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

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

author	cmzmasek <cmzmasek@ca865154-3058-d1c3-3e42-d8f55a55bdbd>
	Sun, 25 Nov 2012 01:45:45 +0000 (01:45 +0000)
committer	cmzmasek <cmzmasek@ca865154-3058-d1c3-3e42-d8f55a55bdbd>
	Sun, 25 Nov 2012 01:45:45 +0000 (01:45 +0000)
commit	03e51d179caedf757b09e2872f9500318bd85a53
tree	dfbaa0a218235d6e997cf7de62f5cb401e661bff	tree \| snapshot
parent	841c7135a24076a444b2f6652cde00ef0cf60239	commit \| diff

rio, lca, refactoring

58 files changed:

forester/java/src/org/forester/analysis/AncestralTaxonomyInference.java		diff \| blob \| history
forester/java/src/org/forester/application/aa.java		diff \| blob \| history
forester/java/src/org/forester/application/confadd.java		diff \| blob \| history
forester/java/src/org/forester/application/decorator.java		diff \| blob \| history
forester/java/src/org/forester/application/goac.java		diff \| blob \| history
forester/java/src/org/forester/application/mcc.java		diff \| blob \| history
forester/java/src/org/forester/application/pfam2go_extractor.java		diff \| blob \| history
forester/java/src/org/forester/application/rio.java		diff \| blob \| history
forester/java/src/org/forester/application/sdi_dir.java		diff \| blob \| history
forester/java/src/org/forester/application/strip.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/MainFrame.java		diff \| blob \| history
forester/java/src/org/forester/archaeopteryx/NodePanel.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/phylogeny/data/RenderableDomainArchitecture.java		diff \| blob \| history
forester/java/src/org/forester/archaeopteryx/phylogeny/data/RenderableVector.java		diff \| blob \| history
forester/java/src/org/forester/datastructures/IntMatrix.java		diff \| blob \| history
forester/java/src/org/forester/development/DevelopmentTools.java		diff \| blob \| history
forester/java/src/org/forester/development/MsaRenderer.java		diff \| blob \| history
forester/java/src/org/forester/development/ResidueRenderer.java		diff \| blob \| history
forester/java/src/org/forester/development/neTest.java		diff \| blob \| history
forester/java/src/org/forester/evoinference/distance/NeighborJoining.java		diff \| blob \| history
forester/java/src/org/forester/evoinference/matrix/character/BasicCharacterStateMatrix.java		diff \| blob \| history
forester/java/src/org/forester/evoinference/matrix/distance/BasicSymmetricalDistanceMatrix.java		diff \| blob \| history
forester/java/src/org/forester/io/parsers/SymmetricalDistanceMatrixParser.java		diff \| blob \| history
forester/java/src/org/forester/msa/MsaCompactor.java		diff \| blob \| history
forester/java/src/org/forester/pccx/TestPccx.java		diff \| blob \| history
forester/java/src/org/forester/phylogeny/Phylogeny.java		diff \| blob \| history
forester/java/src/org/forester/phylogeny/PhylogenyBranch.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/NodeData.java		diff \| blob \| history
forester/java/src/org/forester/phylogeny/data/ProteinDomain.java		diff \| blob \| history
forester/java/src/org/forester/phylogeny/data/Taxonomy.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/sdi/GSDI.java		diff \| blob \| history
forester/java/src/org/forester/sdi/ORcount.java		diff \| blob \| history
forester/java/src/org/forester/sdi/RIO.java		diff \| blob \| history
forester/java/src/org/forester/sdi/SDI.java		diff \| blob \| history
forester/java/src/org/forester/sdi/SDIse.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/CountsBasedPairwiseDomainSimilarity.java		diff \| blob \| history
forester/java/src/org/forester/surfacing/DomainCountsDifferenceUtil.java		diff \| blob \| history
forester/java/src/org/forester/surfacing/PrintableSpeciesSpecificDomainSimilariyData.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/PhylogenyDecorator.java		diff \| blob \| history
forester/java/src/org/forester/tools/TreeSplitMatrix.java		diff \| blob \| history
forester/java/src/org/forester/util/AsciiHistogram.java		diff \| blob \| history
forester/java/src/org/forester/util/BasicTable.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/ForesterUtil.java		diff \| blob \| history

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