[ViewVC] Revision 1305 of: owl

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Author:	jmduarteg
Date:	Fri Jan 21 10:11:16 2011 UTC (11 years, 3 months ago)
Log Message:	Renaming all xxxxError named exceptions to xxxxException. Long overdue thing (was historical because it came from python). Learnt just recently that java does have a concept of Error too.

Changed paths

Path	Details
trunk/src/addSeq2Mcma.java	modified , text changed
trunk/src/benchmarkGraphAlgorithm.java	modified , text changed
trunk/src/calculateGridDensity.java	modified , text changed
trunk/src/compareAlignments.java	modified , text changed
trunk/src/dumppdb.java	modified , text changed
trunk/src/dumpseq.java	modified , text changed
trunk/src/examples/HelloAGLappe.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/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/MapStru2Seq.java	modified , text changed
trunk/src/owl/core/connections/GTGHit.java	modified , text changed
trunk/src/owl/core/connections/GTGHitList.java	modified , text changed
trunk/src/owl/core/connections/GTGParser.java	modified , text changed
trunk/src/owl/core/runners/DaliRunner.java	modified , text changed
trunk/src/owl/core/runners/TcoffeeRunner.java	modified , text changed
trunk/src/owl/core/runners/blast/BlastHsp.java	modified , text changed
trunk/src/owl/core/runners/tinker/TinkerRunner.java	modified , text changed
trunk/src/owl/core/sequence/UniprotHomologList.java	modified , text changed
trunk/src/owl/core/sequence/alignment/AlignmentConstructionError.java	deleted
trunk/src/owl/core/sequence/alignment/AlignmentConstructionException.java (Copied from trunk/src/owl/core/sequence/alignment/AlignmentConstructionError.java, r1304)	added , text changed
trunk/src/owl/core/sequence/alignment/MultipleSequenceAlignment.java	modified , text changed
trunk/src/owl/core/sequence/alignment/PairwiseAlignmentConverter.java	modified , text changed
trunk/src/owl/core/structure/CiffilePdb.java	modified , text changed
trunk/src/owl/core/structure/ConformationsNotSameSizeError.java	deleted
trunk/src/owl/core/structure/ConformationsNotSameSizeException.java (Copied from trunk/src/owl/core/structure/ConformationsNotSameSizeError.java, r1304)	added , text changed
trunk/src/owl/core/structure/Pdb.java	modified , text changed
trunk/src/owl/core/structure/PdbAsymUnit.java	modified , text changed
trunk/src/owl/core/structure/PdbChainCodeNotFoundError.java	deleted
trunk/src/owl/core/structure/PdbChainCodeNotFoundException.java (Copied from trunk/src/owl/core/structure/PdbChainCodeNotFoundError.java, r1304)	added , text changed
trunk/src/owl/core/structure/PdbCodeNotFoundError.java	deleted
trunk/src/owl/core/structure/PdbCodeNotFoundException.java (Copied from trunk/src/owl/core/structure/PdbCodeNotFoundError.java, r1304)	added , text changed
trunk/src/owl/core/structure/PdbSet.java	modified , text changed
trunk/src/owl/core/structure/PdbaseInconsistencyError.java	deleted
trunk/src/owl/core/structure/PdbaseInconsistencyException.java (Copied from trunk/src/owl/core/structure/PdbaseInconsistencyError.java, r1304)	added , text changed
trunk/src/owl/core/structure/PdbasePdb.java	modified , text changed
trunk/src/owl/core/structure/PdbfilePdb.java	modified , text changed
trunk/src/owl/core/structure/Template.java	modified , text changed
trunk/src/owl/core/structure/TemplateList.java	modified , text changed
trunk/src/owl/core/structure/alignment/PaulStructAligner.java	modified , text changed
trunk/src/owl/core/structure/alignment/StructAligner.java	modified , text changed
trunk/src/owl/core/structure/alignment/StructAlignmentError.java	deleted
trunk/src/owl/core/structure/alignment/StructAlignmentException.java (Copied from trunk/src/owl/core/structure/alignment/StructAlignmentError.java, r1304)	added , text changed
trunk/src/owl/core/structure/alignment/StructureAlignmentEvaluator.java	modified , text changed
trunk/src/owl/core/structure/graphs/GraphIOGDLFile.java	modified , text changed
trunk/src/owl/core/structure/graphs/RIGEnsemble.java	modified , text changed
trunk/src/owl/core/structure/graphs/RIGMatrix.java	modified , text changed
trunk/src/owl/decoyScoring/AtomCountScorer.java	modified , text changed
trunk/src/owl/decoyScoring/AtomTripletScorer.java	modified , text changed
trunk/src/owl/decoyScoring/AtomTypeScorer.java	modified , text changed
trunk/src/owl/decoyScoring/DistanceScorer.java	modified , text changed
trunk/src/owl/decoyScoring/ResCountScorer.java	modified , text changed
trunk/src/owl/decoyScoring/ResTripletScorer.java	modified , text changed
trunk/src/owl/decoyScoring/ResTypeScorer.java	modified , text changed
trunk/src/owl/embed/ConePeeler.java	modified , text changed
trunk/src/owl/embed/Distiller.java	modified , text changed
trunk/src/owl/embed/Scorer.java	modified , text changed
trunk/src/owl/embed/SetScore.java	modified , text changed
trunk/src/owl/embed/contactmaps/CMDMErrorEvaluator.java	modified , text changed
trunk/src/owl/embed/contactmaps/CMGrabber.java	modified , text changed
trunk/src/owl/embed/contactmaps/CompareIndis.java	modified , text changed
trunk/src/owl/embed/contactmaps/ContactMap.java	modified , text changed
trunk/src/owl/embed/contactmaps/ContactMapEvolver.java	modified , text changed
trunk/src/owl/embed/contactmaps/ContactMapWeighted.java	modified , text changed
trunk/src/owl/embed/contactmaps/ContactMatrix.java	modified , text changed
trunk/src/owl/embed/contactmaps/Demes.java	modified , text changed
trunk/src/owl/embed/contactmaps/DistMatrix.java	modified , text changed
trunk/src/owl/embed/contactmaps/Individuals.java	modified , text changed
trunk/src/owl/embed/contactmaps/Metric2.java	modified , text changed
trunk/src/owl/embed/contactmaps/NbhStringRanker.java	modified , text changed
trunk/src/owl/embed/contactmaps/NeighbourhoodString.java	modified , text changed
trunk/src/owl/embed/contactmaps/Species.java	modified , text changed
trunk/src/owl/embed/contactmaps/Stripper.java	modified , text changed
trunk/src/owl/graphAveraging/GraphAverager.java	modified , text changed
trunk/src/owl/graphAveraging/GraphAveragerError.java	deleted
trunk/src/owl/graphAveraging/GraphAveragerException.java (Copied from trunk/src/owl/graphAveraging/GraphAveragerError.java, r1304)	added , text changed
trunk/src/owl/sadp/ContactMapConstructorError.java	deleted
trunk/src/owl/sadp/ContactMapConstructorException.java (Copied from trunk/src/owl/sadp/ContactMapConstructorError.java, r1304)	added , text changed
trunk/src/owl/sadp/SADP.java	modified , text changed
trunk/src/owl/sadp/SADPContactMap.java	modified , text changed
trunk/src/owl/tests/core/connections/SiftsConnectionTest.java	modified , text changed
trunk/src/owl/tests/core/runners/tinker/TinkerRunnerTest.java	modified , text changed
trunk/src/owl/tests/core/structure/PdbAsymUnitTest.java	modified , text changed
trunk/src/owl/tests/core/structure/PdbParsersTest.java	modified , text changed
trunk/src/owl/tests/core/structure/PdbTest.java	modified , text changed
trunk/src/reconstruct.java	modified , text changed
trunk/src/scorePdbSet.java	modified , text changed
trunk/src/superimposeMult.java	modified , text changed
trunk/src/testJUNGframework.java	modified , text changed
trunk/src/testPdb.java	modified , text changed
trunk/src/writeSASAtoBFactor.java	modified , text changed