[Bioperl-guts-l] [bioperl/bioperl-live] 1ef660: rectify a conflict in behavior between PrimarySeq:...

noreply at github.com noreply at github.com
Sat Mar 12 22:27:06 EST 2011 

Branch: refs/heads/release-1-6-2
Home:   https://github.com/bioperl/bioperl-live

Commit: 1ef6600ac4fef830844a86ea44afe8aa18d465ec
    https://github.com/bioperl/bioperl-live/commit/1ef6600ac4fef830844a86ea44afe8aa18d465ec
Author: Chris Fields <cjfields at bioperl.org>
Date:   2011-01-18 (Tue, 18 Jan 2011)

Changed paths:
  M Bio/PrimarySeqI.pm
  M Bio/Tools/CodonTable.pm
  M t/Seq/Seq.t

Log Message:
-----------
rectify a conflict in behavior between PrimarySeq::translate and CodonTable::translate(); sequences to be translated are not automatically assumed to be codons, add a flag (-complete_codons) that allows partial codons to be translated, but off by default (thanks to Amir Karger for pointing this out)


Commit: 68979de93da4b0559c80860d77e2f8ff5d87ed49
    https://github.com/bioperl/bioperl-live/commit/68979de93da4b0559c80860d77e2f8ff5d87ed49
Author: Johan Viklund <johan.viklund at gmail.com>
Date:   2011-01-25 (Tue, 25 Jan 2011)

Changed paths:
  R .shipit
  M Bio/Align/AlignI.pm
  M Bio/Align/DNAStatistics.pm
  M Bio/Align/PairwiseStatistics.pm
  M Bio/Align/ProteinStatistics.pm
  M Bio/Align/StatisticsI.pm
  M Bio/Align/Utilities.pm
  M Bio/AlignIO.pm
  M Bio/AlignIO/arp.pm
  M Bio/AlignIO/bl2seq.pm
  M Bio/AlignIO/clustalw.pm
  M Bio/AlignIO/emboss.pm
  M Bio/AlignIO/fasta.pm
  M Bio/AlignIO/maf.pm
  M Bio/AlignIO/mase.pm
  M Bio/AlignIO/mega.pm
  M Bio/AlignIO/meme.pm
  M Bio/AlignIO/metafasta.pm
  M Bio/AlignIO/msf.pm
  M Bio/AlignIO/nexml.pm
  M Bio/AlignIO/nexus.pm
  M Bio/AlignIO/pfam.pm
  M Bio/AlignIO/phylip.pm
  M Bio/AlignIO/proda.pm
  M Bio/AlignIO/prodom.pm
  M Bio/AlignIO/psi.pm
  M Bio/AlignIO/selex.pm
  M Bio/AlignIO/stockholm.pm
  M Bio/AlignIO/xmfa.pm
  M Bio/AnalysisI.pm
  M Bio/AnalysisParserI.pm
  M Bio/AnalysisResultI.pm
  M Bio/AnnotatableI.pm
  M Bio/Annotation/AnnotationFactory.pm
  M Bio/Annotation/Collection.pm
  M Bio/Annotation/Comment.pm
  M Bio/Annotation/DBLink.pm
  M Bio/Annotation/OntologyTerm.pm
  M Bio/Annotation/Reference.pm
  M Bio/Annotation/SimpleValue.pm
  M Bio/Annotation/StructuredValue.pm
  M Bio/Annotation/Target.pm
  M Bio/Annotation/TypeManager.pm
  M Bio/AnnotationCollectionI.pm
  M Bio/AnnotationI.pm
  M Bio/Assembly/Contig.pm
  M Bio/Assembly/ContigAnalysis.pm
  M Bio/Assembly/IO/ace.pm
  M Bio/Assembly/IO/bowtie.pm
  M Bio/Assembly/IO/maq.pm
  M Bio/Assembly/IO/phrap.pm
  M Bio/Assembly/IO/sam.pm
  M Bio/Assembly/IO/tigr.pm
  M Bio/Assembly/Scaffold.pm
  M Bio/Assembly/ScaffoldI.pm
  M Bio/Assembly/Singlet.pm
  M Bio/Assembly/Tools/ContigSpectrum.pm
  M Bio/Biblio.pm
  M Bio/Biblio/Article.pm
  M Bio/Biblio/BiblioBase.pm
  M Bio/Biblio/Book.pm
  M Bio/Biblio/BookArticle.pm
  M Bio/Biblio/IO.pm
  M Bio/Biblio/IO/medline2ref.pm
  M Bio/Biblio/IO/medlinexml.pm
  M Bio/Biblio/IO/pubmed2ref.pm
  M Bio/Biblio/IO/pubmedxml.pm
  M Bio/Biblio/Journal.pm
  M Bio/Biblio/JournalArticle.pm
  M Bio/Biblio/MedlineArticle.pm
  M Bio/Biblio/MedlineBook.pm
  M Bio/Biblio/MedlineBookArticle.pm
  M Bio/Biblio/MedlineJournal.pm
  M Bio/Biblio/MedlineJournalArticle.pm
  M Bio/Biblio/Organisation.pm
  M Bio/Biblio/Patent.pm
  M Bio/Biblio/Person.pm
  M Bio/Biblio/Proceeding.pm
  M Bio/Biblio/Provider.pm
  M Bio/Biblio/PubmedArticle.pm
  M Bio/Biblio/PubmedBookArticle.pm
  M Bio/Biblio/PubmedJournalArticle.pm
  M Bio/Biblio/Ref.pm
  M Bio/Biblio/Service.pm
  M Bio/Biblio/TechReport.pm
  M Bio/Biblio/Thesis.pm
  M Bio/Biblio/WebResource.pm
  M Bio/Cluster/ClusterFactory.pm
  M Bio/Cluster/SequenceFamily.pm
  M Bio/Cluster/UniGene.pm
  M Bio/Cluster/UniGeneI.pm
  M Bio/ClusterI.pm
  M Bio/ClusterIO.pm
  M Bio/ClusterIO/dbsnp.pm
  M Bio/ClusterIO/unigene.pm
  M Bio/CodonUsage/IO.pm
  M Bio/CodonUsage/Table.pm
  M Bio/Coordinate/Chain.pm
  M Bio/Coordinate/Collection.pm
  M Bio/Coordinate/ExtrapolatingPair.pm
  M Bio/Coordinate/GeneMapper.pm
  M Bio/Coordinate/Graph.pm
  M Bio/Coordinate/MapperI.pm
  M Bio/Coordinate/Pair.pm
  M Bio/Coordinate/Result.pm
  M Bio/Coordinate/Result/Gap.pm
  M Bio/Coordinate/Result/Match.pm
  M Bio/Coordinate/ResultI.pm
  M Bio/Coordinate/Utils.pm
  M Bio/DB/Ace.pm
  M Bio/DB/Biblio/biofetch.pm
  M Bio/DB/Biblio/eutils.pm
  M Bio/DB/Biblio/soap.pm
  M Bio/DB/BiblioI.pm
  M Bio/DB/BioFetch.pm
  M Bio/DB/CUTG.pm
  M Bio/DB/DBFetch.pm
  M Bio/DB/EMBL.pm
  M Bio/DB/EUtilities.pm
  M Bio/DB/EntrezGene.pm
  M Bio/DB/Expression.pm
  M Bio/DB/Failover.pm
  M Bio/DB/Fasta.pm
  M Bio/DB/FileCache.pm
  M Bio/DB/Flat.pm
  M Bio/DB/Flat/BDB.pm
  M Bio/DB/Flat/BDB/embl.pm
  M Bio/DB/Flat/BDB/fasta.pm
  M Bio/DB/Flat/BDB/genbank.pm
  M Bio/DB/Flat/BDB/swiss.pm
  M Bio/DB/Flat/BinarySearch.pm
  M Bio/DB/GFF.pm
  M Bio/DB/GFF/Adaptor/berkeleydb.pm
  M Bio/DB/GFF/Adaptor/berkeleydb/iterator.pm
  M Bio/DB/GFF/Adaptor/dbi.pm
  M Bio/DB/GFF/Adaptor/dbi/mysql.pm
  M Bio/DB/GFF/Adaptor/dbi/oracle.pm
  M Bio/DB/GFF/Adaptor/dbi/pg.pm
  M Bio/DB/GFF/Adaptor/dbi/pg_fts.pm
  M Bio/DB/GFF/Adaptor/memory.pm
  M Bio/DB/GFF/Adaptor/memory/feature_serializer.pm
  M Bio/DB/GFF/Adaptor/memory/iterator.pm
  M Bio/DB/GenBank.pm
  M Bio/DB/GenPept.pm
  M Bio/DB/GenericWebAgent.pm
  M Bio/DB/InMemoryCache.pm
  M Bio/DB/LocationI.pm
  M Bio/DB/MeSH.pm
  M Bio/DB/NCBIHelper.pm
  M Bio/DB/Qual.pm
  M Bio/DB/Query/GenBank.pm
  M Bio/DB/Query/WebQuery.pm
  M Bio/DB/QueryI.pm
  M Bio/DB/RandomAccessI.pm
  M Bio/DB/RefSeq.pm
  M Bio/DB/ReferenceI.pm
  M Bio/DB/Registry.pm
  M Bio/DB/SeqFeature.pm
  M Bio/DB/SeqFeature/NormalizedFeature.pm
  M Bio/DB/SeqFeature/NormalizedFeatureI.pm
  M Bio/DB/SeqFeature/NormalizedTableFeatureI.pm
  M Bio/DB/SeqFeature/Segment.pm
  M Bio/DB/SeqFeature/Store.pm
  M Bio/DB/SeqFeature/Store/DBI/Iterator.pm
  M Bio/DB/SeqFeature/Store/DBI/Pg.pm
  M Bio/DB/SeqFeature/Store/DBI/SQLite.pm
  M Bio/DB/SeqFeature/Store/DBI/mysql.pm
  M Bio/DB/SeqFeature/Store/FeatureFileLoader.pm
  M Bio/DB/SeqFeature/Store/GFF3Loader.pm
  M Bio/DB/SeqFeature/Store/LoadHelper.pm
  M Bio/DB/SeqFeature/Store/Loader.pm
  M Bio/DB/SeqFeature/Store/bdb.pm
  M Bio/DB/SeqFeature/Store/berkeleydb.pm
  M Bio/DB/SeqFeature/Store/berkeleydb3.pm
  M Bio/DB/SeqFeature/Store/memory.pm
  M Bio/DB/SeqI.pm
  M Bio/DB/SeqVersion.pm
  M Bio/DB/SeqVersion/gi.pm
  M Bio/DB/SwissProt.pm
  M Bio/DB/Taxonomy.pm
  M Bio/DB/Taxonomy/entrez.pm
  M Bio/DB/Taxonomy/flatfile.pm
  M Bio/DB/Taxonomy/list.pm
  M Bio/DB/UpdateableSeqI.pm
  M Bio/DB/WebDBSeqI.pm
  M Bio/DBLinkContainerI.pm
  M Bio/Das/FeatureTypeI.pm
  M Bio/Das/SegmentI.pm
  M Bio/DasI.pm
  M Bio/DescribableI.pm
  M Bio/Event/EventGeneratorI.pm
  M Bio/Event/EventHandlerI.pm
  R Bio/Expression/Contact.pm
  R Bio/Expression/DataSet.pm
  R Bio/Expression/FeatureGroup.pm
  R Bio/Expression/FeatureGroup/FeatureGroupMas50.pm
  R Bio/Expression/FeatureI.pm
  R Bio/Expression/FeatureSet/FeatureSetMas50.pm
  R Bio/Expression/Platform.pm
  R Bio/Expression/ProbeI.pm
  R Bio/Expression/Sample.pm
  M Bio/Factory/AnalysisI.pm
  M Bio/Factory/ApplicationFactoryI.pm
  M Bio/Factory/DriverFactory.pm
  M Bio/Factory/FTLocationFactory.pm
  M Bio/Factory/LocationFactoryI.pm
  M Bio/Factory/MapFactoryI.pm
  M Bio/Factory/ObjectBuilderI.pm
  M Bio/Factory/ObjectFactory.pm
  M Bio/Factory/ObjectFactoryI.pm
  M Bio/Factory/SeqAnalysisParserFactory.pm
  M Bio/Factory/SeqAnalysisParserFactoryI.pm
  M Bio/Factory/SequenceFactoryI.pm
  M Bio/Factory/SequenceProcessorI.pm
  M Bio/Factory/SequenceStreamI.pm
  M Bio/Factory/TreeFactoryI.pm
  M Bio/FeatureHolderI.pm
  M Bio/FeatureIO.pm
  M Bio/FeatureIO/gff.pm
  M Bio/FeatureIO/gtf.pm
  M Bio/HandlerBaseI.pm
  M Bio/IdCollectionI.pm
  M Bio/IdentifiableI.pm
  M Bio/Index/Abstract.pm
  M Bio/Index/AbstractSeq.pm
  M Bio/Index/Blast.pm
  M Bio/Index/BlastTable.pm
  M Bio/Index/EMBL.pm
  M Bio/Index/Fasta.pm
  M Bio/Index/GenBank.pm
  M Bio/Index/Qual.pm
  M Bio/Index/Stockholm.pm
  M Bio/Index/SwissPfam.pm
  M Bio/Index/Swissprot.pm
  M Bio/LiveSeq/AARange.pm
  M Bio/LiveSeq/Chain.pm
  M Bio/LiveSeq/ChainI.pm
  M Bio/LiveSeq/DNA.pm
  M Bio/LiveSeq/Exon.pm
  M Bio/LiveSeq/Gene.pm
  M Bio/LiveSeq/IO/BioPerl.pm
  M Bio/LiveSeq/IO/Loader.pm
  M Bio/LiveSeq/Intron.pm
  M Bio/LiveSeq/Mutation.pm
  M Bio/LiveSeq/Mutator.pm
  M Bio/LiveSeq/Prim_Transcript.pm
  M Bio/LiveSeq/Range.pm
  M Bio/LiveSeq/Repeat_Region.pm
  M Bio/LiveSeq/Repeat_Unit.pm
  M Bio/LiveSeq/SeqI.pm
  M Bio/LiveSeq/Transcript.pm
  M Bio/LiveSeq/Translation.pm
  M Bio/LocatableSeq.pm
  M Bio/Location/Atomic.pm
  M Bio/Location/AvWithinCoordPolicy.pm
  M Bio/Location/CoordinatePolicyI.pm
  M Bio/Location/Fuzzy.pm
  M Bio/Location/FuzzyLocationI.pm
  M Bio/Location/NarrowestCoordPolicy.pm
  M Bio/Location/Simple.pm
  M Bio/Location/Split.pm
  M Bio/Location/SplitLocationI.pm
  M Bio/Location/WidestCoordPolicy.pm
  M Bio/LocationI.pm
  M Bio/Map/Clone.pm
  M Bio/Map/Contig.pm
  M Bio/Map/CytoMap.pm
  M Bio/Map/CytoMarker.pm
  M Bio/Map/CytoPosition.pm
  M Bio/Map/EntityI.pm
  M Bio/Map/FPCMarker.pm
  M Bio/Map/MapI.pm
  M Bio/Map/Mappable.pm
  M Bio/Map/MappableI.pm
  M Bio/Map/Marker.pm
  M Bio/Map/MarkerI.pm
  M Bio/Map/Physical.pm
  M Bio/Map/Position.pm
  M Bio/Map/PositionHandler.pm
  M Bio/Map/PositionHandlerI.pm
  M Bio/Map/PositionI.pm
  M Bio/Map/Relative.pm
  M Bio/Map/RelativeI.pm
  M Bio/Map/SimpleMap.pm
  M Bio/MapIO.pm
  M Bio/MapIO/mapmaker.pm
  M Bio/Matrix/Generic.pm
  M Bio/Matrix/IO.pm
  M Bio/Matrix/IO/mlagan.pm
  M Bio/Matrix/IO/phylip.pm
  M Bio/Matrix/IO/scoring.pm
  M Bio/Matrix/Mlagan.pm
  M Bio/Matrix/PSM/IO.pm
  M Bio/Matrix/PSM/IO/mast.pm
  M Bio/Matrix/PSM/IO/masta.pm
  M Bio/Matrix/PSM/IO/meme.pm
  M Bio/Matrix/PSM/IO/psiblast.pm
  M Bio/Matrix/PSM/IO/transfac.pm
  M Bio/Matrix/PSM/InstanceSite.pm
  M Bio/Matrix/PSM/InstanceSiteI.pm
  M Bio/Matrix/PSM/ProtMatrix.pm
  M Bio/Matrix/PSM/ProtPsm.pm
  M Bio/Matrix/PSM/Psm.pm
  M Bio/Matrix/PSM/PsmHeader.pm
  M Bio/Matrix/PSM/PsmHeaderI.pm
  M Bio/Matrix/PSM/PsmI.pm
  M Bio/Matrix/PSM/SiteMatrix.pm
  M Bio/Matrix/PSM/SiteMatrixI.pm
  M Bio/Matrix/PhylipDist.pm
  M Bio/Matrix/Scoring.pm
  R Bio/Microarray/Tools/MitoChipV2Parser.pm
  R Bio/Microarray/Tools/ReseqChip.pm
  M Bio/MolEvol/CodonModel.pm
  M Bio/Ontology/DocumentRegistry.pm
  M Bio/Ontology/GOterm.pm
  M Bio/Ontology/InterProTerm.pm
  M Bio/Ontology/OBOEngine.pm
  M Bio/Ontology/OBOterm.pm
  M Bio/Ontology/Ontology.pm
  M Bio/Ontology/OntologyEngineI.pm
  M Bio/Ontology/OntologyI.pm
  M Bio/Ontology/OntologyStore.pm
  M Bio/Ontology/Path.pm
  M Bio/Ontology/PathI.pm
  M Bio/Ontology/Relationship.pm
  M Bio/Ontology/RelationshipFactory.pm
  M Bio/Ontology/RelationshipI.pm
  M Bio/Ontology/RelationshipType.pm
  M Bio/Ontology/SimpleOntologyEngine.pm
  M Bio/Ontology/Term.pm
  M Bio/Ontology/TermFactory.pm
  M Bio/Ontology/TermI.pm
  M Bio/OntologyIO.pm
  M Bio/OntologyIO/Handlers/BaseSAXHandler.pm
  M Bio/OntologyIO/Handlers/InterProHandler.pm
  M Bio/OntologyIO/Handlers/InterPro_BioSQL_Handler.pm
  M Bio/OntologyIO/InterProParser.pm
  M Bio/OntologyIO/dagflat.pm
  M Bio/OntologyIO/goflat.pm
  M Bio/OntologyIO/obo.pm
  M Bio/OntologyIO/simplehierarchy.pm
  M Bio/OntologyIO/soflat.pm
  M Bio/ParameterBaseI.pm
  M Bio/Perl.pm
  M Bio/Phenotype/Correlate.pm
  M Bio/Phenotype/MeSH/Term.pm
  M Bio/Phenotype/MeSH/Twig.pm
  M Bio/Phenotype/Measure.pm
  M Bio/Phenotype/OMIM/MiniMIMentry.pm
  M Bio/Phenotype/OMIM/OMIMentry.pm
  M Bio/Phenotype/OMIM/OMIMentryAllelicVariant.pm
  M Bio/Phenotype/OMIM/OMIMparser.pm
  M Bio/Phenotype/Phenotype.pm
  M Bio/Phenotype/PhenotypeI.pm
  M Bio/PhyloNetwork.pm
  M Bio/PhyloNetwork/Factory.pm
  M Bio/PhyloNetwork/FactoryX.pm
  M Bio/PhyloNetwork/GraphViz.pm
  M Bio/PhyloNetwork/RandomFactory.pm
  M Bio/PhyloNetwork/TreeFactory.pm
  M Bio/PhyloNetwork/TreeFactoryMulti.pm
  M Bio/PhyloNetwork/TreeFactoryX.pm
  M Bio/PhyloNetwork/muVector.pm
  M Bio/PopGen/Genotype.pm
  M Bio/PopGen/IO.pm
  M Bio/PopGen/IO/csv.pm
  M Bio/PopGen/IO/hapmap.pm
  M Bio/PopGen/IO/phase.pm
  M Bio/PopGen/IO/prettybase.pm
  M Bio/PopGen/Individual.pm
  M Bio/PopGen/Marker.pm
  M Bio/PopGen/PopStats.pm
  M Bio/PopGen/Population.pm
  M Bio/PopGen/PopulationI.pm
  M Bio/PopGen/Simulation/Coalescent.pm
  M Bio/PopGen/Simulation/GeneticDrift.pm
  M Bio/PopGen/Statistics.pm
  M Bio/PopGen/Utilities.pm
  M Bio/PrimarySeq.pm
  M Bio/PrimarySeqI.pm
  M Bio/PullParserI.pm
  M Bio/Range.pm
  M Bio/RangeI.pm
  M Bio/Restriction/Analysis.pm
  M Bio/Restriction/Enzyme.pm
  M Bio/Restriction/Enzyme/MultiCut.pm
  M Bio/Restriction/Enzyme/MultiSite.pm
  M Bio/Restriction/EnzymeCollection.pm
  M Bio/Restriction/EnzymeI.pm
  M Bio/Restriction/IO.pm
  M Bio/Restriction/IO/bairoch.pm
  M Bio/Restriction/IO/base.pm
  M Bio/Restriction/IO/itype2.pm
  M Bio/Restriction/IO/prototype.pm
  M Bio/Restriction/IO/withrefm.pm
  M Bio/Root/Build.pm
  M Bio/Root/Exception.pm
  M Bio/Root/HTTPget.pm
  M Bio/Root/IO.pm
  M Bio/Root/Root.pm
  M Bio/Root/RootI.pm
  M Bio/Root/Storable.pm
  M Bio/Root/Test.pm
  M Bio/Root/Test/Warn.pm
  M Bio/Root/Utilities.pm
  M Bio/Root/Version.pm
  M Bio/Search/DatabaseI.pm
  M Bio/Search/GenericDatabase.pm
  M Bio/Search/HSP/BlastHSP.pm
  M Bio/Search/HSP/BlastPullHSP.pm
  M Bio/Search/HSP/FastaHSP.pm
  M Bio/Search/HSP/GenericHSP.pm
  M Bio/Search/HSP/HMMERHSP.pm
  M Bio/Search/HSP/HSPFactory.pm
  M Bio/Search/HSP/HSPI.pm
  M Bio/Search/HSP/HmmpfamHSP.pm
  M Bio/Search/HSP/ModelHSP.pm
  M Bio/Search/HSP/PSLHSP.pm
  M Bio/Search/HSP/PsiBlastHSP.pm
  M Bio/Search/HSP/PullHSPI.pm
  M Bio/Search/HSP/WABAHSP.pm
  A Bio/Search/HSP/hmmer3HSP.pm
  M Bio/Search/Hit/BlastHit.pm
  M Bio/Search/Hit/BlastPullHit.pm
  M Bio/Search/Hit/Fasta.pm
  M Bio/Search/Hit/GenericHit.pm
  M Bio/Search/Hit/HMMERHit.pm
  M Bio/Search/Hit/HitFactory.pm
  M Bio/Search/Hit/HitI.pm
  M Bio/Search/Hit/HmmpfamHit.pm
  M Bio/Search/Hit/ModelHit.pm
  M Bio/Search/Hit/PsiBlastHit.pm
  M Bio/Search/Hit/PullHitI.pm
  A Bio/Search/Hit/hmmer3Hit.pm
  M Bio/Search/Iteration/GenericIteration.pm
  M Bio/Search/Iteration/IterationI.pm
  M Bio/Search/Result/BlastPullResult.pm
  M Bio/Search/Result/BlastResult.pm
  M Bio/Search/Result/CrossMatchResult.pm
  M Bio/Search/Result/GenericResult.pm
  M Bio/Search/Result/HMMERResult.pm
  M Bio/Search/Result/HmmpfamResult.pm
  M Bio/Search/Result/PullResultI.pm
  M Bio/Search/Result/ResultFactory.pm
  M Bio/Search/Result/ResultI.pm
  M Bio/Search/Result/WABAResult.pm
  A Bio/Search/Result/hmmer3Result.pm
  M Bio/Search/Tiling/MapTiling.pm
  M Bio/Search/Tiling/TilingI.pm
  M Bio/SearchDist.pm
  M Bio/SearchIO.pm
  M Bio/SearchIO/EventHandlerI.pm
  M Bio/SearchIO/FastHitEventBuilder.pm
  M Bio/SearchIO/IteratedSearchResultEventBuilder.pm
  M Bio/SearchIO/SearchResultEventBuilder.pm
  M Bio/SearchIO/SearchWriterI.pm
  M Bio/SearchIO/Writer/BSMLResultWriter.pm
  M Bio/SearchIO/Writer/GbrowseGFF.pm
  M Bio/SearchIO/Writer/HSPTableWriter.pm
  M Bio/SearchIO/Writer/HTMLResultWriter.pm
  M Bio/SearchIO/Writer/HitTableWriter.pm
  M Bio/SearchIO/Writer/ResultTableWriter.pm
  M Bio/SearchIO/Writer/TextResultWriter.pm
  M Bio/SearchIO/XML/BlastHandler.pm
  M Bio/SearchIO/XML/PsiBlastHandler.pm
  M Bio/SearchIO/axt.pm
  M Bio/SearchIO/blast.pm
  M Bio/SearchIO/blast_pull.pm
  M Bio/SearchIO/blasttable.pm
  M Bio/SearchIO/blastxml.pm
  M Bio/SearchIO/cross_match.pm
  M Bio/SearchIO/erpin.pm
  M Bio/SearchIO/exonerate.pm
  M Bio/SearchIO/fasta.pm
  M Bio/SearchIO/hmmer.pm
  A Bio/SearchIO/hmmer2.pm
  A Bio/SearchIO/hmmer3.pm
  M Bio/SearchIO/hmmer_pull.pm
  M Bio/SearchIO/infernal.pm
  M Bio/SearchIO/megablast.pm
  M Bio/SearchIO/psl.pm
  M Bio/SearchIO/rnamotif.pm
  M Bio/SearchIO/sim4.pm
  M Bio/SearchIO/waba.pm
  M Bio/SearchIO/wise.pm
  M Bio/Seq.pm
  M Bio/Seq/BaseSeqProcessor.pm
  M Bio/Seq/EncodedSeq.pm
  M Bio/Seq/LargePrimarySeq.pm
  M Bio/Seq/LargeSeq.pm
  M Bio/Seq/LargeSeqI.pm
  M Bio/Seq/Meta.pm
  M Bio/Seq/Meta/Array.pm
  M Bio/Seq/MetaI.pm
  M Bio/Seq/PrimaryQual.pm
  M Bio/Seq/PrimedSeq.pm
  M Bio/Seq/QualI.pm
  M Bio/Seq/Quality.pm
  M Bio/Seq/RichSeq.pm
  M Bio/Seq/RichSeqI.pm
  M Bio/Seq/SeqBuilder.pm
  M Bio/Seq/SeqFactory.pm
  M Bio/Seq/SeqFastaSpeedFactory.pm
  M Bio/Seq/SeqWithQuality.pm
  M Bio/Seq/SequenceTrace.pm
  M Bio/SeqAnalysisParserI.pm
  M Bio/SeqEvolution/DNAPoint.pm
  M Bio/SeqEvolution/EvolutionI.pm
  M Bio/SeqEvolution/Factory.pm
  M Bio/SeqFeature/Annotated.pm
  M Bio/SeqFeature/AnnotationAdaptor.pm
  M Bio/SeqFeature/Collection.pm
  M Bio/SeqFeature/CollectionI.pm
  M Bio/SeqFeature/Computation.pm
  M Bio/SeqFeature/FeaturePair.pm
  M Bio/SeqFeature/Gene/Exon.pm
  M Bio/SeqFeature/Gene/ExonI.pm
  M Bio/SeqFeature/Gene/GeneStructure.pm
  M Bio/SeqFeature/Gene/GeneStructureI.pm
  M Bio/SeqFeature/Gene/Intron.pm
  M Bio/SeqFeature/Gene/NC_Feature.pm
  M Bio/SeqFeature/Gene/Poly_A_site.pm
  M Bio/SeqFeature/Gene/Promoter.pm
  M Bio/SeqFeature/Gene/Transcript.pm
  M Bio/SeqFeature/Gene/TranscriptI.pm
  M Bio/SeqFeature/Gene/UTR.pm
  M Bio/SeqFeature/Generic.pm
  M Bio/SeqFeature/Lite.pm
  M Bio/SeqFeature/PositionProxy.pm
  M Bio/SeqFeature/Primer.pm
  M Bio/SeqFeature/SiRNA/Oligo.pm
  M Bio/SeqFeature/SiRNA/Pair.pm
  M Bio/SeqFeature/Similarity.pm
  M Bio/SeqFeature/SimilarityPair.pm
  M Bio/SeqFeature/Tools/FeatureNamer.pm
  M Bio/SeqFeature/Tools/IDHandler.pm
  M Bio/SeqFeature/Tools/TypeMapper.pm
  M Bio/SeqFeature/Tools/Unflattener.pm
  M Bio/SeqFeature/TypedSeqFeatureI.pm
  M Bio/SeqFeatureI.pm
  M Bio/SeqI.pm
  M Bio/SeqIO.pm
  M Bio/SeqIO/FTHelper.pm
  M Bio/SeqIO/Handler/GenericRichSeqHandler.pm
  M Bio/SeqIO/MultiFile.pm
  M Bio/SeqIO/abi.pm
  M Bio/SeqIO/ace.pm
  M Bio/SeqIO/alf.pm
  M Bio/SeqIO/asciitree.pm
  M Bio/SeqIO/bsml_sax.pm
  M Bio/SeqIO/chadoxml.pm
  M Bio/SeqIO/chaos.pm
  M Bio/SeqIO/chaosxml.pm
  M Bio/SeqIO/ctf.pm
  M Bio/SeqIO/embl.pm
  M Bio/SeqIO/embldriver.pm
  M Bio/SeqIO/entrezgene.pm
  M Bio/SeqIO/excel.pm
  M Bio/SeqIO/exp.pm
  M Bio/SeqIO/fasta.pm
  M Bio/SeqIO/fastq.pm
  M Bio/SeqIO/flybase_chadoxml.pm
  M Bio/SeqIO/game.pm
  M Bio/SeqIO/game/featHandler.pm
  M Bio/SeqIO/game/gameSubs.pm
  M Bio/SeqIO/game/gameWriter.pm
  M Bio/SeqIO/game/seqHandler.pm
  M Bio/SeqIO/gbdriver.pm
  M Bio/SeqIO/gcg.pm
  M Bio/SeqIO/genbank.pm
  M Bio/SeqIO/interpro.pm
  M Bio/SeqIO/kegg.pm
  M Bio/SeqIO/largefasta.pm
  M Bio/SeqIO/lasergene.pm
  M Bio/SeqIO/locuslink.pm
  A Bio/SeqIO/mbsout.pm
  M Bio/SeqIO/metafasta.pm
  A Bio/SeqIO/msout.pm
  M Bio/SeqIO/nexml.pm
  M Bio/SeqIO/phd.pm
  M Bio/SeqIO/pir.pm
  M Bio/SeqIO/pln.pm
  M Bio/SeqIO/qual.pm
  M Bio/SeqIO/raw.pm
  M Bio/SeqIO/scf.pm
  M Bio/SeqIO/seqxml.pm
  M Bio/SeqIO/strider.pm
  M Bio/SeqIO/swiss.pm
  M Bio/SeqIO/swissdriver.pm
  M Bio/SeqIO/tab.pm
  M Bio/SeqIO/table.pm
  M Bio/SeqIO/tigr.pm
  M Bio/SeqIO/tigrxml.pm
  M Bio/SeqIO/ztr.pm
  M Bio/SeqUtils.pm
  M Bio/SimpleAlign.pm
  M Bio/SimpleAnalysisI.pm
  M Bio/Species.pm
  M Bio/Structure/Atom.pm
  M Bio/Structure/Chain.pm
  M Bio/Structure/Entry.pm
  M Bio/Structure/IO.pm
  M Bio/Structure/IO/pdb.pm
  M Bio/Structure/Model.pm
  M Bio/Structure/Residue.pm
  M Bio/Structure/StructureI.pm
  M Bio/Symbol/Alphabet.pm
  M Bio/Symbol/AlphabetI.pm
  M Bio/Symbol/DNAAlphabet.pm
  M Bio/Symbol/ProteinAlphabet.pm
  M Bio/Symbol/Symbol.pm
  M Bio/Symbol/SymbolI.pm
  M Bio/Taxon.pm
  M Bio/Taxonomy.pm
  M Bio/Taxonomy/Node.pm
  M Bio/Taxonomy/Taxon.pm
  M Bio/Taxonomy/Tree.pm
  M Bio/Tools/AlignFactory.pm
  M Bio/Tools/Alignment/Consed.pm
  M Bio/Tools/Alignment/Trim.pm
  M Bio/Tools/Analysis/DNA/ESEfinder.pm
  M Bio/Tools/Analysis/Protein/ELM.pm
  M Bio/Tools/Analysis/Protein/NetPhos.pm
  M Bio/Tools/Analysis/Protein/Scansite.pm
  M Bio/Tools/Analysis/SimpleAnalysisBase.pm
  M Bio/Tools/AnalysisResult.pm
  M Bio/Tools/Blat.pm
  M Bio/Tools/CodonTable.pm
  M Bio/Tools/Coil.pm
  M Bio/Tools/ECnumber.pm
  M Bio/Tools/EMBOSS/Palindrome.pm
  M Bio/Tools/EPCR.pm
  M Bio/Tools/ERPIN.pm
  M Bio/Tools/ESTScan.pm
  M Bio/Tools/EUtilities.pm
  R Bio/Tools/EUtilities/Cookie.pm
  M Bio/Tools/EUtilities/EUtilDataI.pm
  M Bio/Tools/EUtilities/EUtilParameters.pm
  M Bio/Tools/EUtilities/History.pm
  M Bio/Tools/EUtilities/HistoryI.pm
  M Bio/Tools/EUtilities/Info.pm
  M Bio/Tools/EUtilities/Info/FieldInfo.pm
  M Bio/Tools/EUtilities/Info/LinkInfo.pm
  M Bio/Tools/EUtilities/Link.pm
  M Bio/Tools/EUtilities/Link/LinkSet.pm
  M Bio/Tools/EUtilities/Link/UrlLink.pm
  M Bio/Tools/EUtilities/Query.pm
  M Bio/Tools/EUtilities/Query/GlobalQuery.pm
  M Bio/Tools/EUtilities/Summary.pm
  M Bio/Tools/EUtilities/Summary/DocSum.pm
  M Bio/Tools/EUtilities/Summary/Item.pm
  M Bio/Tools/EUtilities/Summary/ItemContainerI.pm
  M Bio/Tools/Eponine.pm
  M Bio/Tools/Est2Genome.pm
  M Bio/Tools/Fgenesh.pm
  M Bio/Tools/FootPrinter.pm
  M Bio/Tools/GFF.pm
  M Bio/Tools/Gel.pm
  M Bio/Tools/Geneid.pm
  M Bio/Tools/Genemark.pm
  M Bio/Tools/Genewise.pm
  M Bio/Tools/Genomewise.pm
  M Bio/Tools/Genscan.pm
  M Bio/Tools/Glimmer.pm
  M Bio/Tools/Grail.pm
  M Bio/Tools/GuessSeqFormat.pm
  M Bio/Tools/HMMER/Domain.pm
  M Bio/Tools/HMMER/Results.pm
  M Bio/Tools/HMMER/Set.pm
  M Bio/Tools/Hmmpfam.pm
  M Bio/Tools/IUPAC.pm
  M Bio/Tools/Infernal.pm
  M Bio/Tools/Lucy.pm
  M Bio/Tools/MZEF.pm
  M Bio/Tools/Phylo/Gumby.pm
  M Bio/Tools/Phylo/Molphy.pm
  M Bio/Tools/Phylo/Molphy/Result.pm
  M Bio/Tools/Phylo/PAML.pm
  M Bio/Tools/Phylo/PAML/Codeml.pm
  M Bio/Tools/Phylo/PAML/ModelResult.pm
  M Bio/Tools/Phylo/PAML/Result.pm
  M Bio/Tools/Phylo/Phylip/ProtDist.pm
  M Bio/Tools/Prediction/Exon.pm
  M Bio/Tools/Prediction/Gene.pm
  M Bio/Tools/Primer/Assessor/Base.pm
  M Bio/Tools/Primer/AssessorI.pm
  M Bio/Tools/Primer/Feature.pm
  M Bio/Tools/Primer/Pair.pm
  M Bio/Tools/Primer3.pm
  M Bio/Tools/Prints.pm
  M Bio/Tools/Profile.pm
  M Bio/Tools/Promoterwise.pm
  M Bio/Tools/Protparam.pm
  M Bio/Tools/Pseudowise.pm
  M Bio/Tools/QRNA.pm
  M Bio/Tools/RNAMotif.pm
  M Bio/Tools/RandomDistFunctions.pm
  M Bio/Tools/RepeatMasker.pm
  M Bio/Tools/Run/GenericParameters.pm
  M Bio/Tools/Run/ParametersI.pm
  M Bio/Tools/Run/RemoteBlast.pm
  M Bio/Tools/Run/StandAloneBlast.pm
  M Bio/Tools/Run/StandAloneNCBIBlast.pm
  M Bio/Tools/Run/StandAloneWUBlast.pm
  M Bio/Tools/Run/WrapperBase.pm
  M Bio/Tools/Run/WrapperBase/CommandExts.pm
  A Bio/Tools/Run/hmmer3.pm
  M Bio/Tools/Seg.pm
  M Bio/Tools/SeqPattern.pm
  M Bio/Tools/SeqStats.pm
  M Bio/Tools/SeqWords.pm
  M Bio/Tools/SiRNA.pm
  M Bio/Tools/Sigcleave.pm
  M Bio/Tools/Signalp.pm
  M Bio/Tools/Signalp/ExtendedSignalp.pm
  M Bio/Tools/Sim4/Exon.pm
  M Bio/Tools/Sim4/Results.pm
  M Bio/Tools/Spidey/Exon.pm
  M Bio/Tools/Spidey/Results.pm
  M Bio/Tools/TargetP.pm
  M Bio/Tools/Tmhmm.pm
  M Bio/Tools/dpAlign.pm
  M Bio/Tools/ipcress.pm
  M Bio/Tools/isPcr.pm
  M Bio/Tools/pICalculator.pm
  M Bio/Tools/pSW.pm
  M Bio/Tools/tRNAscanSE.pm
  M Bio/Tree/AlleleNode.pm
  M Bio/Tree/Compatible.pm
  M Bio/Tree/DistanceFactory.pm
  M Bio/Tree/Draw/Cladogram.pm
  M Bio/Tree/Node.pm
  M Bio/Tree/NodeI.pm
  M Bio/Tree/NodeNHX.pm
  M Bio/Tree/RandomFactory.pm
  M Bio/Tree/Statistics.pm
  M Bio/Tree/Tree.pm
  M Bio/Tree/TreeFunctionsI.pm
  M Bio/Tree/TreeI.pm
  M Bio/TreeIO.pm
  A Bio/TreeIO/NewickParser.pm
  M Bio/TreeIO/TreeEventBuilder.pm
  M Bio/TreeIO/cluster.pm
  M Bio/TreeIO/lintree.pm
  M Bio/TreeIO/newick.pm
  M Bio/TreeIO/nexml.pm
  M Bio/TreeIO/nexus.pm
  M Bio/TreeIO/nhx.pm
  M Bio/TreeIO/pag.pm
  M Bio/TreeIO/tabtree.pm
  M Bio/UpdateableSeqI.pm
  M Bio/Variation/AAChange.pm
  M Bio/Variation/AAReverseMutate.pm
  M Bio/Variation/Allele.pm
  M Bio/Variation/DNAMutation.pm
  M Bio/Variation/IO.pm
  M Bio/Variation/IO/flat.pm
  M Bio/Variation/IO/xml.pm
  M Bio/Variation/RNAChange.pm
  M Bio/Variation/SNP.pm
  M Bio/Variation/SeqDiff.pm
  M Bio/Variation/VariantI.pm
  M Bio/WebAgent.pm
  M Build.PL
  M Changes
  M DEPRECATED
  M MANIFEST
  M examples/align/aligntutorial.pl
  M examples/align/clustalw.pl
  M examples/align/simplealign.pl
  M examples/biblio/biblio-eutils-example.pl
  M examples/biblio/biblio-soap-example.pl
  M examples/contributed/nmrpdb_parse.pl
  M examples/contributed/prosite2perl.pl
  M examples/db/dbfetch
  M examples/liveseq/change_gene.pl
  M examples/make_primers.pl
  M examples/popgen/parse_calc_stats.pl
  M examples/rev_and_trans.pl
  M examples/root/exceptions1.pl
  M examples/root/exceptions2.pl
  M examples/root/exceptions3.pl
  M examples/root/exceptions4.pl
  M examples/searchio/custom_writer.pl
  M examples/searchio/hitwriter.pl
  M examples/searchio/hspwriter.pl
  M examples/searchio/htmlwriter.pl
  M examples/searchio/psiblast_features.pl
  M examples/searchio/psiblast_iterations.pl
  M examples/searchio/rawwriter.pl
  M examples/searchio/resultwriter.pl
  M examples/tools/extract_genes.pl
  M examples/tools/psw.pl
  M examples/tools/reverse-translate.pl
  M examples/tools/run_primer3.pl
  M examples/tools/seq_pattern.pl
  M examples/tools/standaloneblast.pl
  M maintenance/authors.pl
  A maintenance/big_split/file_classification.csv
  A maintenance/big_split/rbuels_notes.txt
  M maintenance/cvs2cl_by_file.pl
  M maintenance/modules.pl
  M maintenance/pod.pl
  M maintenance/symlink_script.pl
  M maintenance/version.pl
  M scripts/Bio-DB-GFF/bulk_load_gff.PLS
  M scripts/Bio-DB-GFF/fast_load_gff.PLS
  M scripts/Bio-DB-GFF/genbank2gff.PLS
  M scripts/Bio-DB-GFF/genbank2gff3.PLS
  M scripts/Bio-DB-GFF/generate_histogram.PLS
  M scripts/Bio-DB-GFF/load_gff.PLS
  M scripts/Bio-DB-GFF/process_sgd.PLS
  M scripts/Bio-SeqFeature-Store/bp_seqfeature_delete.PLS
  M scripts/Bio-SeqFeature-Store/bp_seqfeature_gff3.PLS
  M scripts/Bio-SeqFeature-Store/bp_seqfeature_load.PLS
  M scripts/DB/biofetch_genbank_proxy.PLS
  M scripts/DB/biogetseq.PLS
  M scripts/DB/flanks.PLS
  M scripts/biblio/biblio.PLS
  A scripts/bioperl_netinstall.pl
  M scripts/das/das_server.pl
  M scripts/index/bp_seqret.PLS
  M scripts/popgen/composite_LD.PLS
  M scripts/popgen/heterogeneity_test.PLS
  M scripts/searchio/filter_search.PLS
  M scripts/searchio/parse_hmmsearch.PLS
  M scripts/seq/extract_feature_seq.PLS
  M scripts/seq/make_mrna_protein.PLS
  M scripts/seq/seqconvert.PLS
  M scripts/seq/seqretsplit.PLS
  M scripts/seq/split_seq.PLS
  M scripts/seq/translate_seq.PLS
  M scripts/seq/unflatten_seq.PLS
  M scripts/seqstats/aacomp.PLS
  M scripts/seqstats/chaos_plot.PLS
  M scripts/seqstats/gccalc.PLS
  M scripts/seqstats/oligo_count.PLS
  M scripts/taxa/classify_hits_kingdom.PLS
  M scripts/utilities/bp_mrtrans.PLS
  M scripts/utilities/bp_nrdb.PLS
  M scripts/utilities/download_query_genbank.PLS
  M scripts/utilities/mask_by_search.PLS
  M scripts/utilities/pairwise_kaks.PLS
  M scripts/utilities/remote_blast.PLS
  M scripts/utilities/revtrans-motif.PLS
  M scripts/utilities/search2BSML.PLS
  M scripts/utilities/search2alnblocks.PLS
  M scripts/utilities/search2gff.PLS
  M scripts/utilities/search2tribe.PLS
  M t/Align/Graphics.t
  M t/AlignIO/phylip.t
  M t/AlignIO/selex.t
  M t/Annotation/Annotation.t
  R t/Assembly/Assembly.t
  M t/Assembly/ContigSpectrum.t
  A t/Assembly/IO/bowtie.t
  A t/Assembly/IO/sam.t
  A t/Assembly/core.t
  M t/LocalDB/DBFasta.t
  M t/LocalDB/SeqFeature.t
  R t/Microarray/Tools/ReseqChip.t
  M t/Ontology/IO/interpro.t
  M t/Ontology/IO/obo.t
  M t/Ontology/Ontology.t
  M t/Ontology/OntologyEngine.t
  M t/RemoteDB/EMBL.t
  M t/RemoteDB/EUtilities.t
  M t/RemoteDB/GenPept.t
  M t/RemoteDB/SwissProt.t
  M t/RemoteDB/Taxonomy.t
  M t/Root/RootI.t
  M t/Root/RootIO.t
  A t/SearchIO/Writer/TextWriter.t
  A t/SearchIO/axt.t
  M t/SearchIO/hmmer.t
  M t/Seq/Seq.t
  A t/SeqFeature/Clone.t
  M t/SeqFeature/SeqFeature.t
  M t/SeqIO/Handler.t
  A t/SeqIO/SeqIO.t
  M t/SeqIO/embl.t
  M t/SeqIO/genbank.t
  A t/SeqIO/mbsout.t
  A t/SeqIO/msout.t
  M t/SeqIO/seqxml.t
  M t/SeqIO/swiss.t
  M t/Species.t
  M t/Tools/Run/StandAloneBlast.t
  M t/Tree/Node.t
  M t/Tree/TreeIO.t
  M t/Tree/TreeIO/newick.t
  M t/Tree/TreeIO/nhx.t
  A t/data/PX1CG.gb
  R t/data/ReseqChip_ExampleData.fasta
  R t/data/ReseqChip_ParamsNcall.csv
  R t/data/ReseqChip_RefSeq.fasta
  R t/data/ReseqChip_mtDNA_design_annotation_file_FINAL.xls
  M t/data/assembly_with_singlets.ace
  A t/data/biorecipe.nhx
  M t/data/dbfa/1.fa
  A t/data/ex1.nucl.nhx
  A t/data/hmmscan.out
  A t/data/hmmscan_multi_domain.out
  A t/data/hmmscan_sec_struct.out
  A t/data/hmmsearch3.out
  A t/data/interpro.xml
  A t/data/interpro_relationship.xml
  A t/data/interpro_sample.xml
  A t/data/mbsout/mbsout_infile1
  A t/data/mbsout/mbsout_infile2
  A t/data/mbsout/mbsout_infile3
  A t/data/msout_infile1
  A t/data/msout_infile1.gz
  A t/data/msout_infile2
  A t/data/msout_infile2.gz
  A t/data/nhx-bacteria.nhx
  M t/data/seqxml.xml
  A t/data/singlet_w_CT.ace
  A t/data/sp_subset.obo
  A t/data/test_data.axt
  M t/data/testaln.selex
  A t/data/tol-2010-02-18.nhx
  A t/data/wellcome_tol.nhx
  M t/lib/Array/Compare.pm

Log Message:
-----------
Merge branch 'master' of git://github.com/bioperl/bioperl-live


Commit: ac84449033e94df2d699641a4d071467cd8497ba
    https://github.com/bioperl/bioperl-live/commit/ac84449033e94df2d699641a4d071467cd8497ba
Author: Johan Viklund <johan.viklund at gmail.com>
Date:   2011-01-26 (Wed, 26 Jan 2011)

Changed paths:
  M Bio/SeqIO/swiss.pm
  M t/SeqIO/swiss.t

Log Message:
-----------
[Bio::SeqIO::swiss] Fixed bug where write_seq() were generating non-standard swiss and added tests for this


Commit: a8d4ecc091edf0fbb7b29593c72801bb3192ead6
    https://github.com/bioperl/bioperl-live/commit/a8d4ecc091edf0fbb7b29593c72801bb3192ead6
Author: Florent Angly <florent.angly at gmail.com>
Date:   2011-01-28 (Fri, 28 Jan 2011)

Changed paths:
  M Bio/DB/SeqFeature/Store.pm

Log Message:
-----------
Checking that features passed for deletions have a primary_id


Commit: 6acb6d2ff622a648c5ee9658d99abc2c21d6f8f9
    https://github.com/bioperl/bioperl-live/commit/6acb6d2ff622a648c5ee9658d99abc2c21d6f8f9
Author: Florent Angly <florent.angly at gmail.com>
Date:   2011-01-28 (Fri, 28 Jan 2011)

Changed paths:
  M Bio/Root/RootI.pm
  M t/Root/RootI.t

Log Message:
-----------
Bugfix: for non-implemented methods, multiple-argument form of throw() is used only if the object is Bio::Root::Root


Commit: 9fc947327f94a04c27c70f9219e159aa92690ff6
    https://github.com/bioperl/bioperl-live/commit/9fc947327f94a04c27c70f9219e159aa92690ff6
Author: Florent Angly <florent.angly at gmail.com>
Date:   2011-01-28 (Fri, 28 Jan 2011)

Changed paths:
  M Bio/DB/SeqFeature/Store/berkeleydb3.pm

Log Message:
-----------
Documentation typo fix


Commit: 03b728011520fd8c8254b82571b7bc45df5471e9
    https://github.com/bioperl/bioperl-live/commit/03b728011520fd8c8254b82571b7bc45df5471e9
Author: Florent Angly <florent.angly at gmail.com>
Date:   2011-01-28 (Fri, 28 Jan 2011)

Changed paths:
  M Bio/DB/SeqFeature/Store/memory.pm

Log Message:
-----------
Documentation typo fix


Commit: 7c5169623be590f7151bbff35451513ff0ee3577
    https://github.com/bioperl/bioperl-live/commit/7c5169623be590f7151bbff35451513ff0ee3577
Author: Florent Angly <florent.angly at gmail.com>
Date:   2011-01-28 (Fri, 28 Jan 2011)

Changed paths:
  M Bio/DB/SeqFeature/Store/memory.pm

Log Message:
-----------
Documentation typo fix


Commit: 5fa0b5f59773a693d8305bb93a45ee6d886fab99
    https://github.com/bioperl/bioperl-live/commit/5fa0b5f59773a693d8305bb93a45ee6d886fab99
Author: Florent Angly <florent.angly at gmail.com>
Date:   2011-01-28 (Fri, 28 Jan 2011)

Changed paths:
  M Bio/DB/SeqFeature/Store/bdb.pm

Log Message:
-----------
POD fix


Commit: f8fced50c8cedda321cb07503b8979f221aef5a2
    https://github.com/bioperl/bioperl-live/commit/f8fced50c8cedda321cb07503b8979f221aef5a2
Author: Florent Angly <florent.angly at gmail.com>
Date:   2011-01-28 (Fri, 28 Jan 2011)

Changed paths:
  M Bio/DB/SeqFeature/Store.pm

Log Message:
-----------
POD doc improvements


Commit: 6f65223ef5aabc3ceaa815d3cb71982f81ae6b30
    https://github.com/bioperl/bioperl-live/commit/6f65223ef5aabc3ceaa815d3cb71982f81ae6b30
Author: Florent Angly <florent.angly at gmail.com>
Date:   2011-01-28 (Fri, 28 Jan 2011)

Changed paths:
  M Bio/DB/SeqFeature/Store.pm
  M Bio/DB/SeqFeature/Store/memory.pm
  M t/LocalDB/SeqFeature.t

Log Message:
-----------
Implementation of a delete feature method for Bio::DB::SeqFeature::Store::memory and various module improvements


Commit: dc327ca28e62ecfab52b4ccb76f47b3dc4c00dc4
    https://github.com/bioperl/bioperl-live/commit/dc327ca28e62ecfab52b4ccb76f47b3dc4c00dc4
Author: Florent Angly <florent.angly at gmail.com>
Date:   2011-01-29 (Sat, 29 Jan 2011)

Changed paths:
  M Bio/DB/SeqFeature/Store.pm
  M t/LocalDB/SeqFeature.t

Log Message:
-----------
Added method alias add_features() for Bio::SeqFeature::CollectionI compliance


Commit: 194ea70931c51d146c61b8641af6b3e192d1ba9a
    https://github.com/bioperl/bioperl-live/commit/194ea70931c51d146c61b8641af6b3e192d1ba9a
Author: Florent Angly <florent.angly at gmail.com>
Date:   2011-01-29 (Sat, 29 Jan 2011)

Changed paths:
  M Bio/DB/SeqFeature/Store.pm
  M t/LocalDB/SeqFeature.t

Log Message:
-----------
Fix: add_features() needs an arrayref, unlike store()


Commit: b92a9c62cee0edbcff7cd90fad56a1ba1efc51d7
    https://github.com/bioperl/bioperl-live/commit/b92a9c62cee0edbcff7cd90fad56a1ba1efc51d7
Author: Florent Angly <florent.angly at gmail.com>
Date:   2011-01-29 (Sat, 29 Jan 2011)

Changed paths:
  M Bio/Assembly/Contig.pm

Log Message:
-----------
Beginning of the implementation of Bio::DB::SeqFeature::Store for contig features


Commit: 8a13d0f753098044ef721fbe81dfb857672fe174
    https://github.com/bioperl/bioperl-live/commit/8a13d0f753098044ef721fbe81dfb857672fe174
Author: Florent Angly <florent.angly at gmail.com>
Date:   2011-01-29 (Sat, 29 Jan 2011)

Changed paths:
  M Bio/DB/SeqFeature/Store.pm
  M t/Assembly/core.t

Log Message:
-----------
Better compatibility with Bio::SeqFeature::Collection


Commit: 5eebf13b8668f9c914a31aaddbb74b3940b94322
    https://github.com/bioperl/bioperl-live/commit/5eebf13b8668f9c914a31aaddbb74b3940b94322
Author: Florent Angly <florent.angly at gmail.com>
Date:   2011-01-29 (Sat, 29 Jan 2011)

Changed paths:
  M Bio/DB/SeqFeature/Store/memory.pm
  M t/LocalDB/SeqFeature.t

Log Message:
-----------
Bug fix for lookup by type in Bio::DB::SeqFeature::Store::memory


Commit: 078a67c6650667f9cd9536eb9c85076eacfe1ba1
    https://github.com/bioperl/bioperl-live/commit/078a67c6650667f9cd9536eb9c85076eacfe1ba1
Author: Florent Angly <florent.angly at gmail.com>
Date:   2011-01-29 (Sat, 29 Jan 2011)

Changed paths:
  M Bio/Assembly/Contig.pm
  M Bio/Assembly/IO/ace.pm
  M Bio/Assembly/IO/tigr.pm
  M Bio/Assembly/Tools/ContigSpectrum.pm

Log Message:
-----------
Most grep() calls to retrieve features replaced by the more efficient get_features_by_type() command


Commit: 0d04f232638604e55b67a370cd17cd779da4ebf3
    https://github.com/bioperl/bioperl-live/commit/0d04f232638604e55b67a370cd17cd779da4ebf3
Author: Florent Angly <florent.angly at gmail.com>
Date:   2011-01-30 (Sun, 30 Jan 2011)

Changed paths:
  M Bio/Assembly/Contig.pm
  M Bio/Assembly/IO/ace.pm

Log Message:
-----------
Tests


Commit: b3d6899c4d6a97ae34d435c63d3e8c323122693a
    https://github.com/bioperl/bioperl-live/commit/b3d6899c4d6a97ae34d435c63d3e8c323122693a
Author: Florent Angly <florent.angly at gmail.com>
Date:   2011-01-30 (Sun, 30 Jan 2011)

Changed paths:
  M Bio/DB/SeqFeature/Store/memory.pm
  M t/LocalDB/SeqFeature.t

Log Message:
-----------
Bugfix: primary_tag containing a ':' were not handled properly by Bio::DB::SeqFeature::Store::memory


Commit: 2eb770291ab23657db9981bb41df0dfd2086d049
    https://github.com/bioperl/bioperl-live/commit/2eb770291ab23657db9981bb41df0dfd2086d049
Author: Florent Angly <florent.angly at gmail.com>
Date:   2011-01-30 (Sun, 30 Jan 2011)

Changed paths:
  M Bio/Assembly/Contig.pm
  M Bio/Assembly/IO/ace.pm
  M t/Assembly/core.t

Log Message:
-----------
Misc housekeeping


Commit: 33e6dd2006136689182aeee72acba28e8f33875e
    https://github.com/bioperl/bioperl-live/commit/33e6dd2006136689182aeee72acba28e8f33875e
Author: Florent Angly <florent.angly at gmail.com>
Date:   2011-01-30 (Sun, 30 Jan 2011)

Changed paths:
  M Bio/Assembly/Contig.pm

Log Message:
-----------
Misc housekeeping


Commit: 90345b8b9ff52cb0186a74a23e8414868b1b2b2b
    https://github.com/bioperl/bioperl-live/commit/90345b8b9ff52cb0186a74a23e8414868b1b2b2b
Author: Florent Angly <florent.angly at gmail.com>
Date:   2011-01-30 (Sun, 30 Jan 2011)

Changed paths:
  M Bio/Assembly/IO/ace.pm

Log Message:
-----------
Is it possible to use $contig->get_seq_feat_by_tag?


Commit: 40069eddd4300602b86ce3873f281b66309e9234
    https://github.com/bioperl/bioperl-live/commit/40069eddd4300602b86ce3873f281b66309e9234
Author: Chris Fields <cjfields at bioperl.org>
Date:   2011-01-30 (Sun, 30 Jan 2011)

Changed paths:
  M Bio/SeqFeature/Collection.pm

Log Message:
-----------
RT#47704: recursively remove code refs for any SeqFeatureI


Commit: aeb590651d970f781c9ecfebd2dd875447fffe2e
    https://github.com/bioperl/bioperl-live/commit/aeb590651d970f781c9ecfebd2dd875447fffe2e
Author: Florent Angly <florent.angly at gmail.com>
Date:   2011-01-30 (Sun, 30 Jan 2011)

Changed paths:
  M t/Assembly/core.t

Log Message:
-----------
Test migration


Commit: 0a144ddece102902ee6fe93c47bf22cfe9df870b
    https://github.com/bioperl/bioperl-live/commit/0a144ddece102902ee6fe93c47bf22cfe9df870b
Author: Florent Angly <florent.angly at gmail.com>
Date:   2011-01-30 (Sun, 30 Jan 2011)

Changed paths:
  M Bio/DB/SeqFeature/Store/memory.pm
  M t/LocalDB/SeqFeature.t

Log Message:
-----------
Minor change and test update


Commit: 9fe84346cdac3665be5e6334c69f41d36a7e2c1f
    https://github.com/bioperl/bioperl-live/commit/9fe84346cdac3665be5e6334c69f41d36a7e2c1f
Author: Florent Angly <florent.angly at gmail.com>
Date:   2011-01-31 (Mon, 31 Jan 2011)

Changed paths:
  M Bio/DB/SeqFeature/Store/memory.pm

Log Message:
-----------
Avoid undef value


Commit: b1c1c6a866d5b30057d893291668dff8136c03ea
    https://github.com/bioperl/bioperl-live/commit/b1c1c6a866d5b30057d893291668dff8136c03ea
Author: Chris Fields <cjfields at bioperl.org>
Date:   2011-01-31 (Mon, 31 Jan 2011)

Changed paths:
  M Bio/SearchIO/blastxml.pm

Log Message:
-----------
[bug RT#54590] add some docs on the -blasttype parameter


Commit: aea9ea9eb36ad64ebc9751d58557744708ed20cb
    https://github.com/bioperl/bioperl-live/commit/aea9ea9eb36ad64ebc9751d58557744708ed20cb
Author: Chris Fields <cjfields at bioperl.org>
Date:   2011-01-31 (Mon, 31 Jan 2011)

Changed paths:
  M Bio/DB/SeqFeature/Store.pm

Log Message:
-----------
[bug RT#58492] small synopsis fix, update->store


Commit: ff6997e78098d6b6b175b08e398ac346be594960
    https://github.com/bioperl/bioperl-live/commit/ff6997e78098d6b6b175b08e398ac346be594960
Author: Chris Fields <cjfields at bioperl.org>
Date:   2011-01-31 (Mon, 31 Jan 2011)

Changed paths:
  M Build.PL

Log Message:
-----------
squash minor warning


Commit: b45e2d33984cf283b846d7c146ec9e0e9ebae67f
    https://github.com/bioperl/bioperl-live/commit/b45e2d33984cf283b846d7c146ec9e0e9ebae67f
Author: Chris Fields <cjfields at bioperl.org>
Date:   2011-01-31 (Mon, 31 Jan 2011)

Changed paths:
  M Bio/Index/Fastq.pm

Log Message:
-----------
[bug 3165] quick fix for fastq indexing, this parser indexes lines starting with @, which could spell trouble down the road


Commit: 0d979f357b8ec089a05eed56c32c68c7039de741
    https://github.com/bioperl/bioperl-live/commit/0d979f357b8ec089a05eed56c32c68c7039de741
Author: Chris Fields <cjfields at bioperl.org>
Date:   2011-01-31 (Mon, 31 Jan 2011)

Changed paths:
  M t/RemoteDB/SeqVersion.t

Log Message:
-----------
future-proof test


Commit: cd418e38de6dab9a4e0dcbea79c6d3cb158c1f08
    https://github.com/bioperl/bioperl-live/commit/cd418e38de6dab9a4e0dcbea79c6d3cb158c1f08
Author: Chris Fields <cjfields at bioperl.org>
Date:   2011-01-31 (Mon, 31 Jan 2011)

Changed paths:
  M Bio/SeqIO.pm

Log Message:
-----------
can have a -string option as well


Commit: 6fffd64dbe689bba604089aee83732670e8780d4
    https://github.com/bioperl/bioperl-live/commit/6fffd64dbe689bba604089aee83732670e8780d4
Author: Chris Fields <cjfields at bioperl.org>
Date:   2011-01-31 (Mon, 31 Jan 2011)

Changed paths:
  M t/Seq/Seq.t

Log Message:
-----------
correct test count


Commit: c67722c41a4281dc57f07aca32f08ca23cd58122
    https://github.com/bioperl/bioperl-live/commit/c67722c41a4281dc57f07aca32f08ca23cd58122
Author: Chris Fields <cjfields at bioperl.org>
Date:   2011-01-31 (Mon, 31 Jan 2011)

Changed paths:
  R t/SeqIO.t
  M t/SeqIO/SeqIO.t

Log Message:
-----------
consolidate tests, fix exception string


Commit: a92f6aa2ee8d9eb81b6a6ee8edd69093ed31f586
    https://github.com/bioperl/bioperl-live/commit/a92f6aa2ee8d9eb81b6a6ee8edd69093ed31f586
Author: Chris Fields <cjfields at bioperl.org>
Date:   2011-01-31 (Mon, 31 Jan 2011)

Changed paths:
  M t/SeqTools/CodonTable.t

Log Message:
-----------
translate() changes


Commit: 8358e42e7925e60adc97005753121310ebc7a77e
    https://github.com/bioperl/bioperl-live/commit/8358e42e7925e60adc97005753121310ebc7a77e
Author: Florent Angly <florent.angly at gmail.com>
Date:   2011-01-31 (Mon, 31 Jan 2011)

Changed paths:
  M Bio/DB/SeqFeature/Store/memory.pm
  M t/LocalDB/SeqFeature.t

Log Message:
-----------
Bug fix for Bio::DB::SeaFeature::Store::memory() -> quotemeta some strings to avoid interpolation in regular expressions


Commit: 0ffc03f77aae82a1b69b07072ed9487e77fa3f00
    https://github.com/bioperl/bioperl-live/commit/0ffc03f77aae82a1b69b07072ed9487e77fa3f00
Author: Florent Angly <florent.angly at gmail.com>
Date:   2011-02-06 (Sun, 06 Feb 2011)

Changed paths:
  M Bio/DB/SeqFeature/Store/memory.pm
  M t/LocalDB/SeqFeature.t

Log Message:
-----------
Changed the internals of Bio::DB::SeqFeatures::Store::memory to make lookup of a feature by type efficient


Commit: 37b4ce5dd7e6887c7128e00e9e2d89b765f45de7
    https://github.com/bioperl/bioperl-live/commit/37b4ce5dd7e6887c7128e00e9e2d89b765f45de7
Author: Florent Angly <florent.angly at gmail.com>
Date:   2011-02-06 (Sun, 06 Feb 2011)

Changed paths:
  M Bio/DB/SeqFeature/Store/memory.pm

Log Message:
-----------
Small Bio::DB::SeqFeature::Store::memory bugfix


Commit: fdc27467ef6cf0888ba6a947a97d49482171c8c7
    https://github.com/bioperl/bioperl-live/commit/fdc27467ef6cf0888ba6a947a97d49482171c8c7
Author: Florent Angly <florent.angly at gmail.com>
Date:   2011-02-06 (Sun, 06 Feb 2011)

Changed paths:
  M Bio/Assembly/Contig.pm
  M Bio/Assembly/IO/ace.pm
  M Bio/Assembly/IO/maq.pm
  M Bio/Assembly/IO/phrap.pm
  M Bio/Assembly/IO/tigr.pm
  M t/Assembly/core.t

Log Message:
-----------
Migration of assembly features from primary_tag to primary_tag and source_tag


Commit: 8bd382a01f0b2cee395e45078c5e0d9a93446b3a
    https://github.com/bioperl/bioperl-live/commit/8bd382a01f0b2cee395e45078c5e0d9a93446b3a
Author: Jonathan "Duke" Leto <jonathan at leto.net>
Date:   2011-02-10 (Thu, 10 Feb 2011)

Changed paths:
  M Bio/Tools/Run/StandAloneBlast.pm
  M Bio/Tools/Run/StandAloneNCBIBlast.pm
  M t/Tools/Run/StandAloneBlast.t

Log Message:
-----------
Add warnings to some StandAloneBlast files


Commit: ef24026216a4aec517f682e7dbacd3e6220ef5b3
    https://github.com/bioperl/bioperl-live/commit/ef24026216a4aec517f682e7dbacd3e6220ef5b3
Author: Chris Fields <cjfields at bioperl.org>
Date:   2011-02-14 (Mon, 14 Feb 2011)

Changed paths:
  M Bio/SeqIO/fastq.pm

Log Message:
-----------
checked each line for definedness, not falseness


Commit: 368ff0c26821d4313aef2b37c6620e103b5505bb
    https://github.com/bioperl/bioperl-live/commit/368ff0c26821d4313aef2b37c6620e103b5505bb
Author: Chris Fields <cjfields at bioperl.org>
Date:   2011-02-14 (Mon, 14 Feb 2011)

Changed paths:
  M Bio/Tools/Run/StandAloneBlast.pm
  M Bio/Tools/Run/StandAloneNCBIBlast.pm
  M t/Tools/Run/StandAloneBlast.t

Log Message:
-----------
Merge branch 'master' of github.com:bioperl/bioperl-live


Commit: 683d884061cd9498ba28bc1f407c8795f94e21c0
    https://github.com/bioperl/bioperl-live/commit/683d884061cd9498ba28bc1f407c8795f94e21c0
Author: Chris Fields <cjfields at bioperl.org>
Date:   2011-02-23 (Wed, 23 Feb 2011)

Changed paths:
  M Bio/Range.pm

Log Message:
-----------
actually have an error message


Commit: 78b7667172d11e17c25d2f13b09d283f3dc2ad69
    https://github.com/bioperl/bioperl-live/commit/78b7667172d11e17c25d2f13b09d283f3dc2ad69
Author: DaveMessina <online at davemessina.com>
Date:   2011-02-24 (Thu, 24 Feb 2011)

Changed paths:
  M Bio/SeqIO/seqxml.pm
  M t/SeqIO/seqxml.t
  M t/data/seqxml.xml

Log Message:
-----------
fixing erroneous fiddly XML namespace blargle.


Commit: a11a54afe4e10a582828ca55d5a75423ac5ac6b9
    https://github.com/bioperl/bioperl-live/commit/a11a54afe4e10a582828ca55d5a75423ac5ac6b9
Author: DaveMessina <online at davemessina.com>
Date:   2011-02-24 (Thu, 24 Feb 2011)

Changed paths:
  M Bio/Range.pm

Log Message:
-----------
Merge branch 'master' of github.com:bioperl/bioperl-live


Commit: 987eca5b4ed9152d2be0d8b1e2a2777144f3562f
    https://github.com/bioperl/bioperl-live/commit/987eca5b4ed9152d2be0d8b1e2a2777144f3562f
Author: Robert Buels <rmb32 at cornell.edu>
Date:   2011-02-24 (Thu, 24 Feb 2011)

Changed paths:
  M Bio/SeqFeature/Generic.pm
  M Bio/SeqFeatureI.pm
  M t/SeqFeature/SeqFeature.t

Log Message:
-----------
add phase attr to Bio::SeqFeatureI, to match Bio::SeqFeature::Lite


Commit: 40ce36c974f06885bec615d58a6532ce6a2da92a
    https://github.com/bioperl/bioperl-live/commit/40ce36c974f06885bec615d58a6532ce6a2da92a
Author: Robert Buels <rmb32 at cornell.edu>
Date:   2011-02-24 (Thu, 24 Feb 2011)

Changed paths:
  M t/SeqFeature/SeqFeature.t

Log Message:
-----------
add a couple more tests for new phase accessor


Commit: d07f441f4a79043845ebe92805aac8946541be96
    https://github.com/bioperl/bioperl-live/commit/d07f441f4a79043845ebe92805aac8946541be96
Author: Florent Angly <florent.angly at gmail.com>
Date:   2011-02-24 (Thu, 24 Feb 2011)

Changed paths:
  M Bio/DB/SeqFeature/Store.pm
  M Bio/Index/Fastq.pm
  M Bio/Range.pm
  M Bio/SearchIO/blastxml.pm
  M Bio/SeqFeature/Collection.pm
  M Bio/SeqFeature/Generic.pm
  M Bio/SeqFeatureI.pm
  M Bio/SeqIO.pm
  M Bio/SeqIO/fastq.pm
  M Bio/SeqIO/seqxml.pm
  M Bio/SeqIO/swiss.pm
  M Bio/Tools/Run/StandAloneBlast.pm
  M Bio/Tools/Run/StandAloneNCBIBlast.pm
  M Build.PL
  M t/RemoteDB/SeqVersion.t
  M t/Seq/Seq.t
  M t/SeqFeature/SeqFeature.t
  R t/SeqIO.t
  M t/SeqIO/SeqIO.t
  M t/SeqIO/seqxml.t
  M t/SeqIO/swiss.t
  M t/SeqTools/CodonTable.t
  M t/Tools/Run/StandAloneBlast.t
  M t/data/seqxml.xml

Log Message:
-----------
Merge branch 'master' of github.com:bioperl/bioperl-live


Commit: 959a713c2709144ef36696478c4d7912fe205ae0
    https://github.com/bioperl/bioperl-live/commit/959a713c2709144ef36696478c4d7912fe205ae0
Author: Chris Fields <cjfields at bioperl.org>
Date:   2011-02-26 (Sat, 26 Feb 2011)

Changed paths:
  M Bio/SeqFeature/Lite.pm

Log Message:
-----------
-tag and -attribute are synonyms with SeqFeatureI


Commit: 444aa404cd947daab0593958eb006bfd72602e84
    https://github.com/bioperl/bioperl-live/commit/444aa404cd947daab0593958eb006bfd72602e84
Author: Florent Angly <florent.angly at gmail.com>
Date:   2011-02-28 (Mon, 28 Feb 2011)

Changed paths:
  M Bio/SeqFeature/Lite.pm

Log Message:
-----------
Merge branch 'master' of github.com:bioperl/bioperl-live


Commit: f4d9ccfe155081501d02e783629df08a869c2f31
    https://github.com/bioperl/bioperl-live/commit/f4d9ccfe155081501d02e783629df08a869c2f31
Author: Florent Angly <florent.angly at gmail.com>
Date:   2011-02-28 (Mon, 28 Feb 2011)

Changed paths:
  M Bio/PrimarySeq.pm
  M t/Seq/PrimarySeq.t

Log Message:
-----------
Improved detection of protein sequences in Bio::PrimarySeq::_guess_alphabet


Commit: 1c8616f55815c8ea278e25680703081ea16fcd79
    https://github.com/bioperl/bioperl-live/commit/1c8616f55815c8ea278e25680703081ea16fcd79
Author: Florent Angly <florent.angly at gmail.com>
Date:   2011-02-28 (Mon, 28 Feb 2011)

Changed paths:
  M Bio/PrimarySeq.pm
  M t/Seq/PrimarySeq.t
  M t/data/sbay_c127.fas

Log Message:
-----------
Bio::PrimarySeq:_guess_alphabet is now IUPAC-compliant and does not count X as a valid DNA letter


Commit: ffc02d931c4ca85d9585f179f05a78fa1c7015d9
    https://github.com/bioperl/bioperl-live/commit/ffc02d931c4ca85d9585f179f05a78fa1c7015d9
Author: Florent Angly <florent.angly at gmail.com>
Date:   2011-03-02 (Wed, 02 Mar 2011)

Changed paths:
  M t/Seq/Seq.t

Log Message:
-----------
Updated number of tests


Commit: b12fadaec1c0b5825ccee35ac7075f019862d738
    https://github.com/bioperl/bioperl-live/commit/b12fadaec1c0b5825ccee35ac7075f019862d738
Author: Florent Angly <florent.angly at gmail.com>
Date:   2011-03-02 (Wed, 02 Mar 2011)

Changed paths:
  M t/Assembly/core.t

Log Message:
-----------
Little test fix


Commit: 3613bd4ded163d2618d5de03c6ae0106c736f3e2
    https://github.com/bioperl/bioperl-live/commit/3613bd4ded163d2618d5de03c6ae0106c736f3e2
Author: Florent Angly <florent.angly at gmail.com>
Date:   2011-03-02 (Wed, 02 Mar 2011)

Changed paths:
  M Bio/DB/SeqFeature/Store.pm

Log Message:
-----------
POD typo


Commit: 77707175b75fdac6756d93c665492b2335c8e30c
    https://github.com/bioperl/bioperl-live/commit/77707175b75fdac6756d93c665492b2335c8e30c
Author: Florent Angly <florent.angly at gmail.com>
Date:   2011-03-02 (Wed, 02 Mar 2011)

Changed paths:
  M Bio/Assembly/Contig.pm
  M Bio/Assembly/IO/ace.pm
  M Bio/Assembly/IO/maq.pm
  M Bio/Assembly/IO/tigr.pm
  M t/Assembly/core.t

Log Message:
-----------
Continued migration to Bio::DB::SeqFeature::Store::memory and removal of inefficient grep() statements


Commit: ec549e966e1f99b7d93a325ceadee0bcb34bdcc9
    https://github.com/bioperl/bioperl-live/commit/ec549e966e1f99b7d93a325ceadee0bcb34bdcc9
Author: Florent Angly <florent.angly at gmail.com>
Date:   2011-03-02 (Wed, 02 Mar 2011)

Changed paths:
  M Bio/DB/SeqFeature/Store/memory.pm

Log Message:
-----------
Automatically generated primary_id when calling Bio::DB::SeqFeature::Store::memory::add_SeqFeature()


Commit: c17c98a9e17a414d89aec81a0d8dd418af26ab9e
    https://github.com/bioperl/bioperl-live/commit/c17c98a9e17a414d89aec81a0d8dd418af26ab9e
Author: Florent Angly <florent.angly at gmail.com>
Date:   2011-03-02 (Wed, 02 Mar 2011)

Changed paths:
  M Bio/DB/SeqFeature/Store.pm

Log Message:
-----------
POD typo fix


Commit: e614d211113465a3f44b4647e1feecebe057cc65
    https://github.com/bioperl/bioperl-live/commit/e614d211113465a3f44b4647e1feecebe057cc65
Author: Christopher Bottoms <molecules at cpan.org>
Date:   2011-03-03 (Thu, 03 Mar 2011)

Changed paths:
  M Bio/AlignIO/stockholm.pm

Log Message:
-----------
Replaced 'phylip' with 'stockholm' in documentation for constructor.


Commit: 1ff8ddc1608f25182d8007af3f4561ea72414acf
    https://github.com/bioperl/bioperl-live/commit/1ff8ddc1608f25182d8007af3f4561ea72414acf
Author: Florent Angly <florent.angly at gmail.com>
Date:   2011-03-03 (Thu, 03 Mar 2011)

Changed paths:
  M Bio/DB/SeqFeature/Store.pm

Log Message:
-----------
POD typo fix


Commit: 810538f2b29ad83adbc0b43c2cba2daf87925a5d
    https://github.com/bioperl/bioperl-live/commit/810538f2b29ad83adbc0b43c2cba2daf87925a5d
Author: Florent Angly <florent.angly at gmail.com>
Date:   2011-03-03 (Thu, 03 Mar 2011)

Changed paths:
  M Bio/DB/SeqFeature/Store.pm

Log Message:
-----------
POD doc clarification


Commit: a17a4f2483c330dcebf62dc563cbd3ded57dcda0
    https://github.com/bioperl/bioperl-live/commit/a17a4f2483c330dcebf62dc563cbd3ded57dcda0
Author: Florent Angly <florent.angly at gmail.com>
Date:   2011-03-03 (Thu, 03 Mar 2011)

Changed paths:
  M Bio/DB/SeqFeature/Store.pm

Log Message:
-----------
Sanity checks in store()
POD clarifications


Commit: fbe77b4e92ebb417d429690442329270cad774e8
    https://github.com/bioperl/bioperl-live/commit/fbe77b4e92ebb417d429690442329270cad774e8
Author: Florent Angly <florent.angly at gmail.com>
Date:   2011-03-03 (Thu, 03 Mar 2011)

Changed paths:
  M Bio/DB/SeqFeature/Store.pm

Log Message:
-----------
POD typo fix


Commit: 5c03c0cdabe9324a10855c198ebc173819e847ea
    https://github.com/bioperl/bioperl-live/commit/5c03c0cdabe9324a10855c198ebc173819e847ea
Author: Florent Angly <florent.angly at gmail.com>
Date:   2011-03-03 (Thu, 03 Mar 2011)

Changed paths:
  M Bio/DB/SeqFeature/Store/memory.pm

Log Message:
-----------
Added test cases for add_SeqFeature and fetch_SeqFeatures


Commit: e0376da23b5d29d6a9a16efb5a792aaeb1b8cdd1
    https://github.com/bioperl/bioperl-live/commit/e0376da23b5d29d6a9a16efb5a792aaeb1b8cdd1
Author: Chris Fields <cjfields at bioperl.org>
Date:   2011-03-04 (Fri, 04 Mar 2011)

Changed paths:
  M Bio/Restriction/Analysis.pm

Log Message:
-----------
fix for bad condition check, via Elia Stupka


Commit: 6a79bde97793b80c96ca108d4aa15ac74b42c537
    https://github.com/bioperl/bioperl-live/commit/6a79bde97793b80c96ca108d4aa15ac74b42c537
Author: Chris Fields <cjfields at bioperl.org>
Date:   2011-03-04 (Fri, 04 Mar 2011)

Changed paths:
  M Bio/Restriction/Analysis.pm
  M t/Restriction/Analysis.t

Log Message:
-----------
add tests and a few other fixes to account for cut matches at beginning


Commit: b243657c2535b72506b52c9976723f1cfbaa66e3
    https://github.com/bioperl/bioperl-live/commit/b243657c2535b72506b52c9976723f1cfbaa66e3
Author: Florent Angly <florent.angly at gmail.com>
Date:   2011-03-04 (Fri, 04 Mar 2011)

Changed paths:
  M Bio/DB/SeqFeature/Store.pm

Log Message:
-----------
Minor clarifications


Commit: 47d40eb698b9ba65c1602524a0ca2b9745541b38
    https://github.com/bioperl/bioperl-live/commit/47d40eb698b9ba65c1602524a0ca2b9745541b38
Author: Florent Angly <florent.angly at gmail.com>
Date:   2011-03-04 (Fri, 04 Mar 2011)

Changed paths:
  M Bio/DB/SeqFeature/Store/memory.pm
  M t/LocalDB/SeqFeature.t

Log Message:
-----------
Changed fetch_seqfeatures() so that it uses direct lookup instead of grep()
Added test cases for adding and retrieving subfeatures


Commit: 8eef131ebd4b7b14d9997b503f4e90bb46a990fd
    https://github.com/bioperl/bioperl-live/commit/8eef131ebd4b7b14d9997b503f4e90bb46a990fd
Author: Florent Angly <florent.angly at gmail.com>
Date:   2011-03-04 (Fri, 04 Mar 2011)

Changed paths:
  M Bio/DB/SeqFeature/Store/memory.pm
  M t/LocalDB/SeqFeature.t

Log Message:
-----------
Little fix for fetch_SeqFeature and more tests


Commit: a2e6ea56015df8264b536ded1e06d2313f8df84d
    https://github.com/bioperl/bioperl-live/commit/a2e6ea56015df8264b536ded1e06d2313f8df84d
Author: Florent Angly <florent.angly at gmail.com>
Date:   2011-03-04 (Fri, 04 Mar 2011)

Changed paths:
  M t/LocalDB/SeqFeature.t

Log Message:
-----------
Little fix for fetch_SeqFeature and more tests


Commit: fef99a49b4feb022a5bb6a4a2243ac3c093ebe24
    https://github.com/bioperl/bioperl-live/commit/fef99a49b4feb022a5bb6a4a2243ac3c093ebe24
Author: Florent Angly <florent.angly at gmail.com>
Date:   2011-03-04 (Fri, 04 Mar 2011)

Changed paths:
  M Bio/Assembly/Contig.pm
  M Bio/Assembly/IO/ace.pm
  M Bio/Assembly/IO/maq.pm
  M Bio/Assembly/IO/sam.pm
  M Bio/Assembly/IO/tigr.pm
  M t/Assembly/core.t

Log Message:
-----------
Migrated SeqFeatures in assemblies to Bio::DB::SeqFeature::Store::memory
This finishes the migration of all Bio::Assembly code to Bio::DB::SeqFeature::Store facility!
As a consequence, assembly-related operations are much faster, have a computation time proportional to the number of reads in contigs (instead of exponential), and are thus more adapted to process high-throughput assemblies


Commit: b77433064ca70873f5330a59366cb70e1ab5c191
    https://github.com/bioperl/bioperl-live/commit/b77433064ca70873f5330a59366cb70e1ab5c191
Author: Florent Angly <florent.angly at gmail.com>
Date:   2011-03-04 (Fri, 04 Mar 2011)

Changed paths:
  M Bio/Assembly/Contig.pm
  M Bio/Assembly/IO/ace.pm
  M Bio/Assembly/IO/maq.pm
  M Bio/Assembly/IO/phrap.pm
  M Bio/Assembly/IO/sam.pm
  M Bio/Assembly/IO/tigr.pm
  M Bio/Assembly/Tools/ContigSpectrum.pm
  M Bio/DB/SeqFeature/Store.pm
  M Bio/DB/SeqFeature/Store/memory.pm
  M t/Assembly/core.t
  M t/LocalDB/SeqFeature.t

Log Message:
-----------
Merge branch 'assembly_seqfeature_store'


Commit: 7407a262fe98bf241ec932bfbcb2aced432abe93
    https://github.com/bioperl/bioperl-live/commit/7407a262fe98bf241ec932bfbcb2aced432abe93
Author: Florent Angly <florent.angly at gmail.com>
Date:   2011-03-04 (Fri, 04 Mar 2011)

Changed paths:
  M Bio/AlignIO/stockholm.pm
  M Bio/Restriction/Analysis.pm
  M t/Restriction/Analysis.t

Log Message:
-----------
Merge branch 'master' of github.com:bioperl/bioperl-live


Commit: 86dbcaea9a33ed298252d02c0bfb4bc267020069
    https://github.com/bioperl/bioperl-live/commit/86dbcaea9a33ed298252d02c0bfb4bc267020069
Author: Robert Buels <rmb32 at cornell.edu>
Date:   2011-03-08 (Tue, 08 Mar 2011)

Changed paths:
  M Bio/Tools/RepeatMasker.pm

Log Message:
-----------
localize $_ if you are going to modify it in a lib function


Commit: 2de6af141cc1867beb7e78e806550c0d642b66bc
    https://github.com/bioperl/bioperl-live/commit/2de6af141cc1867beb7e78e806550c0d642b66bc
Author: Robert Buels <rmb32 at cornell.edu>
Date:   2011-03-08 (Tue, 08 Mar 2011)

Changed paths:
  M Bio/Tools/RepeatMasker.pm
  M t/Tools/RepeatMasker.t
  M t/data/repeatmasker.fa.out

Log Message:
-----------
bugfix to Bio::Tools::RepeatMasker, reverse matches were wrong


Commit: 532dcfc730e0e77e902cf1a15d6c61fe6e074a07
    https://github.com/bioperl/bioperl-live/commit/532dcfc730e0e77e902cf1a15d6c61fe6e074a07
Author: Lincoln Stein <lincoln.stein at gmail.com>
Date:   2011-03-09 (Wed, 09 Mar 2011)

Changed paths:
  M Bio/DB/SeqFeature/Store.pm
  M Bio/DB/SeqFeature/Store/DBI/Pg.pm
  M Bio/DB/SeqFeature/Store/DBI/SQLite.pm
  M Bio/DB/SeqFeature/Store/DBI/mysql.pm
  M Bio/DB/SeqFeature/Store/GFF3Loader.pm
  M Bio/DB/SeqFeature/Store/berkeleydb.pm
  M Bio/DB/SeqFeature/Store/berkeleydb3.pm
  M t/LocalDB/SeqFeature.t

Log Message:
-----------
Worked around changes in memory adapter without abolishing the features
that Florent added to the memory adapter. Please revisit the decision to
allow arbitrary primary_ids in features that can be stored to the database.


Commit: 455ed6fe184610a8b75dc49b831ff012f67a15c3
    https://github.com/bioperl/bioperl-live/commit/455ed6fe184610a8b75dc49b831ff012f67a15c3
Author: Lincoln Stein <lincoln.stein at gmail.com>
Date:   2011-03-09 (Wed, 09 Mar 2011)

Changed paths:
  M Bio/DB/SeqFeature/Store.pm
  M Bio/DB/SeqFeature/Store/berkeleydb3.pm
  M t/LocalDB/SeqFeature.t

Log Message:
-----------
improved performance of SQLite and mysql adaptors when loading many DNA sequences; fixed berkeleydb3 adaptor to return correct result from get_features_by_type() when called with a primary_tag and no source


Commit: 1c2cf247fd97c4d536054b2136282af69644e4e8
    https://github.com/bioperl/bioperl-live/commit/1c2cf247fd97c4d536054b2136282af69644e4e8
Author: Lincoln Stein <lincoln.stein at gmail.com>
Date:   2011-03-09 (Wed, 09 Mar 2011)

Changed paths:
  M Bio/DB/SeqFeature/Store/DBI/Pg.pm
  M Bio/DB/SeqFeature/Store/DBI/SQLite.pm
  M Bio/DB/SeqFeature/Store/DBI/mysql.pm
  M Bio/DB/SeqFeature/Store/berkeleydb.pm
  M Bio/DB/SeqFeature/Store/berkeleydb3.pm
  M t/LocalDB/SeqFeature.t

Log Message:
-----------
fixed up berkeleydb adaptor to pass new set of regression tests


Commit: 8267ea5ee96ec13d6ca8937d3232ac02597879d1
    https://github.com/bioperl/bioperl-live/commit/8267ea5ee96ec13d6ca8937d3232ac02597879d1
Author: Chris Fields <cjfields at bioperl.org>
Date:   2011-03-10 (Thu, 10 Mar 2011)

Changed paths:
  M README

Log Message:
-----------
not using subversion


Commit: 82f72dae0ed990a98bf31fa25a1c16cb0d06f7d6
    https://github.com/bioperl/bioperl-live/commit/82f72dae0ed990a98bf31fa25a1c16cb0d06f7d6
Author: Chris Fields <cjfields at bioperl.org>
Date:   2011-03-10 (Thu, 10 Mar 2011)

Changed paths:
  M README

Log Message:
-----------
test redmine


Commit: 8c585196d891576fabc0cab0974767379d545705
    https://github.com/bioperl/bioperl-live/commit/8c585196d891576fabc0cab0974767379d545705
Author: Chris Fields <cjfields at bioperl.org>
Date:   2011-03-10 (Thu, 10 Mar 2011)

Changed paths:
  M README

Log Message:
-----------
test redmine post-receive hook


Commit: 7602f98a567babb7245c0e97ef6258ace36a42ba
    https://github.com/bioperl/bioperl-live/commit/7602f98a567babb7245c0e97ef6258ace36a42ba
Author: Chris Fields <cjfields at bioperl.org>
Date:   2011-03-11 (Fri, 11 Mar 2011)

Changed paths:
  M Bio/Assembly/IO/ace.pm

Log Message:
-----------
please use a source tag


Commit: 5f45546e7e42906f9c3f49bb3d72fa3ff566235f
    https://github.com/bioperl/bioperl-live/commit/5f45546e7e42906f9c3f49bb3d72fa3ff566235f
Author: Chris Fields <cjfields at bioperl.org>
Date:   2011-03-11 (Fri, 11 Mar 2011)

Changed paths:
  M Bio/Assembly/IO/ace.pm

Log Message:
-----------
only add tags if the value is defined


Commit: a81e18faf95e929e0c7d57ede113a83cd1f6f09b
    https://github.com/bioperl/bioperl-live/commit/a81e18faf95e929e0c7d57ede113a83cd1f6f09b
Author: Chris Fields <cjfields at bioperl.org>
Date:   2011-03-12 (Sat, 12 Mar 2011)

Changed paths:
  M Bio/DB/SeqFeature/Store/memory.pm

Log Message:
-----------
squash warning


Commit: a8c109d76ddc51ccfec8b03d70e2a35424d09229
    https://github.com/bioperl/bioperl-live/commit/a8c109d76ddc51ccfec8b03d70e2a35424d09229
Author: Chris Fields <cjfields at bioperl.org>
Date:   2011-03-12 (Sat, 12 Mar 2011)

Changed paths:
  M Bio/Assembly/IO/sam.pm

Log Message:
-----------
commented out accidentally uncommented code


Commit: 9cda9c335637966dac7f486f0ad2faa60fa68d46
    https://github.com/bioperl/bioperl-live/commit/9cda9c335637966dac7f486f0ad2faa60fa68d46
Author: Chris Fields <cjfields at bioperl.org>
Date:   2011-03-12 (Sat, 12 Mar 2011)

Changed paths:
  M Bio/Assembly/IO/ace.pm

Log Message:
-----------
use 'ace' as the default source, make sure that undef values are not used (this should probably be cleaned up, should we have possibly undef source here?)


Commit: 597808b1003804610bbaa90afcc5d82be3c45293
    https://github.com/bioperl/bioperl-live/commit/597808b1003804610bbaa90afcc5d82be3c45293
Author: Chris Fields <cjfields at bioperl.org>
Date:   2011-03-12 (Sat, 12 Mar 2011)

Changed paths:
  M Bio/SeqIO/seqxml.pm

Log Message:
-----------
squash XML::Writer issue, still get a warning though


Commit: e9d49ea570cda06065da4cb413fc1842ff5fc58c
    https://github.com/bioperl/bioperl-live/commit/e9d49ea570cda06065da4cb413fc1842ff5fc58c
Author: Chris Fields <cjfields at bioperl.org>
Date:   2011-03-12 (Sat, 12 Mar 2011)

Changed paths:
  M t/Root/RootI.t

Log Message:
-----------
use Test::Exception methods exported from Bio::Root::Test


Commit: 8e493d2227be6d0fd492fe063279daf9e46828a3
    https://github.com/bioperl/bioperl-live/commit/8e493d2227be6d0fd492fe063279daf9e46828a3
Author: Chris Fields <cjfields at bioperl.org>
Date:   2011-03-12 (Sat, 12 Mar 2011)

Changed paths:
  M Bio/DB/SeqFeature/Store/memory.pm

Log Message:
-----------
a bit more perl 5.12 warning squashing


Commit: e4e70a6c1ea50e041cca87ace08275c117237141
    https://github.com/bioperl/bioperl-live/commit/e4e70a6c1ea50e041cca87ace08275c117237141
Author: Chris Fields <cjfields at bioperl.org>
Date:   2011-03-12 (Sat, 12 Mar 2011)

Changed paths:
  M Bio/Root/Root.pm
  M t/Root/RootI.t

Log Message:
-----------
make exception messages match whether one has Error.pm installed or not


Commit: 4b69c5e4333990821def4a3a5db2b8645da71b6c
    https://github.com/bioperl/bioperl-live/commit/4b69c5e4333990821def4a3a5db2b8645da71b6c
Author: Chris Fields <cjfields at bioperl.org>
Date:   2011-03-12 (Sat, 12 Mar 2011)

Changed paths:
  M t/Map/Map.t

Log Message:
-----------
volatile data broke test


Commit: 7fabbfde1a0569af13df4318b9dd91dbc8959bb6
    https://github.com/bioperl/bioperl-live/commit/7fabbfde1a0569af13df4318b9dd91dbc8959bb6
Author: Chris Fields <cjfields at bioperl.org>
Date:   2011-03-12 (Sat, 12 Mar 2011)

Changed paths:
  M t/RemoteDB/CUTG.t

Log Message:
-----------
fix CUTG skipped test count


Commit: e7c4300db759ddf4420a40c8a7e00ab61a32c74c
    https://github.com/bioperl/bioperl-live/commit/e7c4300db759ddf4420a40c8a7e00ab61a32c74c
Author: Chris Fields <cjfields at bioperl.org>
Date:   2011-03-12 (Sat, 12 Mar 2011)

Changed paths:
  M Bio/Tree/TreeFunctionsI.pm

Log Message:
-----------
reduce warning message, was overly verbose and gave warnings when nodes didn't have a defined name


Compare: https://github.com/bioperl/bioperl-live/compare/53a0361...e7c4300

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