[ViewVC] Revision 1009 of: owl

Jump to revision:
Author:	hstehr
Date:	Wed Mar 31 15:50:04 2010 UTC (14 years, 6 months ago)
Log Message:	refactoring: moved many many classes to more appropriate packages; created new packages owl.core.sequence.alignment, owl.core.structure.alignment, owl.core.structure.features

Changed paths

Only 100 changes shown, display 112 more changes...

Path	Details
trunk/src/addSeq2Mcma.java	modified , text changed
trunk/src/alignSeq.java	modified , text changed
trunk/src/averageGraph.java	modified , text changed
trunk/src/benchmarkGraphAlgorithm.java	modified , text changed
trunk/src/compareAlignments.java	modified , text changed
trunk/src/compareCMs.java	modified , text changed
trunk/src/computeEnergies.java	modified , text changed
trunk/src/genDbGraph.java	modified , text changed
trunk/src/genGraph.java	modified , text changed
trunk/src/mapMutations.java	modified , text changed
trunk/src/owl/casp/benchmarking/Benchmarking.java	modified , text changed
trunk/src/owl/casp/pipeline/RunAll.java	modified , text changed
trunk/src/owl/casp/pipeline/TargetToTemplatesAlignment.java	modified , text changed
trunk/src/owl/casp/pipeline/TemplateSelection.java	modified , text changed
trunk/src/owl/casp/pipeline/TemplatesAlignment.java	modified , text changed
trunk/src/owl/casp/tools/DisplaySecStructMatching.java	modified , text changed
trunk/src/owl/casp/tools/MapStru2Seq.java	modified , text changed
trunk/src/owl/core/connections/GTGHit.java (Copied from trunk/src/owl/core/sequence/GTGHit.java, r1007)	added , text changed
trunk/src/owl/core/connections/GTGHitList.java (Copied from trunk/src/owl/core/sequence/GTGHitList.java, r1007)	added , text changed
trunk/src/owl/core/connections/GTGParser.java (Copied from trunk/src/owl/core/sequence/GTGParser.java, r1007)	added , text changed
trunk/src/owl/core/connections/PrositeHit.java (Copied from trunk/src/owl/core/structure/PrositeHit.java, r1007)	added , text changed
trunk/src/owl/core/connections/PrositeScanner.java (Copied from trunk/src/owl/core/structure/PrositeScanner.java, r1007)	added , text changed
trunk/src/owl/core/features/CsaFeature.java	modified , text changed
trunk/src/owl/core/features/PrositeFeature.java	modified , text changed
trunk/src/owl/core/runners/DaliRunner.java (Copied from trunk/src/owl/core/structure/DaliRunner.java, r1007)	added , text changed
trunk/src/owl/core/runners/DsspRunner.java	modified , text changed
trunk/src/owl/core/runners/MaxClusterRunner.java (Copied from trunk/src/owl/core/structure/MaxClusterRunner.java, r1007)	added , text changed
trunk/src/owl/core/runners/PolyposeRunner.java (Copied from trunk/src/owl/core/structure/PolyposeRunner.java, r1007)	added , text changed
trunk/src/owl/core/runners/PsipredError.java (Copied from trunk/src/owl/core/sequence/PsipredError.java, r1007)	added , text changed
trunk/src/owl/core/runners/PsipredRunner.java (Copied from trunk/src/owl/core/sequence/PsipredRunner.java, r1007)	added , text changed
trunk/src/owl/core/runners/TcoffeeError.java (Copied from trunk/src/owl/core/sequence/TcoffeeError.java, r1007)	added , text changed
trunk/src/owl/core/runners/TcoffeeRunner.java (Copied from trunk/src/owl/core/sequence/TcoffeeRunner.java, r1007)	added , text changed
trunk/src/owl/core/runners/blast/BlastError.java (Copied from trunk/src/owl/core/sequence/BlastError.java, r1007)	added , text changed
trunk/src/owl/core/runners/blast/BlastHit.java (Copied from trunk/src/owl/core/sequence/BlastHit.java, r1007)	added , text changed
trunk/src/owl/core/runners/blast/BlastHitList.java (Copied from trunk/src/owl/core/sequence/BlastHitList.java, r1007)	added , text changed
trunk/src/owl/core/runners/blast/BlastRunner.java (Copied from trunk/src/owl/core/sequence/BlastRunner.java, r1007)	added , text changed
trunk/src/owl/core/runners/blast/BlastTabularParser.java (Copied from trunk/src/owl/core/sequence/BlastTabularParser.java, r1007)	added , text changed
trunk/src/owl/core/runners/blast/BlastUtils.java (Copied from trunk/src/owl/core/sequence/BlastUtils.java, r1007)	added , text changed
trunk/src/owl/core/runners/blast/BlastXMLParser.java (Copied from trunk/src/owl/core/sequence/BlastXMLParser.java, r1007)	added , text changed
trunk/src/owl/core/runners/gromacs/GromacsError.java (Copied from trunk/src/owl/core/runners/tinker/GromacsError.java, r1007)	added , text changed
trunk/src/owl/core/runners/gromacs/GromacsMDP.java (Copied from trunk/src/owl/core/runners/tinker/GromacsMDP.java, r1007)	added , text changed
trunk/src/owl/core/runners/gromacs/GromacsRunner.java (Copied from trunk/src/owl/core/runners/tinker/GromacsRunner.java, r1007)	added , text changed
trunk/src/owl/core/runners/tinker/ConstraintsMaker.java	modified , text changed
trunk/src/owl/core/runners/tinker/GromacsError.java	deleted
trunk/src/owl/core/runners/tinker/GromacsMDP.java	deleted
trunk/src/owl/core/runners/tinker/GromacsRunner.java	deleted
trunk/src/owl/core/runners/tinker/TinkerRunner.java	modified , text changed
trunk/src/owl/core/sequence/BlastError.java	deleted
trunk/src/owl/core/sequence/BlastHit.java	deleted
trunk/src/owl/core/sequence/BlastHitList.java	deleted
trunk/src/owl/core/sequence/BlastRunner.java	deleted
trunk/src/owl/core/sequence/BlastTabularParser.java	deleted
trunk/src/owl/core/sequence/BlastUtils.java	deleted
trunk/src/owl/core/sequence/BlastXMLParser.java	deleted
trunk/src/owl/core/sequence/GTGHit.java	deleted
trunk/src/owl/core/sequence/GTGHitList.java	deleted
trunk/src/owl/core/sequence/GTGParser.java	deleted
trunk/src/owl/core/sequence/PsipredError.java	deleted
trunk/src/owl/core/sequence/PsipredRunner.java	deleted
trunk/src/owl/core/sequence/Sequence.java	modified , text changed
trunk/src/owl/core/sequence/TcoffeeError.java	deleted
trunk/src/owl/core/sequence/TcoffeeRunner.java	deleted
trunk/src/owl/core/sequence/alignment/	added
trunk/src/owl/core/sequence/alignment/AlignmentConstructionError.java (Copied from trunk/src/owl/core/structure/AlignmentConstructionError.java, r1007)	added , text changed
trunk/src/owl/core/sequence/alignment/MultipleSequenceAlignment.java (Copied from trunk/src/owl/core/structure/Alignment.java, r1007)	added , text changed
trunk/src/owl/core/sequence/alignment/PairwiseAlignmentConverter.java (Copied from trunk/src/owl/core/structure/PairwiseAlignmentConverter.java, r1007)	added , text changed
trunk/src/owl/core/sequence/alignment/PairwiseSequenceAlignment.java (Copied from trunk/src/owl/core/structure/PairwiseSequenceAlignment.java, r1007)	added , text changed
trunk/src/owl/core/structure/AIGEdge.java	deleted
trunk/src/owl/core/structure/AIGNode.java	deleted
trunk/src/owl/core/structure/AIGraph.java	deleted
trunk/src/owl/core/structure/Alignment.java	deleted
trunk/src/owl/core/structure/AlignmentConstructionError.java	deleted
trunk/src/owl/core/structure/AlignmentEvaluator.java	deleted
trunk/src/owl/core/structure/BackboneCoords.java	modified , text changed
trunk/src/owl/core/structure/Box.java	deleted
trunk/src/owl/core/structure/CaspRRFileData.java	deleted
trunk/src/owl/core/structure/CaspRRFileRIGraph.java	deleted
trunk/src/owl/core/structure/CatalSiteSet.java	deleted
trunk/src/owl/core/structure/CatalyticSite.java	deleted
trunk/src/owl/core/structure/CiffilePdb.java	modified , text changed
trunk/src/owl/core/structure/DaliRunner.java	deleted
trunk/src/owl/core/structure/DbRIGraph.java	deleted
trunk/src/owl/core/structure/EC.java	deleted
trunk/src/owl/core/structure/ECRegion.java	deleted
trunk/src/owl/core/structure/FileFormatError.java	deleted
trunk/src/owl/core/structure/FileRIGraph.java	deleted
trunk/src/owl/core/structure/FileTypeGuesser.java	deleted
trunk/src/owl/core/structure/GeometryTools.java	deleted
trunk/src/owl/core/structure/GraphIODb.java	deleted
trunk/src/owl/core/structure/GraphIOGDLFile.java	deleted
trunk/src/owl/core/structure/GraphIdNotFoundError.java	deleted
trunk/src/owl/core/structure/HashGrid.java	deleted
trunk/src/owl/core/structure/MaxClusterRunner.java	deleted
trunk/src/owl/core/structure/NbhProbDistribution.java	deleted
trunk/src/owl/core/structure/NbhoodBackgrnd.java	deleted
trunk/src/owl/core/structure/PairwiseAlignmentConverter.java	deleted
trunk/src/owl/core/structure/PairwiseSequenceAlignment.java	deleted
trunk/src/owl/core/structure/PaulStructAligner.java	deleted
trunk/src/owl/core/structure/Pdb.java	modified , text changed
trunk/src/owl/core/structure/PdbSet.java	modified , text changed