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Jar File Download » b » biojava   Download biojava-1.7.1.jar  Files contained in biojava-1.7.1.jar:  META-INF/MANIFEST.MF org.biojava.bibliography.BibRef.class org.biojava.bibliography.BibRefException.class org.biojava.bibliography.BibRefQuery.class org.biojava.bibliography.BibRefSupport.class org.biojava.bibliography.BiblioArticle.class org.biojava.bibliography.BiblioBook.class org.biojava.bibliography.BiblioBookArticle.class org.biojava.bibliography.BiblioCriterion.class org.biojava.bibliography.BiblioDescription.class org.biojava.bibliography.BiblioEntryStatus.class org.biojava.bibliography.BiblioJournal.class org.biojava.bibliography.BiblioJournalArticle.class org.biojava.bibliography.BiblioOrganisation.class org.biojava.bibliography.BiblioPatent.class org.biojava.bibliography.BiblioPerson.class org.biojava.bibliography.BiblioProceeding.class org.biojava.bibliography.BiblioProvider.class org.biojava.bibliography.BiblioScope.class org.biojava.bibliography.BiblioService.class org.biojava.bibliography.BiblioSubject.class org.biojava.bibliography.BiblioTechReport.class org.biojava.bibliography.BiblioThesis.class org.biojava.bibliography.BiblioWebResource.class org.biojava.bio.AbstractAnnotation.class org.biojava.bio.Annotatable.class org.biojava.bio.Annotation.class org.biojava.bio.AnnotationChanger.class org.biojava.bio.AnnotationRenamer.class org.biojava.bio.AnnotationTools.class org.biojava.bio.AnnotationType.class org.biojava.bio.AnyPropertyConstraint.class org.biojava.bio.BeanAsAnnotation.class org.biojava.bio.BioError.class org.biojava.bio.BioException.class org.biojava.bio.BioRuntimeException.class org.biojava.bio.CardinalityConstraint.class org.biojava.bio.CollectionConstraint.class org.biojava.bio.EcNumber.class org.biojava.bio.EmptyAnnotation.class org.biojava.bio.MergeAnnotation.class org.biojava.bio.NoneCollectionConstraint.class org.biojava.bio.NonePropertyConstraint.class org.biojava.bio.OverlayAnnotation.class org.biojava.bio.PropertyConstraint.class org.biojava.bio.SimpleAnnotation.class org.biojava.bio.SmallAnnotation.class org.biojava.bio.alignment.ARAlignment.class org.biojava.bio.alignment.AbstractULAlignment.class org.biojava.bio.alignment.AlignmentElement.class org.biojava.bio.alignment.EditableAlignment.class org.biojava.bio.alignment.FlexibleAlignment.class org.biojava.bio.alignment.IllegalAlignmentEditException.class org.biojava.bio.alignment.NeedlemanWunsch.class org.biojava.bio.alignment.QualitativeAlignment.class org.biojava.bio.alignment.SequenceAlignment.class org.biojava.bio.alignment.SimpleAlignmentElement.class org.biojava.bio.alignment.SmithWaterman.class org.biojava.bio.alignment.SubstitutionMatrix.class org.biojava.bio.alignment.UnequalLengthAlignment.class org.biojava.bio.annodb.AnnotationDB.class org.biojava.bio.annodb.EmptyAnnotationDB.class org.biojava.bio.annodb.IndexedAnnotationDB.class org.biojava.bio.annodb.LazyFilteredAnnotationDB.class org.biojava.bio.annodb.LazySearchedAnnotationDB.class org.biojava.bio.annodb.MergingAnnotationDB.class org.biojava.bio.annodb.SimpleAnnotationDB.class org.biojava.bio.chromatogram.AbstractChromatogram.class org.biojava.bio.chromatogram.Chromatogram.class org.biojava.bio.chromatogram.ChromatogramFactory.class org.biojava.bio.chromatogram.ChromatogramTools.class org.biojava.bio.chromatogram.SimpleChromatogram.class org.biojava.bio.chromatogram.UnsupportedChromatogramFormatException.class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic.class org.biojava.bio.chromatogram.graphic.ChromatogramNonlinearScaler.class org.biojava.bio.chromatogram.graphic.FixedBaseWidthScaler.class org.biojava.bio.dist.AbstractDistribution.class org.biojava.bio.dist.AbstractOrderNDistribution.class org.biojava.bio.dist.Count.class org.biojava.bio.dist.Distribution.class org.biojava.bio.dist.DistributionFactory.class org.biojava.bio.dist.DistributionTools.class org.biojava.bio.dist.DistributionTrainer.class org.biojava.bio.dist.DistributionTrainerContext.class org.biojava.bio.dist.GapDistribution.class org.biojava.bio.dist.GeneralNthOrderDistribution.class org.biojava.bio.dist.IgnoreCountsTrainer.class org.biojava.bio.dist.IndexedCount.class org.biojava.bio.dist.IndexedNthOrderDistribution.class org.biojava.bio.dist.OrderNDistribution.class org.biojava.bio.dist.OrderNDistributionFactory.class org.biojava.bio.dist.PairDistribution.class org.biojava.bio.dist.SimpleDistribution.class org.biojava.bio.dist.SimpleDistributionTrainer.class org.biojava.bio.dist.SimpleDistributionTrainerContext.class org.biojava.bio.dist.TranslatedDistribution.class org.biojava.bio.dist.UniformDistribution.class org.biojava.bio.dist.UntrainableDistribution.class org.biojava.bio.dist.XMLDistributionReader.class org.biojava.bio.dist.XMLDistributionWriter.class org.biojava.bio.dp.AbstractTrainer.class org.biojava.bio.dp.BackPointer.class org.biojava.bio.dp.BaumWelchSampler.class org.biojava.bio.dp.BaumWelchTrainer.class org.biojava.bio.dp.DP.class org.biojava.bio.dp.DPFactory.class org.biojava.bio.dp.DPMatrix.class org.biojava.bio.dp.DotState.class org.biojava.bio.dp.EmissionState.class org.biojava.bio.dp.FlatModel.class org.biojava.bio.dp.HMMTrainer.class org.biojava.bio.dp.IllegalTransitionException.class org.biojava.bio.dp.MagicalState.class org.biojava.bio.dp.MarkovModel.class org.biojava.bio.dp.ModelInState.class org.biojava.bio.dp.ModelTrainer.class org.biojava.bio.dp.ProfileHMM.class org.biojava.bio.dp.ScoreType.class org.biojava.bio.dp.SimpleDotState.class org.biojava.bio.dp.SimpleEmissionState.class org.biojava.bio.dp.SimpleHMMTrainer.class org.biojava.bio.dp.SimpleMarkovModel.class org.biojava.bio.dp.SimpleModelInState.class org.biojava.bio.dp.SimpleModelTrainer.class org.biojava.bio.dp.SimpleStatePath.class org.biojava.bio.dp.SimpleWeightMatrix.class org.biojava.bio.dp.State.class org.biojava.bio.dp.StatePath.class org.biojava.bio.dp.StoppingCriteria.class org.biojava.bio.dp.Trainable.class org.biojava.bio.dp.TrainerTransition.class org.biojava.bio.dp.TrainingAlgorithm.class org.biojava.bio.dp.Transition.class org.biojava.bio.dp.TransitionTrainer.class org.biojava.bio.dp.WMAsMM.class org.biojava.bio.dp.WeightMatrix.class org.biojava.bio.dp.WeightMatrixAnnotator.class org.biojava.bio.dp.XmlMarkovModel.class org.biojava.bio.dp.onehead.AbstractCursor.class org.biojava.bio.dp.onehead.DPCursor.class org.biojava.bio.dp.onehead.MatrixCursor.class org.biojava.bio.dp.onehead.SingleDP.class org.biojava.bio.dp.onehead.SingleDPMatrix.class org.biojava.bio.dp.onehead.SmallCursor.class org.biojava.bio.dp.twohead.AbstractMatrixPairDPCursor.class org.biojava.bio.dp.twohead.BackMatrixPairDPCursor.class org.biojava.bio.dp.twohead.Cell.class org.biojava.bio.dp.twohead.CellCalculator.class org.biojava.bio.dp.twohead.CellCalculatorFactory.class org.biojava.bio.dp.twohead.CellCalculatorFactoryMaker.class org.biojava.bio.dp.twohead.DPCompiler.class org.biojava.bio.dp.twohead.DPInterpreter.class org.biojava.bio.dp.twohead.EmissionCache.class org.biojava.bio.dp.twohead.LightPairDPCursor.class org.biojava.bio.dp.twohead.MatrixPairDPCursor.class org.biojava.bio.dp.twohead.PairDPCursor.class org.biojava.bio.dp.twohead.PairDPMatrix.class org.biojava.bio.dp.twohead.PairwiseDP.class org.biojava.bio.gui.BarLogoPainter.class org.biojava.bio.gui.BlockPainter.class org.biojava.bio.gui.DNAStyle.class org.biojava.bio.gui.DistributionLogo.class org.biojava.bio.gui.FeatureTree.class org.biojava.bio.gui.LogoContext.class org.biojava.bio.gui.LogoPainter.class org.biojava.bio.gui.PlainBlock.class org.biojava.bio.gui.PlainStyle.class org.biojava.bio.gui.SimpleSymbolStyle.class org.biojava.bio.gui.StackedLogoPainter.class org.biojava.bio.gui.SymbolStyle.class org.biojava.bio.gui.TextBlock.class org.biojava.bio.gui.TextLogoPainter.class org.biojava.bio.gui.glyph.ArrowGlyph.class org.biojava.bio.gui.glyph.Glyph.class org.biojava.bio.gui.glyph.GlyphUtils.class org.biojava.bio.gui.glyph.HelixGlyph.class org.biojava.bio.gui.glyph.RectangleGlyph.class org.biojava.bio.gui.glyph.TurnGlyph.class org.biojava.bio.gui.glyph.TwoHeadedArrowGlyph.class org.biojava.bio.gui.sequence.AbiTraceRenderer.class org.biojava.bio.gui.sequence.AbstractBeadRenderer.class org.biojava.bio.gui.sequence.AbstractPeptideDigestRenderer.class org.biojava.bio.gui.sequence.AlignmentRenderer.class org.biojava.bio.gui.sequence.ArrowedFeatureRenderer.class org.biojava.bio.gui.sequence.BasicFeatureRenderer.class org.biojava.bio.gui.sequence.BasicImapRenderer.class org.biojava.bio.gui.sequence.BeadFeatureRenderer.class org.biojava.bio.gui.sequence.BumpedRenderer.class org.biojava.bio.gui.sequence.CircularFeatureFilteringRenderer.class org.biojava.bio.gui.sequence.CircularFeatureRenderer.class org.biojava.bio.gui.sequence.CircularFeaturesRenderer.class org.biojava.bio.gui.sequence.CircularMLR.class org.biojava.bio.gui.sequence.CircularPaddedRenderer.class org.biojava.bio.gui.sequence.CircularRenderer.class org.biojava.bio.gui.sequence.CircularRendererContext.class org.biojava.bio.gui.sequence.CircularRendererPanel.class org.biojava.bio.gui.sequence.CrosshairRenderer.class org.biojava.bio.gui.sequence.EllipticalBeadRenderer.class org.biojava.bio.gui.sequence.FeatureBlockSequenceRenderer.class org.biojava.bio.gui.sequence.FeatureLabelRenderer.class org.biojava.bio.gui.sequence.FeatureRenderer.class org.biojava.bio.gui.sequence.FeatureSource.class org.biojava.bio.gui.sequence.FilteringRenderer.class org.biojava.bio.gui.sequence.GUITools.class org.biojava.bio.gui.sequence.GappedRenderer.class org.biojava.bio.gui.sequence.GlyphFeatureRenderer.class org.biojava.bio.gui.sequence.HeadlessRenderContext.class org.biojava.bio.gui.sequence.ImageMap.class org.biojava.bio.gui.sequence.ImageMapRenderer.class org.biojava.bio.gui.sequence.LabelRenderer.class org.biojava.bio.gui.sequence.LabelledSequenceRenderer.class org.biojava.bio.gui.sequence.LayeredRenderer.class org.biojava.bio.gui.sequence.LineInfo.class org.biojava.bio.gui.sequence.MultiLineRenderer.class org.biojava.bio.gui.sequence.OffsetRulerRenderer.class org.biojava.bio.gui.sequence.OverlayMarker.class org.biojava.bio.gui.sequence.OverlayRendererWrapper.class org.biojava.bio.gui.sequence.PaddingRenderer.class org.biojava.bio.gui.sequence.PairwiseDiagonalRenderer.class org.biojava.bio.gui.sequence.PairwiseFilteringRenderer.class org.biojava.bio.gui.sequence.PairwiseOverlayRenderer.class org.biojava.bio.gui.sequence.PairwiseRenderContext.class org.biojava.bio.gui.sequence.PairwiseSequencePanel.class org.biojava.bio.gui.sequence.PairwiseSequenceRenderer.class org.biojava.bio.gui.sequence.PeptideDigestRenderer.class org.biojava.bio.gui.sequence.RectangularBeadRenderer.class org.biojava.bio.gui.sequence.RectangularImapRenderer.class org.biojava.bio.gui.sequence.RoundRectangularBeadRenderer.class org.biojava.bio.gui.sequence.RulerRenderer.class org.biojava.bio.gui.sequence.SecondaryStructureFeatureRenderer.class org.biojava.bio.gui.sequence.SequencePanel.class org.biojava.bio.gui.sequence.SequencePanelWrapper.class org.biojava.bio.gui.sequence.SequencePoster.class org.biojava.bio.gui.sequence.SequenceRenderContext.class org.biojava.bio.gui.sequence.SequenceRenderer.class org.biojava.bio.gui.sequence.SequenceRendererWrapper.class org.biojava.bio.gui.sequence.SequenceViewerEvent.class org.biojava.bio.gui.sequence.SequenceViewerListener.class org.biojava.bio.gui.sequence.SequenceViewerMotionListener.class org.biojava.bio.gui.sequence.SequenceViewerMotionSupport.class org.biojava.bio.gui.sequence.SequenceViewerSupport.class org.biojava.bio.gui.sequence.SimpleLabelRenderer.class org.biojava.bio.gui.sequence.SixFrameRenderer.class org.biojava.bio.gui.sequence.SixFrameZiggyRenderer.class org.biojava.bio.gui.sequence.StackedFeatureRenderer.class org.biojava.bio.gui.sequence.StopRenderer.class org.biojava.bio.gui.sequence.SubCircularRendererContext.class org.biojava.bio.gui.sequence.SubPairwiseRenderContext.class org.biojava.bio.gui.sequence.SubSequenceRenderContext.class org.biojava.bio.gui.sequence.SymbolSequenceRenderer.class org.biojava.bio.gui.sequence.TickFeatureRenderer.class org.biojava.bio.gui.sequence.TranslatedSequencePanel.class org.biojava.bio.gui.sequence.ZiggyFeatureRenderer.class org.biojava.bio.gui.sequence.ZiggyImapRenderer.class org.biojava.bio.gui.sequence.tracklayout.SimpleTrackLayout.class org.biojava.bio.gui.sequence.tracklayout.TrackLayout.class org.biojava.bio.gui.sequence.tracklayout.UserDefinedTrackLayout.class org.biojava.bio.molbio.Composition.class org.biojava.bio.molbio.DNAComposition.class org.biojava.bio.molbio.RestrictionEnzyme.class org.biojava.bio.molbio.RestrictionEnzymeManager.class org.biojava.bio.molbio.RestrictionMapper.class org.biojava.bio.molbio.RestrictionSite.class org.biojava.bio.molbio.RestrictionSiteFinder.class org.biojava.bio.program.BlastLikeToXMLConverter.class org.biojava.bio.program.Meme.class org.biojava.bio.program.PdbToXMLConverter.class org.biojava.bio.program.abi.ABIFChromatogram.class org.biojava.bio.program.abi.ABIFParser.class org.biojava.bio.program.abi.ABITools.class org.biojava.bio.program.abi.ABITrace.class org.biojava.bio.program.blast2html.AbstractAlignmentStyler.class org.biojava.bio.program.blast2html.AlignmentMarker.class org.biojava.bio.program.blast2html.AlignmentStyler.class org.biojava.bio.program.blast2html.Blast2HTMLHandler.class org.biojava.bio.program.blast2html.BlastLikeAlignment.class org.biojava.bio.program.blast2html.BlastMatrixAlignmentStyler.class org.biojava.bio.program.blast2html.ColourCommand.class org.biojava.bio.program.blast2html.DatabaseURLGenerator.class org.biojava.bio.program.blast2html.DefaultURLGeneratorFactory.class org.biojava.bio.program.blast2html.DetailHit.class org.biojava.bio.program.blast2html.EbiDatabaseURLGenerator.class org.biojava.bio.program.blast2html.HSP.class org.biojava.bio.program.blast2html.HSPSummary.class org.biojava.bio.program.blast2html.HTMLRenderer.class org.biojava.bio.program.blast2html.HitDescription.class org.biojava.bio.program.blast2html.HitId.class org.biojava.bio.program.blast2html.HitSummary.class org.biojava.bio.program.blast2html.NcbiDatabaseURLGenerator.class org.biojava.bio.program.blast2html.Sequence.class org.biojava.bio.program.blast2html.SimpleAlignmentStyler.class org.biojava.bio.program.blast2html.URLGeneratorFactory.class org.biojava.bio.program.das.ComponentFeatureHandler.class org.biojava.bio.program.das.DAS.class org.biojava.bio.program.das.DASAnnotationDistDataSource.class org.biojava.bio.program.das.DASCapabilities.class org.biojava.bio.program.das.DASComponentFeature.class org.biojava.bio.program.das.DASDistDataSource.class org.biojava.bio.program.das.DASFeatureSet.class org.biojava.bio.program.das.DASGFFFeatureHandler.class org.biojava.bio.program.das.DASLink.class org.biojava.bio.program.das.DASLinkHandler.class org.biojava.bio.program.das.DASRawSymbolList.class org.biojava.bio.program.das.DASSequence.class org.biojava.bio.program.das.DASSequenceDB.class org.biojava.bio.program.das.DASSequenceDBProvider.class org.biojava.bio.program.das.DASSequenceI.class org.biojava.bio.program.das.DataSource.class org.biojava.bio.program.das.FeatureFetcher.class org.biojava.bio.program.das.FeatureRequestManager.class org.biojava.bio.program.das.Fetcher.class org.biojava.bio.program.das.RawAnnotationSequence.class org.biojava.bio.program.das.ReferenceServer.class org.biojava.bio.program.das.Segment.class org.biojava.bio.program.das.TypesFetcher.class org.biojava.bio.program.das.TypesListener.class org.biojava.bio.program.das.dasalignment.Alignment.class org.biojava.bio.program.das.dasalignment.DASAlignmentCall.class org.biojava.bio.program.das.dasalignment.DASAlignmentClient.class org.biojava.bio.program.das.dasalignment.DASAlignmentXMLResponseParser.class org.biojava.bio.program.das.dasalignment.DASException.class org.biojava.bio.program.das.dasstructure.DASStructureCall.class org.biojava.bio.program.das.dasstructure.DASStructureXMLResponseParser.class org.biojava.bio.program.fastq.AbstractFastqReader.class org.biojava.bio.program.fastq.AbstractFastqWriter.class org.biojava.bio.program.fastq.Fastq.class org.biojava.bio.program.fastq.FastqBuilder.class org.biojava.bio.program.fastq.FastqReader.class org.biojava.bio.program.fastq.FastqVariant.class org.biojava.bio.program.fastq.FastqWriter.class org.biojava.bio.program.fastq.IlluminaFastqReader.class org.biojava.bio.program.fastq.IlluminaFastqWriter.class org.biojava.bio.program.fastq.SangerFastqReader.class org.biojava.bio.program.fastq.SangerFastqWriter.class org.biojava.bio.program.fastq.SolexaFastqReader.class org.biojava.bio.program.fastq.SolexaFastqWriter.class org.biojava.bio.program.formats.Embl.class org.biojava.bio.program.formats.Enzyme.class org.biojava.bio.program.formats.Format.class org.biojava.bio.program.formats.FormatTools.class org.biojava.bio.program.formats.Ligand.class org.biojava.bio.program.formats.Swissprot.class org.biojava.bio.program.gff3.GFF3DocumentHandler.class org.biojava.bio.program.gff3.GFF3Parser.class org.biojava.bio.program.gff3.GFF3Record.class org.biojava.bio.program.gff.GFFComparator.class org.biojava.bio.program.gff.GFFDocumentHandler.class org.biojava.bio.program.gff.GFFEntrySet.class org.biojava.bio.program.gff.GFFErrorHandler.class org.biojava.bio.program.gff.GFFFilterer.class org.biojava.bio.program.gff.GFFParser.class org.biojava.bio.program.gff.GFFRecord.class org.biojava.bio.program.gff.GFFRecordFilter.class org.biojava.bio.program.gff.GFFTools.class org.biojava.bio.program.gff.GFFWriter.class org.biojava.bio.program.gff.IgnoreRecordException.class org.biojava.bio.program.gff.SequencesAsGFF.class org.biojava.bio.program.gff.SimpleGFFRecord.class org.biojava.bio.program.hmmer.FullHmmerProfileHMM.class org.biojava.bio.program.hmmer.HmmerProfileHMM.class org.biojava.bio.program.hmmer.HmmerProfileParser.class org.biojava.bio.program.hmmer.ProfileEmissionState.class org.biojava.bio.program.homologene.AbstractOrthoPairCollection.class org.biojava.bio.program.homologene.AbstractOrthoPairSet.class org.biojava.bio.program.homologene.AbstractOrthologueSet.class org.biojava.bio.program.homologene.DuplicateTaxonException.class org.biojava.bio.program.homologene.HomologeneBuilder.class org.biojava.bio.program.homologene.HomologeneDB.class org.biojava.bio.program.homologene.HomologeneTools.class org.biojava.bio.program.homologene.OrthoPair.class org.biojava.bio.program.homologene.OrthoPairCollection.class org.biojava.bio.program.homologene.OrthoPairFilter.class org.biojava.bio.program.homologene.OrthoPairSet.class org.biojava.bio.program.homologene.OrthoPairSetFilter.class org.biojava.bio.program.homologene.Orthologue.class org.biojava.bio.program.homologene.OrthologueFilter.class org.biojava.bio.program.homologene.OrthologueSet.class org.biojava.bio.program.homologene.SimilarityType.class org.biojava.bio.program.homologene.SimpleHomologeneBuilder.class org.biojava.bio.program.homologene.SimpleHomologeneDB.class org.biojava.bio.program.homologene.SimpleOrthoPair.class org.biojava.bio.program.homologene.SimpleOrthoPairCollection.class org.biojava.bio.program.homologene.SimpleOrthoPairSet.class org.biojava.bio.program.homologene.SimpleOrthologue.class org.biojava.bio.program.homologene.SimpleOrthologueSet.class org.biojava.bio.program.homologene.Taxon.class org.biojava.bio.program.indexdb.BioStore.class org.biojava.bio.program.indexdb.BioStoreFactory.class org.biojava.bio.program.indexdb.CacheList.class org.biojava.bio.program.indexdb.ConfigFile.class org.biojava.bio.program.indexdb.IndexStore.class org.biojava.bio.program.indexdb.IndexTools.class org.biojava.bio.program.indexdb.KeyPair.class org.biojava.bio.program.indexdb.PrimaryIDList.class org.biojava.bio.program.indexdb.PropertiesAnnotation.class org.biojava.bio.program.indexdb.Record.class org.biojava.bio.program.indexdb.SearchableFileAsList.class org.biojava.bio.program.indexdb.SearchableList.class org.biojava.bio.program.indexdb.SecondaryFileAsList.class org.biojava.bio.program.phred.PhredFormat.class org.biojava.bio.program.phred.PhredSequence.class org.biojava.bio.program.phred.PhredTools.class org.biojava.bio.program.phred.Qualitative.class org.biojava.bio.program.sax.AbstractNativeAppSAXParser.class org.biojava.bio.program.sax.BaseXMLWriterTestHelper.class org.biojava.bio.program.sax.BlastLikeAlignmentSAXParser.class org.biojava.bio.program.sax.BlastLikeSAXParser.class org.biojava.bio.program.sax.BlastLikeVersionSupport.class org.biojava.bio.program.sax.BlastSAXParser.class org.biojava.bio.program.sax.ClustalWAlignmentSAXParser.class org.biojava.bio.program.sax.DomainSectionSAXParser.class org.biojava.bio.program.sax.FastaSearchParser.class org.biojava.bio.program.sax.FastaSearchSAXParser.class org.biojava.bio.program.sax.FastaSequenceSAXParser.class org.biojava.bio.program.sax.GCGBlastSummaryLineHelper.class org.biojava.bio.program.sax.GenericSAXParserTest.class org.biojava.bio.program.sax.HSPSummaryHelper.class org.biojava.bio.program.sax.HitSectionSAXParser.class org.biojava.bio.program.sax.HmmerAlignmentSAXParser.class org.biojava.bio.program.sax.HmmerSummaryLineHelper.class org.biojava.bio.program.sax.NamespaceConfigurationIF.class org.biojava.bio.program.sax.NcbiBlastSummaryLineHelper.class org.biojava.bio.program.sax.NeedleAlignmentSAXParser.class org.biojava.bio.program.sax.PdbSAXParser.class org.biojava.bio.program.sax.QName.class org.biojava.bio.program.sax.SequenceAlignmentSAXParser.class org.biojava.bio.program.sax.SimpleXMLEmitterTestHelper.class org.biojava.bio.program.sax.SummaryLineHelperIF.class org.biojava.bio.program.sax.WuBlastSummaryLineHelper.class org.biojava.bio.program.sax.blastxml.BlastAggregator.class org.biojava.bio.program.sax.blastxml.BlastOutputHandler.class org.biojava.bio.program.sax.blastxml.BlastOutputIterationsHandler.class org.biojava.bio.program.sax.blastxml.BlastXMLParser.class org.biojava.bio.program.sax.blastxml.BlastXMLParserFacade.class org.biojava.bio.program.sax.blastxml.HitHandler.class org.biojava.bio.program.sax.blastxml.HitHspsHandler.class org.biojava.bio.program.sax.blastxml.HspHandler.class org.biojava.bio.program.sax.blastxml.IterationHandler.class org.biojava.bio.program.sax.blastxml.IterationHitsHandler.class org.biojava.bio.program.sax.blastxml.StAXFeatureHandler.class org.biojava.bio.program.sax.blastxml.StAXFeatureHandlerMod.class org.biojava.bio.program.sax.blastxml.StAXHandlerFactory.class org.biojava.bio.program.scf.SCF.class org.biojava.bio.program.ssaha.CompactedDataStore.class org.biojava.bio.program.ssaha.CompactedDataStoreFactory.class org.biojava.bio.program.ssaha.DataStore.class org.biojava.bio.program.ssaha.DataStoreFactory.class org.biojava.bio.program.ssaha.HitMerger.class org.biojava.bio.program.ssaha.MappedDataStore.class org.biojava.bio.program.ssaha.MappedDataStoreFactory.class org.biojava.bio.program.ssaha.NIODataStore.class org.biojava.bio.program.ssaha.NIODataStoreFactory.class org.biojava.bio.program.ssaha.SearchException.class org.biojava.bio.program.ssaha.SearchListener.class org.biojava.bio.program.ssaha.SequenceStreamer.class org.biojava.bio.program.ssbind.AlignmentStAXHandler.class org.biojava.bio.program.ssbind.AlphabetResolver.class org.biojava.bio.program.ssbind.AnnotationFactory.class org.biojava.bio.program.ssbind.BlastLikeHomologyBuilder.class org.biojava.bio.program.ssbind.BlastLikeSearchBuilder.class org.biojava.bio.program.ssbind.HSPStAXHandler.class org.biojava.bio.program.ssbind.HSPSummaryStAXHandler.class org.biojava.bio.program.ssbind.HeaderStAXHandler.class org.biojava.bio.program.ssbind.HitStAXHandler.class org.biojava.bio.program.ssbind.SeqSimilarityAdapter.class org.biojava.bio.program.ssbind.SeqSimilarityStAXAdapter.class org.biojava.bio.program.ssbind.SeqSimilarityStAXHandler.class org.biojava.bio.program.ssbind.SimilarityPairBuilder.class org.biojava.bio.program.ssbind.StAXHandlerBinding.class org.biojava.bio.program.ssbind.StAXHandlerFactory.class org.biojava.bio.program.ssbind.ViewSequenceFactory.class org.biojava.bio.program.tagvalue.AbstractWrapper.class org.biojava.bio.program.tagvalue.Aggregator.class org.biojava.bio.program.tagvalue.AnnotationBuilder.class org.biojava.bio.program.tagvalue.BoundaryFinder.class org.biojava.bio.program.tagvalue.ChangeTable.class org.biojava.bio.program.tagvalue.Echo.class org.biojava.bio.program.tagvalue.Formats.class org.biojava.bio.program.tagvalue.Index2Model.class org.biojava.bio.program.tagvalue.Indexer.class org.biojava.bio.program.tagvalue.Indexer2.class org.biojava.bio.program.tagvalue.LineSplitParser.class org.biojava.bio.program.tagvalue.MultiTagger.class org.biojava.bio.program.tagvalue.Parser.class org.biojava.bio.program.tagvalue.ParserListener.class org.biojava.bio.program.tagvalue.PropertyChanger.class org.biojava.bio.program.tagvalue.RegexChanger.class org.biojava.bio.program.tagvalue.RegexFieldFinder.class org.biojava.bio.program.tagvalue.RegexParser.class org.biojava.bio.program.tagvalue.RegexSplitter.class org.biojava.bio.program.tagvalue.SimpleTagValueWrapper.class org.biojava.bio.program.tagvalue.StateMachine.class org.biojava.bio.program.tagvalue.TagDelegator.class org.biojava.bio.program.tagvalue.TagDropper.class org.biojava.bio.program.tagvalue.TagMapper.class org.biojava.bio.program.tagvalue.TagRenamer.class org.biojava.bio.program.tagvalue.TagValue.class org.biojava.bio.program.tagvalue.TagValueContext.class org.biojava.bio.program.tagvalue.TagValueListener.class org.biojava.bio.program.tagvalue.TagValueParser.class org.biojava.bio.program.tagvalue.TagValueWrapper.class org.biojava.bio.program.tagvalue.ValueChanger.class org.biojava.bio.program.unigene.FlatFileUnigeneDB.class org.biojava.bio.program.unigene.FlatFileUnigeneFactory.class org.biojava.bio.program.unigene.SQLUnigeneDB.class org.biojava.bio.program.unigene.SQLUnigeneFactory.class org.biojava.bio.program.unigene.UnigeneCluster.class org.biojava.bio.program.unigene.UnigeneDB.class org.biojava.bio.program.unigene.UnigeneFactory.class org.biojava.bio.program.unigene.UnigeneTools.class org.biojava.bio.program.xff.BasicXFFHelper.class org.biojava.bio.program.xff.ElementRecognizer.class org.biojava.bio.program.xff.FeatureHandler.class org.biojava.bio.program.xff.LocationHandlerBase.class org.biojava.bio.program.xff.PropDetailHandler.class org.biojava.bio.program.xff.PropertyWriter.class org.biojava.bio.program.xff.StrandedFeatureHandler.class org.biojava.bio.program.xff.XFFFeatureSetHandler.class org.biojava.bio.program.xff.XFFHelper.class org.biojava.bio.program.xff.XFFPartHandlerFactory.class org.biojava.bio.program.xff.XFFTools.class org.biojava.bio.program.xff.XFFWriter.class org.biojava.bio.program.xml.BaseXMLWriter.class org.biojava.bio.program.xml.SimpleXMLEmitter.class org.biojava.bio.proteomics.Digest.class org.biojava.bio.proteomics.IsoelectricPointCalc.class org.biojava.bio.proteomics.MassCalc.class org.biojava.bio.proteomics.Protease.class org.biojava.bio.proteomics.ProteaseManager.class org.biojava.bio.proteomics.StructureTools.class org.biojava.bio.proteomics.aaindex.AAindex.class org.biojava.bio.proteomics.aaindex.AAindexStreamReader.class org.biojava.bio.proteomics.aaindex.SimpleSymbolPropertyTableDB.class org.biojava.bio.proteomics.aaindex.SymbolPropertyTableDB.class org.biojava.bio.proteomics.aaindex.SymbolPropertyTableIterator.class org.biojava.bio.search.BioMatcher.class org.biojava.bio.search.BioPattern.class org.biojava.bio.search.BlastLikeSearchFilter.class org.biojava.bio.search.FilterTest.class org.biojava.bio.search.FilteringContentHandler.class org.biojava.bio.search.KnuthMorrisPrattSearch.class org.biojava.bio.search.MaxMismatchMatcher.class org.biojava.bio.search.MaxMismatchPattern.class org.biojava.bio.search.SearchBuilder.class org.biojava.bio.search.SearchContentAdapter.class org.biojava.bio.search.SearchContentFilter.class org.biojava.bio.search.SearchContentHandler.class org.biojava.bio.search.SearchContentHandlerDebugger.class org.biojava.bio.search.SeqContentMatcher.class org.biojava.bio.search.SeqContentPattern.class org.biojava.bio.search.SeqSimilaritySearchHit.class org.biojava.bio.search.SeqSimilaritySearchResult.class org.biojava.bio.search.SeqSimilaritySearchSubHit.class org.biojava.bio.search.SeqSimilaritySearcher.class org.biojava.bio.search.SequenceDBSearchHit.class org.biojava.bio.search.SequenceDBSearchResult.class org.biojava.bio.search.SequenceDBSearchSubHit.class org.biojava.bio.search.SimpleSeqSimilaritySearchHit.class org.biojava.bio.search.SimpleSeqSimilaritySearchResult.class org.biojava.bio.search.SimpleSeqSimilaritySearchSubHit.class org.biojava.bio.seq.AbstractFeatureHolder.class org.biojava.bio.seq.AcceptAllFilter.class org.biojava.bio.seq.AcceptNoneFilter.class org.biojava.bio.seq.ByHierarchy.class org.biojava.bio.seq.ByLocationMinMaxComparator.class org.biojava.bio.seq.ByLocationMinMaxFeatureComparator.class org.biojava.bio.seq.CircularView.class org.biojava.bio.seq.ComponentFeature.class org.biojava.bio.seq.DNATools.class org.biojava.bio.seq.Down.class org.biojava.bio.seq.Feature.class org.biojava.bio.seq.FeatureFilter.class org.biojava.bio.seq.FeatureHolder.class org.biojava.bio.seq.FeatureHolderUtils.class org.biojava.bio.seq.FeatureRealizer.class org.biojava.bio.seq.FeatureTypes.class org.biojava.bio.seq.FilterUtils.class org.biojava.bio.seq.Frame.class org.biojava.bio.seq.FramedFeature.class org.biojava.bio.seq.GappedSequence.class org.biojava.bio.seq.GeneticCodes.class org.biojava.bio.seq.IsLeaf.class org.biojava.bio.seq.IsTopLevel.class org.biojava.bio.seq.LazyFeatureHolder.class org.biojava.bio.seq.MergeFeatureHolder.class org.biojava.bio.seq.NewSimpleAssembly.class org.biojava.bio.seq.NucleotideTools.class org.biojava.bio.seq.OptimizableFilter.class org.biojava.bio.seq.ProteinTools.class org.biojava.bio.seq.RNATools.class org.biojava.bio.seq.RealizingFeatureHolder.class org.biojava.bio.seq.RemoteFeature.class org.biojava.bio.seq.Sequence.class org.biojava.bio.seq.SequenceAnnotator.class org.biojava.bio.seq.SequenceFactory.class org.biojava.bio.seq.SequenceIterator.class org.biojava.bio.seq.SequenceTools.class org.biojava.bio.seq.SimpleAssembly.class org.biojava.bio.seq.SimpleComponentFeature.class org.biojava.bio.seq.SimpleFeatureHolder.class org.biojava.bio.seq.SimpleFeatureRealizer.class org.biojava.bio.seq.StrandParser.class org.biojava.bio.seq.StrandedFeature.class org.biojava.bio.seq.Up.class org.biojava.bio.seq.db.AbstractSequenceDB.class org.biojava.bio.seq.db.AnnotatedSequenceDB.class org.biojava.bio.seq.db.BioIndex.class org.biojava.bio.seq.db.CachingSequenceDB.class org.biojava.bio.seq.db.DummySequenceDB.class org.biojava.bio.seq.db.DummySequenceDBInstallation.class org.biojava.bio.seq.db.EmblCDROMIndexStore.class org.biojava.bio.seq.db.FetchURL.class org.biojava.bio.seq.db.GenbankSequenceDB.class org.biojava.bio.seq.db.GenpeptSequenceDB.class org.biojava.bio.seq.db.HashSequenceDB.class org.biojava.bio.seq.db.IDMaker.class org.biojava.bio.seq.db.IllegalIDException.class org.biojava.bio.seq.db.Index.class org.biojava.bio.seq.db.IndexStore.class org.biojava.bio.seq.db.IndexedSequenceDB.class org.biojava.bio.seq.db.NCBISequenceDB.class org.biojava.bio.seq.db.SequenceDB.class org.biojava.bio.seq.db.SequenceDBInstallation.class org.biojava.bio.seq.db.SequenceDBLite.class org.biojava.bio.seq.db.SequenceDBWrapper.class org.biojava.bio.seq.db.SimpleIndex.class org.biojava.bio.seq.db.SimpleSequenceDBInstallation.class org.biojava.bio.seq.db.SubSequenceDB.class org.biojava.bio.seq.db.SwissprotSequenceDB.class org.biojava.bio.seq.db.TabIndexStore.class org.biojava.bio.seq.db.ViewingSequenceDB.class org.biojava.bio.seq.db.WebSequenceDB.class org.biojava.bio.seq.db.biofetch.BioFetchSequenceDB.class org.biojava.bio.seq.db.biofetch.BioFetchSequenceDBProvider.class org.biojava.bio.seq.db.biosql.BioSQLAllFeatures.class org.biojava.bio.seq.db.biosql.BioSQLAssembly.class org.biojava.bio.seq.db.biosql.BioSQLComponentFeature.class org.biojava.bio.seq.db.biosql.BioSQLEntryAnnotationChangeHub.class org.biojava.bio.seq.db.biosql.BioSQLEntryChangeHub.class org.biojava.bio.seq.db.biosql.BioSQLFeature.class org.biojava.bio.seq.db.biosql.BioSQLFeatureAnnotation.class org.biojava.bio.seq.db.biosql.BioSQLFeatureAnnotationChangeHub.class org.biojava.bio.seq.db.biosql.BioSQLFeatureChangeHub.class org.biojava.bio.seq.db.biosql.BioSQLFeatureReceiver.class org.biojava.bio.seq.db.biosql.BioSQLSequence.class org.biojava.bio.seq.db.biosql.BioSQLSequenceAnnotation.class org.biojava.bio.seq.db.biosql.BioSQLSequenceDB.class org.biojava.bio.seq.db.biosql.BioSQLSequenceDBProvider.class org.biojava.bio.seq.db.biosql.BioSQLSequenceI.class org.biojava.bio.seq.db.biosql.BioSQLStrandedFeature.class org.biojava.bio.seq.db.biosql.BioSQLTiledFeatures.class org.biojava.bio.seq.db.biosql.DBHelper.class org.biojava.bio.seq.db.biosql.FeaturesSQL.class org.biojava.bio.seq.db.biosql.HypersonicDBHelper.class org.biojava.bio.seq.db.biosql.MySQLDBHelper.class org.biojava.bio.seq.db.biosql.OntologySQL.class org.biojava.bio.seq.db.biosql.OracleDBHelper.class org.biojava.bio.seq.db.biosql.PostgreSQLDBHelper.class org.biojava.bio.seq.db.biosql.TaxonSQL.class org.biojava.bio.seq.db.biosql.UnknownDBHelper.class org.biojava.bio.seq.db.emblcd.AcnumHitReader.class org.biojava.bio.seq.db.emblcd.AcnumTrgReader.class org.biojava.bio.seq.db.emblcd.DivisionLkpReader.class org.biojava.bio.seq.db.emblcd.EmblCDROMIndexReader.class org.biojava.bio.seq.db.emblcd.EmblCDROMRandomAccess.class org.biojava.bio.seq.db.emblcd.EntryNamIdxReader.class org.biojava.bio.seq.db.emblcd.EntryNamRandomAccess.class org.biojava.bio.seq.db.emblcd.RecordParser.class org.biojava.bio.seq.db.flat.FlatSequenceDB.class org.biojava.bio.seq.db.flat.FlatSequenceDBProvider.class org.biojava.bio.seq.distributed.DistComponentFeature.class org.biojava.bio.seq.distributed.DistDataSource.class org.biojava.bio.seq.distributed.DistProjectionContext.class org.biojava.bio.seq.distributed.DistributedSequence.class org.biojava.bio.seq.distributed.DistributedSequenceDB.class org.biojava.bio.seq.distributed.GFFDataSource.class org.biojava.bio.seq.distributed.SequenceDBDataSource.class org.biojava.bio.seq.filter.FilterTransformer.class org.biojava.bio.seq.homol.Homology.class org.biojava.bio.seq.homol.HomologyDB.class org.biojava.bio.seq.homol.HomologyFeature.class org.biojava.bio.seq.homol.SimilarityPairFeature.class org.biojava.bio.seq.homol.SimpleHomology.class org.biojava.bio.seq.impl.AssembledSymbolList.class org.biojava.bio.seq.impl.DummySequence.class org.biojava.bio.seq.impl.FeatureImpl.class org.biojava.bio.seq.impl.LazyFilterFeatureHolder.class org.biojava.bio.seq.impl.NewAssembledSymbolList.class org.biojava.bio.seq.impl.RevCompSequence.class org.biojava.bio.seq.impl.SimpleFeature.class org.biojava.bio.seq.impl.SimpleFramedFeature.class org.biojava.bio.seq.impl.SimpleGappedSequence.class org.biojava.bio.seq.impl.SimpleHomologyFeature.class org.biojava.bio.seq.impl.SimpleRemoteFeature.class org.biojava.bio.seq.impl.SimpleRestrictionSite.class org.biojava.bio.seq.impl.SimpleSequence.class org.biojava.bio.seq.impl.SimpleSequenceFactory.class org.biojava.bio.seq.impl.SimpleSimilarityPairFeature.class org.biojava.bio.seq.impl.SimpleStrandedFeature.class org.biojava.bio.seq.impl.SubSequence.class org.biojava.bio.seq.impl.TemplateUtils.class org.biojava.bio.seq.impl.ViewSequence.class org.biojava.bio.seq.io.AbstractGenEmblFileFormer.class org.biojava.bio.seq.io.AlignIOConstants.class org.biojava.bio.seq.io.AlignmentFormat.class org.biojava.bio.seq.io.AlternateTokenization.class org.biojava.bio.seq.io.CharacterTokenization.class org.biojava.bio.seq.io.ChunkedSymbolListFactory.class org.biojava.bio.seq.io.CrossProductTokenization.class org.biojava.bio.seq.io.DoubleTokenization.class org.biojava.bio.seq.io.EmblFileFormer.class org.biojava.bio.seq.io.EmblLikeFormat.class org.biojava.bio.seq.io.EmblLikeLocationParser.class org.biojava.bio.seq.io.EmblProcessor.class org.biojava.bio.seq.io.EmblReferenceComparator.class org.biojava.bio.seq.io.FastaAlignmentFormat.class org.biojava.bio.seq.io.FastaDescriptionLineParser.class org.biojava.bio.seq.io.FastaFormat.class org.biojava.bio.seq.io.FeatureTableParser.class org.biojava.bio.seq.io.GAMEFormat.class org.biojava.bio.seq.io.GenEmblFeatureComparator.class org.biojava.bio.seq.io.GenEmblPropertyComparator.class org.biojava.bio.seq.io.GenbankContext.class org.biojava.bio.seq.io.GenbankFileFormer.class org.biojava.bio.seq.io.GenbankFormat.class org.biojava.bio.seq.io.GenbankProcessor.class org.biojava.bio.seq.io.GenbankXmlFormat.class org.biojava.bio.seq.io.GenpeptFileFormer.class org.biojava.bio.seq.io.GenpeptFormat.class org.biojava.bio.seq.io.IntegerTokenization.class org.biojava.bio.seq.io.MSFAlignmentFormat.class org.biojava.bio.seq.io.NameTokenization.class org.biojava.bio.seq.io.OrganismParser.class org.biojava.bio.seq.io.ParseException.class org.biojava.bio.seq.io.ProteinRefSeqFileFormer.class org.biojava.bio.seq.io.ProteinRefSeqProcessor.class org.biojava.bio.seq.io.ReferenceAnnotation.class org.biojava.bio.seq.io.SeqFileFormer.class org.biojava.bio.seq.io.SeqIOAdapter.class org.biojava.bio.seq.io.SeqIOConstants.class org.biojava.bio.seq.io.SeqIOEventEmitter.class org.biojava.bio.seq.io.SeqIOFilter.class org.biojava.bio.seq.io.SeqIOListener.class org.biojava.bio.seq.io.SeqIOTools.class org.biojava.bio.seq.io.SequenceBuilder.class org.biojava.bio.seq.io.SequenceBuilderBase.class org.biojava.bio.seq.io.SequenceBuilderFactory.class org.biojava.bio.seq.io.SequenceBuilderFilter.class org.biojava.bio.seq.io.SequenceDBSequenceBuilder.class org.biojava.bio.seq.io.SequenceFormat.class org.biojava.bio.seq.io.SimpleAssemblyBuilder.class org.biojava.bio.seq.io.SimpleSequenceBuilder.class org.biojava.bio.seq.io.SmartSequenceBuilder.class org.biojava.bio.seq.io.StreamParser.class org.biojava.bio.seq.io.StreamReader.class org.biojava.bio.seq.io.StreamWriter.class org.biojava.bio.seq.io.SubIntegerTokenization.class org.biojava.bio.seq.io.SwissprotFeatureTableParser.class org.biojava.bio.seq.io.SwissprotFileFormer.class org.biojava.bio.seq.io.SwissprotProcessor.class org.biojava.bio.seq.io.SymbolListCharSequence.class org.biojava.bio.seq.io.SymbolReader.class org.biojava.bio.seq.io.SymbolTokenization.class org.biojava.bio.seq.io.WordTokenization.class org.biojava.bio.seq.io.agave.AGAVEAltIdsPropHandler.class org.biojava.bio.seq.io.agave.AGAVEAnnotFilter.class org.biojava.bio.seq.io.agave.AGAVEAnnotFilterFactory.class org.biojava.bio.seq.io.agave.AGAVEAnnotationsHandler.class org.biojava.bio.seq.io.agave.AGAVEAssemblyHandler.class org.biojava.bio.seq.io.agave.AGAVEBioSeqCallbackItf.class org.biojava.bio.seq.io.agave.AGAVEBioSeqHandler.class org.biojava.bio.seq.io.agave.AGAVEBioSequenceHandler.class org.biojava.bio.seq.io.agave.AGAVECallbackItf.class org.biojava.bio.seq.io.agave.AGAVECdsHandler.class org.biojava.bio.seq.io.agave.AGAVEChromosomeCallbackItf.class org.biojava.bio.seq.io.agave.AGAVEChromosomeHandler.class org.biojava.bio.seq.io.agave.AGAVEClassificationHandler.class org.biojava.bio.seq.io.agave.AGAVECompResultHandler.class org.biojava.bio.seq.io.agave.AGAVEComputationHandler.class org.biojava.bio.seq.io.agave.AGAVEContigCallbackItf.class org.biojava.bio.seq.io.agave.AGAVEContigHandler.class org.biojava.bio.seq.io.agave.AGAVEDbId.class org.biojava.bio.seq.io.agave.AGAVEDbIdCallbackItf.class org.biojava.bio.seq.io.agave.AGAVEDbIdPropCallbackItf.class org.biojava.bio.seq.io.agave.AGAVEDbIdPropHandler.class org.biojava.bio.seq.io.agave.AGAVEDescPropHandler.class org.biojava.bio.seq.io.agave.AGAVEElementIdPropHandler.class org.biojava.bio.seq.io.agave.AGAVEEvidenceCallbackItf.class org.biojava.bio.seq.io.agave.AGAVEEvidenceHandler.class org.biojava.bio.seq.io.agave.AGAVEExonsPropHandler.class org.biojava.bio.seq.io.agave.AGAVEFeatureCallbackItf.class org.biojava.bio.seq.io.agave.AGAVEFragmentOrderHandler.class org.biojava.bio.seq.io.agave.AGAVEFragmentOrientationHandler.class org.biojava.bio.seq.io.agave.AGAVEGeneHandler.class org.biojava.bio.seq.io.agave.AGAVEHandler.class org.biojava.bio.seq.io.agave.AGAVEIdAlias.class org.biojava.bio.seq.io.agave.AGAVEIdAliasCallbackItf.class org.biojava.bio.seq.io.agave.AGAVEIdAliasPropHandler.class org.biojava.bio.seq.io.agave.AGAVEKeywordPropHandler.class org.biojava.bio.seq.io.agave.AGAVEMapLocation.class org.biojava.bio.seq.io.agave.AGAVEMapLocationPropHandler.class org.biojava.bio.seq.io.agave.AGAVEMapPosition.class org.biojava.bio.seq.io.agave.AGAVEMapPositionPropHandler.class org.biojava.bio.seq.io.agave.AGAVEMatchAlignPropHandler.class org.biojava.bio.seq.io.agave.AGAVEMatchDescPropHandler.class org.biojava.bio.seq.io.agave.AGAVEMatchRegion.class org.biojava.bio.seq.io.agave.AGAVEMatchRegionPropHandler.class org.biojava.bio.seq.io.agave.AGAVEMrnaHandler.class org.biojava.bio.seq.io.agave.AGAVENotePropHandler.class org.biojava.bio.seq.io.agave.AGAVEPredictedProteinHandler.class org.biojava.bio.seq.io.agave.AGAVEProperty.class org.biojava.bio.seq.io.agave.AGAVEQualifierPropHandler.class org.biojava.bio.seq.io.agave.AGAVEQueryRegion.class org.biojava.bio.seq.io.agave.AGAVEQueryRegionPropHandler.class org.biojava.bio.seq.io.agave.AGAVERelatedAnnot.class org.biojava.bio.seq.io.agave.AGAVERelatedAnnotPropHandler.class org.biojava.bio.seq.io.agave.AGAVEResultGroupHandler.class org.biojava.bio.seq.io.agave.AGAVEResultPropertyPropHandler.class org.biojava.bio.seq.io.agave.AGAVESciPropertyPropHandler.class org.biojava.bio.seq.io.agave.AGAVESeqFeatureHandler.class org.biojava.bio.seq.io.agave.AGAVESeqLocationPropHandler.class org.biojava.bio.seq.io.agave.AGAVESeqMapHandler.class org.biojava.bio.seq.io.agave.AGAVESeqPropHandler.class org.biojava.bio.seq.io.agave.AGAVETranscriptHandler.class org.biojava.bio.seq.io.agave.AGAVEUnorderedFragmentsHandler.class org.biojava.bio.seq.io.agave.AGAVEViewPropHandler.class org.biojava.bio.seq.io.agave.AGAVEXref.class org.biojava.bio.seq.io.agave.AGAVEXrefCallbackItf.class org.biojava.bio.seq.io.agave.AGAVEXrefPropHandler.class org.biojava.bio.seq.io.agave.AGAVEXrefPropPropHandler.class org.biojava.bio.seq.io.agave.AGAVEXrefs.class org.biojava.bio.seq.io.agave.AGAVEXrefsPropHandler.class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter.class org.biojava.bio.seq.io.agave.AgaveWriter.class org.biojava.bio.seq.io.agave.DelegationManager.class org.biojava.bio.seq.io.agave.ElementRecognizer.class org.biojava.bio.seq.io.agave.Embl2AgaveAnnotFilter.class org.biojava.bio.seq.io.agave.PCDATAFilterWriter.class org.biojava.bio.seq.io.agave.SAX2StAXAdaptor.class org.biojava.bio.seq.io.agave.SequenceHandler.class org.biojava.bio.seq.io.agave.SimpleAnnotFilter.class org.biojava.bio.seq.io.agave.StAXContentHandler.class org.biojava.bio.seq.io.agave.StAXContentHandlerBase.class org.biojava.bio.seq.io.agave.StAXFeatureHandler.class org.biojava.bio.seq.io.agave.StAXHandlerFactory.class org.biojava.bio.seq.io.agave.StAXPropertyHandler.class org.biojava.bio.seq.io.agave.UtilHelper.class org.biojava.bio.seq.io.filterxml.QName.class org.biojava.bio.seq.io.filterxml.XMLAnnotationTypeHandler.class org.biojava.bio.seq.io.filterxml.XMLAnnotationTypeWriter.class org.biojava.bio.seq.io.filterxml.XMLFilterHandler.class org.biojava.bio.seq.io.filterxml.XMLFilterWriter.class org.biojava.bio.seq.io.game12.GAMEAnnotationHandler.class org.biojava.bio.seq.io.game12.GAMEAspectHandler.class org.biojava.bio.seq.io.game12.GAMEDbxrefHandler.class org.biojava.bio.seq.io.game12.GAMEFeatureSetHandler.class org.biojava.bio.seq.io.game12.GAMEFeatureSpanHandler.class org.biojava.bio.seq.io.game12.GAMEGeneHandler.class org.biojava.bio.seq.io.game12.GAMEHandler.class org.biojava.bio.seq.io.game12.GAMEPropertyHandler.class org.biojava.bio.seq.io.game12.GAMESeqHandler.class org.biojava.bio.seq.io.game12.GAMESeqRelHandler.class org.biojava.bio.seq.io.game12.GAMESpanHandler.class org.biojava.bio.seq.io.game12.StAXFeatureHandler.class org.biojava.bio.seq.io.game12.StAXHandlerFactory.class org.biojava.bio.seq.io.game.ElementRecognizer.class org.biojava.bio.seq.io.game.GAMEAnnotationHandler.class org.biojava.bio.seq.io.game.GAMEAspectPropHandler.class org.biojava.bio.seq.io.game.GAMEDbxrefPropHandler.class org.biojava.bio.seq.io.game.GAMEDescriptionPropHandler.class org.biojava.bio.seq.io.game.GAMEFeatureCallbackItf.class org.biojava.bio.seq.io.game.GAMEFeatureSetHandler.class org.biojava.bio.seq.io.game.GAMEFeatureSetPropHandler.class org.biojava.bio.seq.io.game.GAMEFeatureSpanHandler.class org.biojava.bio.seq.io.game.GAMEGenePropHandler.class org.biojava.bio.seq.io.game.GAMEHandler.class org.biojava.bio.seq.io.game.GAMEMapPosPropHandler.class org.biojava.bio.seq.io.game.GAMENameCallbackItf.class org.biojava.bio.seq.io.game.GAMENamePropHandler.class org.biojava.bio.seq.io.game.GAMEResiduesPropHandler.class org.biojava.bio.seq.io.game.GAMESeqPropHandler.class org.biojava.bio.seq.io.game.GAMESeqRelPropHandler.class org.biojava.bio.seq.io.game.GAMESpanPropHandler.class org.biojava.bio.seq.io.game.GAMETranscriptCallbackItf.class org.biojava.bio.seq.io.game.GAMETypePropHandler.class org.biojava.bio.seq.io.game.SequenceContentHandlerBase.class org.biojava.bio.seq.io.game.StAXFeatureHandler.class org.biojava.bio.seq.io.game.StAXHandlerFactory.class org.biojava.bio.seq.io.game.StAXPropertyHandler.class org.biojava.bio.seq.projection.ProjectedFeature.class org.biojava.bio.seq.projection.ProjectedFeatureHolder.class org.biojava.bio.seq.projection.Projection.class org.biojava.bio.seq.projection.ProjectionContext.class org.biojava.bio.seq.projection.ProjectionEngine.class org.biojava.bio.seq.projection.ProjectionUtils.class org.biojava.bio.seq.projection.ReparentContext.class org.biojava.bio.seq.projection.TranslateFlipContext.class org.biojava.bio.structure.AlphaCTools.class org.biojava.bio.structure.AminoAcid.class org.biojava.bio.structure.AminoAcidImpl.class org.biojava.bio.structure.Atom.class org.biojava.bio.structure.AtomImpl.class org.biojava.bio.structure.AtomIterator.class org.biojava.bio.structure.Author.class org.biojava.bio.structure.Calc.class org.biojava.bio.structure.Chain.class org.biojava.bio.structure.ChainImpl.class org.biojava.bio.structure.Compound.class org.biojava.bio.structure.DBRef.class org.biojava.bio.structure.Group.class org.biojava.bio.structure.GroupIterator.class org.biojava.bio.structure.GroupType.class org.biojava.bio.structure.HetatomImpl.class org.biojava.bio.structure.JournalArticle.class org.biojava.bio.structure.Mutator.class org.biojava.bio.structure.NucleotideImpl.class org.biojava.bio.structure.PDBHeader.class org.biojava.bio.structure.PDBRecord.class org.biojava.bio.structure.SSBond.class org.biojava.bio.structure.SVDSuperimposer.class org.biojava.bio.structure.StandardAminoAcid.class org.biojava.bio.structure.Structure.class org.biojava.bio.structure.StructureException.class org.biojava.bio.structure.StructureImpl.class org.biojava.bio.structure.StructureTools.class org.biojava.bio.structure.align.ClusterAltAligs.class org.biojava.bio.structure.align.StrucAligParameters.class org.biojava.bio.structure.align.StructurePairAligner.class org.biojava.bio.structure.align.helper.AligMatEl.class org.biojava.bio.structure.align.helper.AlignTools.class org.biojava.bio.structure.align.helper.GapArray.class org.biojava.bio.structure.align.helper.IndexPair.class org.biojava.bio.structure.align.helper.JointFragments.class org.biojava.bio.structure.align.pairwise.AligNPE.class org.biojava.bio.structure.align.pairwise.Alignable.class org.biojava.bio.structure.align.pairwise.AltAligComparator.class org.biojava.bio.structure.align.pairwise.AlternativeAlignment.class org.biojava.bio.structure.align.pairwise.FragmentJoiner.class org.biojava.bio.structure.align.pairwise.FragmentPair.class org.biojava.bio.structure.align.pairwise.Gotoh.class org.biojava.bio.structure.align.pairwise.JointFragmentsComparator.class org.biojava.bio.structure.align.pairwise.StrCompAlignment.class org.biojava.bio.structure.gui.AlignmentGui.class org.biojava.bio.structure.gui.BiojavaJmol.class org.biojava.bio.structure.gui.JMatrixPanel.class org.biojava.bio.structure.gui.ProgressThreadDrawer.class org.biojava.bio.structure.gui.RasmolCommandListener.class org.biojava.bio.structure.gui.ScaleableMatrixPanel.class org.biojava.bio.structure.gui.SequenceDisplay.class org.biojava.bio.structure.gui.events.AlignmentPositionListener.class org.biojava.bio.structure.gui.events.JmolAlignedPositionListener.class org.biojava.bio.structure.gui.util.AlignedPosition.class org.biojava.bio.structure.gui.util.AlignmentCalc.class org.biojava.bio.structure.gui.util.AlternativeAlignmentFrame.class org.biojava.bio.structure.gui.util.ChooseAction.class org.biojava.bio.structure.gui.util.ChooseDirAction.class org.biojava.bio.structure.gui.util.CoordManager.class org.biojava.bio.structure.gui.util.JButtonTableCellRenderer.class org.biojava.bio.structure.gui.util.JTableDataButtonModel.class org.biojava.bio.structure.gui.util.JTableMouseButtonListener.class org.biojava.bio.structure.gui.util.MatrixMouseListener.class org.biojava.bio.structure.gui.util.MenuCreator.class org.biojava.bio.structure.gui.util.MyButtonMouseListener.class org.biojava.bio.structure.gui.util.PDBDirPanel.class org.biojava.bio.structure.gui.util.PDBServerPanel.class org.biojava.bio.structure.gui.util.PDBUploadPanel.class org.biojava.bio.structure.gui.util.SequenceMouseListener.class org.biojava.bio.structure.gui.util.SequenceScalePanel.class org.biojava.bio.structure.gui.util.StructurePairSelector.class org.biojava.bio.structure.io.CAConverter.class org.biojava.bio.structure.io.DASStructureClient.class org.biojava.bio.structure.io.FileConvert.class org.biojava.bio.structure.io.MMCIFFileReader.class org.biojava.bio.structure.io.PDBFileParser.class org.biojava.bio.structure.io.PDBFileReader.class org.biojava.bio.structure.io.PDBMSDReader.class org.biojava.bio.structure.io.PDBParseException.class org.biojava.bio.structure.io.PDBSRSReader.class org.biojava.bio.structure.io.SeqRes2AtomAligner.class org.biojava.bio.structure.io.StructureIO.class org.biojava.bio.structure.io.StructureIOFile.class org.biojava.bio.structure.io.mmcif.ChemCompConsumer.class org.biojava.bio.structure.io.mmcif.ChemicalComponentDictionary.class org.biojava.bio.structure.io.mmcif.MMcifConsumer.class org.biojava.bio.structure.io.mmcif.MMcifParser.class org.biojava.bio.structure.io.mmcif.SimpleMMcifConsumer.class org.biojava.bio.structure.io.mmcif.SimpleMMcifParser.class org.biojava.bio.structure.io.mmcif.chem.ChemCompTools.class org.biojava.bio.structure.io.mmcif.chem.PolymerType.class org.biojava.bio.structure.io.mmcif.chem.ResidueType.class org.biojava.bio.structure.io.mmcif.model.AbstractBean.class org.biojava.bio.structure.io.mmcif.model.AtomSite.class org.biojava.bio.structure.io.mmcif.model.ChemComp.class org.biojava.bio.structure.io.mmcif.model.DatabasePDBremark.class org.biojava.bio.structure.io.mmcif.model.DatabasePDBrev.class org.biojava.bio.structure.io.mmcif.model.Entity.class org.biojava.bio.structure.io.mmcif.model.EntityPolySeq.class org.biojava.bio.structure.io.mmcif.model.Exptl.class org.biojava.bio.structure.io.mmcif.model.PdbxEntityNonPoly.class org.biojava.bio.structure.io.mmcif.model.PdbxNonPolyScheme.class org.biojava.bio.structure.io.mmcif.model.PdbxPolySeqScheme.class org.biojava.bio.structure.io.mmcif.model.Refine.class org.biojava.bio.structure.io.mmcif.model.Struct.class org.biojava.bio.structure.io.mmcif.model.StructAsym.class org.biojava.bio.structure.io.mmcif.model.StructKeywords.class org.biojava.bio.structure.io.mmcif.model.StructRef.class org.biojava.bio.structure.io.mmcif.model.StructRefSeq.class org.biojava.bio.structure.jama.CholeskyDecomposition.class org.biojava.bio.structure.jama.EigenvalueDecomposition.class org.biojava.bio.structure.jama.LUDecomposition.class org.biojava.bio.structure.jama.Maths.class org.biojava.bio.structure.jama.Matrix.class org.biojava.bio.structure.jama.QRDecomposition.class org.biojava.bio.structure.jama.SingularValueDecomposition.class org.biojava.bio.structure.server.DemoStructureServer.class org.biojava.bio.structure.server.FlatFileInstallation.class org.biojava.bio.structure.server.MMCIFFileInstallation.class org.biojava.bio.structure.server.PDBFilter.class org.biojava.bio.structure.server.PDBInstallation.class org.biojava.bio.structure.server.PrepareIndexFile.class org.biojava.bio.structure.server.PrepareMMcifIndexFile.class org.biojava.bio.structure.server.SimpleStructureServer.class org.biojava.bio.structure.server.StructureEvent.class org.biojava.bio.structure.server.StructureEventImpl.class org.biojava.bio.structure.server.StructureFetcherRunnable.class org.biojava.bio.structure.server.StructureListener.class org.biojava.bio.structure.server.StructureServer.class org.biojava.bio.symbol.AbstractAlphabet.class org.biojava.bio.symbol.AbstractLocation.class org.biojava.bio.symbol.AbstractLocationDecorator.class org.biojava.bio.symbol.AbstractManyToOneTranslationTable.class org.biojava.bio.symbol.AbstractRangeLocation.class org.biojava.bio.symbol.AbstractReversibleTranslationTable.class org.biojava.bio.symbol.AbstractSimpleBasisSymbol.class org.biojava.bio.symbol.AbstractSymbol.class org.biojava.bio.symbol.AbstractSymbolList.class org.biojava.bio.symbol.AbstractTranslationTable.class org.biojava.bio.symbol.Alignment.class org.biojava.bio.symbol.Alphabet.class org.biojava.bio.symbol.AlphabetIndex.class org.biojava.bio.symbol.AlphabetManager.class org.biojava.bio.symbol.AtomicSymbol.class org.biojava.bio.symbol.BasisSymbol.class org.biojava.bio.symbol.BetweenLocation.class org.biojava.bio.symbol.BetweenLocationTools.class org.biojava.bio.symbol.ChunkedSymbolList.class org.biojava.bio.symbol.CircularLocation.class org.biojava.bio.symbol.CircularLocationTools.class org.biojava.bio.symbol.CodonPref.class org.biojava.bio.symbol.CodonPrefFilter.class org.biojava.bio.symbol.CodonPrefTools.class org.biojava.bio.symbol.CompoundLocation.class org.biojava.bio.symbol.CrossProductAlphabetIndex.class org.biojava.bio.symbol.DNAAmbPack.class org.biojava.bio.symbol.DNANoAmbPack.class org.biojava.bio.symbol.DoubleAlphabet.class org.biojava.bio.symbol.DummySymbolList.class org.biojava.bio.symbol.Edit.class org.biojava.bio.symbol.EmptyAlphabet.class org.biojava.bio.symbol.EmptyLocation.class org.biojava.bio.symbol.EmptySymbolList.class org.biojava.bio.symbol.FiniteAlphabet.class org.biojava.bio.symbol.FullDnaAlphabetIndex.class org.biojava.bio.symbol.FundamentalAtomicSymbol.class org.biojava.bio.symbol.FuzzyLocation.class org.biojava.bio.symbol.FuzzyPointLocation.class org.biojava.bio.symbol.GappedSymbolList.class org.biojava.bio.symbol.HashedAlphabetIndex.class org.biojava.bio.symbol.IllegalAlphabetException.class org.biojava.bio.symbol.IllegalSymbolException.class org.biojava.bio.symbol.IndexedNoAmbPack.class org.biojava.bio.symbol.InfiniteCrossProductAlphabet.class org.biojava.bio.symbol.IntegerAlphabet.class org.biojava.bio.symbol.LinearAlphabetIndex.class org.biojava.bio.symbol.Location.class org.biojava.bio.symbol.LocationComparator.class org.biojava.bio.symbol.LocationTools.class org.biojava.bio.symbol.ManyToOneTranslationTable.class org.biojava.bio.symbol.MergeLocation.class org.biojava.bio.symbol.MotifTools.class org.biojava.bio.symbol.OrderNSymbolList.class org.biojava.bio.symbol.PackedSymbolList.class org.biojava.bio.symbol.PackedSymbolListFactory.class org.biojava.bio.symbol.Packing.class org.biojava.bio.symbol.PackingFactory.class org.biojava.bio.symbol.PointLocation.class org.biojava.bio.symbol.RangeLocation.class org.biojava.bio.symbol.RelabeledAlignment.class org.biojava.bio.symbol.ReverseSymbolList.class org.biojava.bio.symbol.ReversibleTranslationTable.class org.biojava.bio.symbol.SimpleAlignment.class org.biojava.bio.symbol.SimpleAlphabet.class org.biojava.bio.symbol.SimpleAtomicSymbol.class org.biojava.bio.symbol.SimpleBasisSymbol.class org.biojava.bio.symbol.SimpleCodonPref.class org.biojava.bio.symbol.SimpleCrossProductAlphabet.class org.biojava.bio.symbol.SimpleGappedSymbolList.class org.biojava.bio.symbol.SimpleGeneticCodeTable.class org.biojava.bio.symbol.SimpleManyToOneTranslationTable.class org.biojava.bio.symbol.SimpleReversibleTranslationTable.class org.biojava.bio.symbol.SimpleSymbol.class org.biojava.bio.symbol.SimpleSymbolList.class org.biojava.bio.symbol.SimpleSymbolListFactory.class org.biojava.bio.symbol.SimpleSymbolPropertyTable.class org.biojava.bio.symbol.SimpleTranslationTable.class org.biojava.bio.symbol.SimpleWobbleDistribution.class org.biojava.bio.symbol.SingletonAlphabet.class org.biojava.bio.symbol.SoftMaskedAlphabet.class org.biojava.bio.symbol.SparseCrossProductAlphabet.class org.biojava.bio.symbol.SubList.class org.biojava.bio.symbol.SuffixTree.class org.biojava.bio.symbol.Symbol.class org.biojava.bio.symbol.SymbolList.class org.biojava.bio.symbol.SymbolListFactory.class org.biojava.bio.symbol.SymbolListViews.class org.biojava.bio.symbol.SymbolPropertyTable.class org.biojava.bio.symbol.TranslatedSymbolList.class org.biojava.bio.symbol.TranslationTable.class org.biojava.bio.symbol.UkkonenSuffixTree.class org.biojava.bio.symbol.WindowedSymbolList.class org.biojava.bio.symbol.WobbleDistribution.class org.biojava.bio.taxa.AbstractTaxon.class org.biojava.bio.taxa.CircularReferenceException.class org.biojava.bio.taxa.EbiFormat.class org.biojava.bio.taxa.SimpleTaxon.class org.biojava.bio.taxa.SimpleTaxonFactory.class org.biojava.bio.taxa.Taxon.class org.biojava.bio.taxa.TaxonFactory.class org.biojava.bio.taxa.TaxonParser.class org.biojava.bio.taxa.WeakTaxon.class org.biojava.bio.taxa.WeakTaxonFactory.class org.biojava.directory.OBDARegistryParser.class org.biojava.directory.ProviderNotFoundException.class org.biojava.directory.Registry.class org.biojava.directory.RegistryConfiguration.class org.biojava.directory.RegistryException.class org.biojava.directory.SequenceDBProvider.class org.biojava.directory.SystemRegistry.class org.biojava.naming.ObdaContext.class org.biojava.naming.ObdaInitialContextFactory.class org.biojava.naming.ObdaUriParser.class org.biojava.ontology.AbstractTerm.class org.biojava.ontology.AlreadyExistsException.class org.biojava.ontology.DefaultOps.class org.biojava.ontology.IntegerOntology.class org.biojava.ontology.InvalidTermException.class org.biojava.ontology.OntoTools.class org.biojava.ontology.Ontology.class org.biojava.ontology.OntologyException.class org.biojava.ontology.OntologyFactory.class org.biojava.ontology.OntologyOps.class org.biojava.ontology.OntologyTerm.class org.biojava.ontology.RemoteTerm.class org.biojava.ontology.Synonym.class org.biojava.ontology.Term.class org.biojava.ontology.Triple.class org.biojava.ontology.Variable.class org.biojava.ontology.io.GOParser.class org.biojava.ontology.io.OboParser.class org.biojava.ontology.io.TabDelimParser.class org.biojava.ontology.obo.NestedValue.class org.biojava.ontology.obo.OboFileEventListener.class org.biojava.ontology.obo.OboFileHandler.class org.biojava.ontology.obo.OboFileParser.class org.biojava.stats.svm.AbstractSVMClassifierModel.class org.biojava.stats.svm.AbstractSVMTarget.class org.biojava.stats.svm.CachingKernel.class org.biojava.stats.svm.DiagonalAddKernel.class org.biojava.stats.svm.DiagonalCachingKernel.class org.biojava.stats.svm.ItemValue.class org.biojava.stats.svm.LinearKernel.class org.biojava.stats.svm.ListSumKernel.class org.biojava.stats.svm.NestedKernel.class org.biojava.stats.svm.NormalizingKernel.class org.biojava.stats.svm.PolynomialKernel.class org.biojava.stats.svm.RadialBaseKernel.class org.biojava.stats.svm.SMORegressionTrainer.class org.biojava.stats.svm.SMOTrainer.class org.biojava.stats.svm.SVMClassifierModel.class org.biojava.stats.svm.SVMKernel.class org.biojava.stats.svm.SVMRegressionModel.class org.biojava.stats.svm.SVMTarget.class org.biojava.stats.svm.SigmoidKernel.class org.biojava.stats.svm.SimpleItemValue.class org.biojava.stats.svm.SimpleSVMClassifierModel.class org.biojava.stats.svm.SimpleSVMTarget.class org.biojava.stats.svm.SparseVector.class org.biojava.stats.svm.TrainingContext.class org.biojava.stats.svm.TrainingEvent.class org.biojava.stats.svm.TrainingListener.class org.biojava.stats.svm.tools.ClassifierExample.class org.biojava.stats.svm.tools.Classify.class org.biojava.stats.svm.tools.SVM_Light.class org.biojava.stats.svm.tools.SuffixTreeKernel.class org.biojava.stats.svm.tools.Train.class org.biojava.stats.svm.tools.TrainRegression.class org.biojava.utils.AbstractChangeable.class org.biojava.utils.ActivityListener.class org.biojava.utils.AssertionFailure.class org.biojava.utils.BeanAsMap.class org.biojava.utils.ChangeAdapter.class org.biojava.utils.ChangeEvent.class org.biojava.utils.ChangeForwarder.class org.biojava.utils.ChangeHub.class org.biojava.utils.ChangeListener.class org.biojava.utils.ChangeSupport.class org.biojava.utils.ChangeType.class org.biojava.utils.ChangeVetoException.class org.biojava.utils.Changeable.class org.biojava.utils.ClassTools.class org.biojava.utils.CommitFailure.class org.biojava.utils.Commitable.class org.biojava.utils.Constants.class org.biojava.utils.ExecRunner.class org.biojava.utils.FileAsList.class org.biojava.utils.IndexedChangeHub.class org.biojava.utils.JDBCConnectionPool.class org.biojava.utils.JDBCPooledDataSource.class org.biojava.utils.ListTools.class org.biojava.utils.MergingIterator.class org.biojava.utils.MergingSet.class org.biojava.utils.ObjectUtil.class org.biojava.utils.OverlayMap.class org.biojava.utils.ParseErrorEvent.class org.biojava.utils.ParseErrorListener.class org.biojava.utils.ParseErrorSource.class org.biojava.utils.ParserException.class org.biojava.utils.ProcessTimeoutException.class org.biojava.utils.ProcessTools.class org.biojava.utils.RepeatedCharSequence.class org.biojava.utils.Services.class org.biojava.utils.SimpleThreadPool.class org.biojava.utils.SingletonList.class org.biojava.utils.SmallMap.class org.biojava.utils.SmallSet.class org.biojava.utils.StaticMemberPlaceHolder.class org.biojava.utils.StreamGobbler.class org.biojava.utils.ThreadPool.class org.biojava.utils.TriState.class org.biojava.utils.TypedProperties.class org.biojava.utils.Unchangeable.class org.biojava.utils.automata.ArrayStateMachineToolkit.class org.biojava.utils.automata.AutomatonException.class org.biojava.utils.automata.DfaBuilder.class org.biojava.utils.automata.FiniteAutomaton.class org.biojava.utils.automata.Nfa.class org.biojava.utils.automata.NfaBuilder.class org.biojava.utils.automata.NfaSubModel.class org.biojava.utils.automata.PatternBlitz.class org.biojava.utils.automata.PatternListener.class org.biojava.utils.automata.PatternMaker.class org.biojava.utils.automata.StateMachineFactory.class org.biojava.utils.automata.StateMachineInstance.class org.biojava.utils.automata.StateMachineToolkit.class org.biojava.utils.cache.Cache.class org.biojava.utils.cache.CacheMap.class org.biojava.utils.cache.CacheReference.class org.biojava.utils.cache.ChangeableCache.class org.biojava.utils.cache.FixedSizeCache.class org.biojava.utils.cache.FixedSizeMap.class org.biojava.utils.cache.KeyedWeakReference.class org.biojava.utils.cache.SoftReferenceCache.class org.biojava.utils.cache.WeakCacheMap.class org.biojava.utils.cache.WeakValueHashMap.class org.biojava.utils.candy.CandyEntry.class org.biojava.utils.candy.CandyException.class org.biojava.utils.candy.CandyFinder.class org.biojava.utils.candy.CandyVocabulary.class org.biojava.utils.io.CachingInputStream.class org.biojava.utils.io.CountedBufferedReader.class org.biojava.utils.io.InputStreamProvider.class org.biojava.utils.io.LargeBuffer.class org.biojava.utils.io.RAF.class org.biojava.utils.io.RandomAccessReader.class org.biojava.utils.io.Seekable.class org.biojava.utils.io.UncompressInputStream.class org.biojava.utils.lsid.Identifiable.class org.biojava.utils.lsid.LifeScienceIdentifier.class org.biojava.utils.lsid.LifeScienceIdentifierParseException.class org.biojava.utils.math.BinarySearch.class org.biojava.utils.math.ComputeObject.class org.biojava.utils.net.URLFactory.class org.biojava.utils.process.ExternalProcess.class org.biojava.utils.process.InputHandler.class org.biojava.utils.process.OutputHandler.class org.biojava.utils.process.ReaderInputHandler.class org.biojava.utils.process.ReaderWriterPipe.class org.biojava.utils.process.SimpleInputHandler.class org.biojava.utils.process.SimpleOutputHandler.class org.biojava.utils.process.StreamPipe.class org.biojava.utils.process.WriterOutputHandler.class org.biojava.utils.regex.Matcher.class org.biojava.utils.regex.Pattern.class org.biojava.utils.regex.PatternChecker.class org.biojava.utils.regex.PatternFactory.class org.biojava.utils.regex.RegexException.class org.biojava.utils.regex.Search.class org.biojava.utils.stax.BooleanElementHandlerBase.class org.biojava.utils.stax.ByteElementHandlerBase.class org.biojava.utils.stax.CharElementHandlerBase.class org.biojava.utils.stax.DelegationManager.class org.biojava.utils.stax.DoubleElementHandlerBase.class org.biojava.utils.stax.FloatElementHandlerBase.class org.biojava.utils.stax.IntElementHandlerBase.class org.biojava.utils.stax.LongElementHandlerBase.class org.biojava.utils.stax.SAX2StAXAdaptor.class org.biojava.utils.stax.StAXContentHandler.class org.biojava.utils.stax.StAXContentHandlerBase.class org.biojava.utils.stax.StringElementHandlerBase.class org.biojava.utils.walker.Visitor.class org.biojava.utils.walker.Walker.class org.biojava.utils.walker.WalkerFactory.class org.biojava.utils.xml.AppBeanRunner.class org.biojava.utils.xml.AppEntry.class org.biojava.utils.xml.AppException.class org.biojava.utils.xml.FastXMLWriter.class org.biojava.utils.xml.Initializable.class org.biojava.utils.xml.PrettyXMLWriter.class org.biojava.utils.xml.ResourceEntityResolver.class org.biojava.utils.xml.XMLBeans.class org.biojava.utils.xml.XMLWritable.class org.biojava.utils.xml.XMLWriter.class org.biojavax.Comment.class org.biojavax.CrossRef.class org.biojavax.CrossReferenceResolutionException.class org.biojavax.CrossReferenceResolver.class org.biojavax.DocRef.class org.biojavax.DocRefAuthor.class org.biojavax.DummyCrossReferenceResolver.class org.biojavax.EmptyRichAnnotation.class org.biojavax.Namespace.class org.biojavax.Note.class org.biojavax.RankedCrossRef.class org.biojavax.RankedCrossRefable.class org.biojavax.RankedDocRef.class org.biojavax.RichAnnotatable.class org.biojavax.RichAnnotation.class org.biojavax.RichObjectBuilder.class org.biojavax.RichObjectFactory.class org.biojavax.SimpleComment.class org.biojavax.SimpleCrossRef.class org.biojavax.SimpleDocRef.class org.biojavax.SimpleDocRefAuthor.class org.biojavax.SimpleNamespace.class org.biojavax.SimpleNote.class org.biojavax.SimpleRankedCrossRef.class org.biojavax.SimpleRankedDocRef.class org.biojavax.SimpleRichAnnotation.class org.biojavax.SimpleRichObjectBuilder.class org.biojavax.bio.BioEntry.class org.biojavax.bio.BioEntryIterator.class org.biojavax.bio.BioEntryRelationship.class org.biojavax.bio.SimpleBioEntry.class org.biojavax.bio.SimpleBioEntryRelationship.class org.biojavax.bio.db.AbstractBioEntryDB.class org.biojavax.bio.db.AbstractRichSequenceDB.class org.biojavax.bio.db.BioEntryDB.class org.biojavax.bio.db.BioEntryDBLite.class org.biojavax.bio.db.HashBioEntryDB.class org.biojavax.bio.db.HashRichSequenceDB.class org.biojavax.bio.db.RichSequenceDB.class org.biojavax.bio.db.RichSequenceDBLite.class org.biojavax.bio.db.biosql.BioSQLAcceptAllFilter.class org.biojavax.bio.db.biosql.BioSQLAcceptNoneFilter.class org.biojavax.bio.db.biosql.BioSQLBioEntryDB.class org.biojavax.bio.db.biosql.BioSQLCrossReferenceResolver.class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.class org.biojavax.bio.db.biosql.BioSQLRichObjectBuilder.class org.biojavax.bio.db.biosql.BioSQLRichSequenceDB.class org.biojavax.bio.db.biosql.BioSQLRichSequenceHandler.class org.biojavax.bio.db.ncbi.GenbankRichSequenceDB.class org.biojavax.bio.db.ncbi.GenpeptRichSequenceDB.class org.biojavax.bio.phylo.DistanceBasedTreeMethod.class org.biojavax.bio.phylo.MultipleHitCorrection.class org.biojavax.bio.phylo.ParsimonyTreeMethod.class org.biojavax.bio.phylo.io.nexus.CharactersBlock.class org.biojavax.bio.phylo.io.nexus.CharactersBlockBuilder.class org.biojavax.bio.phylo.io.nexus.CharactersBlockListener.class org.biojavax.bio.phylo.io.nexus.CharactersBlockParser.class org.biojavax.bio.phylo.io.nexus.DataBlock.class org.biojavax.bio.phylo.io.nexus.DataBlockBuilder.class org.biojavax.bio.phylo.io.nexus.DataBlockListener.class org.biojavax.bio.phylo.io.nexus.DataBlockParser.class org.biojavax.bio.phylo.io.nexus.DistancesBlock.class org.biojavax.bio.phylo.io.nexus.DistancesBlockBuilder.class org.biojavax.bio.phylo.io.nexus.DistancesBlockListener.class org.biojavax.bio.phylo.io.nexus.DistancesBlockParser.class org.biojavax.bio.phylo.io.nexus.NexusBlock.class org.biojavax.bio.phylo.io.nexus.NexusBlockBuilder.class org.biojavax.bio.phylo.io.nexus.NexusBlockListener.class org.biojavax.bio.phylo.io.nexus.NexusBlockParser.class org.biojavax.bio.phylo.io.nexus.NexusComment.class org.biojavax.bio.phylo.io.nexus.NexusFile.class org.biojavax.bio.phylo.io.nexus.NexusFileBuilder.class org.biojavax.bio.phylo.io.nexus.NexusFileFormat.class org.biojavax.bio.phylo.io.nexus.NexusFileListener.class org.biojavax.bio.phylo.io.nexus.NexusObject.class org.biojavax.bio.phylo.io.nexus.TaxaBlock.class org.biojavax.bio.phylo.io.nexus.TaxaBlockBuilder.class org.biojavax.bio.phylo.io.nexus.TaxaBlockListener.class org.biojavax.bio.phylo.io.nexus.TaxaBlockParser.class org.biojavax.bio.phylo.io.nexus.TreesBlock.class org.biojavax.bio.phylo.io.nexus.TreesBlockBuilder.class org.biojavax.bio.phylo.io.nexus.TreesBlockListener.class org.biojavax.bio.phylo.io.nexus.TreesBlockParser.class org.biojavax.bio.phylo.io.phylip.PHYLIPFileBuilder.class org.biojavax.bio.phylo.io.phylip.PHYLIPFileFormat.class org.biojavax.bio.phylo.io.phylip.PHYLIPFileListener.class org.biojavax.bio.seq.CompoundRichLocation.class org.biojavax.bio.seq.DummyRichSequenceHandler.class org.biojavax.bio.seq.EmptyRichLocation.class org.biojavax.bio.seq.InfinitelyAmbiguousSymbolList.class org.biojavax.bio.seq.MultiSourceCompoundRichLocation.class org.biojavax.bio.seq.Position.class org.biojavax.bio.seq.PositionResolver.class org.biojavax.bio.seq.RichFeature.class org.biojavax.bio.seq.RichFeatureRelationship.class org.biojavax.bio.seq.RichFeatureRelationshipHolder.class org.biojavax.bio.seq.RichLocation.class org.biojavax.bio.seq.RichSequence.class org.biojavax.bio.seq.RichSequenceHandler.class org.biojavax.bio.seq.RichSequenceIterator.class org.biojavax.bio.seq.SimplePosition.class org.biojavax.bio.seq.SimpleRichFeature.class org.biojavax.bio.seq.SimpleRichFeatureRelationship.class org.biojavax.bio.seq.SimpleRichLocation.class org.biojavax.bio.seq.SimpleRichSequence.class org.biojavax.bio.seq.ThinRichSequence.class org.biojavax.bio.seq.io.DebuggingRichSeqIOListener.class org.biojavax.bio.seq.io.EMBLFormat.class org.biojavax.bio.seq.io.EMBLxmlFormat.class org.biojavax.bio.seq.io.FastaFormat.class org.biojavax.bio.seq.io.FastaHeader.class org.biojavax.bio.seq.io.GenbankFormat.class org.biojavax.bio.seq.io.GenbankLocationParser.class org.biojavax.bio.seq.io.HashedFastaIterator.class org.biojavax.bio.seq.io.INSDseqFormat.class org.biojavax.bio.seq.io.MyRichSeqIOListener.class org.biojavax.bio.seq.io.RichSeqIOAdapter.class org.biojavax.bio.seq.io.RichSeqIOListener.class org.biojavax.bio.seq.io.RichSequenceBuilder.class org.biojavax.bio.seq.io.RichSequenceBuilderFactory.class org.biojavax.bio.seq.io.RichSequenceFormat.class org.biojavax.bio.seq.io.RichStreamReader.class org.biojavax.bio.seq.io.RichStreamWriter.class org.biojavax.bio.seq.io.SimpleRichSequenceBuilder.class org.biojavax.bio.seq.io.SimpleRichSequenceBuilderFactory.class org.biojavax.bio.seq.io.UniProtCommentParser.class org.biojavax.bio.seq.io.UniProtFormat.class org.biojavax.bio.seq.io.UniProtLocationParser.class org.biojavax.bio.seq.io.UniProtXMLFormat.class org.biojavax.bio.taxa.NCBITaxon.class org.biojavax.bio.taxa.SimpleNCBITaxon.class org.biojavax.bio.taxa.SimpleNCBITaxonName.class org.biojavax.bio.taxa.io.NCBITaxonomyLoader.class org.biojavax.bio.taxa.io.SimpleNCBITaxonomyLoader.class org.biojavax.ga.GAStoppingCriteria.class org.biojavax.ga.GeneticAlgorithm.class org.biojavax.ga.Organism.class org.biojavax.ga.Population.class org.biojavax.ga.exception.IllegalOrganismException.class org.biojavax.ga.functions.AbstractCrossOverFunction.class org.biojavax.ga.functions.AbstractMutationFunction.class org.biojavax.ga.functions.CrossOverFunction.class org.biojavax.ga.functions.FitnessFunction.class org.biojavax.ga.functions.GACross.class org.biojavax.ga.functions.GACrossResult.class org.biojavax.ga.functions.MutationFunction.class org.biojavax.ga.functions.OrderCrossover.class org.biojavax.ga.functions.ProportionalSelection.class org.biojavax.ga.functions.SelectionFunction.class org.biojavax.ga.functions.SimpleCrossOverFunction.class org.biojavax.ga.functions.SimpleGACrossResult.class org.biojavax.ga.functions.SimpleMutationFunction.class org.biojavax.ga.functions.SwapMutationFunction.class org.biojavax.ga.functions.TournamentSelection.class org.biojavax.ga.impl.AbstractGeneticAlgorithm.class org.biojavax.ga.impl.AbstractOrganism.class org.biojavax.ga.impl.AbstractPopulation.class org.biojavax.ga.impl.SimpleGeneticAlgorithm.class org.biojavax.ga.impl.SimpleOrganism.class org.biojavax.ga.impl.SimplePopulation.class org.biojavax.ga.util.GATools.class org.biojavax.ga.util.WeightedSet.class org.biojavax.ontology.ComparableOntology.class org.biojavax.ontology.ComparableTerm.class org.biojavax.ontology.ComparableTriple.class org.biojavax.ontology.SimpleComparableOntology.class org.biojavax.ontology.SimpleComparableTerm.class org.biojavax.ontology.SimpleComparableTriple.class org.biojavax.utils.CRC64Checksum.class org.biojavax.utils.StringTools.class org.biojavax.utils.XMLTools.class META-INF/services/org.biojava.bio.program.formats.Format META-INF/services/org.biojava.directory.SequenceDBProvider obda/naming/core.xml org/biojava/bio/gui/sequence/NoDesc.html org/biojava/bio/gui/sequence/NoSample.txt org/biojava/bio/gui/sequence/aprDesc.html org/biojava/bio/gui/sequence/aprExamp.apr org/biojava/bio/gui/sequence/fastaDesc.html org/biojava/bio/gui/sequence/fastaExamp.fasta org/biojava/bio/gui/sequence/msfDesc.html org/biojava/bio/gui/sequence/msfExamp.msf org/biojava/bio/molbio/RestrictionEnzymeManager.properties org/biojava/bio/molbio/rebase_common.dat org/biojava/bio/program/sax/blastxml/NCBI_BlastOutput.dtd org/biojava/bio/program/sax/blastxml/NCBI_BlastOutput.mod org/biojava/bio/program/sax/blastxml/NCBI_Entity.mod org/biojava/bio/program/unigene/createUnigene.sql org/biojava/bio/proteomics/ProteaseManager.xml org/biojava/bio/seq/TranslationTables.xml org/biojava/bio/seq/io/FeatureQualifier.xml org/biojava/bio/structure/blosum62.mat org/biojava/bio/structure/standardaminos.pdb org/biojava/bio/symbol/AlphabetManager.xml org/biojava/bio/symbol/CodonPrefTables.xml org/biojava/bio/symbol/ResidueProperties.xml org/biojava/ontology/colonel-west.pred org/biojava/ontology/core.agregate.pred org/biojava/ontology/core.list.pred org/biojava/ontology/core.onto org/biojava/ontology/core.pred org/biojava/ontology/core.set.pred org/biojava/ontology/ontology.pred                          biojava/biojava-1.7.1.jar.zip( 3,248 k) Related examples in the same category 1. Download biojava-1.4.jar 2. Download biojava-1.4cvs.jar 3. Download biojava-1.6-bin.jar 4. Download biojava-1.6.jar 5. Download biojava-1.7.jar 6. Download biojava-ensembl.jar 7. Download biojava-live.jar