source.jalview.org Git - jalview.git/commit

git://source.jalview.org / jalview.git / commit

author	cmzmasek@gmail.com <cmzmasek@gmail.com@ca865154-3058-d1c3-3e42-d8f55a55bdbd>
	Tue, 18 Nov 2014 22:49:47 +0000 (22:49 +0000)
committer	cmzmasek@gmail.com <cmzmasek@gmail.com@ca865154-3058-d1c3-3e42-d8f55a55bdbd>
	Tue, 18 Nov 2014 22:49:47 +0000 (22:49 +0000)
commit	10297bd8b8a4b4ab198a17a42fc6ff24ae2ed49b
tree	fff763976763953892ce5477b380c70d28432a09	tree \| snapshot
parent	28cf1afacf61a15e72411b1e58c3694f78d6d0dd	commit \| diff

192 files changed:

forester/java/src/org/forester/analysis/AncestralTaxonomyInference.java		diff \| blob \| history
forester/java/src/org/forester/analysis/TaxonomyDataManager.java		diff \| blob \| history
forester/java/src/org/forester/application/annotator.java		diff \| blob \| history
forester/java/src/org/forester/application/confadd.java		diff \| blob \| history
forester/java/src/org/forester/application/count_support.java		diff \| blob \| history
forester/java/src/org/forester/application/decorator.java		diff \| blob \| history
forester/java/src/org/forester/application/dom_dup.java		diff \| blob \| history
forester/java/src/org/forester/application/gene_tree_preprocess.java		diff \| blob \| history
forester/java/src/org/forester/application/goac.java		diff \| blob \| history
forester/java/src/org/forester/application/gsdi.java		diff \| blob \| history
forester/java/src/org/forester/application/meta_ontologizer.java		diff \| blob \| history
forester/java/src/org/forester/application/msa_compactor.java		diff \| blob \| history
forester/java/src/org/forester/application/nj.java		diff \| blob \| history
forester/java/src/org/forester/application/obo_tool.java		diff \| blob \| history
forester/java/src/org/forester/application/pccx.java		diff \| blob \| history
forester/java/src/org/forester/application/pfam2go_extractor.java		diff \| blob \| history
forester/java/src/org/forester/application/pfam_go.java		diff \| blob \| history
forester/java/src/org/forester/application/pfamacc2go.java		diff \| blob \| history
forester/java/src/org/forester/application/phylostrip.java		diff \| blob \| history
forester/java/src/org/forester/application/phyloxml_converter.java		diff \| blob \| history
forester/java/src/org/forester/application/rio.java		diff \| blob \| history
forester/java/src/org/forester/application/support_statistics.java		diff \| blob \| history
forester/java/src/org/forester/application/support_transfer.java		diff \| blob \| history
forester/java/src/org/forester/application/surfacing.java		diff \| blob \| history
forester/java/src/org/forester/archaeopteryx/AptxUtil.java		diff \| blob \| history
forester/java/src/org/forester/archaeopteryx/ArchaeopteryxA.java		diff \| blob \| history
forester/java/src/org/forester/archaeopteryx/ArchaeopteryxE.java		diff \| blob \| history
forester/java/src/org/forester/archaeopteryx/Configuration.java		diff \| blob \| history
forester/java/src/org/forester/archaeopteryx/ControlPanel.java		diff \| blob \| history
forester/java/src/org/forester/archaeopteryx/MainFrame.java		diff \| blob \| history
forester/java/src/org/forester/archaeopteryx/MainFrameApplet.java		diff \| blob \| history
forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java		diff \| blob \| history
forester/java/src/org/forester/archaeopteryx/Options.java		diff \| blob \| history
forester/java/src/org/forester/archaeopteryx/Printer.java		diff \| blob \| history
forester/java/src/org/forester/archaeopteryx/TextFrame.java		diff \| blob \| history
forester/java/src/org/forester/archaeopteryx/TreeColorSet.java		diff \| blob \| history
forester/java/src/org/forester/archaeopteryx/TreePanel.java		diff \| blob \| history
forester/java/src/org/forester/archaeopteryx/TreePanelUtil.java		diff \| blob \| history
forester/java/src/org/forester/archaeopteryx/phylogeny/data/RenderableDomainArchitecture.java		diff \| blob \| history
forester/java/src/org/forester/archaeopteryx/phylogeny/data/RenderablePhylogenyData.java		diff \| blob \| history
forester/java/src/org/forester/archaeopteryx/tools/Blast.java		diff \| blob \| history
forester/java/src/org/forester/archaeopteryx/tools/ImageLoader.java		diff \| blob \| history
forester/java/src/org/forester/archaeopteryx/tools/InferenceManager.java		diff \| blob \| history
forester/java/src/org/forester/archaeopteryx/tools/PhyloInferenceDialog.java		diff \| blob \| history
forester/java/src/org/forester/archaeopteryx/tools/PhylogeneticInferrer.java		diff \| blob \| history
forester/java/src/org/forester/archaeopteryx/tools/RunnableProcess.java		diff \| blob \| history
forester/java/src/org/forester/archaeopteryx/tools/SequenceDataRetriver.java		diff \| blob \| history
forester/java/src/org/forester/archaeopteryx/webservices/PhylogeniesWebserviceClient.java		diff \| blob \| history
forester/java/src/org/forester/archaeopteryx/webservices/WebserviceUtil.java		diff \| blob \| history
forester/java/src/org/forester/datastructures/Queue.java		diff \| blob \| history
forester/java/src/org/forester/development/AbstractRenderer.java		diff \| blob \| history
forester/java/src/org/forester/development/DevelopmentTools.java		diff \| blob \| history
forester/java/src/org/forester/development/ResidueRenderer.java		diff \| blob \| history
forester/java/src/org/forester/development/Test.java		diff \| blob \| history
forester/java/src/org/forester/development/neTest.java		diff \| blob \| history
forester/java/src/org/forester/evoinference/TestPhylogenyReconstruction.java		diff \| blob \| history
forester/java/src/org/forester/evoinference/distance/NeighborJoining.java		diff \| blob \| history
forester/java/src/org/forester/evoinference/distance/NeighborJoiningF.java		diff \| blob \| history
forester/java/src/org/forester/evoinference/distance/NeighborJoiningR.java		diff \| blob \| history
forester/java/src/org/forester/evoinference/distance/PairwiseDistanceCalculator.java		diff \| blob \| history
forester/java/src/org/forester/evoinference/distance/Sarray.java		diff \| blob \| history
forester/java/src/org/forester/evoinference/distance/Sset.java		diff \| blob \| history
forester/java/src/org/forester/evoinference/matrix/character/BasicCharacterStateMatrix.java		diff \| blob \| history
forester/java/src/org/forester/evoinference/parsimony/DolloParsimony.java		diff \| blob \| history
forester/java/src/org/forester/evoinference/parsimony/FitchParsimony.java		diff \| blob \| history
forester/java/src/org/forester/evoinference/parsimony/SankoffParsimony.java		diff \| blob \| history
forester/java/src/org/forester/go/BasicGoRelationship.java		diff \| blob \| history
forester/java/src/org/forester/go/BasicGoSubset.java		diff \| blob \| history
forester/java/src/org/forester/go/BasicGoTerm.java		diff \| blob \| history
forester/java/src/org/forester/go/BasicGoXRef.java		diff \| blob \| history
forester/java/src/org/forester/go/GoUtils.java		diff \| blob \| history
forester/java/src/org/forester/go/PfamToGoMapping.java		diff \| blob \| history
forester/java/src/org/forester/go/TestGo.java		diff \| blob \| history
forester/java/src/org/forester/go/etc/MetaOntologizer.java		diff \| blob \| history
forester/java/src/org/forester/go/etc/OntologizerResult.java		diff \| blob \| history
forester/java/src/org/forester/io/parsers/FastaParser.java		diff \| blob \| history
forester/java/src/org/forester/io/parsers/GeneralMsaParser.java		diff \| blob \| history
forester/java/src/org/forester/io/parsers/HmmPfamOutputParser.java		diff \| blob \| history
forester/java/src/org/forester/io/parsers/HmmscanPerDomainTableParser.java		diff \| blob \| history
forester/java/src/org/forester/io/parsers/PhylogenyParser.java		diff \| blob \| history
forester/java/src/org/forester/io/parsers/SymmetricalDistanceMatrixParser.java		diff \| blob \| history
forester/java/src/org/forester/io/parsers/nhx/NHXParser.java		diff \| blob \| history
forester/java/src/org/forester/io/parsers/phyloxml/PhyloXmlHandler.java		diff \| blob \| history
forester/java/src/org/forester/io/parsers/phyloxml/PhyloXmlParser.java		diff \| blob \| history
forester/java/src/org/forester/io/parsers/phyloxml/PhyloXmlUtil.java		diff \| blob \| history
forester/java/src/org/forester/io/parsers/phyloxml/XmlElement.java		diff \| blob \| history
forester/java/src/org/forester/io/parsers/phyloxml/data/AnnotationParser.java		diff \| blob \| history
forester/java/src/org/forester/io/parsers/phyloxml/data/BinaryCharactersParser.java		diff \| blob \| history
forester/java/src/org/forester/io/parsers/phyloxml/data/ConfidenceParser.java		diff \| blob \| history
forester/java/src/org/forester/io/parsers/phyloxml/data/DomainArchitectureParser.java		diff \| blob \| history
forester/java/src/org/forester/io/parsers/phyloxml/data/ProteinDomainParser.java		diff \| blob \| history
forester/java/src/org/forester/io/parsers/phyloxml/data/SequenceParser.java		diff \| blob \| history
forester/java/src/org/forester/io/parsers/phyloxml/data/SequenceRelationParser.java		diff \| blob \| history
forester/java/src/org/forester/io/parsers/tol/TolParser.java		diff \| blob \| history
forester/java/src/org/forester/io/parsers/tol/TolXmlHandler.java		diff \| blob \| history
forester/java/src/org/forester/io/parsers/util/ParserUtils.java		diff \| blob \| history
forester/java/src/org/forester/io/parsers/util/PhylogenyParserException.java		diff \| blob \| history
forester/java/src/org/forester/io/writers/PhyloXmlNodeWriter.java		diff \| blob \| history
forester/java/src/org/forester/io/writers/PhylogenyWriter.java		diff \| blob \| history
forester/java/src/org/forester/msa/BasicMsa.java		diff \| blob \| history
forester/java/src/org/forester/msa/ClustalOmega.java		diff \| blob \| history
forester/java/src/org/forester/msa/Mafft.java		diff \| blob \| history
forester/java/src/org/forester/msa/MsaInferrer.java		diff \| blob \| history
forester/java/src/org/forester/msa/MsaMethods.java		diff \| blob \| history
forester/java/src/org/forester/msa/ResampleableMsa.java		diff \| blob \| history
forester/java/src/org/forester/msa_compactor/MsaCompactor.java		diff \| blob \| history
forester/java/src/org/forester/pccx/BasicExternalNodeBasedCoverageExtender.java		diff \| blob \| history
forester/java/src/org/forester/pccx/BranchCountingBasedScoringMethod.java		diff \| blob \| history
forester/java/src/org/forester/pccx/BranchLengthBasedScoringMethod.java		diff \| blob \| history
forester/java/src/org/forester/pccx/ExternalNodeBasedCoverageMethod.java		diff \| blob \| history
forester/java/src/org/forester/pccx/ExternalNodeBasedCoverageMethodOptions.java		diff \| blob \| history
forester/java/src/org/forester/pccx/LogBranchLengthBasedScoringMethod.java		diff \| blob \| history
forester/java/src/org/forester/pccx/ScoringMethodForExternalNode.java		diff \| blob \| history
forester/java/src/org/forester/phylogeny/Phylogeny.java		diff \| blob \| history
forester/java/src/org/forester/phylogeny/PhylogenyMethods.java		diff \| blob \| history
forester/java/src/org/forester/phylogeny/PhylogenyNode.java		diff \| blob \| history
forester/java/src/org/forester/phylogeny/data/BinaryCharacters.java		diff \| blob \| history
forester/java/src/org/forester/phylogeny/data/BranchColor.java		diff \| blob \| history
forester/java/src/org/forester/phylogeny/data/BranchData.java		diff \| blob \| history
forester/java/src/org/forester/phylogeny/data/Confidence.java		diff \| blob \| history
forester/java/src/org/forester/phylogeny/data/Date.java		diff \| blob \| history
forester/java/src/org/forester/phylogeny/data/DomainArchitecture.java		diff \| blob \| history
forester/java/src/org/forester/phylogeny/data/Event.java		diff \| blob \| history
forester/java/src/org/forester/phylogeny/data/NodeData.java		diff \| blob \| history
forester/java/src/org/forester/phylogeny/data/NodeVisualData.java		diff \| blob \| history
forester/java/src/org/forester/phylogeny/data/PhylogenyData.java		diff \| blob \| history
forester/java/src/org/forester/phylogeny/data/PhylogenyDataUtil.java		diff \| blob \| history
forester/java/src/org/forester/phylogeny/data/Point.java		diff \| blob \| history
forester/java/src/org/forester/phylogeny/data/Property.java		diff \| blob \| history
forester/java/src/org/forester/phylogeny/data/Sequence.java		diff \| blob \| history
forester/java/src/org/forester/phylogeny/data/Taxonomy.java		diff \| blob \| history
forester/java/src/org/forester/phylogeny/factories/PhylogenyFactory.java		diff \| blob \| history
forester/java/src/org/forester/phylogeny/iterators/ExternalForwardIterator.java		diff \| blob \| history
forester/java/src/org/forester/phylogeny/iterators/LevelOrderTreeIterator.java		diff \| blob \| history
forester/java/src/org/forester/phylogeny/iterators/PhylogenyNodeIterator.java		diff \| blob \| history
forester/java/src/org/forester/phylogeny/iterators/PostOrderStackObject.java		diff \| blob \| history
forester/java/src/org/forester/phylogeny/iterators/PreorderTreeIterator.java		diff \| blob \| history
forester/java/src/org/forester/protein/BasicDomain.java		diff \| blob \| history
forester/java/src/org/forester/protein/BasicProtein.java		diff \| blob \| history
forester/java/src/org/forester/protein/Protein.java		diff \| blob \| history
forester/java/src/org/forester/protein/ProteinId.java		diff \| blob \| history
forester/java/src/org/forester/rio/RIO.java		diff \| blob \| history
forester/java/src/org/forester/rio/RIOException.java		diff \| blob \| history
forester/java/src/org/forester/rio/TestRIO.java		diff \| blob \| history
forester/java/src/org/forester/sdi/GSDI.java		diff \| blob \| history
forester/java/src/org/forester/sdi/GSDIR.java		diff \| blob \| history
forester/java/src/org/forester/sdi/SDI.java		diff \| blob \| history
forester/java/src/org/forester/sdi/SDIException.java		diff \| blob \| history
forester/java/src/org/forester/sdi/SDIR.java		diff \| blob \| history
forester/java/src/org/forester/sdi/SDIutil.java		diff \| blob \| history
forester/java/src/org/forester/sdi/TestGSDI.java		diff \| blob \| history
forester/java/src/org/forester/sequence/BasicSequence.java		diff \| blob \| history
forester/java/src/org/forester/surfacing/BasicGenomeWideCombinableDomains.java		diff \| blob \| history
forester/java/src/org/forester/surfacing/CombinableDomains.java		diff \| blob \| history
forester/java/src/org/forester/surfacing/CountsBasedPairwiseDomainSimilarity.java		diff \| blob \| history
forester/java/src/org/forester/surfacing/DomainArchitectureBasedGenomeSimilarityCalculator.java		diff \| blob \| history
forester/java/src/org/forester/surfacing/DomainCountsDifferenceUtil.java		diff \| blob \| history
forester/java/src/org/forester/surfacing/DomainLengths.java		diff \| blob \| history
forester/java/src/org/forester/surfacing/DomainLengthsTable.java		diff \| blob \| history
forester/java/src/org/forester/surfacing/DomainParsimonyCalculator.java		diff \| blob \| history
forester/java/src/org/forester/surfacing/DomainSimilarity.java		diff \| blob \| history
forester/java/src/org/forester/surfacing/DomainSimilarityCalculator.java		diff \| blob \| history
forester/java/src/org/forester/surfacing/GenomeWideCombinableDomains.java		diff \| blob \| history
forester/java/src/org/forester/surfacing/PairwiseDomainSimilarity.java		diff \| blob \| history
forester/java/src/org/forester/surfacing/PairwiseGenomeComparator.java		diff \| blob \| history
forester/java/src/org/forester/surfacing/PrintableSpeciesSpecificDcData.java		diff \| blob \| history
forester/java/src/org/forester/surfacing/SpeciesSpecificDcData.java		diff \| blob \| history
forester/java/src/org/forester/surfacing/SurfacingUtil.java		diff \| blob \| history
forester/java/src/org/forester/surfacing/TestSurfacing.java		diff \| blob \| history
forester/java/src/org/forester/test/Test.java		diff \| blob \| history
forester/java/src/org/forester/tools/ConfidenceAssessor.java		diff \| blob \| history
forester/java/src/org/forester/tools/PhylogenyDecorator.java		diff \| blob \| history
forester/java/src/org/forester/tools/SupportCount.java		diff \| blob \| history
forester/java/src/org/forester/tools/TreeSplitMatrix.java		diff \| blob \| history
forester/java/src/org/forester/util/BasicDescriptiveStatistics.java		diff \| blob \| history
forester/java/src/org/forester/util/BasicTableParser.java		diff \| blob \| history
forester/java/src/org/forester/util/CommandLineArguments.java		diff \| blob \| history
forester/java/src/org/forester/util/CommandProcessBuilder.java		diff \| blob \| history
forester/java/src/org/forester/util/DescriptiveStatistics.java		diff \| blob \| history
forester/java/src/org/forester/util/FailedConditionCheckException.java		diff \| blob \| history
forester/java/src/org/forester/util/ForesterUtil.java		diff \| blob \| history
forester/java/src/org/forester/util/IllegalFormatUseException.java		diff \| blob \| history
forester/java/src/org/forester/util/SequenceAccessionTools.java		diff \| blob \| history
forester/java/src/org/forester/util/SystemCommandExecutor.java		diff \| blob \| history
forester/java/src/org/forester/util/ThreadedStreamHandler.java		diff \| blob \| history
forester/java/src/org/forester/util/WindowsUtils.java		diff \| blob \| history
forester/java/src/org/forester/ws/seqdb/EbiDbEntry.java		diff \| blob \| history
forester/java/src/org/forester/ws/seqdb/SequenceDbWsTools.java		diff \| blob \| history
forester/java/src/org/forester/ws/seqdb/UniProtEntry.java		diff \| blob \| history
forester/java/src/org/forester/ws/seqdb/UniProtTaxonomy.java		diff \| blob \| history
forester/java/src/org/forester/ws/wabi/RestUtil.java		diff \| blob \| history
forester/java/src/org/forester/ws/wabi/TxSearch.java		diff \| blob \| history

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