XMLAnnotationTypeWriter.XMLPropertyConstraintWriter.html/XMLAnnotationTypeWriter.XMLCollectionConstraintWriter.html/XMLAnnotationTypeHandler.html/XMLAnnotationTypeHandler.PropertyConstraintHandlerFactory.html/XMLAnnotationTypeHandler.PropertyConstraintHandler.html/XMLAnnotationTypeHandler.CollectionConstraintHandlerFactory.html/XMLAnnotationTypeHandler.CollectionConstraintHandler.html


dirname: /usr/share/javadoc/biojava-1.7.1/org/biojava/utils
filetypes: dddddddddddddfffffffffffffffffffffffffffffffffffffffffffffffffffffffff
filenames:
  xml/walker/stax/regex/process/net/math/lsid/io/class-use/candy/cache/automata/package-use.html/package-tree.html/package-summary.html/package-frame.html/Unchangeable.html/TypedProperties.html/TriState.html/ThreadPool.html/StaticMemberPlaceHolder.html/SmallSet.html/SmallMap.html/SingletonList.html/SimpleThreadPool.html/Services.html/RepeatedCharSequence.html/ProcessTools.html/ProcessTimeoutException.html/ParserException.html/ParseErrorSource.html/ParseErrorListener.html/ParseErrorEvent.html/OverlayMap.html/ObjectUtil.html/MergingSet.html/MergingIterator.html/ListTools.html/ListTools.Triplet.html/ListTools.SeriesList.html/ListTools.Mapper.html/ListTools.Doublet.html/JDBCPooledDataSource.html/JDBCConnectionPool.html/IndexedChangeHub.html/IndexedChangeHub.ListenerMemento.html/FileAsList.html/ExecRunner.html/Constants.html/Commitable.html/CommitFailure.html/ClassTools.html/Changeable.html/ChangeVetoException.html/ChangeType.html/ChangeSupport.html/ChangeListener.html/ChangeListener.LoggingListener.html/ChangeListener.ChangeEventRecorder.html/ChangeListener.AlwaysVetoListener.html/ChangeHub.html/ChangeForwarder.html/ChangeForwarder.Retyper.html/ChangeEvent.html/ChangeAdapter.html/BeanAsMap.html/AssertionFailure.html/ActivityListener.html/AbstractChangeable.html


dirname: /usr/share/javadoc/biojava-1.7.1/org/biojavax/bio/phylo/io/nexus
filetypes: dfffffffffffffffffffffffffffffffffffffff
filenames:
  class-use/package-use.html/package-tree.html/package-summary.html/package-frame.html/TreesBlockParser.html/TreesBlockListener.html/TreesBlockBuilder.html/TreesBlock.html/TreesBlock.NewickTreeString.html/TaxaBlockParser.html/TaxaBlockListener.html/TaxaBlockBuilder.html/TaxaBlock.html/NexusObject.html/NexusFileListener.html/NexusFileListener.Abstract.html/NexusFileFormat.html/NexusFileBuilder.html/NexusFile.html/NexusComment.html/NexusBlockParser.html/NexusBlockParser.Abstract.html/NexusBlockListener.html/NexusBlockBuilder.html/NexusBlockBuilder.Abstract.html/NexusBlock.html/NexusBlock.Abstract.html/DistancesBlockParser.html/DistancesBlockListener.html/DistancesBlockBuilder.html/DistancesBlock.html/DataBlockParser.html/DataBlockListener.html/DataBlockBuilder.html/DataBlock.html/CharactersBlockParser.html/CharactersBlockListener.html/CharactersBlockBuilder.html/CharactersBlock.html


dirname: /usr/share/javadoc/biojava-1.7.1/org/biojava/utils/io
filetypes: dffffffffffff
filenames:
  class-use/package-use.html/package-tree.html/package-summary.html/package-frame.html/UncompressInputStream.html/Seekable.html/RandomAccessReader.html/RAF.html/LargeBuffer.html/InputStreamProvider.html/CountedBufferedReader.html/CachingInputStream.html


dirname: /usr/share/javadoc/biojava-1.7.1/org/biojava/bio/program/fastq
filetypes: dfffffffffffffff
filenames:
  class-use/package-use.html/package-tree.html/package-summary.html/package-frame.html/SolexaFastqWriter.html/SolexaFastqReader.html/SangerFastqWriter.html/SangerFastqReader.html/IlluminaFastqWriter.html/IlluminaFastqReader.html/FastqWriter.html/FastqVariant.html/FastqReader.html/FastqBuilder.html/Fastq.html


dirname: /usr/share/javadoc/biojava-1.7.1/org/biojava/bio/chromatogram
filetypes: ddffffffffff
filenames:
  graphic/class-use/package-use.html/package-tree.html/package-summary.html/package-frame.html/UnsupportedChromatogramFormatException.html/SimpleChromatogram.html/ChromatogramTools.html/ChromatogramFactory.html/Chromatogram.html/AbstractChromatogram.html


dirname: /usr/share/javadoc/biojava-1.7.1/org/biojava/bio/class-use
filetypes: fffffffffffffffffffffffffffffffffff
filenames:
  SmallAnnotation.html/SimpleAnnotation.html/PropertyConstraint.html/PropertyConstraint.Or.html/PropertyConstraint.ExactValue.html/PropertyConstraint.Enumeration.html/PropertyConstraint.ByClass.html/PropertyConstraint.ByAnnotationType.html/PropertyConstraint.And.html/OverlayAnnotation.html/OverlayAnnotation.PropertyForwarder.html/MergeAnnotation.html/MergeAnnotation.PropertyForwarder.html/EcNumber.html/EcNumber.Impl.html/CollectionConstraint.html/CollectionConstraint.Or.html/CollectionConstraint.Contains.html/CollectionConstraint.And.html/CollectionConstraint.AllValuesIn.html/CardinalityConstraint.html/BioRuntimeException.html/BioException.html/BioError.html/BeanAsAnnotation.html/AnnotationType.html/AnnotationType.Impl.html/AnnotationType.Abstract.html/AnnotationTools.html/AnnotationRenamer.html/AnnotationChanger.html/Annotation.html/Annotatable.html/Annotatable.AnnotationForwarder.html/AbstractAnnotation.html


dirname: /usr/share/javadoc/biojava-1.7.1/org/biojava/bio/gui/glyph/class-use
filetypes: fffffff
filenames:
  TwoHeadedArrowGlyph.html/TurnGlyph.html/RectangleGlyph.html/HelixGlyph.html/GlyphUtils.html/Glyph.html/ArrowGlyph.html


dirname: /usr/share/javadoc/biojava-1.7.1/org/biojava/bio/alignment/class-use
filetypes: fffffffffffffff
filenames:
  UnequalLengthAlignment.html/SubstitutionMatrix.html/SmithWaterman.html/SimpleAlignmentElement.html/SequenceAlignment.html/QualitativeAlignment.html/NeedlemanWunsch.html/IllegalAlignmentEditException.html/FlexibleAlignment.html/EditableAlignment.html/AlignmentElement.html/AbstractULAlignment.html/AbstractULAlignment.SubULAlignment.html/AbstractULAlignment.LeftRightLocationComparator.html/ARAlignment.html


dirname: /usr/share/javadoc/biojava-1.7.1/org/biojava/utils/io/class-use
filetypes: ffffffff
filenames:
  UncompressInputStream.html/Seekable.html/RandomAccessReader.html/RAF.html/LargeBuffer.html/InputStreamProvider.html/CountedBufferedReader.html/CachingInputStream.html


dirname: /usr/share/javadoc/biojava-1.7.1/org/biojava/bio/structure/gui/util
filetypes: dfffffffffffffff
filenames:
  class-use/package-use.html/package-tree.html/package-summary.html/package-frame.html/StructurePairSelector.html/SequenceScalePanel.html/SequenceMouseListener.html/PDBUploadPanel.html/PDBServerPanel.html/PDBDirPanel.html/MenuCreator.html/CoordManager.html/AlternativeAlignmentFrame.html/AlignmentCalc.html/AlignedPosition.html


dirname: /usr/share/javadoc/biojava-1.7.1/org/biojava/utils/automata
filetypes: dffffffffffffffff
filenames:
  class-use/package-use.html/package-tree.html/package-summary.html/package-frame.html/StateMachineInstance.html/StateMachineFactory.html/PatternMaker.html/PatternListener.html/PatternBlitz.html/NfaSubModel.html/NfaBuilder.html/Nfa.html/FiniteAutomaton.html/DfaBuilder.html/AutomatonException.html/ArrayStateMachineToolkit.html


dirname: /usr/share/javadoc/biojava-1.7.1/org/biojavax/bio/db
filetypes: dddffffffffffff
filenames:
  ncbi/class-use/biosql/package-use.html/package-tree.html/package-summary.html/package-frame.html/RichSequenceDBLite.html/RichSequenceDB.html/HashRichSequenceDB.html/HashBioEntryDB.html/BioEntryDBLite.html/BioEntryDB.html/AbstractRichSequenceDB.html/AbstractBioEntryDB.html


dirname: /usr/share/javadoc/biojava-1.7.1/org/biojava/bio/structure/server
filetypes: dfffffffffffffffff
filenames:
  class-use/package-use.html/package-tree.html/package-summary.html/package-frame.html/StructureServer.html/StructureListener.html/StructureFetcherRunnable.html/StructureEventImpl.html/StructureEvent.html/SimpleStructureServer.html/PrepareMMcifIndexFile.html/PrepareIndexFile.html/PDBInstallation.html/PDBFilter.html/MMCIFFileInstallation.html/FlatFileInstallation.html/DemoStructureServer.html


dirname: /usr/share/javadoc/biojava-1.7.1/org/biojava/bio/program/tagvalue
filetypes: dffffffffffffffffffffffffffffffffffffffffffff
filenames:
  class-use/package-use.html/package-tree.html/package-summary.html/package-frame.html/ValueChanger.html/TagValueWrapper.html/TagValueParser.html/TagValueListener.html/TagValueContext.html/TagValue.html/TagRenamer.html/TagMapper.html/TagDropper.html/TagDelegator.html/StateMachine.html/StateMachine.TransitionTable.html/StateMachine.Transition.html/StateMachine.State.html/StateMachine.SimpleStateListener.html/StateMachine.ExitNotification.html/StateMachine.BasicState.html/SimpleTagValueWrapper.html/RegexSplitter.html/RegexParser.html/RegexFieldFinder.html/RegexChanger.html/PropertyChanger.html/ParserListener.html/Parser.html/MultiTagger.html/LineSplitParser.html/Indexer2.html/Indexer.html/Index2Model.html/Formats.html/Echo.html/ChangeTable.html/ChangeTable.Splitter.html/ChangeTable.Changer.html/ChangeTable.ChainedChanger.html/BoundaryFinder.html/AnnotationBuilder.html/Aggregator.html/AbstractWrapper.html


dirname: /usr/share/javadoc/biojava-1.7.1/org/biojava/ontology/obo
filetypes: dffffffff
filenames:
  class-use/package-use.html/package-tree.html/package-summary.html/package-frame.html/OboFileParser.html/OboFileParser.SOPair.html/OboFileHandler.html/OboFileEventListener.html


dirname: /usr/share/javadoc/biojava-1.7.1/org/biojava/stats/svm
filetypes: ddfffffffffffffffffffffffffffffff
filenames:
  tools/class-use/package-use.html/package-tree.html/package-summary.html/package-frame.html/TrainingListener.html/TrainingEvent.html/TrainingContext.html/SparseVector.html/SparseVector.NormalizingKernel.html/SimpleSVMTarget.html/SimpleSVMClassifierModel.html/SimpleItemValue.html/SigmoidKernel.html/SVMTarget.html/SVMRegressionModel.html/SVMKernel.html/SVMClassifierModel.html/SMOTrainer.html/SMORegressionTrainer.html/RadialBaseKernel.html/PolynomialKernel.html/NormalizingKernel.html/NestedKernel.html/ListSumKernel.html/LinearKernel.html/ItemValue.html/DiagonalCachingKernel.html/DiagonalAddKernel.html/CachingKernel.html/AbstractSVMTarget.html/AbstractSVMClassifierModel.html


dirname: /usr/share/javadoc/biojava-1.7.1/org/biojava/bio/annodb
filetypes: dffffffffffff
filenames:
  class-use/package-use.html/package-tree.html/package-summary.html/package-frame.html/SimpleAnnotationDB.html/MergingAnnotationDB.html/LazySearchedAnnotationDB.html/LazyFilteredAnnotationDB.html/IndexedAnnotationDB.html/IndexedAnnotationDB.StaticMethodRPFactory.html/IndexedAnnotationDB.ParserListenerFactory.html/AnnotationDB.html


dirname: /usr/share/javadoc/biojava-1.7.1/org/biojavax/bio/class-use
filetypes: fffff
filenames:
  SimpleBioEntryRelationship.html/SimpleBioEntry.html/BioEntryRelationship.html/BioEntryIterator.html/BioEntry.html


dirname: /usr/share/javadoc/biojava-1.7.1/org/biojava/bio/molbio/class-use
filetypes: fffffff
filenames:
  RestrictionSite.html/RestrictionSite.Template.html/RestrictionMapper.html/RestrictionEnzymeManager.html/RestrictionEnzyme.html/DNAComposition.html/Composition.html


dirname: /usr/share/javadoc/biojava-1.7.1/org/biojava/bio/gui/class-use
filetypes: ffffffffffffff
filenames:
  TextLogoPainter.html/TextBlock.html/SymbolStyle.html/StackedLogoPainter.html/SimpleSymbolStyle.html/PlainStyle.html/PlainBlock.html/LogoPainter.html/LogoContext.html/FeatureTree.html/DistributionLogo.html/DNAStyle.html/BlockPainter.html/BarLogoPainter.html


dirname: /usr/share/javadoc/biojava-1.7.1/org/biojava/bio/symbol/class-use
filetypes: ffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffff
filenames:
  WobbleDistribution.html/UkkonenSuffixTree.html/UkkonenSuffixTree.SuffixNode.html/TranslationTable.html/SymbolPropertyTable.html/SymbolListViews.html/SymbolListFactory.html/SymbolList.html/Symbol.html/SuffixTree.html/SuffixTree.SuffixNode.html/SoftMaskedAlphabet.html/SoftMaskedAlphabet.MaskingDetector.html/SoftMaskedAlphabet.MaskingDetector.DefaultMaskingDetector.html/SoftMaskedAlphabet.CaseSensitiveTokenization.html/SingletonAlphabet.html/SimpleTranslationTable.html/SimpleSymbolPropertyTable.html/SimpleSymbolListFactory.html/SimpleSymbolList.html/SimpleReversibleTranslationTable.html/SimpleManyToOneTranslationTable.html/SimpleGeneticCodeTable.html/SimpleGappedSymbolList.html/SimpleGappedSymbolList.Block.html/SimpleCodonPref.html/SimpleAtomicSymbol.html/SimpleAlphabet.html/SimpleAlignment.html/ReversibleTranslationTable.html/RelabeledAlignment.html/RangeLocation.html/PointLocation.html/PackingFactory.html/Packing.html/PackedSymbolListFactory.html/PackedSymbolList.html/MotifTools.html/MergeLocation.html/ManyToOneTranslationTable.html/LocationTools.html/Location.html/IntegerAlphabet.html/IntegerAlphabet.SubIntegerAlphabet.html/IntegerAlphabet.IntegerSymbol.html/IllegalSymbolException.html/IllegalAlphabetException.html/GappedSymbolList.html/FuzzyPointLocation.html/FuzzyPointLocation.PointResolver.html/FuzzyLocation.html/FuzzyLocation.RangeResolver.html/FundamentalAtomicSymbol.html/FiniteAlphabet.html/Edit.html/DummySymbolList.html/DoubleAlphabet.html/DoubleAlphabet.SubDoubleAlphabet.html/DoubleAlphabet.DoubleSymbol.html/DoubleAlphabet.DoubleRange.html/DNANoAmbPack.html/DNAAmbPack.html/CodonPrefTools.html/CodonPrefFilter.html/CodonPrefFilter.EverythingToXML.html/CodonPrefFilter.ByName.html/CodonPrefFilter.AcceptAll.html/CodonPref.html/CircularLocation.html/ChunkedSymbolList.html/BetweenLocation.html/BasisSymbol.html/AtomicSymbol.html/AlphabetManager.html/AlphabetIndex.html/Alphabet.html/Alignment.html/Alignment.SymbolListIterator.html/AbstractSymbolList.html/AbstractSymbolList.EditTranslater.html/AbstractSymbolList.EditScreener.html/AbstractSymbol.html/AbstractReversibleTranslationTable.html/AbstractRangeLocation.html/AbstractManyToOneTranslationTable.html/AbstractLocationDecorator.html/AbstractLocation.html/AbstractAlphabet.html


dirname: /usr/share/javadoc/biojava-1.7.1/org/biojava/bio/alignment
filetypes: dfffffffffffffffffff
filenames:
  class-use/package-use.html/package-tree.html/package-summary.html/package-frame.html/UnequalLengthAlignment.html/SubstitutionMatrix.html/SmithWaterman.html/SimpleAlignmentElement.html/SequenceAlignment.html/QualitativeAlignment.html/NeedlemanWunsch.html/IllegalAlignmentEditException.html/FlexibleAlignment.html/EditableAlignment.html/AlignmentElement.html/AbstractULAlignment.html/AbstractULAlignment.SubULAlignment.html/AbstractULAlignment.LeftRightLocationComparator.html/ARAlignment.html


dirname: /usr/share/javadoc/biojava-1.7.1/org/biojava/bio/structure/gui/events
filetypes: dffffff
filenames:
  class-use/package-use.html/package-tree.html/package-summary.html/package-frame.html/JmolAlignedPositionListener.html/AlignmentPositionListener.html


dirname: /usr/share/javadoc/biojava-1.7.1/org/biojava/bio/seq/io/class-use
filetypes: fffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffff
filenames:
  WordTokenization.html/SymbolTokenization.html/SymbolTokenization.TokenType.html/SymbolReader.html/SymbolListCharSequence.html/SwissprotProcessor.html/SwissprotProcessor.Factory.html/SwissprotFileFormer.html/SubIntegerTokenization.html/StreamWriter.html/StreamReader.html/StreamParser.html/SmartSequenceBuilder.html/SimpleSequenceBuilder.html/SimpleAssemblyBuilder.html/SequenceFormat.html/SequenceDBSequenceBuilder.html/SequenceBuilderFilter.html/SequenceBuilderFactory.html/SequenceBuilderBase.html/SequenceBuilder.html/SeqIOTools.html/SeqIOListener.html/SeqIOFilter.html/SeqIOEventEmitter.html/SeqIOConstants.html/SeqIOAdapter.html/SeqFileFormer.html/ReferenceAnnotation.html/ProteinRefSeqProcessor.html/ProteinRefSeqProcessor.Factory.html/ProteinRefSeqFileFormer.html/ParseException.html/OrganismParser.html/OrganismParser.Factory.html/NameTokenization.html/MSFAlignmentFormat.html/IntegerTokenization.html/GenpeptFormat.html/GenbankXmlFormat.html/GenbankProcessor.html/GenbankProcessor.Factory.html/GenbankFormat.html/GenbankFileFormer.html/GenEmblPropertyComparator.html/GenEmblFeatureComparator.html/GAMEFormat.html/FeatureTableParser.html/FastaFormat.html/FastaDescriptionLineParser.html/FastaDescriptionLineParser.Factory.html/FastaAlignmentFormat.html/EmblReferenceComparator.html/EmblProcessor.html/EmblProcessor.Factory.html/EmblLikeLocationParser.html/EmblLikeFormat.html/EmblFileFormer.html/DoubleTokenization.html/CrossProductTokenization.html/ChunkedSymbolListFactory.html/CharacterTokenization.html/AlternateTokenization.html/AlignmentFormat.html/AlignIOConstants.html


dirname: /usr/share/javadoc/biojava-1.7.1/org/biojava/bio/seq/io/agave/class-use
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filenames:
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dirname: /usr/share/javadoc/biojava-1.7.1/org/biojava/bio/seq/db/emblcd/class-use
filetypes: fffffff
filenames:
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dirname: /usr/share/javadoc/biojava-1.7.1/org/biojava/bio/proteomics
filetypes: ddfffffffffff
filenames:
  class-use/aaindex/package-use.html/package-tree.html/package-summary.html/package-frame.html/StructureTools.html/ProteaseManager.html/Protease.html/MassCalc.html/IsoelectricPointCalc.html/IsoelectricPointCalc.ChargeCalculator.html/Digest.html


dirname: /usr/share/javadoc/biojava-1.7.1/org/biojava/bio/structure/io
filetypes: ddffffffffffffffff
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