permissions = sandbox
authorcmzmasek@gmail.com <cmzmasek@gmail.com@ca865154-3058-d1c3-3e42-d8f55a55bdbd>
Wed, 18 Feb 2015 17:51:23 +0000 (17:51 +0000)
committercmzmasek@gmail.com <cmzmasek@gmail.com@ca865154-3058-d1c3-3e42-d8f55a55bdbd>
Wed, 18 Feb 2015 17:51:23 +0000 (17:51 +0000)
511 files changed:
forester/java/archaeopteryx_applets.jar
forester/java/classes/org/forester/analysis/AncestralTaxonomyInference.class
forester/java/classes/org/forester/analysis/AncestralTaxonomyInferenceException.class
forester/java/classes/org/forester/analysis/TaxonomyDataManager$1.class
forester/java/classes/org/forester/analysis/TaxonomyDataManager$QUERY_TYPE.class
forester/java/classes/org/forester/analysis/TaxonomyDataManager.class
forester/java/classes/org/forester/application/annotator.class
forester/java/classes/org/forester/application/check_fasta.class
forester/java/classes/org/forester/application/confadd.class
forester/java/classes/org/forester/application/count_support.class
forester/java/classes/org/forester/application/decorator.class
forester/java/classes/org/forester/application/decoratorX.class
forester/java/classes/org/forester/application/dom_dup.class
forester/java/classes/org/forester/application/gene_tree_preprocess.class
forester/java/classes/org/forester/application/goac.class
forester/java/classes/org/forester/application/gsdi.class
forester/java/classes/org/forester/application/mcc.class
forester/java/classes/org/forester/application/meta_ontologizer.class
forester/java/classes/org/forester/application/msa_compactor.class
forester/java/classes/org/forester/application/nj.class
forester/java/classes/org/forester/application/obo_tool.class
forester/java/classes/org/forester/application/pccx.class
forester/java/classes/org/forester/application/pfam2go_extractor.class
forester/java/classes/org/forester/application/pfam_go.class
forester/java/classes/org/forester/application/pfamacc2go.class
forester/java/classes/org/forester/application/pfamacc2pfamid.class
forester/java/classes/org/forester/application/phylostrip.class
forester/java/classes/org/forester/application/phyloxml_converter.class
forester/java/classes/org/forester/application/rio$1.class
forester/java/classes/org/forester/application/rio.class
forester/java/classes/org/forester/application/support_statistics.class
forester/java/classes/org/forester/application/support_transfer.class
forester/java/classes/org/forester/application/surfacing$1.class
forester/java/classes/org/forester/application/surfacing.class
forester/java/classes/org/forester/archaeopteryx/AptxUtil$GraphicsExportType.class
forester/java/classes/org/forester/archaeopteryx/AptxUtil.class
forester/java/classes/org/forester/archaeopteryx/Archaeopteryx.class
forester/java/classes/org/forester/archaeopteryx/ArchaeopteryxA.class
forester/java/classes/org/forester/archaeopteryx/ArchaeopteryxE$1.class
forester/java/classes/org/forester/archaeopteryx/ArchaeopteryxE$2.class
forester/java/classes/org/forester/archaeopteryx/ArchaeopteryxE$3.class
forester/java/classes/org/forester/archaeopteryx/ArchaeopteryxE.class
forester/java/classes/org/forester/archaeopteryx/ColorSchemeChooser$1.class
forester/java/classes/org/forester/archaeopteryx/ColorSchemeChooser$2.class
forester/java/classes/org/forester/archaeopteryx/ColorSchemeChooser$3.class
forester/java/classes/org/forester/archaeopteryx/ColorSchemeChooser.class
forester/java/classes/org/forester/archaeopteryx/Configuration$EXT_NODE_DATA_RETURN_ON.class
forester/java/classes/org/forester/archaeopteryx/Configuration$TRIPLET.class
forester/java/classes/org/forester/archaeopteryx/Configuration$UI.class
forester/java/classes/org/forester/archaeopteryx/Configuration.class
forester/java/classes/org/forester/archaeopteryx/Constants.class
forester/java/classes/org/forester/archaeopteryx/ControlPanel$1.class
forester/java/classes/org/forester/archaeopteryx/ControlPanel$2.class
forester/java/classes/org/forester/archaeopteryx/ControlPanel$3.class
forester/java/classes/org/forester/archaeopteryx/ControlPanel$4.class
forester/java/classes/org/forester/archaeopteryx/ControlPanel$5.class
forester/java/classes/org/forester/archaeopteryx/ControlPanel$6.class
forester/java/classes/org/forester/archaeopteryx/ControlPanel$7.class
forester/java/classes/org/forester/archaeopteryx/ControlPanel$NodeClickAction.class
forester/java/classes/org/forester/archaeopteryx/ControlPanel.class
forester/java/classes/org/forester/archaeopteryx/DefaultFilter.class
forester/java/classes/org/forester/archaeopteryx/FontChooser.class
forester/java/classes/org/forester/archaeopteryx/GraphicsFileFilter.class
forester/java/classes/org/forester/archaeopteryx/MainFrame$1.class
forester/java/classes/org/forester/archaeopteryx/MainFrame$2.class
forester/java/classes/org/forester/archaeopteryx/MainFrame.class
forester/java/classes/org/forester/archaeopteryx/MainFrameApplet$1.class
forester/java/classes/org/forester/archaeopteryx/MainFrameApplet$2.class
forester/java/classes/org/forester/archaeopteryx/MainFrameApplet$3.class
forester/java/classes/org/forester/archaeopteryx/MainFrameApplet.class
forester/java/classes/org/forester/archaeopteryx/MainFrameApplication$1.class
forester/java/classes/org/forester/archaeopteryx/MainFrameApplication$2.class
forester/java/classes/org/forester/archaeopteryx/MainFrameApplication$3.class
forester/java/classes/org/forester/archaeopteryx/MainFrameApplication$4.class
forester/java/classes/org/forester/archaeopteryx/MainFrameApplication.class
forester/java/classes/org/forester/archaeopteryx/MainPanel$1.class
forester/java/classes/org/forester/archaeopteryx/MainPanel$2.class
forester/java/classes/org/forester/archaeopteryx/MainPanel$3.class
forester/java/classes/org/forester/archaeopteryx/MainPanel$4.class
forester/java/classes/org/forester/archaeopteryx/MainPanel$5.class
forester/java/classes/org/forester/archaeopteryx/MainPanel.class
forester/java/classes/org/forester/archaeopteryx/MainPanelApplets.class
forester/java/classes/org/forester/archaeopteryx/MouseListener.class
forester/java/classes/org/forester/archaeopteryx/MsaFileFilter.class
forester/java/classes/org/forester/archaeopteryx/NHFilter.class
forester/java/classes/org/forester/archaeopteryx/NHXFilter.class
forester/java/classes/org/forester/archaeopteryx/NexusFilter.class
forester/java/classes/org/forester/archaeopteryx/NodeEditPanel$1.class
forester/java/classes/org/forester/archaeopteryx/NodeEditPanel$2.class
forester/java/classes/org/forester/archaeopteryx/NodeEditPanel$3.class
forester/java/classes/org/forester/archaeopteryx/NodeEditPanel$PHYLOXML_TAG.class
forester/java/classes/org/forester/archaeopteryx/NodeEditPanel$TagNumber.class
forester/java/classes/org/forester/archaeopteryx/NodeEditPanel.class
forester/java/classes/org/forester/archaeopteryx/NodeFrame$1.class
forester/java/classes/org/forester/archaeopteryx/NodeFrame$2.class
forester/java/classes/org/forester/archaeopteryx/NodeFrame.class
forester/java/classes/org/forester/archaeopteryx/NodePanel.class
forester/java/classes/org/forester/archaeopteryx/Options$CLADOGRAM_TYPE.class
forester/java/classes/org/forester/archaeopteryx/Options$NODE_LABEL_DIRECTION.class
forester/java/classes/org/forester/archaeopteryx/Options$OVERVIEW_PLACEMENT_TYPE.class
forester/java/classes/org/forester/archaeopteryx/Options$PHYLOGENY_GRAPHICS_TYPE.class
forester/java/classes/org/forester/archaeopteryx/Options.class
forester/java/classes/org/forester/archaeopteryx/PdfExporter.class
forester/java/classes/org/forester/archaeopteryx/PdfFilter.class
forester/java/classes/org/forester/archaeopteryx/Printer.class
forester/java/classes/org/forester/archaeopteryx/SequencesFileFilter.class
forester/java/classes/org/forester/archaeopteryx/TextFrame$1.class
forester/java/classes/org/forester/archaeopteryx/TextFrame.class
forester/java/classes/org/forester/archaeopteryx/TolFilter.class
forester/java/classes/org/forester/archaeopteryx/TreeColorSet.class
forester/java/classes/org/forester/archaeopteryx/TreeFontSet.class
forester/java/classes/org/forester/archaeopteryx/TreePanel$1.class
forester/java/classes/org/forester/archaeopteryx/TreePanel$2.class
forester/java/classes/org/forester/archaeopteryx/TreePanel$3.class
forester/java/classes/org/forester/archaeopteryx/TreePanel$NodeColorizationActionListener.class
forester/java/classes/org/forester/archaeopteryx/TreePanel$SubtreeColorizationActionListener.class
forester/java/classes/org/forester/archaeopteryx/TreePanel.class
forester/java/classes/org/forester/archaeopteryx/TreePanelUtil.class
forester/java/classes/org/forester/archaeopteryx/UrlTreeReader$1.class
forester/java/classes/org/forester/archaeopteryx/UrlTreeReader.class
forester/java/classes/org/forester/archaeopteryx/XMLFilter.class
forester/java/classes/org/forester/archaeopteryx/phylogeny/data/RenderableDomainArchitecture.class
forester/java/classes/org/forester/archaeopteryx/phylogeny/data/RenderableMsaSequence.class [new file with mode: 0644]
forester/java/classes/org/forester/archaeopteryx/phylogeny/data/RenderablePhylogenyData.class
forester/java/classes/org/forester/archaeopteryx/phylogeny/data/RenderableVector.class
forester/java/classes/org/forester/archaeopteryx/tools/AncestralTaxonomyInferrer.class
forester/java/classes/org/forester/archaeopteryx/tools/Blast.class
forester/java/classes/org/forester/archaeopteryx/tools/ImageLoader.class
forester/java/classes/org/forester/archaeopteryx/tools/InferenceManager.class
forester/java/classes/org/forester/archaeopteryx/tools/PhyloInferenceDialog$1.class
forester/java/classes/org/forester/archaeopteryx/tools/PhyloInferenceDialog.class
forester/java/classes/org/forester/archaeopteryx/tools/PhylogeneticInferenceOptions.class
forester/java/classes/org/forester/archaeopteryx/tools/PhylogeneticInferrer$1.class
forester/java/classes/org/forester/archaeopteryx/tools/PhylogeneticInferrer$MSA_PRG.class
forester/java/classes/org/forester/archaeopteryx/tools/PhylogeneticInferrer.class
forester/java/classes/org/forester/archaeopteryx/tools/ProcessPool.class
forester/java/classes/org/forester/archaeopteryx/tools/ProcessRunning.class
forester/java/classes/org/forester/archaeopteryx/tools/RunnableProcess.class
forester/java/classes/org/forester/archaeopteryx/tools/SequenceDataRetriver.class
forester/java/classes/org/forester/archaeopteryx/webservices/BasicPhylogeniesWebserviceClient.class
forester/java/classes/org/forester/archaeopteryx/webservices/PhylogeniesWebserviceClient.class
forester/java/classes/org/forester/archaeopteryx/webservices/WebserviceUtil.class
forester/java/classes/org/forester/archaeopteryx/webservices/WebservicesManager$WsPhylogenyFormat.class
forester/java/classes/org/forester/archaeopteryx/webservices/WebservicesManager.class
forester/java/classes/org/forester/datastructures/IntMatrix.class
forester/java/classes/org/forester/datastructures/Queue.class
forester/java/classes/org/forester/development/AbstractRenderer.class
forester/java/classes/org/forester/development/DevelopmentTools.class
forester/java/classes/org/forester/development/Hello3d.class
forester/java/classes/org/forester/development/HmmerRest.class
forester/java/classes/org/forester/development/MsaRenderer$1.class
forester/java/classes/org/forester/development/MsaRenderer$2.class
forester/java/classes/org/forester/development/MsaRenderer.class
forester/java/classes/org/forester/development/RandomThing.class
forester/java/classes/org/forester/development/ResidueRenderer.class
forester/java/classes/org/forester/development/Test.class
forester/java/classes/org/forester/development/Time.class
forester/java/classes/org/forester/development/neTest$DoublePointer.class
forester/java/classes/org/forester/development/neTest.class
forester/java/classes/org/forester/evoinference/TestPhylogenyReconstruction.class
forester/java/classes/org/forester/evoinference/distance/NeighborJoining.class
forester/java/classes/org/forester/evoinference/distance/NeighborJoiningF.class
forester/java/classes/org/forester/evoinference/distance/NeighborJoiningR.class
forester/java/classes/org/forester/evoinference/distance/PairwiseDistanceCalculator$PWD_DISTANCE_METHOD.class
forester/java/classes/org/forester/evoinference/distance/PairwiseDistanceCalculator.class
forester/java/classes/org/forester/evoinference/distance/Sarray.class
forester/java/classes/org/forester/evoinference/distance/Sset.class
forester/java/classes/org/forester/evoinference/matrix/character/BasicCharacterStateMatrix$1.class
forester/java/classes/org/forester/evoinference/matrix/character/BasicCharacterStateMatrix.class
forester/java/classes/org/forester/evoinference/matrix/character/CharacterStateMatrix$1.class
forester/java/classes/org/forester/evoinference/matrix/character/CharacterStateMatrix$BinaryStates.class
forester/java/classes/org/forester/evoinference/matrix/character/CharacterStateMatrix$Format.class
forester/java/classes/org/forester/evoinference/matrix/character/CharacterStateMatrix$GainLossStates.class
forester/java/classes/org/forester/evoinference/matrix/character/CharacterStateMatrix$NucleotideStates.class
forester/java/classes/org/forester/evoinference/matrix/character/CharacterStateMatrix.class
forester/java/classes/org/forester/evoinference/matrix/distance/BasicSymmetricalDistanceMatrix$1.class
forester/java/classes/org/forester/evoinference/matrix/distance/BasicSymmetricalDistanceMatrix.class
forester/java/classes/org/forester/evoinference/matrix/distance/DistanceMatrix$Format.class
forester/java/classes/org/forester/evoinference/matrix/distance/DistanceMatrix.class
forester/java/classes/org/forester/evoinference/parsimony/DolloParsimony.class
forester/java/classes/org/forester/evoinference/parsimony/FitchParsimony.class
forester/java/classes/org/forester/evoinference/parsimony/SankoffParsimony.class
forester/java/classes/org/forester/evoinference/tools/BootstrapResampler.class
forester/java/classes/org/forester/go/BasicGoRelationship$1.class
forester/java/classes/org/forester/go/BasicGoRelationship.class
forester/java/classes/org/forester/go/BasicGoSubset$1.class
forester/java/classes/org/forester/go/BasicGoSubset.class
forester/java/classes/org/forester/go/BasicGoTerm.class
forester/java/classes/org/forester/go/BasicGoXRef$1.class
forester/java/classes/org/forester/go/BasicGoXRef.class
forester/java/classes/org/forester/go/GoId.class
forester/java/classes/org/forester/go/GoNameSpace$1.class
forester/java/classes/org/forester/go/GoNameSpace$GoNamespaceType.class
forester/java/classes/org/forester/go/GoNameSpace.class
forester/java/classes/org/forester/go/GoRelationship$Type.class
forester/java/classes/org/forester/go/GoRelationship.class
forester/java/classes/org/forester/go/GoSubset$Type.class
forester/java/classes/org/forester/go/GoSubset.class
forester/java/classes/org/forester/go/GoTerm.class
forester/java/classes/org/forester/go/GoUtils.class
forester/java/classes/org/forester/go/GoXRef$Type.class
forester/java/classes/org/forester/go/GoXRef.class
forester/java/classes/org/forester/go/Mapping.class
forester/java/classes/org/forester/go/OBOparser$1.class
forester/java/classes/org/forester/go/OBOparser$ReturnType.class
forester/java/classes/org/forester/go/OBOparser.class
forester/java/classes/org/forester/go/PfamToGoMapping.class
forester/java/classes/org/forester/go/PfamToGoParser.class
forester/java/classes/org/forester/go/TestGo.class
forester/java/classes/org/forester/go/etc/MetaOntologizer$1.class
forester/java/classes/org/forester/go/etc/MetaOntologizer.class
forester/java/classes/org/forester/go/etc/OntologizerResult$TYPE.class
forester/java/classes/org/forester/go/etc/OntologizerResult.class
forester/java/classes/org/forester/io/parsers/FastaParser.class
forester/java/classes/org/forester/io/parsers/GeneralMsaParser.class
forester/java/classes/org/forester/io/parsers/HmmPfamOutputParser$FilterType.class
forester/java/classes/org/forester/io/parsers/HmmPfamOutputParser$ReturnType.class
forester/java/classes/org/forester/io/parsers/HmmPfamOutputParser.class
forester/java/classes/org/forester/io/parsers/HmmscanPerDomainTableParser$FilterType.class
forester/java/classes/org/forester/io/parsers/HmmscanPerDomainTableParser$INDIVIDUAL_SCORE_CUTOFF.class
forester/java/classes/org/forester/io/parsers/HmmscanPerDomainTableParser$ReturnType.class
forester/java/classes/org/forester/io/parsers/HmmscanPerDomainTableParser.class
forester/java/classes/org/forester/io/parsers/IteratingPhylogenyParser.class
forester/java/classes/org/forester/io/parsers/PhylogenyParser.class
forester/java/classes/org/forester/io/parsers/SymmetricalDistanceMatrixParser$1.class
forester/java/classes/org/forester/io/parsers/SymmetricalDistanceMatrixParser$InputMatrixType.class
forester/java/classes/org/forester/io/parsers/SymmetricalDistanceMatrixParser.class
forester/java/classes/org/forester/io/parsers/nexus/NexusBinaryStatesMatrixParser.class
forester/java/classes/org/forester/io/parsers/nexus/NexusCharactersParser.class
forester/java/classes/org/forester/io/parsers/nexus/NexusConstants.class
forester/java/classes/org/forester/io/parsers/nexus/NexusFormatException.class
forester/java/classes/org/forester/io/parsers/nexus/NexusPhylogeniesParser.class
forester/java/classes/org/forester/io/parsers/nexus/PaupLogParser.class
forester/java/classes/org/forester/io/parsers/nhx/NHXFormatException.class
forester/java/classes/org/forester/io/parsers/nhx/NHXParser$TAXONOMY_EXTRACTION.class
forester/java/classes/org/forester/io/parsers/nhx/NHXParser.class
forester/java/classes/org/forester/io/parsers/nhx/NHXtags.class
forester/java/classes/org/forester/io/parsers/phyloxml/PhyloXmlDataFormatException.class
forester/java/classes/org/forester/io/parsers/phyloxml/PhyloXmlException.class
forester/java/classes/org/forester/io/parsers/phyloxml/PhyloXmlHandler.class
forester/java/classes/org/forester/io/parsers/phyloxml/PhyloXmlMapping.class
forester/java/classes/org/forester/io/parsers/phyloxml/PhyloXmlParser$1.class
forester/java/classes/org/forester/io/parsers/phyloxml/PhyloXmlParser$PhyloXmlParserErrorHandler.class
forester/java/classes/org/forester/io/parsers/phyloxml/PhyloXmlParser.class
forester/java/classes/org/forester/io/parsers/phyloxml/PhyloXmlUtil.class
forester/java/classes/org/forester/io/parsers/phyloxml/XmlElement.class
forester/java/classes/org/forester/io/parsers/phyloxml/data/AccessionParser.class
forester/java/classes/org/forester/io/parsers/phyloxml/data/AnnotationParser.class
forester/java/classes/org/forester/io/parsers/phyloxml/data/BinaryCharactersParser.class
forester/java/classes/org/forester/io/parsers/phyloxml/data/BranchWidthParser.class
forester/java/classes/org/forester/io/parsers/phyloxml/data/ColorParser.class
forester/java/classes/org/forester/io/parsers/phyloxml/data/ConfidenceParser.class
forester/java/classes/org/forester/io/parsers/phyloxml/data/DateParser.class
forester/java/classes/org/forester/io/parsers/phyloxml/data/DistributionParser.class
forester/java/classes/org/forester/io/parsers/phyloxml/data/DomainArchitectureParser.class
forester/java/classes/org/forester/io/parsers/phyloxml/data/EventParser.class
forester/java/classes/org/forester/io/parsers/phyloxml/data/IdentifierParser.class
forester/java/classes/org/forester/io/parsers/phyloxml/data/PhylogenyDataPhyloXmlParser.class
forester/java/classes/org/forester/io/parsers/phyloxml/data/PointParser.class
forester/java/classes/org/forester/io/parsers/phyloxml/data/PolygonParser.class
forester/java/classes/org/forester/io/parsers/phyloxml/data/PropertyParser.class
forester/java/classes/org/forester/io/parsers/phyloxml/data/ProteinDomainParser.class
forester/java/classes/org/forester/io/parsers/phyloxml/data/ReferenceParser.class
forester/java/classes/org/forester/io/parsers/phyloxml/data/SequenceParser.class
forester/java/classes/org/forester/io/parsers/phyloxml/data/SequenceRelationParser.class
forester/java/classes/org/forester/io/parsers/phyloxml/data/TaxonomyParser.class
forester/java/classes/org/forester/io/parsers/phyloxml/data/UriParser.class
forester/java/classes/org/forester/io/parsers/tol/TolParser$1.class
forester/java/classes/org/forester/io/parsers/tol/TolParser$TolParserErrorHandler.class
forester/java/classes/org/forester/io/parsers/tol/TolParser.class
forester/java/classes/org/forester/io/parsers/tol/TolXmlHandler.class
forester/java/classes/org/forester/io/parsers/tol/TolXmlMapping.class
forester/java/classes/org/forester/io/parsers/util/ParserUtils.class
forester/java/classes/org/forester/io/parsers/util/PhylogenyParserException.class
forester/java/classes/org/forester/io/writers/PhyloXmlNodeWriter.class
forester/java/classes/org/forester/io/writers/PhylogenyWriter$FORMAT.class
forester/java/classes/org/forester/io/writers/PhylogenyWriter.class
forester/java/classes/org/forester/io/writers/SequenceWriter$1.class
forester/java/classes/org/forester/io/writers/SequenceWriter$SEQ_FORMAT.class
forester/java/classes/org/forester/io/writers/SequenceWriter.class
forester/java/classes/org/forester/msa/BasicMsa$1.class
forester/java/classes/org/forester/msa/BasicMsa.class
forester/java/classes/org/forester/msa/ClustalOmega.class
forester/java/classes/org/forester/msa/DeleteableMsa.class
forester/java/classes/org/forester/msa/Mafft.class
forester/java/classes/org/forester/msa/Msa$MSA_FORMAT.class
forester/java/classes/org/forester/msa/Msa.class
forester/java/classes/org/forester/msa/MsaFormatException.class
forester/java/classes/org/forester/msa/MsaInferrer.class
forester/java/classes/org/forester/msa/MsaMethods.class
forester/java/classes/org/forester/msa/ResampleableMsa.class
forester/java/classes/org/forester/msa_compactor/Chart.class
forester/java/classes/org/forester/msa_compactor/GapContribution.class
forester/java/classes/org/forester/msa_compactor/MsaCompactor$1.class
forester/java/classes/org/forester/msa_compactor/MsaCompactor.class
forester/java/classes/org/forester/msa_compactor/MsaProperties.class
forester/java/classes/org/forester/pccx/BasicExternalNodeBasedCoverageExtender.class
forester/java/classes/org/forester/pccx/BranchCountingBasedScoringMethod.class
forester/java/classes/org/forester/pccx/BranchLengthBasedScoringMethod.class
forester/java/classes/org/forester/pccx/Coverage.class
forester/java/classes/org/forester/pccx/CoverageCalculationMethod.class
forester/java/classes/org/forester/pccx/CoverageCalculationOptions.class
forester/java/classes/org/forester/pccx/CoverageCalculator.class
forester/java/classes/org/forester/pccx/CoverageExtender.class
forester/java/classes/org/forester/pccx/ExternalNodeBasedCoverage.class
forester/java/classes/org/forester/pccx/ExternalNodeBasedCoverageMethod.class
forester/java/classes/org/forester/pccx/ExternalNodeBasedCoverageMethodOptions.class
forester/java/classes/org/forester/pccx/LogBranchLengthBasedScoringMethod.class
forester/java/classes/org/forester/pccx/ModelingUtils.class
forester/java/classes/org/forester/pccx/ScoringMethodForExternalNode.class
forester/java/classes/org/forester/pccx/TestPccx.class
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forester/java/classes/org/forester/phylogeny/PhylogenyBranch.class
forester/java/classes/org/forester/phylogeny/PhylogenyMethods$1.class
forester/java/classes/org/forester/phylogeny/PhylogenyMethods$DESCENDANT_SORT_PRIORITY.class
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forester/java/classes/org/forester/phylogeny/PhylogenyMethods$PhylogenyNodeField.class
forester/java/classes/org/forester/phylogeny/PhylogenyMethods$PhylogenyNodeSortNodeNamePriority.class [new file with mode: 0644]
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forester/java/classes/org/forester/phylogeny/PhylogenyMethods$PhylogenyNodeSortTaxonomyPriority.class [new file with mode: 0644]
forester/java/classes/org/forester/phylogeny/PhylogenyMethods.class
forester/java/classes/org/forester/phylogeny/PhylogenyNode$NH_CONVERSION_SUPPORT_VALUE_STYLE.class
forester/java/classes/org/forester/phylogeny/PhylogenyNode.class
forester/java/classes/org/forester/phylogeny/data/Accession$1.class
forester/java/classes/org/forester/phylogeny/data/Accession$Source.class
forester/java/classes/org/forester/phylogeny/data/Accession.class
forester/java/classes/org/forester/phylogeny/data/Annotation.class
forester/java/classes/org/forester/phylogeny/data/BinaryCharacters.class
forester/java/classes/org/forester/phylogeny/data/BranchColor.class
forester/java/classes/org/forester/phylogeny/data/BranchData.class
forester/java/classes/org/forester/phylogeny/data/BranchWidth.class
forester/java/classes/org/forester/phylogeny/data/Confidence.class
forester/java/classes/org/forester/phylogeny/data/Date.class
forester/java/classes/org/forester/phylogeny/data/Distribution.class
forester/java/classes/org/forester/phylogeny/data/DomainArchitecture.class
forester/java/classes/org/forester/phylogeny/data/Event$EventType.class
forester/java/classes/org/forester/phylogeny/data/Event.class
forester/java/classes/org/forester/phylogeny/data/Identifier.class
forester/java/classes/org/forester/phylogeny/data/MultipleUris.class
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forester/java/classes/org/forester/phylogeny/data/NodeDataField$1.class [new file with mode: 0644]
forester/java/classes/org/forester/phylogeny/data/NodeDataField.class [new file with mode: 0644]
forester/java/classes/org/forester/phylogeny/data/NodeVisualData$FontType.class
forester/java/classes/org/forester/phylogeny/data/NodeVisualData$NodeFill.class
forester/java/classes/org/forester/phylogeny/data/NodeVisualData$NodeShape.class
forester/java/classes/org/forester/phylogeny/data/NodeVisualData.class
forester/java/classes/org/forester/phylogeny/data/PhylogenyData.class
forester/java/classes/org/forester/phylogeny/data/PhylogenyDataUtil.class
forester/java/classes/org/forester/phylogeny/data/Point.class
forester/java/classes/org/forester/phylogeny/data/Polygon.class
forester/java/classes/org/forester/phylogeny/data/PropertiesMap.class
forester/java/classes/org/forester/phylogeny/data/Property$1.class
forester/java/classes/org/forester/phylogeny/data/Property$AppliesTo$1.class
forester/java/classes/org/forester/phylogeny/data/Property$AppliesTo$2.class
forester/java/classes/org/forester/phylogeny/data/Property$AppliesTo$3.class
forester/java/classes/org/forester/phylogeny/data/Property$AppliesTo$4.class
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forester/java/classes/org/forester/phylogeny/data/Property$AppliesTo.class
forester/java/classes/org/forester/phylogeny/data/Property.class
forester/java/classes/org/forester/phylogeny/data/ProteinDomain.class
forester/java/classes/org/forester/phylogeny/data/Reference.class
forester/java/classes/org/forester/phylogeny/data/Sequence.class
forester/java/classes/org/forester/phylogeny/data/SequenceRelation$SEQUENCE_RELATION_TYPE.class
forester/java/classes/org/forester/phylogeny/data/SequenceRelation.class
forester/java/classes/org/forester/phylogeny/data/Taxonomy.class
forester/java/classes/org/forester/phylogeny/data/Uri.class
forester/java/classes/org/forester/phylogeny/factories/ParserBasedPhylogenyFactory.class
forester/java/classes/org/forester/phylogeny/factories/PhylogenyFactory.class
forester/java/classes/org/forester/phylogeny/iterators/ExternalForwardIterator.class
forester/java/classes/org/forester/phylogeny/iterators/LevelOrderTreeIterator.class
forester/java/classes/org/forester/phylogeny/iterators/PhylogenyNodeIterator.class
forester/java/classes/org/forester/phylogeny/iterators/PostOrderStackObject.class
forester/java/classes/org/forester/phylogeny/iterators/PostorderTreeIterator.class
forester/java/classes/org/forester/phylogeny/iterators/PreorderTreeIterator.class
forester/java/classes/org/forester/protein/BasicDomain.class
forester/java/classes/org/forester/protein/BasicProtein$1.class
forester/java/classes/org/forester/protein/BasicProtein.class
forester/java/classes/org/forester/protein/BinaryDomainCombination$DomainCombinationType.class
forester/java/classes/org/forester/protein/BinaryDomainCombination$OutputFormat.class
forester/java/classes/org/forester/protein/BinaryDomainCombination.class
forester/java/classes/org/forester/protein/Domain.class
forester/java/classes/org/forester/protein/Protein.class
forester/java/classes/org/forester/protein/ProteinId.class
forester/java/classes/org/forester/rio/RIO$1.class
forester/java/classes/org/forester/rio/RIO$REROOTING.class
forester/java/classes/org/forester/rio/RIO.class
forester/java/classes/org/forester/rio/RIOException.class
forester/java/classes/org/forester/rio/TestRIO.class
forester/java/classes/org/forester/sdi/GSDI.class
forester/java/classes/org/forester/sdi/GSDII.class
forester/java/classes/org/forester/sdi/GSDIR.class
forester/java/classes/org/forester/sdi/GSDIsummaryResult.class
forester/java/classes/org/forester/sdi/NodesLinkingResult.class
forester/java/classes/org/forester/sdi/SDI.class
forester/java/classes/org/forester/sdi/SDIException.class
forester/java/classes/org/forester/sdi/SDIR.class
forester/java/classes/org/forester/sdi/SDIutil$1.class
forester/java/classes/org/forester/sdi/SDIutil$ALGORITHM.class
forester/java/classes/org/forester/sdi/SDIutil$TaxonomyComparisonBase$1.class
forester/java/classes/org/forester/sdi/SDIutil$TaxonomyComparisonBase$2.class
forester/java/classes/org/forester/sdi/SDIutil$TaxonomyComparisonBase$3.class
forester/java/classes/org/forester/sdi/SDIutil$TaxonomyComparisonBase.class
forester/java/classes/org/forester/sdi/SDIutil.class
forester/java/classes/org/forester/sdi/TestGSDI.class
forester/java/classes/org/forester/sequence/BasicSequence.class
forester/java/classes/org/forester/sequence/MolecularSequence$TYPE.class [new file with mode: 0644]
forester/java/classes/org/forester/sequence/MolecularSequence.class [new file with mode: 0644]
forester/java/classes/org/forester/species/BasicSpecies.class
forester/java/classes/org/forester/species/Species.class
forester/java/classes/org/forester/surfacing/AdjactantDirectedBinaryDomainCombination.class
forester/java/classes/org/forester/surfacing/AdjactantDirectedCombinableDomains.class
forester/java/classes/org/forester/surfacing/BasicBinaryDomainCombination$1.class
forester/java/classes/org/forester/surfacing/BasicBinaryDomainCombination.class
forester/java/classes/org/forester/surfacing/BasicCombinableDomains.class
forester/java/classes/org/forester/surfacing/BasicDomainSimilarityCalculator.class
forester/java/classes/org/forester/surfacing/BasicGenomeWideCombinableDomains$1.class
forester/java/classes/org/forester/surfacing/BasicGenomeWideCombinableDomains$2.class
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forester/java/classes/org/forester/surfacing/CombinableDomains.class
forester/java/classes/org/forester/surfacing/CombinationsBasedPairwiseDomainSimilarity.class
forester/java/classes/org/forester/surfacing/CombinationsBasedPairwiseDomainSimilarityCalculator.class
forester/java/classes/org/forester/surfacing/CountsBasedPairwiseDomainSimilarity.class
forester/java/classes/org/forester/surfacing/DirectedBinaryDomainCombination.class
forester/java/classes/org/forester/surfacing/DirectedCombinableDomains.class
forester/java/classes/org/forester/surfacing/DomainArchitectureBasedGenomeSimilarityCalculator.class
forester/java/classes/org/forester/surfacing/DomainCountsBasedPairwiseSimilarityCalculator.class
forester/java/classes/org/forester/surfacing/DomainCountsDifferenceUtil$1.class
forester/java/classes/org/forester/surfacing/DomainCountsDifferenceUtil$COPY_CALCULATION_MODE.class
forester/java/classes/org/forester/surfacing/DomainCountsDifferenceUtil.class
forester/java/classes/org/forester/surfacing/DomainLengths.class
forester/java/classes/org/forester/surfacing/DomainLengthsTable.class
forester/java/classes/org/forester/surfacing/DomainParsimonyCalculator.class
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forester/java/classes/org/forester/surfacing/DomainSimilarity$DomainSimilarityScoring.class
forester/java/classes/org/forester/surfacing/DomainSimilarity$DomainSimilaritySortField.class
forester/java/classes/org/forester/surfacing/DomainSimilarity$PRINT_OPTION.class
forester/java/classes/org/forester/surfacing/DomainSimilarity$ValueComparator.class
forester/java/classes/org/forester/surfacing/DomainSimilarity.class
forester/java/classes/org/forester/surfacing/DomainSimilarityCalculator$Detailedness.class
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forester/java/classes/org/forester/surfacing/DomainSimilarityCalculator.class
forester/java/classes/org/forester/surfacing/GenomeWideCombinableDomains$GenomeWideCombinableDomainsSortOrder.class
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forester/java/classes/org/forester/surfacing/MappingResults.class
forester/java/classes/org/forester/surfacing/PairwiseDomainSimilarity.class
forester/java/classes/org/forester/surfacing/PairwiseDomainSimilarityCalculator.class
forester/java/classes/org/forester/surfacing/PairwiseGenomeComparator$1.class
forester/java/classes/org/forester/surfacing/PairwiseGenomeComparator.class
forester/java/classes/org/forester/surfacing/PrintableSpeciesSpecificDcData.class
forester/java/classes/org/forester/surfacing/ProteinCountsBasedPairwiseDomainSimilarityCalculator.class
forester/java/classes/org/forester/surfacing/SimpleDomain.class
forester/java/classes/org/forester/surfacing/SpeciesSpecificDcData.class
forester/java/classes/org/forester/surfacing/SurfacingConstants.class
forester/java/classes/org/forester/surfacing/SurfacingUtil$1.class
forester/java/classes/org/forester/surfacing/SurfacingUtil$2.class
forester/java/classes/org/forester/surfacing/SurfacingUtil$DomainComparator.class
forester/java/classes/org/forester/surfacing/SurfacingUtil.class
forester/java/classes/org/forester/surfacing/TestSurfacing.class
forester/java/classes/org/forester/test/Test.class
forester/java/classes/org/forester/test/examples/Example1.class
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forester/java/classes/org/forester/tools/ConfidenceAssessor.class
forester/java/classes/org/forester/tools/PhylogenyDecorator$1.class
forester/java/classes/org/forester/tools/PhylogenyDecorator$FIELD.class
forester/java/classes/org/forester/tools/PhylogenyDecorator.class
forester/java/classes/org/forester/tools/SupportCount.class
forester/java/classes/org/forester/tools/TreeSplitMatrix.class
forester/java/classes/org/forester/util/AsciiHistogram.class
forester/java/classes/org/forester/util/BasicDescriptiveStatistics.class
forester/java/classes/org/forester/util/BasicTable.class
forester/java/classes/org/forester/util/BasicTableParser.class
forester/java/classes/org/forester/util/CommandLineArguments.class
forester/java/classes/org/forester/util/CommandProcessBuilder.class
forester/java/classes/org/forester/util/DescriptiveStatistics.class
forester/java/classes/org/forester/util/EasyWriter.class
forester/java/classes/org/forester/util/ExternalProgram.class
forester/java/classes/org/forester/util/FailedConditionCheckException.class
forester/java/classes/org/forester/util/ForesterConstants$PhylogeneticTreeFormats.class
forester/java/classes/org/forester/util/ForesterConstants.class
forester/java/classes/org/forester/util/ForesterUtil.class
forester/java/classes/org/forester/util/GeneralTable.class
forester/java/classes/org/forester/util/IllegalFormatUseException.class
forester/java/classes/org/forester/util/SequenceAccessionTools.class
forester/java/classes/org/forester/util/StringInt$DescendingIntComparator.class [new file with mode: 0644]
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forester/java/classes/org/forester/util/SystemCommandExecutor.class
forester/java/classes/org/forester/util/TaxonomyColors.class
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forester/java/classes/org/forester/util/TaxonomyUtil.class
forester/java/classes/org/forester/util/ThreadedStreamHandler.class
forester/java/classes/org/forester/util/WindowsUtils$StreamReader.class
forester/java/classes/org/forester/util/WindowsUtils.class
forester/java/classes/org/forester/ws/hmmer/Test.class
forester/java/classes/org/forester/ws/seqdb/EbiDbEntry.class
forester/java/classes/org/forester/ws/seqdb/SequenceDatabaseEntry.class
forester/java/classes/org/forester/ws/seqdb/SequenceDbWsTools.class
forester/java/classes/org/forester/ws/seqdb/UniProtEntry.class
forester/java/classes/org/forester/ws/seqdb/UniProtTaxonomy.class
forester/java/classes/org/forester/ws/wabi/RestUtil.class
forester/java/classes/org/forester/ws/wabi/TxSearch$RANKS.class
forester/java/classes/org/forester/ws/wabi/TxSearch$TAX_NAME_CLASS.class
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forester/java/classes/org/forester/ws/wabi/WabiTools.class
forester/java/src/org/forester/archaeopteryx/Constants.java

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@@ -43,7 +43,7 @@ public final class Constants {
     public final static boolean ALLOW_DDBJ_BLAST                                              = false;
     public final static String  PRG_NAME                                                      = "Archaeopteryx";
     final static String         VERSION                                                       = "0.9904 beta";
-    final static String         PRG_DATE                                                      = "150212";
+    final static String         PRG_DATE                                                      = "150218";
     final static String         DEFAULT_CONFIGURATION_FILE_NAME                               = "_aptx_configuration_file";
     final static String[]       DEFAULT_FONT_CHOICES                                          = { "Arial", "Helvetica",
             "Verdana", "Tahoma", "Dialog", "Lucida Sans", "SansSerif", "Sans-serif", "Sans"  };