| | | Download biojava-1.6.jar |
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Files contained in biojava-1.6.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/bibliography/doc-files/BibRefQuery_corba.jpg
org/biojava/bibliography/doc-files/BibRefQuery_simple.jpg
org/biojava/bibliography/doc-files/BibRefQuery_soap.jpg
org/biojava/bibliography/doc-files/bibobjects_java.jpg
org/biojava/bibliography/package.html
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/alignment/package.html
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/annodb/package.html
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/chromatogram/graphic/package.html
org/biojava/bio/chromatogram/package.html
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/dist/package.html
org/biojava/bio/dist/package.inf
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/onehead/package.inf
org/biojava/bio/dp/package.html
org/biojava/bio/dp/package.inf
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/dp/twohead/package.inf
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/glyph/package.html
org/biojava/bio/gui/package.html
org/biojava/bio/gui/package.inf
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/NoDesc.html
org/biojava/bio/gui/sequence/NoSample.txt
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/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/gui/sequence/package.html
org/biojava/bio/gui/sequence/package.inf
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/gui/sequence/tracklayout/package.html
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/RestrictionEnzymeManager.properties
org.biojava.bio.molbio.RestrictionMapper.class
org.biojava.bio.molbio.RestrictionSite.class
org.biojava.bio.molbio.RestrictionSiteFinder.class
org/biojava/bio/molbio/package.html
org/biojava/bio/molbio/rebase_common.dat
org/biojava/bio/package.html
org/biojava/bio/package.inf
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/abi/package.html
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/blast2html/package.html
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/dasalignment/package.html
org.biojava.bio.program.das.dasstructure.DASStructureCall.class
org.biojava.bio.program.das.dasstructure.DASStructureXMLResponseParser.class
org/biojava/bio/program/das/dasstructure/package.html
org/biojava/bio/program/das/package.html
org/biojava/bio/program/das/package.inf
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/formats/package.html
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/gff3/package.html
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/gff/package.html
org/biojava/bio/program/gff/package.inf
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/hmmer/package.html
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/homologene/package.html
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/indexdb/package.html
org/biojava/bio/program/package.html
org/biojava/bio/program/package.inf
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/phred/package.html
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
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org.biojava.utils.io.Seekable.class
org.biojava.utils.io.UncompressInputStream.class
org/biojava/utils/io/package.html
org.biojava.utils.lsid.Identifiable.class
org.biojava.utils.lsid.LifeScienceIdentifier.class
org.biojava.utils.lsid.LifeScienceIdentifierParseException.class
org/biojava/utils/lsid/package.html
org.biojava.utils.math.BinarySearch.class
org.biojava.utils.math.ComputeObject.class
org/biojava/utils/math/package.html
org.biojava.utils.net.URLFactory.class
org/biojava/utils/net/package.html
org/biojava/utils/package.html
org/biojava/utils/package.inf
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/process/package.html
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/regex/package.html
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/stax/package.html
org/biojava/utils/stax/package.inf
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/biojava/utils/xml/package.html
org/biojava/utils/xml/package.inf
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/biosql/hsqldb/BioEntry.hbm.xml
org/biojavax/bio/db/biosql/hsqldb/BioEntryRelationship.hbm.xml
org/biojavax/bio/db/biosql/hsqldb/Comment.hbm.xml
org/biojavax/bio/db/biosql/hsqldb/CrossRef.hbm.xml
org/biojavax/bio/db/biosql/hsqldb/DocRef.hbm.xml
org/biojavax/bio/db/biosql/hsqldb/Feature.hbm.xml
org/biojavax/bio/db/biosql/hsqldb/FeatureRelationship.hbm.xml
org/biojavax/bio/db/biosql/hsqldb/Location.hbm.xml
org/biojavax/bio/db/biosql/hsqldb/Namespace.hbm.xml
org/biojavax/bio/db/biosql/hsqldb/Ontology.hbm.xml
org/biojavax/bio/db/biosql/hsqldb/Taxon.hbm.xml
org/biojavax/bio/db/biosql/hsqldb/Term.hbm.xml
org/biojavax/bio/db/biosql/hsqldb/Triple.hbm.xml
org/biojavax/bio/db/biosql/hsqldb/hibernate.cfg.xml
org/biojavax/bio/db/biosql/mysql/BioEntry.hbm.xml
org/biojavax/bio/db/biosql/mysql/BioEntryRelationship.hbm.xml
org/biojavax/bio/db/biosql/mysql/Comment.hbm.xml
org/biojavax/bio/db/biosql/mysql/CrossRef.hbm.xml
org/biojavax/bio/db/biosql/mysql/DocRef.hbm.xml
org/biojavax/bio/db/biosql/mysql/Feature.hbm.xml
org/biojavax/bio/db/biosql/mysql/FeatureRelationship.hbm.xml
org/biojavax/bio/db/biosql/mysql/Location.hbm.xml
org/biojavax/bio/db/biosql/mysql/Namespace.hbm.xml
org/biojavax/bio/db/biosql/mysql/Ontology.hbm.xml
org/biojavax/bio/db/biosql/mysql/Taxon.hbm.xml
org/biojavax/bio/db/biosql/mysql/Term.hbm.xml
org/biojavax/bio/db/biosql/mysql/Triple.hbm.xml
org/biojavax/bio/db/biosql/mysql/hibernate.cfg.xml
org/biojavax/bio/db/biosql/oracle/BioEntry.hbm.xml
org/biojavax/bio/db/biosql/oracle/BioEntryRelationship.hbm.xml
org/biojavax/bio/db/biosql/oracle/Comment.hbm.xml
org/biojavax/bio/db/biosql/oracle/CrossRef.hbm.xml
org/biojavax/bio/db/biosql/oracle/DocRef.hbm.xml
org/biojavax/bio/db/biosql/oracle/Feature.hbm.xml
org/biojavax/bio/db/biosql/oracle/FeatureRelationship.hbm.xml
org/biojavax/bio/db/biosql/oracle/Location.hbm.xml
org/biojavax/bio/db/biosql/oracle/Namespace.hbm.xml
org/biojavax/bio/db/biosql/oracle/Ontology.hbm.xml
org/biojavax/bio/db/biosql/oracle/Taxon.hbm.xml
org/biojavax/bio/db/biosql/oracle/Term.hbm.xml
org/biojavax/bio/db/biosql/oracle/Triple.hbm.xml
org/biojavax/bio/db/biosql/oracle/hibernate.cfg.xml
org/biojavax/bio/db/biosql/package.html
org/biojavax/bio/db/biosql/pg/BioEntry.hbm.xml
org/biojavax/bio/db/biosql/pg/BioEntryRelationship.hbm.xml
org/biojavax/bio/db/biosql/pg/Comment.hbm.xml
org/biojavax/bio/db/biosql/pg/CrossRef.hbm.xml
org/biojavax/bio/db/biosql/pg/DocRef.hbm.xml
org/biojavax/bio/db/biosql/pg/Feature.hbm.xml
org/biojavax/bio/db/biosql/pg/FeatureRelationship.hbm.xml
org/biojavax/bio/db/biosql/pg/Location.hbm.xml
org/biojavax/bio/db/biosql/pg/Namespace.hbm.xml
org/biojavax/bio/db/biosql/pg/Ontology.hbm.xml
org/biojavax/bio/db/biosql/pg/Taxon.hbm.xml
org/biojavax/bio/db/biosql/pg/Term.hbm.xml
org/biojavax/bio/db/biosql/pg/Triple.hbm.xml
org/biojavax/bio/db/biosql/pg/hibernate.cfg.xml
org.biojavax.bio.db.ncbi.GenbankRichSequenceDB.class
org.biojavax.bio.db.ncbi.GenpeptRichSequenceDB.class
org/biojavax/bio/db/ncbi/package.html
org/biojavax/bio/db/package.html
org/biojavax/bio/package.html
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/nexus/package.html
org/biojavax/bio/phylo/io/package.html
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/phylo/io/phylip/package.html
org/biojavax/bio/phylo/package.html
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.INSDseqFormat.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/seq/io/package.html
org/biojavax/bio/seq/package.html
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/bio/taxa/package.html
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/exception/package.html
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/functions/package.html
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/impl/package.html
org/biojavax/ga/package.html
org.biojavax.ga.util.GATools.class
org.biojavax.ga.util.WeightedSet.class
org/biojavax/ga/util/package.html
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/ontology/package.html
org/biojavax/package.html
org.biojavax.utils.CRC64Checksum.class
org.biojavax.utils.StringTools.class
org.biojavax.utils.XMLTools.class
org/biojavax/utils/package.html
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 biojava/biojava-1.6.jar.zip( 3,448 k) |
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