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initial commit
authorcmzmasek@gmail.com <cmzmasek@gmail.com@ca865154-3058-d1c3-3e42-d8f55a55bdbd>
Wed, 9 Feb 2011 01:09:48 +0000 (01:09 +0000)
committercmzmasek@gmail.com <cmzmasek@gmail.com@ca865154-3058-d1c3-3e42-d8f55a55bdbd>
Wed, 9 Feb 2011 01:09:48 +0000 (01:09 +0000)
commit48f7a89be9d34f1930a1f863e608235cc27184c5
tree128c293c713129fe05fd45bf2b4816c343847566tree | snapshot
parenteccc2fdb674f76be1815fd7984295661bff8a2becommit | diff
initial commit
211 files changed:
forester/java/src/org/forester/go/BasicGoRelationship.java [new file with mode: 0644] blob
forester/java/src/org/forester/go/BasicGoSubset.java [new file with mode: 0644] blob
forester/java/src/org/forester/go/BasicGoTerm.java [new file with mode: 0644] blob
forester/java/src/org/forester/go/BasicGoXRef.java [new file with mode: 0644] blob
forester/java/src/org/forester/go/GoId.java [new file with mode: 0644] blob
forester/java/src/org/forester/go/GoNameSpace.java [new file with mode: 0644] blob
forester/java/src/org/forester/go/GoRelationship.java [new file with mode: 0644] blob
forester/java/src/org/forester/go/GoSubset.java [new file with mode: 0644] blob
forester/java/src/org/forester/go/GoTerm.java [new file with mode: 0644] blob
forester/java/src/org/forester/go/GoUtils.java [new file with mode: 0644] blob
forester/java/src/org/forester/go/GoXRef.java [new file with mode: 0644] blob
forester/java/src/org/forester/go/Mapping.java [new file with mode: 0644] blob
forester/java/src/org/forester/go/OBOparser.java [new file with mode: 0644] blob
forester/java/src/org/forester/go/PfamToGoMapping.java [new file with mode: 0644] blob
forester/java/src/org/forester/go/PfamToGoParser.java [new file with mode: 0644] blob
forester/java/src/org/forester/go/TestGo.java [new file with mode: 0644] blob
forester/java/src/org/forester/go/etc/MetaOntologizer.java [new file with mode: 0644] blob
forester/java/src/org/forester/go/etc/OntologizerResult.java [new file with mode: 0644] blob
forester/java/src/org/forester/io/parsers/FastaParser.java [new file with mode: 0644] blob
forester/java/src/org/forester/io/parsers/GeneralMsaParser.java [new file with mode: 0644] blob
forester/java/src/org/forester/io/parsers/HmmPfamOutputParser.java [new file with mode: 0644] blob
forester/java/src/org/forester/io/parsers/HmmscanPerDomainTableParser.java [new file with mode: 0644] blob
forester/java/src/org/forester/io/parsers/PhylogenyParser.java [new file with mode: 0644] blob
forester/java/src/org/forester/io/parsers/SymmetricalDistanceMatrixParser.java [new file with mode: 0644] blob
forester/java/src/org/forester/io/parsers/nexus/NexusBinaryStatesMatrixParser.java [new file with mode: 0644] blob
forester/java/src/org/forester/io/parsers/nexus/NexusCharactersParser.java [new file with mode: 0644] blob
forester/java/src/org/forester/io/parsers/nexus/NexusConstants.java [new file with mode: 0644] blob
forester/java/src/org/forester/io/parsers/nexus/NexusFormatException.java [new file with mode: 0644] blob
forester/java/src/org/forester/io/parsers/nexus/NexusPhylogeniesParser.java [new file with mode: 0644] blob
forester/java/src/org/forester/io/parsers/nexus/PaupLogParser.java [new file with mode: 0644] blob
forester/java/src/org/forester/io/parsers/nhx/NHXFormatException.java [new file with mode: 0644] blob
forester/java/src/org/forester/io/parsers/nhx/NHXParser.java [new file with mode: 0644] blob
forester/java/src/org/forester/io/parsers/nhx/NHXtags.java [new file with mode: 0644] blob
forester/java/src/org/forester/io/parsers/phyloxml/PhyloXmlDataFormatException.java [new file with mode: 0644] blob
forester/java/src/org/forester/io/parsers/phyloxml/PhyloXmlException.java [new file with mode: 0644] blob
forester/java/src/org/forester/io/parsers/phyloxml/PhyloXmlHandler.java [new file with mode: 0644] blob
forester/java/src/org/forester/io/parsers/phyloxml/PhyloXmlMapping.java [new file with mode: 0644] blob
forester/java/src/org/forester/io/parsers/phyloxml/PhyloXmlParser.java [new file with mode: 0644] blob
forester/java/src/org/forester/io/parsers/phyloxml/PhyloXmlUtil.java [new file with mode: 0644] blob
forester/java/src/org/forester/io/parsers/phyloxml/XmlElement.java [new file with mode: 0644] blob
forester/java/src/org/forester/io/parsers/phyloxml/data/AccessionParser.java [new file with mode: 0644] blob
forester/java/src/org/forester/io/parsers/phyloxml/data/AnnotationParser.java [new file with mode: 0644] blob
forester/java/src/org/forester/io/parsers/phyloxml/data/BinaryCharactersParser.java [new file with mode: 0644] blob
forester/java/src/org/forester/io/parsers/phyloxml/data/BranchWidthParser.java [new file with mode: 0644] blob
forester/java/src/org/forester/io/parsers/phyloxml/data/ColorParser.java [new file with mode: 0644] blob
forester/java/src/org/forester/io/parsers/phyloxml/data/ConfidenceParser.java [new file with mode: 0644] blob
forester/java/src/org/forester/io/parsers/phyloxml/data/DateParser.java [new file with mode: 0644] blob
forester/java/src/org/forester/io/parsers/phyloxml/data/DistributionParser.java [new file with mode: 0644] blob
forester/java/src/org/forester/io/parsers/phyloxml/data/DomainArchitectureParser.java [new file with mode: 0644] blob
forester/java/src/org/forester/io/parsers/phyloxml/data/EventParser.java [new file with mode: 0644] blob
forester/java/src/org/forester/io/parsers/phyloxml/data/IdentifierParser.java [new file with mode: 0644] blob
forester/java/src/org/forester/io/parsers/phyloxml/data/PhylogenyDataPhyloXmlParser.java [new file with mode: 0644] blob
forester/java/src/org/forester/io/parsers/phyloxml/data/PointParser.java [new file with mode: 0644] blob
forester/java/src/org/forester/io/parsers/phyloxml/data/PolygonParser.java [new file with mode: 0644] blob
forester/java/src/org/forester/io/parsers/phyloxml/data/PropertyParser.java [new file with mode: 0644] blob
forester/java/src/org/forester/io/parsers/phyloxml/data/ProteinDomainParser.java [new file with mode: 0644] blob
forester/java/src/org/forester/io/parsers/phyloxml/data/ReferenceParser.java [new file with mode: 0644] blob
forester/java/src/org/forester/io/parsers/phyloxml/data/SequenceParser.java [new file with mode: 0644] blob
forester/java/src/org/forester/io/parsers/phyloxml/data/SequenceRelationParser.java [new file with mode: 0644] blob
forester/java/src/org/forester/io/parsers/phyloxml/data/TaxonomyParser.java [new file with mode: 0644] blob
forester/java/src/org/forester/io/parsers/phyloxml/data/UriParser.java [new file with mode: 0644] blob
forester/java/src/org/forester/io/parsers/tol/TolParser.java [new file with mode: 0644] blob
forester/java/src/org/forester/io/parsers/tol/TolXmlHandler.java [new file with mode: 0644] blob
forester/java/src/org/forester/io/parsers/tol/TolXmlMapping.java [new file with mode: 0644] blob
forester/java/src/org/forester/io/parsers/util/ParserUtils.java [new file with mode: 0644] blob
forester/java/src/org/forester/io/parsers/util/PhylogenyParserException.java [new file with mode: 0644] blob
forester/java/src/org/forester/io/writers/PhyloXmlNodeWriter.java [new file with mode: 0644] blob
forester/java/src/org/forester/io/writers/PhylogenyWriter.java [new file with mode: 0644] blob
forester/java/src/org/forester/io/writers/SequenceWriter.java [new file with mode: 0644] blob
forester/java/src/org/forester/msa/BasicMsa.java [new file with mode: 0644] blob
forester/java/src/org/forester/msa/Mafft.java [new file with mode: 0644] blob
forester/java/src/org/forester/msa/MafftOLD.java [new file with mode: 0644] blob
forester/java/src/org/forester/msa/Msa.java [new file with mode: 0644] blob
forester/java/src/org/forester/msa/MsaFormatException.java [new file with mode: 0644] blob
forester/java/src/org/forester/msa/MsaInferrer.java [new file with mode: 0644] blob
forester/java/src/org/forester/msa/MsaTools.java [new file with mode: 0644] blob
forester/java/src/org/forester/msa/ResampleableMsa.java [new file with mode: 0644] blob
forester/java/src/org/forester/pccx/BasicExternalNodeBasedCoverageExtender.java [new file with mode: 0644] blob
forester/java/src/org/forester/pccx/BranchCountingBasedScoringMethod.java [new file with mode: 0644] blob
forester/java/src/org/forester/pccx/BranchLengthBasedScoringMethod.java [new file with mode: 0644] blob
forester/java/src/org/forester/pccx/Coverage.java [new file with mode: 0644] blob
forester/java/src/org/forester/pccx/CoverageCalculationMethod.java [new file with mode: 0644] blob
forester/java/src/org/forester/pccx/CoverageCalculationOptions.java [new file with mode: 0644] blob
forester/java/src/org/forester/pccx/CoverageCalculator.java [new file with mode: 0644] blob
forester/java/src/org/forester/pccx/CoverageExtender.java [new file with mode: 0644] blob
forester/java/src/org/forester/pccx/ExternalNodeBasedCoverage.java [new file with mode: 0644] blob
forester/java/src/org/forester/pccx/ExternalNodeBasedCoverageMethod.java [new file with mode: 0644] blob
forester/java/src/org/forester/pccx/ExternalNodeBasedCoverageMethodOptions.java [new file with mode: 0644] blob
forester/java/src/org/forester/pccx/LogBranchLengthBasedScoringMethod.java [new file with mode: 0644] blob
forester/java/src/org/forester/pccx/ModelingUtils.java [new file with mode: 0644] blob
forester/java/src/org/forester/pccx/ScoringMethodForExternalNode.java [new file with mode: 0644] blob
forester/java/src/org/forester/pccx/TestPccx.java [new file with mode: 0644] blob
forester/java/src/org/forester/phylogeny/Edge.java [new file with mode: 0644] blob
forester/java/src/org/forester/phylogeny/Phylogeny.java [new file with mode: 0644] blob
forester/java/src/org/forester/phylogeny/PhylogenyBranch.java [new file with mode: 0644] blob
forester/java/src/org/forester/phylogeny/PhylogenyMethods.java [new file with mode: 0644] blob
forester/java/src/org/forester/phylogeny/PhylogenyNode.java [new file with mode: 0644] blob
forester/java/src/org/forester/phylogeny/PhylogenyNodeI.java [new file with mode: 0644] blob
forester/java/src/org/forester/phylogeny/data/Accession.java [new file with mode: 0644] blob
forester/java/src/org/forester/phylogeny/data/Annotation.java [new file with mode: 0644] blob
forester/java/src/org/forester/phylogeny/data/BinaryCharacters.java [new file with mode: 0644] blob
forester/java/src/org/forester/phylogeny/data/BranchColor.java [new file with mode: 0644] blob
forester/java/src/org/forester/phylogeny/data/BranchData.java [new file with mode: 0644] blob
forester/java/src/org/forester/phylogeny/data/BranchWidth.java [new file with mode: 0644] blob
forester/java/src/org/forester/phylogeny/data/Confidence.java [new file with mode: 0644] blob
forester/java/src/org/forester/phylogeny/data/Date.java [new file with mode: 0644] blob
forester/java/src/org/forester/phylogeny/data/Distribution.java [new file with mode: 0644] blob
forester/java/src/org/forester/phylogeny/data/DomainArchitecture.java [new file with mode: 0644] blob
forester/java/src/org/forester/phylogeny/data/Event.java [new file with mode: 0644] blob
forester/java/src/org/forester/phylogeny/data/Identifier.java [new file with mode: 0644] blob
forester/java/src/org/forester/phylogeny/data/MultipleUris.java [new file with mode: 0644] blob
forester/java/src/org/forester/phylogeny/data/NodeData.java [new file with mode: 0644] blob
forester/java/src/org/forester/phylogeny/data/PhylogenyData.java [new file with mode: 0644] blob
forester/java/src/org/forester/phylogeny/data/PhylogenyDataUtil.java [new file with mode: 0644] blob
forester/java/src/org/forester/phylogeny/data/Point.java [new file with mode: 0644] blob
forester/java/src/org/forester/phylogeny/data/Polygon.java [new file with mode: 0644] blob
forester/java/src/org/forester/phylogeny/data/PropertiesMap.java [new file with mode: 0644] blob
forester/java/src/org/forester/phylogeny/data/Property.java [new file with mode: 0644] blob
forester/java/src/org/forester/phylogeny/data/ProteinDomain.java [new file with mode: 0644] blob
forester/java/src/org/forester/phylogeny/data/Reference.java [new file with mode: 0644] blob
forester/java/src/org/forester/phylogeny/data/Sequence.java [new file with mode: 0644] blob
forester/java/src/org/forester/phylogeny/data/SequenceRelation.java [new file with mode: 0644] blob
forester/java/src/org/forester/phylogeny/data/Taxonomy.java [new file with mode: 0644] blob
forester/java/src/org/forester/phylogeny/data/Uri.java [new file with mode: 0644] blob
forester/java/src/org/forester/phylogeny/factories/BasicPhylogenyFactory.java [new file with mode: 0644] blob
forester/java/src/org/forester/phylogeny/factories/ParserBasedPhylogenyFactory.java [new file with mode: 0644] blob
forester/java/src/org/forester/phylogeny/factories/PhylogenyFactory.java [new file with mode: 0644] blob
forester/java/src/org/forester/phylogeny/iterators/ChildNodeIteratorForward.java [new file with mode: 0644] blob
forester/java/src/org/forester/phylogeny/iterators/ExternalForwardIterator.java [new file with mode: 0644] blob
forester/java/src/org/forester/phylogeny/iterators/LevelOrderTreeIterator.java [new file with mode: 0644] blob
forester/java/src/org/forester/phylogeny/iterators/PhylogenyNodeIterator.java [new file with mode: 0644] blob
forester/java/src/org/forester/phylogeny/iterators/PostOrderStackObject.java [new file with mode: 0644] blob
forester/java/src/org/forester/phylogeny/iterators/PostorderTreeIterator.java [new file with mode: 0644] blob
forester/java/src/org/forester/phylogeny/iterators/PreorderTreeIterator.java [new file with mode: 0644] blob
forester/java/src/org/forester/sdi/DistanceCalculator.java [new file with mode: 0644] blob
forester/java/src/org/forester/sdi/GSDI.java [new file with mode: 0644] blob
forester/java/src/org/forester/sdi/ORcount.java [new file with mode: 0644] blob
forester/java/src/org/forester/sdi/RIO.java [new file with mode: 0644] blob
forester/java/src/org/forester/sdi/RIOn.java [new file with mode: 0644] blob
forester/java/src/org/forester/sdi/SDI.java [new file with mode: 0644] blob
forester/java/src/org/forester/sdi/SDIR.java [new file with mode: 0644] blob
forester/java/src/org/forester/sdi/SDIse.java [new file with mode: 0644] blob
forester/java/src/org/forester/sdi/Shin.java [new file with mode: 0644] blob
forester/java/src/org/forester/sdi/TaxonomyAssigner.java [new file with mode: 0644] blob
forester/java/src/org/forester/sdi/TestGSDI.java [new file with mode: 0644] blob
forester/java/src/org/forester/sdi/Tuplet.java [new file with mode: 0644] blob
forester/java/src/org/forester/sequence/BasicSequence.java [new file with mode: 0644] blob
forester/java/src/org/forester/sequence/Sequence.java [new file with mode: 0644] blob
forester/java/src/org/forester/surfacing/AdjactantDirectedBinaryDomainCombination.java [new file with mode: 0644] blob
forester/java/src/org/forester/surfacing/AdjactantDirectedCombinableDomains.java [new file with mode: 0644] blob
forester/java/src/org/forester/surfacing/BasicBinaryDomainCombination.java [new file with mode: 0644] blob
forester/java/src/org/forester/surfacing/BasicCombinableDomains.java [new file with mode: 0644] blob
forester/java/src/org/forester/surfacing/BasicDomain.java [new file with mode: 0644] blob
forester/java/src/org/forester/surfacing/BasicDomainSimilarityCalculator.java [new file with mode: 0644] blob
forester/java/src/org/forester/surfacing/BasicGenomeWideCombinableDomains.java [new file with mode: 0644] blob
forester/java/src/org/forester/surfacing/BasicProtein.java [new file with mode: 0644] blob
forester/java/src/org/forester/surfacing/BasicSpecies.java [new file with mode: 0644] blob
forester/java/src/org/forester/surfacing/BinaryDomainCombination.java [new file with mode: 0644] blob
forester/java/src/org/forester/surfacing/CombinableDomains.java [new file with mode: 0644] blob
forester/java/src/org/forester/surfacing/CombinationsBasedPairwiseDomainSimilarity.java [new file with mode: 0644] blob
forester/java/src/org/forester/surfacing/CombinationsBasedPairwiseDomainSimilarityCalculator.java [new file with mode: 0644] blob
forester/java/src/org/forester/surfacing/CountsBasedPairwiseDomainSimilarity.java [new file with mode: 0644] blob
forester/java/src/org/forester/surfacing/DirectedBinaryDomainCombination.java [new file with mode: 0644] blob
forester/java/src/org/forester/surfacing/DirectedCombinableDomains.java [new file with mode: 0644] blob
forester/java/src/org/forester/surfacing/Domain.java [new file with mode: 0644] blob
forester/java/src/org/forester/surfacing/DomainArchitectureBasedGenomeSimilarityCalculator.java [new file with mode: 0644] blob
forester/java/src/org/forester/surfacing/DomainCountsBasedPairwiseSimilarityCalculator.java [new file with mode: 0644] blob
forester/java/src/org/forester/surfacing/DomainCountsDifferenceUtil.java [new file with mode: 0644] blob
forester/java/src/org/forester/surfacing/DomainId.java [new file with mode: 0644] blob
forester/java/src/org/forester/surfacing/DomainLengths.java [new file with mode: 0644] blob
forester/java/src/org/forester/surfacing/DomainLengthsTable.java [new file with mode: 0644] blob
forester/java/src/org/forester/surfacing/DomainParsimonyCalculator.java [new file with mode: 0644] blob
forester/java/src/org/forester/surfacing/DomainSimilarity.java [new file with mode: 0644] blob
forester/java/src/org/forester/surfacing/DomainSimilarityCalculator.java [new file with mode: 0644] blob
forester/java/src/org/forester/surfacing/GenomeWideCombinableDomains.java [new file with mode: 0644] blob
forester/java/src/org/forester/surfacing/MappingResults.java [new file with mode: 0644] blob
forester/java/src/org/forester/surfacing/PairwiseDomainSimilarity.java [new file with mode: 0644] blob
forester/java/src/org/forester/surfacing/PairwiseDomainSimilarityCalculator.java [new file with mode: 0644] blob
forester/java/src/org/forester/surfacing/PairwiseGenomeComparator.java [new file with mode: 0644] blob
forester/java/src/org/forester/surfacing/PrintableDomainSimilarity.java [new file with mode: 0644] blob
forester/java/src/org/forester/surfacing/PrintableSpeciesSpecificDomainSimilariyData.java [new file with mode: 0644] blob
forester/java/src/org/forester/surfacing/Protein.java [new file with mode: 0644] blob
forester/java/src/org/forester/surfacing/ProteinCountsBasedPairwiseDomainSimilarityCalculator.java [new file with mode: 0644] blob
forester/java/src/org/forester/surfacing/ProteinId.java [new file with mode: 0644] blob
forester/java/src/org/forester/surfacing/SimpleDomain.java [new file with mode: 0644] blob
forester/java/src/org/forester/surfacing/Species.java [new file with mode: 0644] blob
forester/java/src/org/forester/surfacing/SpeciesSpecificDomainSimilariyData.java [new file with mode: 0644] blob
forester/java/src/org/forester/surfacing/SurfacingConstants.java [new file with mode: 0644] blob
forester/java/src/org/forester/surfacing/SurfacingUtil.java [new file with mode: 0644] blob
forester/java/src/org/forester/surfacing/TestSurfacing.java [new file with mode: 0644] blob
forester/java/src/org/forester/test/Test.java [new file with mode: 0644] blob
forester/java/src/org/forester/tools/ConfidenceAssessor.java [new file with mode: 0644] blob
forester/java/src/org/forester/tools/PhylogenyDecorator.java [new file with mode: 0644] blob
forester/java/src/org/forester/tools/SupportCount.java [new file with mode: 0644] blob
forester/java/src/org/forester/tools/TreeSplitMatrix.java [new file with mode: 0644] blob
forester/java/src/org/forester/util/AsciiHistogram.java [new file with mode: 0644] blob
forester/java/src/org/forester/util/BasicDescriptiveStatistics.java [new file with mode: 0644] blob
forester/java/src/org/forester/util/BasicTable.java [new file with mode: 0644] blob
forester/java/src/org/forester/util/BasicTableParser.java [new file with mode: 0644] blob
forester/java/src/org/forester/util/CommandLineArguments.java [new file with mode: 0644] blob
forester/java/src/org/forester/util/CommandProcessBuilder.java [new file with mode: 0644] blob
forester/java/src/org/forester/util/DescriptiveStatistics.java [new file with mode: 0644] blob
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forester/java/src/org/forester/util/FailedConditionCheckException.java [new file with mode: 0644] blob
forester/java/src/org/forester/util/ForesterConstants.java [new file with mode: 0644] blob
forester/java/src/org/forester/util/ForesterUtil.java [new file with mode: 0644] blob
forester/java/src/org/forester/util/GeneralTable.java [new file with mode: 0644] blob
forester/java/src/org/forester/util/IllegalFormatUseException.java [new file with mode: 0644] blob
forester/java/src/org/forester/util/SystemCommandExecutor.java [new file with mode: 0644] blob
forester/java/src/org/forester/util/ThreadedStreamHandler.java [new file with mode: 0644] blob
forester/java/src/org/forester/util/WindowsUtils.java [new file with mode: 0644] blob