Public Git Hosting - bioperl-live.git/commit

commit	7814d898d40bc874743e7cac623d4d0eee4e1b4f
author	Chris Fields <cjfields@bioperl.org>
	Mon, 21 Apr 2014 04:14:51 +0000 (20 23:14 -0500)
committer	Chris Fields <cjfields@bioperl.org>
	Mon, 21 Apr 2014 04:14:51 +0000 (20 23:14 -0500)
tree	51c4181c53c42fb8eb9e880dfc43b7cb482b1e56	tree \| snapshot (tar.gz zip)
parent	c682abd1a61cc73f7a15c8015f06f942d4e16a79	commit \| diff

changes all issue tracking in preparation for switch to github issues

718 files changed:

BUGS		diff \| blob \| blame \| history
Bio/Align/AlignI.pm		diff \| blob \| blame \| history
Bio/Align/DNAStatistics.pm		diff \| blob \| blame \| history
Bio/Align/PairwiseStatistics.pm		diff \| blob \| blame \| history
Bio/Align/ProteinStatistics.pm		diff \| blob \| blame \| history
Bio/Align/StatisticsI.pm		diff \| blob \| blame \| history
Bio/Align/Utilities.pm		diff \| blob \| blame \| history
Bio/AlignIO.pm		diff \| blob \| blame \| history
Bio/AlignIO/Handler/GenericAlignHandler.pm		diff \| blob \| blame \| history
Bio/AlignIO/arp.pm		diff \| blob \| blame \| history
Bio/AlignIO/bl2seq.pm		diff \| blob \| blame \| history
Bio/AlignIO/clustalw.pm		diff \| blob \| blame \| history
Bio/AlignIO/emboss.pm		diff \| blob \| blame \| history
Bio/AlignIO/fasta.pm		diff \| blob \| blame \| history
Bio/AlignIO/largemultifasta.pm		diff \| blob \| blame \| history
Bio/AlignIO/maf.pm		diff \| blob \| blame \| history
Bio/AlignIO/mase.pm		diff \| blob \| blame \| history
Bio/AlignIO/mega.pm		diff \| blob \| blame \| history
Bio/AlignIO/meme.pm		diff \| blob \| blame \| history
Bio/AlignIO/metafasta.pm		diff \| blob \| blame \| history
Bio/AlignIO/msf.pm		diff \| blob \| blame \| history
Bio/AlignIO/nexml.pm		diff \| blob \| blame \| history
Bio/AlignIO/nexus.pm		diff \| blob \| blame \| history
Bio/AlignIO/pfam.pm		diff \| blob \| blame \| history
Bio/AlignIO/phylip.pm		diff \| blob \| blame \| history
Bio/AlignIO/po.pm		diff \| blob \| blame \| history
Bio/AlignIO/proda.pm		diff \| blob \| blame \| history
Bio/AlignIO/prodom.pm		diff \| blob \| blame \| history
Bio/AlignIO/psi.pm		diff \| blob \| blame \| history
Bio/AlignIO/selex.pm		diff \| blob \| blame \| history
Bio/AlignIO/stockholm.pm		diff \| blob \| blame \| history
Bio/AlignIO/xmfa.pm		diff \| blob \| blame \| history
Bio/AnalysisI.pm		diff \| blob \| blame \| history
Bio/AnalysisParserI.pm		diff \| blob \| blame \| history
Bio/AnalysisResultI.pm		diff \| blob \| blame \| history
Bio/AnnotatableI.pm		diff \| blob \| blame \| history
Bio/Annotation/AnnotationFactory.pm		diff \| blob \| blame \| history
Bio/Annotation/Collection.pm		diff \| blob \| blame \| history
Bio/Annotation/OntologyTerm.pm		diff \| blob \| blame \| history
Bio/Annotation/Relation.pm		diff \| blob \| blame \| history
Bio/Annotation/SimpleValue.pm		diff \| blob \| blame \| history
Bio/Annotation/StructuredValue.pm		diff \| blob \| blame \| history
Bio/Annotation/TagTree.pm		diff \| blob \| blame \| history
Bio/Annotation/TypeManager.pm		diff \| blob \| blame \| history
Bio/AnnotationCollectionI.pm		diff \| blob \| blame \| history
Bio/AnnotationI.pm		diff \| blob \| blame \| history
Bio/Assembly/Contig.pm		diff \| blob \| blame \| history
Bio/Assembly/ContigAnalysis.pm		diff \| blob \| blame \| history
Bio/Assembly/IO.pm		diff \| blob \| blame \| history
Bio/Assembly/IO/ace.pm		diff \| blob \| blame \| history
Bio/Assembly/IO/bowtie.pm		diff \| blob \| blame \| history
Bio/Assembly/IO/maq.pm		diff \| blob \| blame \| history
Bio/Assembly/IO/phrap.pm		diff \| blob \| blame \| history
Bio/Assembly/IO/sam.pm		diff \| blob \| blame \| history
Bio/Assembly/IO/tigr.pm		diff \| blob \| blame \| history
Bio/Assembly/Scaffold.pm		diff \| blob \| blame \| history
Bio/Assembly/ScaffoldI.pm		diff \| blob \| blame \| history
Bio/Assembly/Singlet.pm		diff \| blob \| blame \| history
Bio/Assembly/Tools/ContigSpectrum.pm		diff \| blob \| blame \| history
Bio/Cluster/ClusterFactory.pm		diff \| blob \| blame \| history
Bio/Cluster/FamilyI.pm		diff \| blob \| blame \| history
Bio/Cluster/SequenceFamily.pm		diff \| blob \| blame \| history
Bio/Cluster/UniGene.pm		diff \| blob \| blame \| history
Bio/Cluster/UniGeneI.pm		diff \| blob \| blame \| history
Bio/ClusterI.pm		diff \| blob \| blame \| history
Bio/ClusterIO.pm		diff \| blob \| blame \| history
Bio/ClusterIO/dbsnp.pm		diff \| blob \| blame \| history
Bio/ClusterIO/unigene.pm		diff \| blob \| blame \| history
Bio/CodonUsage/IO.pm		diff \| blob \| blame \| history
Bio/CodonUsage/Table.pm		diff \| blob \| blame \| history
Bio/DB/Ace.pm		diff \| blob \| blame \| history
Bio/DB/BioFetch.pm		diff \| blob \| blame \| history
Bio/DB/CUTG.pm		diff \| blob \| blame \| history
Bio/DB/DBFetch.pm		diff \| blob \| blame \| history
Bio/DB/EMBL.pm		diff \| blob \| blame \| history
Bio/DB/EntrezGene.pm		diff \| blob \| blame \| history
Bio/DB/Expression.pm		diff \| blob \| blame \| history
Bio/DB/Expression/geo.pm		diff \| blob \| blame \| history
Bio/DB/Failover.pm		diff \| blob \| blame \| history
Bio/DB/FileCache.pm		diff \| blob \| blame \| history
Bio/DB/Flat.pm		diff \| blob \| blame \| history
Bio/DB/Flat/BDB.pm		diff \| blob \| blame \| history
Bio/DB/Flat/BDB/embl.pm		diff \| blob \| blame \| history
Bio/DB/Flat/BDB/fasta.pm		diff \| blob \| blame \| history
Bio/DB/Flat/BDB/genbank.pm		diff \| blob \| blame \| history
Bio/DB/Flat/BDB/swiss.pm		diff \| blob \| blame \| history
Bio/DB/Flat/BinarySearch.pm		diff \| blob \| blame \| history
Bio/DB/GenBank.pm		diff \| blob \| blame \| history
Bio/DB/GenPept.pm		diff \| blob \| blame \| history
Bio/DB/GenericWebAgent.pm		diff \| blob \| blame \| history
Bio/DB/HIV.pm		diff \| blob \| blame \| history
Bio/DB/HIV/HIVAnnotProcessor.pm		diff \| blob \| blame \| history
Bio/DB/HIV/HIVQueryHelper.pm		diff \| blob \| blame \| history
Bio/DB/InMemoryCache.pm		diff \| blob \| blame \| history
Bio/DB/LocationI.pm		diff \| blob \| blame \| history
Bio/DB/MeSH.pm		diff \| blob \| blame \| history
Bio/DB/NCBIHelper.pm		diff \| blob \| blame \| history
Bio/DB/Query/GenBank.pm		diff \| blob \| blame \| history
Bio/DB/Query/HIVQuery.pm		diff \| blob \| blame \| history
Bio/DB/Query/WebQuery.pm		diff \| blob \| blame \| history
Bio/DB/QueryI.pm		diff \| blob \| blame \| history
Bio/DB/RandomAccessI.pm		diff \| blob \| blame \| history
Bio/DB/RefSeq.pm		diff \| blob \| blame \| history
Bio/DB/ReferenceI.pm		diff \| blob \| blame \| history
Bio/DB/Registry.pm		diff \| blob \| blame \| history
Bio/DB/SeqI.pm		diff \| blob \| blame \| history
Bio/DB/SeqVersion.pm		diff \| blob \| blame \| history
Bio/DB/SeqVersion/gi.pm		diff \| blob \| blame \| history
Bio/DB/SwissProt.pm		diff \| blob \| blame \| history
Bio/DB/TFBS.pm		diff \| blob \| blame \| history
Bio/DB/TFBS/transfac_pro.pm		diff \| blob \| blame \| history
Bio/DB/Taxonomy.pm		diff \| blob \| blame \| history
Bio/DB/Taxonomy/entrez.pm		diff \| blob \| blame \| history
Bio/DB/Taxonomy/flatfile.pm		diff \| blob \| blame \| history
Bio/DB/Taxonomy/greengenes.pm		diff \| blob \| blame \| history
Bio/DB/Taxonomy/list.pm		diff \| blob \| blame \| history
Bio/DB/Taxonomy/silva.pm		diff \| blob \| blame \| history
Bio/DB/Universal.pm		diff \| blob \| blame \| history
Bio/DB/UpdateableSeqI.pm		diff \| blob \| blame \| history
Bio/DB/WebDBSeqI.pm		diff \| blob \| blame \| history
Bio/DBLinkContainerI.pm		diff \| blob \| blame \| history
Bio/Das/FeatureTypeI.pm		diff \| blob \| blame \| history
Bio/Das/SegmentI.pm		diff \| blob \| blame \| history
Bio/DasI.pm		diff \| blob \| blame \| history
Bio/DescribableI.pm		diff \| blob \| blame \| history
Bio/Draw/Pictogram.pm		diff \| blob \| blame \| history
Bio/Event/EventGeneratorI.pm		diff \| blob \| blame \| history
Bio/Event/EventHandlerI.pm		diff \| blob \| blame \| history
Bio/Factory/AnalysisI.pm		diff \| blob \| blame \| history
Bio/Factory/ApplicationFactoryI.pm		diff \| blob \| blame \| history
Bio/Factory/DriverFactory.pm		diff \| blob \| blame \| history
Bio/Factory/FTLocationFactory.pm		diff \| blob \| blame \| history
Bio/Factory/LocationFactoryI.pm		diff \| blob \| blame \| history
Bio/Factory/MapFactoryI.pm		diff \| blob \| blame \| history
Bio/Factory/ObjectBuilderI.pm		diff \| blob \| blame \| history
Bio/Factory/ObjectFactory.pm		diff \| blob \| blame \| history
Bio/Factory/ObjectFactoryI.pm		diff \| blob \| blame \| history
Bio/Factory/SeqAnalysisParserFactory.pm		diff \| blob \| blame \| history
Bio/Factory/SeqAnalysisParserFactoryI.pm		diff \| blob \| blame \| history
Bio/Factory/SequenceFactoryI.pm		diff \| blob \| blame \| history
Bio/Factory/SequenceProcessorI.pm		diff \| blob \| blame \| history
Bio/Factory/SequenceStreamI.pm		diff \| blob \| blame \| history
Bio/Factory/TreeFactoryI.pm		diff \| blob \| blame \| history
Bio/FeatureHolderI.pm		diff \| blob \| blame \| history
Bio/HandlerBaseI.pm		diff \| blob \| blame \| history
Bio/IdCollectionI.pm		diff \| blob \| blame \| history
Bio/IdentifiableI.pm		diff \| blob \| blame \| history
Bio/Index/Abstract.pm		diff \| blob \| blame \| history
Bio/Index/AbstractSeq.pm		diff \| blob \| blame \| history
Bio/Index/Blast.pm		diff \| blob \| blame \| history
Bio/Index/BlastTable.pm		diff \| blob \| blame \| history
Bio/Index/EMBL.pm		diff \| blob \| blame \| history
Bio/Index/Fasta.pm		diff \| blob \| blame \| history
Bio/Index/Fastq.pm		diff \| blob \| blame \| history
Bio/Index/GenBank.pm		diff \| blob \| blame \| history
Bio/Index/Hmmer.pm		diff \| blob \| blame \| history
Bio/Index/Qual.pm		diff \| blob \| blame \| history
Bio/Index/Stockholm.pm		diff \| blob \| blame \| history
Bio/Index/SwissPfam.pm		diff \| blob \| blame \| history
Bio/Index/Swissprot.pm		diff \| blob \| blame \| history
Bio/LiveSeq/ChainI.pm		diff \| blob \| blame \| history
Bio/LiveSeq/Mutation.pm		diff \| blob \| blame \| history
Bio/LiveSeq/Mutator.pm		diff \| blob \| blame \| history
Bio/LiveSeq/SeqI.pm		diff \| blob \| blame \| history
Bio/LocatableSeq.pm		diff \| blob \| blame \| history
Bio/Location/Atomic.pm		diff \| blob \| blame \| history
Bio/Location/AvWithinCoordPolicy.pm		diff \| blob \| blame \| history
Bio/Location/CoordinatePolicyI.pm		diff \| blob \| blame \| history
Bio/Location/Fuzzy.pm		diff \| blob \| blame \| history
Bio/Location/FuzzyLocationI.pm		diff \| blob \| blame \| history
Bio/Location/NarrowestCoordPolicy.pm		diff \| blob \| blame \| history
Bio/Location/Simple.pm		diff \| blob \| blame \| history
Bio/Location/Split.pm		diff \| blob \| blame \| history
Bio/Location/SplitLocationI.pm		diff \| blob \| blame \| history
Bio/Location/WidestCoordPolicy.pm		diff \| blob \| blame \| history
Bio/LocationI.pm		diff \| blob \| blame \| history
Bio/Map/Clone.pm		diff \| blob \| blame \| history
Bio/Map/Contig.pm		diff \| blob \| blame \| history
Bio/Map/CytoMap.pm		diff \| blob \| blame \| history
Bio/Map/CytoMarker.pm		diff \| blob \| blame \| history
Bio/Map/CytoPosition.pm		diff \| blob \| blame \| history
Bio/Map/EntityI.pm		diff \| blob \| blame \| history
Bio/Map/FPCMarker.pm		diff \| blob \| blame \| history
Bio/Map/Gene.pm		diff \| blob \| blame \| history
Bio/Map/GeneMap.pm		diff \| blob \| blame \| history
Bio/Map/GenePosition.pm		diff \| blob \| blame \| history
Bio/Map/GeneRelative.pm		diff \| blob \| blame \| history
Bio/Map/LinkageMap.pm		diff \| blob \| blame \| history
Bio/Map/LinkagePosition.pm		diff \| blob \| blame \| history
Bio/Map/MapI.pm		diff \| blob \| blame \| history
Bio/Map/Mappable.pm		diff \| blob \| blame \| history
Bio/Map/MappableI.pm		diff \| blob \| blame \| history
Bio/Map/Marker.pm		diff \| blob \| blame \| history
Bio/Map/MarkerI.pm		diff \| blob \| blame \| history
Bio/Map/Microsatellite.pm		diff \| blob \| blame \| history
Bio/Map/OrderedPosition.pm		diff \| blob \| blame \| history
Bio/Map/OrderedPositionWithDistance.pm		diff \| blob \| blame \| history
Bio/Map/Physical.pm		diff \| blob \| blame \| history
Bio/Map/Position.pm		diff \| blob \| blame \| history
Bio/Map/PositionHandler.pm		diff \| blob \| blame \| history
Bio/Map/PositionHandlerI.pm		diff \| blob \| blame \| history
Bio/Map/PositionI.pm		diff \| blob \| blame \| history
Bio/Map/PositionWithSequence.pm		diff \| blob \| blame \| history
Bio/Map/Prediction.pm		diff \| blob \| blame \| history
Bio/Map/Relative.pm		diff \| blob \| blame \| history
Bio/Map/RelativeI.pm		diff \| blob \| blame \| history
Bio/Map/SimpleMap.pm		diff \| blob \| blame \| history
Bio/Map/TranscriptionFactor.pm		diff \| blob \| blame \| history
Bio/MapIO.pm		diff \| blob \| blame \| history
Bio/MapIO/fpc.pm		diff \| blob \| blame \| history
Bio/MapIO/mapmaker.pm		diff \| blob \| blame \| history
Bio/Matrix/Generic.pm		diff \| blob \| blame \| history
Bio/Matrix/IO.pm		diff \| blob \| blame \| history
Bio/Matrix/IO/mlagan.pm		diff \| blob \| blame \| history
Bio/Matrix/IO/phylip.pm		diff \| blob \| blame \| history
Bio/Matrix/IO/scoring.pm		diff \| blob \| blame \| history
Bio/Matrix/MatrixI.pm		diff \| blob \| blame \| history
Bio/Matrix/Mlagan.pm		diff \| blob \| blame \| history
Bio/Matrix/PSM/IO.pm		diff \| blob \| blame \| history
Bio/Matrix/PSM/IO/mast.pm		diff \| blob \| blame \| history
Bio/Matrix/PSM/IO/masta.pm		diff \| blob \| blame \| history
Bio/Matrix/PSM/IO/meme.pm		diff \| blob \| blame \| history
Bio/Matrix/PSM/IO/psiblast.pm		diff \| blob \| blame \| history
Bio/Matrix/PSM/IO/transfac.pm		diff \| blob \| blame \| history
Bio/Matrix/PSM/InstanceSite.pm		diff \| blob \| blame \| history
Bio/Matrix/PSM/InstanceSiteI.pm		diff \| blob \| blame \| history
Bio/Matrix/PSM/ProtMatrix.pm		diff \| blob \| blame \| history
Bio/Matrix/PSM/ProtPsm.pm		diff \| blob \| blame \| history
Bio/Matrix/PSM/Psm.pm		diff \| blob \| blame \| history
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Bio/Matrix/PSM/PsmHeaderI.pm		diff \| blob \| blame \| history
Bio/Matrix/PSM/PsmI.pm		diff \| blob \| blame \| history
Bio/Matrix/PSM/SiteMatrix.pm		diff \| blob \| blame \| history
Bio/Matrix/PSM/SiteMatrixI.pm		diff \| blob \| blame \| history
Bio/Matrix/PhylipDist.pm		diff \| blob \| blame \| history
Bio/Matrix/Scoring.pm		diff \| blob \| blame \| history
Bio/MolEvol/CodonModel.pm		diff \| blob \| blame \| history
Bio/Nexml/Factory.pm		diff \| blob \| blame \| history
Bio/NexmlIO.pm		diff \| blob \| blame \| history
Bio/Ontology/DocumentRegistry.pm		diff \| blob \| blame \| history
Bio/Ontology/GOterm.pm		diff \| blob \| blame \| history
Bio/Ontology/InterProTerm.pm		diff \| blob \| blame \| history
Bio/Ontology/OBOEngine.pm		diff \| blob \| blame \| history
Bio/Ontology/OBOterm.pm		diff \| blob \| blame \| history
Bio/Ontology/Ontology.pm		diff \| blob \| blame \| history
Bio/Ontology/OntologyEngineI.pm		diff \| blob \| blame \| history
Bio/Ontology/OntologyI.pm		diff \| blob \| blame \| history
Bio/Ontology/OntologyStore.pm		diff \| blob \| blame \| history
Bio/Ontology/Path.pm		diff \| blob \| blame \| history
Bio/Ontology/PathI.pm		diff \| blob \| blame \| history
Bio/Ontology/Relationship.pm		diff \| blob \| blame \| history
Bio/Ontology/RelationshipFactory.pm		diff \| blob \| blame \| history
Bio/Ontology/RelationshipI.pm		diff \| blob \| blame \| history
Bio/Ontology/RelationshipType.pm		diff \| blob \| blame \| history
Bio/Ontology/SimpleGOEngine/GraphAdaptor.pm		diff \| blob \| blame \| history
Bio/Ontology/SimpleOntologyEngine.pm		diff \| blob \| blame \| history
Bio/Ontology/Term.pm		diff \| blob \| blame \| history
Bio/Ontology/TermFactory.pm		diff \| blob \| blame \| history
Bio/Ontology/TermI.pm		diff \| blob \| blame \| history
Bio/OntologyIO.pm		diff \| blob \| blame \| history
Bio/OntologyIO/Handlers/BaseSAXHandler.pm		diff \| blob \| blame \| history
Bio/OntologyIO/Handlers/InterProHandler.pm		diff \| blob \| blame \| history
Bio/OntologyIO/InterProParser.pm		diff \| blob \| blame \| history
Bio/OntologyIO/dagflat.pm		diff \| blob \| blame \| history
Bio/OntologyIO/goflat.pm		diff \| blob \| blame \| history
Bio/OntologyIO/obo.pm		diff \| blob \| blame \| history
Bio/OntologyIO/simplehierarchy.pm		diff \| blob \| blame \| history
Bio/OntologyIO/soflat.pm		diff \| blob \| blame \| history
Bio/ParameterBaseI.pm		diff \| blob \| blame \| history
Bio/Perl.pm		diff \| blob \| blame \| history
Bio/Phenotype/Correlate.pm		diff \| blob \| blame \| history
Bio/Phenotype/MeSH/Term.pm		diff \| blob \| blame \| history
Bio/Phenotype/MeSH/Twig.pm		diff \| blob \| blame \| history
Bio/Phenotype/Measure.pm		diff \| blob \| blame \| history
Bio/Phenotype/OMIM/MiniMIMentry.pm		diff \| blob \| blame \| history
Bio/Phenotype/OMIM/OMIMentry.pm		diff \| blob \| blame \| history
Bio/Phenotype/OMIM/OMIMentryAllelicVariant.pm		diff \| blob \| blame \| history
Bio/Phenotype/OMIM/OMIMparser.pm		diff \| blob \| blame \| history
Bio/Phenotype/Phenotype.pm		diff \| blob \| blame \| history
Bio/Phenotype/PhenotypeI.pm		diff \| blob \| blame \| history
Bio/PopGen/Genotype.pm		diff \| blob \| blame \| history
Bio/PopGen/GenotypeI.pm		diff \| blob \| blame \| history
Bio/PopGen/HtSNP.pm		diff \| blob \| blame \| history
Bio/PopGen/IO.pm		diff \| blob \| blame \| history
Bio/PopGen/IO/csv.pm		diff \| blob \| blame \| history
Bio/PopGen/IO/hapmap.pm		diff \| blob \| blame \| history
Bio/PopGen/IO/phase.pm		diff \| blob \| blame \| history
Bio/PopGen/IO/prettybase.pm		diff \| blob \| blame \| history
Bio/PopGen/Individual.pm		diff \| blob \| blame \| history
Bio/PopGen/IndividualI.pm		diff \| blob \| blame \| history
Bio/PopGen/Marker.pm		diff \| blob \| blame \| history
Bio/PopGen/MarkerI.pm		diff \| blob \| blame \| history
Bio/PopGen/PopStats.pm		diff \| blob \| blame \| history
Bio/PopGen/Population.pm		diff \| blob \| blame \| history
Bio/PopGen/PopulationI.pm		diff \| blob \| blame \| history
Bio/PopGen/Simulation/Coalescent.pm		diff \| blob \| blame \| history
Bio/PopGen/Simulation/GeneticDrift.pm		diff \| blob \| blame \| history
Bio/PopGen/Statistics.pm		diff \| blob \| blame \| history
Bio/PopGen/TagHaplotype.pm		diff \| blob \| blame \| history
Bio/PopGen/Utilities.pm		diff \| blob \| blame \| history
Bio/PrimarySeq.pm		diff \| blob \| blame \| history
Bio/PrimarySeqI.pm		diff \| blob \| blame \| history
Bio/PullParserI.pm		diff \| blob \| blame \| history
Bio/Range.pm		diff \| blob \| blame \| history
Bio/RangeI.pm		diff \| blob \| blame \| history
Bio/Restriction/Analysis.pm		diff \| blob \| blame \| history
Bio/Restriction/Enzyme.pm		diff \| blob \| blame \| history
Bio/Restriction/Enzyme/MultiCut.pm		diff \| blob \| blame \| history
Bio/Restriction/Enzyme/MultiSite.pm		diff \| blob \| blame \| history
Bio/Restriction/EnzymeCollection.pm		diff \| blob \| blame \| history
Bio/Restriction/EnzymeI.pm		diff \| blob \| blame \| history
Bio/Restriction/IO.pm		diff \| blob \| blame \| history
Bio/Restriction/IO/bairoch.pm		diff \| blob \| blame \| history
Bio/Restriction/IO/base.pm		diff \| blob \| blame \| history
Bio/Restriction/IO/itype2.pm		diff \| blob \| blame \| history
Bio/Restriction/IO/prototype.pm		diff \| blob \| blame \| history
Bio/Restriction/IO/withrefm.pm		diff \| blob \| blame \| history
Bio/Root/HTTPget.pm		diff \| blob \| blame \| history
Bio/Search/BlastStatistics.pm		diff \| blob \| blame \| history
Bio/Search/DatabaseI.pm		diff \| blob \| blame \| history
Bio/Search/GenericDatabase.pm		diff \| blob \| blame \| history
Bio/Search/GenericStatistics.pm		diff \| blob \| blame \| history
Bio/Search/HSP/BlastHSP.pm		diff \| blob \| blame \| history
Bio/Search/HSP/BlastPullHSP.pm		diff \| blob \| blame \| history
Bio/Search/HSP/FastaHSP.pm		diff \| blob \| blame \| history
Bio/Search/HSP/GenericHSP.pm		diff \| blob \| blame \| history
Bio/Search/HSP/HMMERHSP.pm		diff \| blob \| blame \| history
Bio/Search/HSP/HSPFactory.pm		diff \| blob \| blame \| history
Bio/Search/HSP/HSPI.pm		diff \| blob \| blame \| history
Bio/Search/HSP/HmmpfamHSP.pm		diff \| blob \| blame \| history
Bio/Search/HSP/ModelHSP.pm		diff \| blob \| blame \| history
Bio/Search/HSP/PSLHSP.pm		diff \| blob \| blame \| history
Bio/Search/HSP/PsiBlastHSP.pm		diff \| blob \| blame \| history
Bio/Search/HSP/PullHSPI.pm		diff \| blob \| blame \| history
Bio/Search/HSP/WABAHSP.pm		diff \| blob \| blame \| history
Bio/Search/Hit/BlastHit.pm		diff \| blob \| blame \| history
Bio/Search/Hit/BlastPullHit.pm		diff \| blob \| blame \| history
Bio/Search/Hit/Fasta.pm		diff \| blob \| blame \| history
Bio/Search/Hit/GenericHit.pm		diff \| blob \| blame \| history
Bio/Search/Hit/HMMERHit.pm		diff \| blob \| blame \| history
Bio/Search/Hit/HitFactory.pm		diff \| blob \| blame \| history
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Bio/Search/Hit/HmmpfamHit.pm		diff \| blob \| blame \| history
Bio/Search/Hit/ModelHit.pm		diff \| blob \| blame \| history
Bio/Search/Hit/PsiBlastHit.pm		diff \| blob \| blame \| history
Bio/Search/Hit/PullHitI.pm		diff \| blob \| blame \| history
Bio/Search/Hit/hmmer3Hit.pm		diff \| blob \| blame \| history
Bio/Search/Iteration/GenericIteration.pm		diff \| blob \| blame \| history
Bio/Search/Iteration/IterationI.pm		diff \| blob \| blame \| history
Bio/Search/Processor.pm		diff \| blob \| blame \| history
Bio/Search/Result/BlastPullResult.pm		diff \| blob \| blame \| history
Bio/Search/Result/BlastResult.pm		diff \| blob \| blame \| history
Bio/Search/Result/CrossMatchResult.pm		diff \| blob \| blame \| history
Bio/Search/Result/GenericResult.pm		diff \| blob \| blame \| history
Bio/Search/Result/HMMERResult.pm		diff \| blob \| blame \| history
Bio/Search/Result/HmmpfamResult.pm		diff \| blob \| blame \| history
Bio/Search/Result/PullResultI.pm		diff \| blob \| blame \| history
Bio/Search/Result/ResultFactory.pm		diff \| blob \| blame \| history
Bio/Search/Result/ResultI.pm		diff \| blob \| blame \| history
Bio/Search/Result/WABAResult.pm		diff \| blob \| blame \| history
Bio/Search/Result/hmmer3Result.pm		diff \| blob \| blame \| history
Bio/Search/StatisticsI.pm		diff \| blob \| blame \| history
Bio/Search/Tiling/MapTiling.pm		diff \| blob \| blame \| history
Bio/Search/Tiling/TilingI.pm		diff \| blob \| blame \| history
Bio/SearchDist.pm		diff \| blob \| blame \| history
Bio/SearchIO.pm		diff \| blob \| blame \| history
Bio/SearchIO/EventHandlerI.pm		diff \| blob \| blame \| history
Bio/SearchIO/FastHitEventBuilder.pm		diff \| blob \| blame \| history
Bio/SearchIO/IteratedSearchResultEventBuilder.pm		diff \| blob \| blame \| history
Bio/SearchIO/SearchResultEventBuilder.pm		diff \| blob \| blame \| history
Bio/SearchIO/Writer/GbrowseGFF.pm		diff \| blob \| blame \| history
Bio/SearchIO/Writer/HSPTableWriter.pm		diff \| blob \| blame \| history
Bio/SearchIO/Writer/HTMLResultWriter.pm		diff \| blob \| blame \| history
Bio/SearchIO/Writer/HitTableWriter.pm		diff \| blob \| blame \| history
Bio/SearchIO/Writer/ResultTableWriter.pm		diff \| blob \| blame \| history
Bio/SearchIO/Writer/TextResultWriter.pm		diff \| blob \| blame \| history
Bio/SearchIO/axt.pm		diff \| blob \| blame \| history
Bio/SearchIO/blast.pm		diff \| blob \| blame \| history
Bio/SearchIO/blast_pull.pm		diff \| blob \| blame \| history
Bio/SearchIO/blasttable.pm		diff \| blob \| blame \| history
Bio/SearchIO/cross_match.pm		diff \| blob \| blame \| history
Bio/SearchIO/erpin.pm		diff \| blob \| blame \| history
Bio/SearchIO/exonerate.pm		diff \| blob \| blame \| history
Bio/SearchIO/fasta.pm		diff \| blob \| blame \| history
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