← Back to branch summary

~ubuntu-branches/ubuntu/saucy/biojava3-live/saucy

~ubuntu-branches/ubuntu/saucy/biojava3-live/saucy

Viewing all changes in revision 5.

Committer: Package Import Robot
Author(s): Ilya Barygin
Date: 2012-12-29 22:52:51 UTC
mfrom: (2.1.3 raring-proposed)
Revision ID: package-import@ubuntu.com-20121229225251-p1cifiucnlc8kr0x

Disable tests that fail without Internet access.

files added:
.pc/fix_ascii_characters_mapping

.pc/fix_ascii_characters_mapping/biojava3-forester

.pc/fix_ascii_characters_mapping/biojava3-forester/src

.pc/fix_ascii_characters_mapping/biojava3-forester/src/main

.pc/fix_ascii_characters_mapping/biojava3-forester/src/main/java

.pc/fix_ascii_characters_mapping/biojava3-forester/src/main/java/org

.pc/fix_ascii_characters_mapping/biojava3-forester/src/main/java/org/forester

.pc/fix_ascii_characters_mapping/biojava3-forester/src/main/java/org/forester/test

.pc/fix_ascii_characters_mapping/biojava3-forester/src/main/java/org/forester/test/Test.java

biojava3-aa-prop/src/main/assembly

biojava3-aa-prop/src/main/assembly/assembly.xml

biojava3-alignment/src/main/java/demo

biojava3-alignment/src/main/java/demo/CookbookMSA.java

biojava3-alignment/src/main/java/demo/DemoLoadSubstMax.java

biojava3-alignment/src/main/java/demo/TestDNANeedlemanWunsch.java

biojava3-alignment/src/main/java/org/biojava3/alignment/io

biojava3-alignment/src/main/java/org/biojava3/alignment/io/StockholmConsensusAnnotation.java

biojava3-alignment/src/main/java/org/biojava3/alignment/io/StockholmFileAnnotation.java

biojava3-alignment/src/main/java/org/biojava3/alignment/io/StockholmFileParser.java

biojava3-alignment/src/main/java/org/biojava3/alignment/io/StockholmResidueAnnotation.java

biojava3-alignment/src/main/java/org/biojava3/alignment/io/StockholmSequenceAnnotation.java

biojava3-alignment/src/main/java/org/biojava3/alignment/io/StockholmStructure.java

biojava3-alignment/src/test/java/org/biojava3/alignment/io

biojava3-alignment/src/test/java/org/biojava3/alignment/io/TestStockholmParser.java

biojava3-alignment/src/test/resources/longTest(Ankyrin repeat).sto

biojava3-alignment/src/test/resources/piwi.sth.gz

biojava3-alignment/src/test/resources/pkinase.sto

biojava3-alignment/src/test/resources/rrm.sto

biojava3-alignment/src/test/resources/test.sth

biojava3-alignment/src/test/resources/test1.sth

biojava3-forester/src/main/java/.classpath

biojava3-forester/src/main/java/.project

biojava3-forester/src/main/java/build.xml

biojava3-forester/src/main/java/classes

biojava3-forester/src/main/java/classes/org

biojava3-forester/src/main/java/classes/org/forester

biojava3-forester/src/main/java/classes/org/forester/analysis

biojava3-forester/src/main/java/classes/org/forester/application

biojava3-forester/src/main/java/classes/org/forester/archaeopteryx

biojava3-forester/src/main/java/classes/org/forester/archaeopteryx/phylogeny

biojava3-forester/src/main/java/classes/org/forester/archaeopteryx/phylogeny/data

biojava3-forester/src/main/java/classes/org/forester/archaeopteryx/tools

biojava3-forester/src/main/java/classes/org/forester/archaeopteryx/webservices

biojava3-forester/src/main/java/classes/org/forester/datastructures

biojava3-forester/src/main/java/classes/org/forester/development

biojava3-forester/src/main/java/classes/org/forester/evoinference

biojava3-forester/src/main/java/classes/org/forester/evoinference/distance

biojava3-forester/src/main/java/classes/org/forester/evoinference/matrix

biojava3-forester/src/main/java/classes/org/forester/evoinference/matrix/character

biojava3-forester/src/main/java/classes/org/forester/evoinference/matrix/distance

biojava3-forester/src/main/java/classes/org/forester/evoinference/parsimony

biojava3-forester/src/main/java/classes/org/forester/evoinference/tools

biojava3-forester/src/main/java/classes/org/forester/go

biojava3-forester/src/main/java/classes/org/forester/go/etc

biojava3-forester/src/main/java/classes/org/forester/io

biojava3-forester/src/main/java/classes/org/forester/io/parsers

biojava3-forester/src/main/java/classes/org/forester/io/parsers/nexus

biojava3-forester/src/main/java/classes/org/forester/io/parsers/nhx

biojava3-forester/src/main/java/classes/org/forester/io/parsers/phyloxml

biojava3-forester/src/main/java/classes/org/forester/io/parsers/phyloxml/data

biojava3-forester/src/main/java/classes/org/forester/io/parsers/tol

biojava3-forester/src/main/java/classes/org/forester/io/parsers/util

biojava3-forester/src/main/java/classes/org/forester/io/writers

biojava3-forester/src/main/java/classes/org/forester/msa

biojava3-forester/src/main/java/classes/org/forester/pccx

biojava3-forester/src/main/java/classes/org/forester/phylogeny

biojava3-forester/src/main/java/classes/org/forester/phylogeny/data

biojava3-forester/src/main/java/classes/org/forester/phylogeny/factories

biojava3-forester/src/main/java/classes/org/forester/phylogeny/iterators

biojava3-forester/src/main/java/classes/org/forester/protein

biojava3-forester/src/main/java/classes/org/forester/sdi

biojava3-forester/src/main/java/classes/org/forester/sequence

biojava3-forester/src/main/java/classes/org/forester/species

biojava3-forester/src/main/java/classes/org/forester/surfacing

biojava3-forester/src/main/java/classes/org/forester/test

biojava3-forester/src/main/java/classes/org/forester/test/examples

biojava3-forester/src/main/java/classes/org/forester/tools

biojava3-forester/src/main/java/classes/org/forester/util

biojava3-forester/src/main/java/classes/org/forester/ws

biojava3-forester/src/main/java/classes/org/forester/ws/hmmer

biojava3-forester/src/main/java/classes/org/forester/ws/seqdb

biojava3-forester/src/main/java/classes/org/forester/ws/uniprot

biojava3-forester/src/main/java/classes/org/forester/ws/wabi

biojava3-forester/src/main/java/forester-1.005-sources-1.005.jar

biojava3-forester/src/main/java/org/forester/analysis

biojava3-forester/src/main/java/org/forester/analysis/AncestralTaxonomyInference.java

biojava3-forester/src/main/java/org/forester/analysis/AncestralTaxonomyInferenceException.java

biojava3-forester/src/main/java/org/forester/analysis/TaxonomyDataManager.java

biojava3-forester/src/main/java/org/forester/application/gene_tree_preprocess.java

biojava3-forester/src/main/java/org/forester/application/gsdi.java

biojava3-forester/src/main/java/org/forester/application/mcc.java

biojava3-forester/src/main/java/org/forester/application/pfamacc2go.java

biojava3-forester/src/main/java/org/forester/application/pfamacc2pfamid.java

biojava3-forester/src/main/java/org/forester/application/sdi_dir.java

biojava3-forester/src/main/java/org/forester/archaeopteryx/AptxUtil.java

biojava3-forester/src/main/java/org/forester/archaeopteryx/phylogeny/data/RenderableVector.java

biojava3-forester/src/main/java/org/forester/archaeopteryx/tools

biojava3-forester/src/main/java/org/forester/archaeopteryx/tools/AncestralTaxonomyInferrer.java

biojava3-forester/src/main/java/org/forester/archaeopteryx/tools/Blast.java

biojava3-forester/src/main/java/org/forester/archaeopteryx/tools/GoAnnotation.java

biojava3-forester/src/main/java/org/forester/archaeopteryx/tools/ImageLoader.java

biojava3-forester/src/main/java/org/forester/archaeopteryx/tools/InferenceManager.java

biojava3-forester/src/main/java/org/forester/archaeopteryx/tools/PhyloInferenceDialog.java

biojava3-forester/src/main/java/org/forester/archaeopteryx/tools/PhylogeneticInferenceOptions.java

biojava3-forester/src/main/java/org/forester/archaeopteryx/tools/PhylogeneticInferrer.java

biojava3-forester/src/main/java/org/forester/archaeopteryx/tools/ProcessPool.java

biojava3-forester/src/main/java/org/forester/archaeopteryx/tools/ProcessRunning.java

biojava3-forester/src/main/java/org/forester/archaeopteryx/tools/RunnableProcess.java

biojava3-forester/src/main/java/org/forester/archaeopteryx/tools/SequenceDataRetriver.java

biojava3-forester/src/main/java/org/forester/development/AbstractRenderer.java

biojava3-forester/src/main/java/org/forester/development/Hello3d.java

biojava3-forester/src/main/java/org/forester/development/HmmerRest.java

biojava3-forester/src/main/java/org/forester/development/MsaRenderer.java

biojava3-forester/src/main/java/org/forester/development/RandomThing.java

biojava3-forester/src/main/java/org/forester/development/ResidueRenderer.java

biojava3-forester/src/main/java/org/forester/development/Time.java

biojava3-forester/src/main/java/org/forester/development/neTest.java

biojava3-forester/src/main/java/org/forester/evoinference

biojava3-forester/src/main/java/org/forester/evoinference/TestPhylogenyReconstruction.java

biojava3-forester/src/main/java/org/forester/evoinference/distance

biojava3-forester/src/main/java/org/forester/evoinference/distance/NeighborJoining.java

biojava3-forester/src/main/java/org/forester/evoinference/distance/PairwiseDistanceCalculator.java

biojava3-forester/src/main/java/org/forester/evoinference/matrix

biojava3-forester/src/main/java/org/forester/evoinference/matrix/character

biojava3-forester/src/main/java/org/forester/evoinference/matrix/character/BasicCharacterStateMatrix.java

biojava3-forester/src/main/java/org/forester/evoinference/matrix/character/CharacterStateMatrix.java

biojava3-forester/src/main/java/org/forester/evoinference/matrix/character/DiscreteState.java

biojava3-forester/src/main/java/org/forester/evoinference/matrix/distance

biojava3-forester/src/main/java/org/forester/evoinference/matrix/distance/BasicSymmetricalDistanceMatrix.java

biojava3-forester/src/main/java/org/forester/evoinference/matrix/distance/DistanceMatrix.java

biojava3-forester/src/main/java/org/forester/evoinference/parsimony

biojava3-forester/src/main/java/org/forester/evoinference/parsimony/DolloParsimony.java

biojava3-forester/src/main/java/org/forester/evoinference/parsimony/FitchParsimony.java

biojava3-forester/src/main/java/org/forester/evoinference/parsimony/SankoffParsimony.java

biojava3-forester/src/main/java/org/forester/evoinference/tools

biojava3-forester/src/main/java/org/forester/evoinference/tools/BootstrapResampler.java

biojava3-forester/src/main/java/org/forester/io/parsers/FastaParser.java

biojava3-forester/src/main/java/org/forester/io/parsers/GeneralMsaParser.java

biojava3-forester/src/main/java/org/forester/io/parsers/SymmetricalDistanceMatrixParser.java

biojava3-forester/src/main/java/org/forester/io/parsers/phyloxml/data

biojava3-forester/src/main/java/org/forester/io/parsers/phyloxml/data/AccessionParser.java

biojava3-forester/src/main/java/org/forester/io/parsers/phyloxml/data/AnnotationParser.java

biojava3-forester/src/main/java/org/forester/io/parsers/phyloxml/data/BinaryCharactersParser.java

biojava3-forester/src/main/java/org/forester/io/parsers/phyloxml/data/BranchWidthParser.java

biojava3-forester/src/main/java/org/forester/io/parsers/phyloxml/data/ColorParser.java

biojava3-forester/src/main/java/org/forester/io/parsers/phyloxml/data/ConfidenceParser.java

biojava3-forester/src/main/java/org/forester/io/parsers/phyloxml/data/DateParser.java

biojava3-forester/src/main/java/org/forester/io/parsers/phyloxml/data/DistributionParser.java

biojava3-forester/src/main/java/org/forester/io/parsers/phyloxml/data/DomainArchitectureParser.java

biojava3-forester/src/main/java/org/forester/io/parsers/phyloxml/data/EventParser.java

biojava3-forester/src/main/java/org/forester/io/parsers/phyloxml/data/IdentifierParser.java

biojava3-forester/src/main/java/org/forester/io/parsers/phyloxml/data/PhylogenyDataPhyloXmlParser.java

biojava3-forester/src/main/java/org/forester/io/parsers/phyloxml/data/PointParser.java

biojava3-forester/src/main/java/org/forester/io/parsers/phyloxml/data/PolygonParser.java

biojava3-forester/src/main/java/org/forester/io/parsers/phyloxml/data/PropertyParser.java

biojava3-forester/src/main/java/org/forester/io/parsers/phyloxml/data/ProteinDomainParser.java

biojava3-forester/src/main/java/org/forester/io/parsers/phyloxml/data/ReferenceParser.java

biojava3-forester/src/main/java/org/forester/io/parsers/phyloxml/data/SequenceParser.java

biojava3-forester/src/main/java/org/forester/io/parsers/phyloxml/data/SequenceRelationParser.java

biojava3-forester/src/main/java/org/forester/io/parsers/phyloxml/data/TaxonomyParser.java

biojava3-forester/src/main/java/org/forester/io/parsers/phyloxml/data/UriParser.java

biojava3-forester/src/main/java/org/forester/io/parsers/util

biojava3-forester/src/main/java/org/forester/io/parsers/util/ParserUtils.java

biojava3-forester/src/main/java/org/forester/io/parsers/util/PhylogenyParserException.java

biojava3-forester/src/main/java/org/forester/io/writers/SequenceWriter.java

biojava3-forester/src/main/java/org/forester/msa

biojava3-forester/src/main/java/org/forester/msa/BasicMsa.java

biojava3-forester/src/main/java/org/forester/msa/Mafft.java

biojava3-forester/src/main/java/org/forester/msa/MafftOLD.java

biojava3-forester/src/main/java/org/forester/msa/Msa.java

biojava3-forester/src/main/java/org/forester/msa/MsaFormatException.java

biojava3-forester/src/main/java/org/forester/msa/MsaInferrer.java

biojava3-forester/src/main/java/org/forester/msa/MsaMethods.java

biojava3-forester/src/main/java/org/forester/msa/ResampleableMsa.java

biojava3-forester/src/main/java/org/forester/phylogeny/data/MultipleUris.java

biojava3-forester/src/main/java/org/forester/phylogeny/data/NodeVisualization.java

biojava3-forester/src/main/java/org/forester/phylogeny/data/Polygon.java

biojava3-forester/src/main/java/org/forester/protein

biojava3-forester/src/main/java/org/forester/protein/BasicDomain.java

biojava3-forester/src/main/java/org/forester/protein/BasicProtein.java

biojava3-forester/src/main/java/org/forester/protein/BinaryDomainCombination.java

biojava3-forester/src/main/java/org/forester/protein/Domain.java

biojava3-forester/src/main/java/org/forester/protein/DomainId.java

biojava3-forester/src/main/java/org/forester/protein/Protein.java

biojava3-forester/src/main/java/org/forester/protein/ProteinId.java

biojava3-forester/src/main/java/org/forester/sdi/SDIException.java

biojava3-forester/src/main/java/org/forester/sequence

biojava3-forester/src/main/java/org/forester/sequence/BasicSequence.java

biojava3-forester/src/main/java/org/forester/sequence/Sequence.java

biojava3-forester/src/main/java/org/forester/species

biojava3-forester/src/main/java/org/forester/species/BasicSpecies.java

biojava3-forester/src/main/java/org/forester/species/Species.java

biojava3-forester/src/main/java/org/forester/test/examples

biojava3-forester/src/main/java/org/forester/test/examples/Example1.java

biojava3-forester/src/main/java/org/forester/test/examples/Example2.java

biojava3-forester/src/main/java/org/forester/test/examples/Example3.java

biojava3-forester/src/main/java/org/forester/test/examples/Example4.java

biojava3-forester/src/main/java/org/forester/test/examples/Example5.java

biojava3-forester/src/main/java/org/forester/tools/SupportCount.java

biojava3-forester/src/main/java/org/forester/util/CommandProcessBuilder.java

biojava3-forester/src/main/java/org/forester/util/EasyWriter.java

biojava3-forester/src/main/java/org/forester/util/ExternalProgram.java

biojava3-forester/src/main/java/org/forester/util/FailedConditionCheckException.java

biojava3-forester/src/main/java/org/forester/util/IllegalFormatUseException.java

biojava3-forester/src/main/java/org/forester/util/SequenceIdParser.java

biojava3-forester/src/main/java/org/forester/util/SystemCommandExecutor.java

biojava3-forester/src/main/java/org/forester/util/ThreadedStreamHandler.java

biojava3-forester/src/main/java/org/forester/ws

biojava3-forester/src/main/java/org/forester/ws/hmmer

biojava3-forester/src/main/java/org/forester/ws/hmmer/Test.java

biojava3-forester/src/main/java/org/forester/ws/seqdb

biojava3-forester/src/main/java/org/forester/ws/seqdb/DatabaseTools.java

biojava3-forester/src/main/java/org/forester/ws/seqdb/EbiDbEntry.java

biojava3-forester/src/main/java/org/forester/ws/seqdb/SequenceDatabaseEntry.java

biojava3-forester/src/main/java/org/forester/ws/seqdb/SequenceDbWsTools.java

biojava3-forester/src/main/java/org/forester/ws/seqdb/UniProtEntry.java

biojava3-forester/src/main/java/org/forester/ws/seqdb/UniProtTaxonomy.java

biojava3-forester/src/main/java/org/forester/ws/uniprot

biojava3-forester/src/main/java/org/forester/ws/uniprot/DatabaseTools.java

biojava3-forester/src/main/java/org/forester/ws/uniprot/EbiDbEntry.java

biojava3-forester/src/main/java/org/forester/ws/uniprot/SequenceDatabaseEntry.java

biojava3-forester/src/main/java/org/forester/ws/uniprot/SequenceDbWsTools.java

biojava3-forester/src/main/java/org/forester/ws/uniprot/UniProtEntry.java

biojava3-forester/src/main/java/org/forester/ws/uniprot/UniProtTaxonomy.java

biojava3-forester/src/main/java/org/forester/ws/wabi

biojava3-forester/src/main/java/org/forester/ws/wabi/RestUtil.java

biojava3-forester/src/main/java/org/forester/ws/wabi/TxSearch.java

biojava3-forester/src/main/java/org/forester/ws/wabi/WabiTools.java

biojava3-forester/src/main/java/resources

biojava3-forester/src/main/java/resources/NOTICE.txt

biojava3-forester/src/main/java/resources/commons-codec-1.5.jar

biojava3-forester/src/main/java/resources/itextpdf-5.1.0.jar

biojava3-protein-disorder/src/main/java/demo

biojava3-protein-disorder/src/main/java/demo/PredictDisorder.java

biojava3-protein-disorder/src/test/java/org/biojava3/ronn/NonstandardProteinCompoundTest.java

biojava3-structure-gui/src/main/java/demo/DemoShowBiolAssembly.java

biojava3-structure-gui/src/main/java/org/biojava/bio/structure/align/gui/MemoryMonitor.java

biojava3-structure-gui/src/main/java/org/biojava/bio/structure/align/gui/StructureLoaderThread.java

biojava3-structure/src/main/java/demo/DemoBerkeleyScop.java

biojava3-structure/src/main/java/demo/DemoCATH.java

biojava3-structure/src/main/java/org/biojava/bio/structure/cath

biojava3-structure/src/main/java/org/biojava/bio/structure/cath/CathCategory.java

biojava3-structure/src/main/java/org/biojava/bio/structure/cath/CathDatabase.java

biojava3-structure/src/main/java/org/biojava/bio/structure/cath/CathDomain.java

biojava3-structure/src/main/java/org/biojava/bio/structure/cath/CathFragment.java

biojava3-structure/src/main/java/org/biojava/bio/structure/cath/CathInstallation.java

biojava3-structure/src/main/java/org/biojava/bio/structure/cath/CathNode.java

biojava3-structure/src/main/java/org/biojava/bio/structure/cath/CathSegment.java

biojava3-structure/src/main/java/org/biojava/bio/structure/domain/PDBDomainProvider.java

biojava3-structure/src/main/java/org/biojava/bio/structure/io/PDBBioAssemblyParser.java

biojava3-structure/src/main/java/org/biojava/bio/structure/io/mmcif/model/PdbxStructAssembly.java

biojava3-structure/src/main/java/org/biojava/bio/structure/io/mmcif/model/PdbxStructAssemblyGen.java

biojava3-structure/src/main/java/org/biojava/bio/structure/io/mmcif/model/PdbxStructAssemblyGenXMLContainer.java

biojava3-structure/src/main/java/org/biojava/bio/structure/io/mmcif/model/PdbxStructAssemblyXMLContainer.java

biojava3-structure/src/main/java/org/biojava/bio/structure/io/mmcif/model/PdbxStructOperList.java

biojava3-structure/src/main/java/org/biojava/bio/structure/io/mmcif/model/PdbxStructOperListXMLContainer.java

biojava3-structure/src/main/java/org/biojava/bio/structure/quaternary

biojava3-structure/src/main/java/org/biojava/bio/structure/quaternary/BioAssemblyTools.java

biojava3-structure/src/main/java/org/biojava/bio/structure/quaternary/BiologicalAssemblyBuilder.java

biojava3-structure/src/main/java/org/biojava/bio/structure/quaternary/CartesianProduct.java

biojava3-structure/src/main/java/org/biojava/bio/structure/quaternary/ModelTransformationMatrix.java

biojava3-structure/src/main/java/org/biojava/bio/structure/quaternary/OperatorResolver.java

biojava3-structure/src/main/java/org/biojava/bio/structure/quaternary/OrderedPair.java

biojava3-structure/src/main/java/org/biojava/bio/structure/quaternary/io

biojava3-structure/src/main/java/org/biojava/bio/structure/quaternary/io/BioUnitDataProvider.java

biojava3-structure/src/main/java/org/biojava/bio/structure/quaternary/io/BioUnitDataProviderFactory.java

biojava3-structure/src/main/java/org/biojava/bio/structure/quaternary/io/FileBasedPDBBioUnitDataProvider.java

biojava3-structure/src/main/java/org/biojava/bio/structure/quaternary/io/MmCifBiolAssemblyProvider.java

biojava3-structure/src/main/java/org/biojava/bio/structure/quaternary/io/MmCifPDBBiolAssemblyProvider.java

biojava3-structure/src/main/java/org/biojava/bio/structure/quaternary/io/PDBBioUnitDataProvider.java

biojava3-structure/src/main/java/org/biojava/bio/structure/quaternary/io/RawBioUnitDataProvider.java

biojava3-structure/src/main/java/org/biojava/bio/structure/quaternary/io/RemoteBioUnitDataProvider.java

biojava3-structure/src/main/java/org/biojava/bio/structure/quaternary/io/RemoteRawBioUnitDataProvider.java

biojava3-structure/src/main/java/org/biojava/bio/structure/secstruc/BridgeType.java

biojava3-structure/src/main/java/org/biojava/bio/structure/secstruc/Ladder.java

biojava3-structure/src/main/java/org/biojava/bio/structure/secstruc/SecStrucType.java

biojava3-structure/src/main/java/org/biojava3

biojava3-structure/src/main/java/org/biojava3/structure

biojava3-structure/src/main/java/org/biojava3/structure/StructureIO.java

biojava3-structure/src/main/resources/about.properties

biojava3-structure/src/test/java/org/biojava/bio/structure/StructureIOTest.java

biojava3-structure/src/test/java/org/biojava/bio/structure/TestCloning.java

biojava3-structure/src/test/java/org/biojava/bio/structure/cath

biojava3-structure/src/test/java/org/biojava/bio/structure/io/TestHardBioUnits.java

biojava3-structure/src/test/java/org/biojava/bio/structure/io/TestQuaternaryStructureProviders.java

debian/patches/fix_ascii_characters_mapping

integrationtest

integrationtest/pom.xml

integrationtest/src

integrationtest/src/main

integrationtest/src/main/java

integrationtest/src/test

integrationtest/src/test/java

integrationtest/src/test/java/org

integrationtest/src/test/java/org/biojava

integrationtest/src/test/java/org/biojava/bio

integrationtest/src/test/java/org/biojava/bio/structure

integrationtest/src/test/java/org/biojava/bio/structure/HeaderOnlyTest.java

integrationtest/src/test/java/org/biojava/bio/structure/MMcifTest.java

integrationtest/src/test/java/org/biojava/bio/structure/PDBFileParserTest.java

integrationtest/src/test/java/org/biojava/bio/structure/StructurePairAlignerTest.java

integrationtest/src/test/java/org/biojava/bio/structure/StructureTest.java

integrationtest/src/test/java/org/biojava/bio/structure/StructureToolsTest.java

integrationtest/src/test/java/org/biojava/bio/structure/Test1a4w.java

integrationtest/src/test/java/org/biojava/bio/structure/TestSECalignment.java

integrationtest/src/test/java/org/biojava/bio/structure/align

integrationtest/src/test/java/org/biojava/bio/structure/align/FlipAFPChainTest.java

integrationtest/src/test/java/org/biojava/bio/structure/align/ce

integrationtest/src/test/java/org/biojava/bio/structure/align/ce/OptimalCECPMainTest.java

integrationtest/src/test/java/org/biojava/bio/structure/align/fatcat

integrationtest/src/test/java/org/biojava/bio/structure/align/fatcat/AFPChainSerialisationTest.java

integrationtest/src/test/java/org/biojava/bio/structure/align/fatcat/FlipAFPChainTest.java

integrationtest/src/test/java/org/biojava/bio/structure/align/fatcat/MyTestHelper.java

integrationtest/src/test/java/org/biojava/bio/structure/align/fatcat/TestFlexibleRotationMatrices.java

integrationtest/src/test/java/org/biojava/bio/structure/align/fatcat/TestOutputStrings.java

integrationtest/src/test/java/org/biojava/bio/structure/cath

integrationtest/src/test/java/org/biojava/bio/structure/cath/CathTest.java

integrationtest/src/test/java/org/biojava/bio/structure/scop

integrationtest/src/test/java/org/biojava/bio/structure/scop/ScopTest.java

integrationtest/src/test/java/org/biojava/bio/structure/util

integrationtest/src/test/java/org/biojava/bio/structure/util/StringManipulationTestsHelper.java

integrationtest/src/test/java/org/integrationtest

integrationtest/src/test/java/org/integrationtest/AppTest.java

integrationtest/src/test/resources

integrationtest/src/test/resources/1a4w.cif

integrationtest/src/test/resources/1a4w.pdb

integrationtest/src/test/resources/1fdo.cif

integrationtest/src/test/resources/1fdo.pdb

integrationtest/src/test/resources/1j59.cif

integrationtest/src/test/resources/1j59.pdb

integrationtest/src/test/resources/1lnl.pdb

integrationtest/src/test/resources/1tap.pdb

integrationtest/src/test/resources/2kc9.cif

integrationtest/src/test/resources/2kc9.pdb

integrationtest/src/test/resources/5pti.cif

integrationtest/src/test/resources/5pti.pdb

integrationtest/src/test/resources/5pti_old.pdb

integrationtest/src/test/resources/ce_1fdo.A_2iv2.X.out

integrationtest/target

integrationtest/target/failsafe-reports

integrationtest/target/failsafe-reports/failsafe-summary.xml

integrationtest/target/generated-site

integrationtest/target/generated-site/xdoc

integrationtest/target/generated-site/xdoc/statscm

integrationtest/target/generated-test-sources

integrationtest/target/generated-test-sources/test-annotations

integrationtest/target/integrationtest-3.0.5.jar

integrationtest/target/javadoc-bundle-options

integrationtest/target/javadoc-bundle-options/javadoc-options-javadoc-resources.xml

integrationtest/target/maven-archiver

integrationtest/target/maven-archiver/pom.properties

integrationtest/target/site

integrationtest/target/site/css

integrationtest/target/site/css/maven-base.css

integrationtest/target/site/css/maven-theme.css

integrationtest/target/site/css/print.css

integrationtest/target/site/css/site.css

integrationtest/target/site/dependencies.html

integrationtest/target/site/dependency-convergence.html

integrationtest/target/site/dependency-info.html

integrationtest/target/site/dependency-management.html

integrationtest/target/site/distribution-management.html

integrationtest/target/site/images

integrationtest/target/site/images/close.gif

integrationtest/target/site/images/collapsed.gif

integrationtest/target/site/images/expanded.gif

integrationtest/target/site/images/external.png

integrationtest/target/site/images/icon_error_sml.gif

integrationtest/target/site/images/icon_info_sml.gif

integrationtest/target/site/images/icon_success_sml.gif

integrationtest/target/site/images/icon_warning_sml.gif

integrationtest/target/site/images/logos

integrationtest/target/site/images/logos/build-by-maven-black.png

integrationtest/target/site/images/logos/build-by-maven-white.png

integrationtest/target/site/images/logos/maven-feather.png

integrationtest/target/site/images/newwindow.png

integrationtest/target/site/index.html

integrationtest/target/site/integration.html

integrationtest/target/site/issue-tracking.html

integrationtest/target/site/license.html

integrationtest/target/site/mail-lists.html

integrationtest/target/site/plugin-management.html

integrationtest/target/site/plugins.html

integrationtest/target/site/project-info.html

integrationtest/target/site/project-reports.html

integrationtest/target/site/project-summary.html

integrationtest/target/site/source-repository.html

integrationtest/target/site/statscm

integrationtest/target/site/statscm/statscm.html

integrationtest/target/site/team-list.html

integrationtest/target/surefire

integrationtest/target/surefire-reports

integrationtest/target/surefire-reports/TEST-org.biojava.bio.structure.HeaderOnlyTest.xml

integrationtest/target/surefire-reports/TEST-org.biojava.bio.structure.MMcifTest.xml

integrationtest/target/surefire-reports/TEST-org.biojava.bio.structure.PDBFileParserTest.xml

integrationtest/target/surefire-reports/TEST-org.biojava.bio.structure.StructurePairAlignerTest.xml

integrationtest/target/surefire-reports/TEST-org.biojava.bio.structure.StructureTest.xml

integrationtest/target/surefire-reports/TEST-org.biojava.bio.structure.StructureToolsTest.xml

integrationtest/target/surefire-reports/TEST-org.biojava.bio.structure.Test1a4w.xml

integrationtest/target/surefire-reports/TEST-org.biojava.bio.structure.TestSECalignment.xml

integrationtest/target/surefire-reports/TEST-org.biojava.bio.structure.align.FlipAFPChainTest.xml

integrationtest/target/surefire-reports/TEST-org.biojava.bio.structure.align.ce.OptimalCECPMainTest.xml

integrationtest/target/surefire-reports/TEST-org.biojava.bio.structure.align.fatcat.AFPChainSerialisationTest.xml

integrationtest/target/surefire-reports/TEST-org.biojava.bio.structure.align.fatcat.FlipAFPChainTest.xml

integrationtest/target/surefire-reports/TEST-org.biojava.bio.structure.align.fatcat.TestFlexibleRotationMatrices.xml

integrationtest/target/surefire-reports/TEST-org.biojava.bio.structure.align.fatcat.TestOutputStrings.xml

integrationtest/target/surefire-reports/TEST-org.biojava.bio.structure.cath.CathTest.xml

integrationtest/target/surefire-reports/TEST-org.biojava.bio.structure.scop.ScopTest.xml

integrationtest/target/surefire-reports/TEST-org.integrationtest.AppTest.xml

integrationtest/target/surefire-reports/org.biojava.bio.structure.HeaderOnlyTest.txt

integrationtest/target/surefire-reports/org.biojava.bio.structure.MMcifTest.txt

integrationtest/target/surefire-reports/org.biojava.bio.structure.PDBFileParserTest.txt

integrationtest/target/surefire-reports/org.biojava.bio.structure.StructurePairAlignerTest.txt

integrationtest/target/surefire-reports/org.biojava.bio.structure.StructureTest.txt

integrationtest/target/surefire-reports/org.biojava.bio.structure.StructureToolsTest.txt

integrationtest/target/surefire-reports/org.biojava.bio.structure.Test1a4w.txt

integrationtest/target/surefire-reports/org.biojava.bio.structure.TestSECalignment.txt

integrationtest/target/surefire-reports/org.biojava.bio.structure.align.FlipAFPChainTest.txt

integrationtest/target/surefire-reports/org.biojava.bio.structure.align.ce.OptimalCECPMainTest.txt

integrationtest/target/surefire-reports/org.biojava.bio.structure.align.fatcat.AFPChainSerialisationTest.txt

integrationtest/target/surefire-reports/org.biojava.bio.structure.align.fatcat.FlipAFPChainTest.txt

integrationtest/target/surefire-reports/org.biojava.bio.structure.align.fatcat.TestFlexibleRotationMatrices.txt

integrationtest/target/surefire-reports/org.biojava.bio.structure.align.fatcat.TestOutputStrings.txt

integrationtest/target/surefire-reports/org.biojava.bio.structure.cath.CathTest.txt

integrationtest/target/surefire-reports/org.biojava.bio.structure.scop.ScopTest.txt

integrationtest/target/surefire-reports/org.integrationtest.AppTest.txt

integrationtest/target/test-classes

integrationtest/target/test-classes/1a4w.cif

integrationtest/target/test-classes/1a4w.pdb

integrationtest/target/test-classes/1fdo.cif

integrationtest/target/test-classes/1fdo.pdb

integrationtest/target/test-classes/1j59.cif

integrationtest/target/test-classes/1j59.pdb

integrationtest/target/test-classes/1lnl.pdb

integrationtest/target/test-classes/1tap.pdb

integrationtest/target/test-classes/2kc9.cif

integrationtest/target/test-classes/2kc9.pdb

integrationtest/target/test-classes/5pti.cif

integrationtest/target/test-classes/5pti.pdb

integrationtest/target/test-classes/5pti_old.pdb

integrationtest/target/test-classes/ce_1fdo.A_2iv2.X.out

integrationtest/target/test-classes/org

integrationtest/target/test-classes/org/biojava

integrationtest/target/test-classes/org/biojava/bio

integrationtest/target/test-classes/org/biojava/bio/structure

integrationtest/target/test-classes/org/biojava/bio/structure/HeaderOnlyTest.class

integrationtest/target/test-classes/org/biojava/bio/structure/MMcifTest.class

integrationtest/target/test-classes/org/biojava/bio/structure/PDBFileParserTest.class

integrationtest/target/test-classes/org/biojava/bio/structure/StructurePairAlignerTest.class

integrationtest/target/test-classes/org/biojava/bio/structure/StructureTest.class

integrationtest/target/test-classes/org/biojava/bio/structure/StructureToolsTest.class

integrationtest/target/test-classes/org/biojava/bio/structure/Test1a4w.class

integrationtest/target/test-classes/org/biojava/bio/structure/TestSECalignment.class

integrationtest/target/test-classes/org/biojava/bio/structure/align

integrationtest/target/test-classes/org/biojava/bio/structure/align/FlipAFPChainTest.class

integrationtest/target/test-classes/org/biojava/bio/structure/align/ce

integrationtest/target/test-classes/org/biojava/bio/structure/align/ce/OptimalCECPMainTest.class

integrationtest/target/test-classes/org/biojava/bio/structure/align/fatcat

integrationtest/target/test-classes/org/biojava/bio/structure/align/fatcat/AFPChainSerialisationTest.class

integrationtest/target/test-classes/org/biojava/bio/structure/align/fatcat/FlipAFPChainTest.class

integrationtest/target/test-classes/org/biojava/bio/structure/align/fatcat/MyTestHelper.class

integrationtest/target/test-classes/org/biojava/bio/structure/align/fatcat/TestFlexibleRotationMatrices.class

integrationtest/target/test-classes/org/biojava/bio/structure/align/fatcat/TestOutputStrings.class

integrationtest/target/test-classes/org/biojava/bio/structure/cath

integrationtest/target/test-classes/org/biojava/bio/structure/cath/CathTest.class

integrationtest/target/test-classes/org/biojava/bio/structure/scop

integrationtest/target/test-classes/org/biojava/bio/structure/scop/ScopTest.class

integrationtest/target/test-classes/org/biojava/bio/structure/util

integrationtest/target/test-classes/org/biojava/bio/structure/util/StringManipulationTestsHelper.class

integrationtest/target/test-classes/org/integrationtest

integrationtest/target/test-classes/org/integrationtest/AppTest.class

protein-comparison-tool

protein-comparison-tool/pom.xml

protein-comparison-tool/src

protein-comparison-tool/src/main

protein-comparison-tool/src/main/assembly

protein-comparison-tool/src/main/assembly/LICENSE

protein-comparison-tool/src/main/assembly/assembly.xml

protein-comparison-tool/src/main/assembly/db.out

protein-comparison-tool/src/main/assembly/example.lst

protein-comparison-tool/src/main/assembly/runCE.sh

protein-comparison-tool/src/main/assembly/runFATCAT.sh

protein-comparison-tool/src/main/assembly/startFarmJob.sh

protein-comparison-tool/target

protein-comparison-tool/target/archive-tmp

protein-comparison-tool/target/generated-site

protein-comparison-tool/target/generated-site/xdoc

protein-comparison-tool/target/generated-site/xdoc/statscm

protein-comparison-tool/target/javadoc-bundle-options

protein-comparison-tool/target/javadoc-bundle-options/javadoc-options-javadoc-resources.xml

protein-comparison-tool/target/maven-archiver

protein-comparison-tool/target/maven-archiver/pom.properties

protein-comparison-tool/target/protein-comparison-tool-3.0.5-bundle.tar.gz

protein-comparison-tool/target/protein-comparison-tool-3.0.5.jar

protein-comparison-tool/target/site

protein-comparison-tool/target/site/css

protein-comparison-tool/target/site/css/maven-base.css

protein-comparison-tool/target/site/css/maven-theme.css

protein-comparison-tool/target/site/css/print.css

protein-comparison-tool/target/site/css/site.css

protein-comparison-tool/target/site/dependencies.html

protein-comparison-tool/target/site/dependency-convergence.html

protein-comparison-tool/target/site/dependency-info.html

protein-comparison-tool/target/site/dependency-management.html

protein-comparison-tool/target/site/distribution-management.html

protein-comparison-tool/target/site/images

protein-comparison-tool/target/site/images/close.gif

protein-comparison-tool/target/site/images/collapsed.gif

protein-comparison-tool/target/site/images/expanded.gif

protein-comparison-tool/target/site/images/external.png

protein-comparison-tool/target/site/images/icon_error_sml.gif

protein-comparison-tool/target/site/images/icon_info_sml.gif

protein-comparison-tool/target/site/images/icon_success_sml.gif

protein-comparison-tool/target/site/images/icon_warning_sml.gif

protein-comparison-tool/target/site/images/logos

protein-comparison-tool/target/site/images/logos/build-by-maven-black.png

protein-comparison-tool/target/site/images/logos/build-by-maven-white.png

protein-comparison-tool/target/site/images/logos/maven-feather.png

protein-comparison-tool/target/site/images/newwindow.png

protein-comparison-tool/target/site/index.html

protein-comparison-tool/target/site/integration.html

protein-comparison-tool/target/site/issue-tracking.html

protein-comparison-tool/target/site/license.html

protein-comparison-tool/target/site/mail-lists.html

protein-comparison-tool/target/site/plugin-management.html

protein-comparison-tool/target/site/plugins.html

protein-comparison-tool/target/site/project-info.html

protein-comparison-tool/target/site/project-reports.html

protein-comparison-tool/target/site/project-summary.html

protein-comparison-tool/target/site/source-repository.html

protein-comparison-tool/target/site/statscm

protein-comparison-tool/target/site/statscm/statscm.html

protein-comparison-tool/target/site/team-list.html

protein-comparison-tool/target/surefire

files removed:
.pc/fix_ascii_character_issue

.pc/fix_ascii_character_issue/biojava3-forester

.pc/fix_ascii_character_issue/biojava3-forester/src

.pc/fix_ascii_character_issue/biojava3-forester/src/main

.pc/fix_ascii_character_issue/biojava3-forester/src/main/java

.pc/fix_ascii_character_issue/biojava3-forester/src/main/java/org

.pc/fix_ascii_character_issue/biojava3-forester/src/main/java/org/forester

.pc/fix_ascii_character_issue/biojava3-forester/src/main/java/org/forester/archaeopteryx

.pc/fix_ascii_character_issue/biojava3-forester/src/main/java/org/forester/archaeopteryx/Blast.java

biojava3-forester/src/main/java/META-INF

biojava3-forester/src/main/java/META-INF/MANIFEST.MF

biojava3-forester/src/main/java/forester-0.955-sources.jar

biojava3-forester/src/main/java/org/forester/application/CheckTreeAccuracy.java

biojava3-forester/src/main/java/org/forester/application/get_distances.java

biojava3-forester/src/main/java/org/forester/application/perfume.java

biojava3-forester/src/main/java/org/forester/application/sdi.java

biojava3-forester/src/main/java/org/forester/application/shin.java

biojava3-forester/src/main/java/org/forester/application/surfacing_old.java

biojava3-forester/src/main/java/org/forester/application/ta.java

biojava3-forester/src/main/java/org/forester/archaeopteryx/Blast.java

biojava3-forester/src/main/java/org/forester/archaeopteryx/PdfWriter.java

biojava3-forester/src/main/java/org/forester/archaeopteryx/Util.java

biojava3-forester/src/main/java/org/forester/development/AminoAcid.java

biojava3-forester/src/main/java/org/forester/development/AminoAcidSequence.java

biojava3-forester/src/main/java/org/forester/development/BasicMsa.java

biojava3-forester/src/main/java/org/forester/development/Factory.java

biojava3-forester/src/main/java/org/forester/development/Msa.java

biojava3-forester/src/main/java/org/forester/development/MsaFactory.java

biojava3-forester/src/main/java/org/forester/development/Sequence.java

biojava3-forester/src/main/java/org/forester/development/SimpleMutableMsa.java

biojava3-forester/src/main/java/org/forester/development/StreamBasedMsaFactory.java

biojava3-forester/src/main/java/org/forester/development/SupportCount.java

biojava3-forester/src/main/java/org/forester/io/parsers/ParserUtils.java

biojava3-forester/src/main/java/org/forester/io/parsers/PhylogenyParserException.java

biojava3-forester/src/main/java/org/forester/io/parsers/phyloxml/phylogenydata

biojava3-forester/src/main/java/org/forester/io/parsers/phyloxml/phylogenydata/AccessionParser.java

biojava3-forester/src/main/java/org/forester/io/parsers/phyloxml/phylogenydata/AnnotationParser.java

biojava3-forester/src/main/java/org/forester/io/parsers/phyloxml/phylogenydata/BinaryCharactersParser.java

biojava3-forester/src/main/java/org/forester/io/parsers/phyloxml/phylogenydata/BranchWidthParser.java

biojava3-forester/src/main/java/org/forester/io/parsers/phyloxml/phylogenydata/ColorParser.java

biojava3-forester/src/main/java/org/forester/io/parsers/phyloxml/phylogenydata/ConfidenceParser.java

biojava3-forester/src/main/java/org/forester/io/parsers/phyloxml/phylogenydata/DateParser.java

biojava3-forester/src/main/java/org/forester/io/parsers/phyloxml/phylogenydata/DistributionParser.java

biojava3-forester/src/main/java/org/forester/io/parsers/phyloxml/phylogenydata/DomainArchitectureParser.java

biojava3-forester/src/main/java/org/forester/io/parsers/phyloxml/phylogenydata/EventParser.java

biojava3-forester/src/main/java/org/forester/io/parsers/phyloxml/phylogenydata/IdentifierParser.java

biojava3-forester/src/main/java/org/forester/io/parsers/phyloxml/phylogenydata/PhylogenyDataPhyloXmlParser.java

biojava3-forester/src/main/java/org/forester/io/parsers/phyloxml/phylogenydata/PointParser.java

biojava3-forester/src/main/java/org/forester/io/parsers/phyloxml/phylogenydata/PropertyParser.java

biojava3-forester/src/main/java/org/forester/io/parsers/phyloxml/phylogenydata/ProteinDomainParser.java

biojava3-forester/src/main/java/org/forester/io/parsers/phyloxml/phylogenydata/ReferenceParser.java

biojava3-forester/src/main/java/org/forester/io/parsers/phyloxml/phylogenydata/SequenceParser.java

biojava3-forester/src/main/java/org/forester/io/parsers/phyloxml/phylogenydata/SequenceRelationParser.java

biojava3-forester/src/main/java/org/forester/io/parsers/phyloxml/phylogenydata/TaxonomyParser.java

biojava3-forester/src/main/java/org/forester/io/parsers/phyloxml/phylogenydata/UriParser.java

biojava3-forester/src/main/java/org/forester/phylogeny/iterators/ChildNodeIteratorForward.java

biojava3-forester/src/main/java/org/forester/phylogenyinference

biojava3-forester/src/main/java/org/forester/phylogenyinference/BasicCharacterStateMatrix.java

biojava3-forester/src/main/java/org/forester/phylogenyinference/BasicSymmetricalDistanceMatrix.java

biojava3-forester/src/main/java/org/forester/phylogenyinference/CharacterStateMatrix.java

biojava3-forester/src/main/java/org/forester/phylogenyinference/DiscreteState.java

biojava3-forester/src/main/java/org/forester/phylogenyinference/DistanceMatrix.java

biojava3-forester/src/main/java/org/forester/phylogenyinference/DistanceMatrixParser.java

biojava3-forester/src/main/java/org/forester/phylogenyinference/DistanceMethod.java

biojava3-forester/src/main/java/org/forester/phylogenyinference/DolloParsimony.java

biojava3-forester/src/main/java/org/forester/phylogenyinference/FitchParsimony.java

biojava3-forester/src/main/java/org/forester/phylogenyinference/NeighborJoining.java

biojava3-forester/src/main/java/org/forester/phylogenyinference/SankoffParsimony.java

biojava3-forester/src/main/java/org/forester/phylogenyinference/SymmetricalDistanceMatrixParser.java

biojava3-forester/src/main/java/org/forester/phylogenyinference/TestPhylogenyReconstruction.java

biojava3-forester/src/main/java/org/forester/sdi/SDIdirectory.java

biojava3-forester/src/main/java/org/forester/sdi/Shin.java

biojava3-forester/src/main/java/org/forester/sdi/TaxonomyAssigner.java

biojava3-forester/src/main/java/org/forester/surfacing/BasicDomain.java

biojava3-forester/src/main/java/org/forester/surfacing/BasicProtein.java

biojava3-forester/src/main/java/org/forester/surfacing/BasicSpecies.java

biojava3-forester/src/main/java/org/forester/surfacing/BinaryDomainCombination.java

biojava3-forester/src/main/java/org/forester/surfacing/Domain.java

biojava3-forester/src/main/java/org/forester/surfacing/DomainId.java

biojava3-forester/src/main/java/org/forester/surfacing/Protein.java

biojava3-forester/src/main/java/org/forester/surfacing/ProteinId.java

biojava3-forester/src/main/java/org/forester/surfacing/Species.java

biojava3-genome/src/test/resources/testoutput/volvox_all.faa

biojava3-genome/src/test/resources/testoutput/volvox_all_genes_exon_uppercase.gff3

biojava3-genome/src/test/resources/testoutput/volvox_length.gff3

biojava3-structure/src/test/java/org/biojava/bio/structure/HeaderOnlyTest.java

biojava3-structure/src/test/java/org/biojava/bio/structure/MMcifTest.java

biojava3-structure/src/test/java/org/biojava/bio/structure/PDBFileParserTest.java

biojava3-structure/src/test/java/org/biojava/bio/structure/StructurePairAlignerTest.java

biojava3-structure/src/test/java/org/biojava/bio/structure/StructureTest.java

biojava3-structure/src/test/java/org/biojava/bio/structure/StructureToolsTest.java

biojava3-structure/src/test/java/org/biojava/bio/structure/Test1a4w.java

biojava3-structure/src/test/java/org/biojava/bio/structure/TestSECalignment.java

biojava3-structure/src/test/java/org/biojava/bio/structure/align/FlipAFPChainTest.java

biojava3-structure/src/test/java/org/biojava/bio/structure/align/ce/OptimalCECPMainTest.java

biojava3-structure/src/test/java/org/biojava/bio/structure/align/fatcat

biojava3-structure/src/test/java/org/biojava/bio/structure/align/fatcat/AFPChainSerialisationTest.java

biojava3-structure/src/test/java/org/biojava/bio/structure/align/fatcat/FlipAFPChainTest.java

biojava3-structure/src/test/java/org/biojava/bio/structure/align/fatcat/MyTestHelper.java

biojava3-structure/src/test/java/org/biojava/bio/structure/align/fatcat/TestFlexibleRotationMatrices.java

biojava3-structure/src/test/java/org/biojava/bio/structure/align/fatcat/TestOutputStrings.java

biojava3-structure/src/test/java/org/biojava/bio/structure/scop/ScopTest.java

biojava3-structure/src/test/java/org/biojava/bio/structure/util/StringManipulationTestsHelper.java

biojava3-structure/src/test/resources/1a4w.cif

biojava3-structure/src/test/resources/1a4w.pdb

biojava3-structure/src/test/resources/1fdo.cif

biojava3-structure/src/test/resources/1fdo.pdb

biojava3-structure/src/test/resources/1j59.cif

biojava3-structure/src/test/resources/1j59.pdb

biojava3-structure/src/test/resources/1lnl.pdb

biojava3-structure/src/test/resources/1tap.pdb

biojava3-structure/src/test/resources/2kc9.cif

biojava3-structure/src/test/resources/2kc9.pdb

biojava3-structure/src/test/resources/5pti.cif

biojava3-structure/src/test/resources/5pti.pdb

biojava3-structure/src/test/resources/5pti_old.pdb

biojava3-structure/src/test/resources/ce_1fdo.A_2iv2.X.out

debian/patches/fix_ascii_character_issue

files modified:
.pc/applied-patches

.pc/use_simple_json/biojava3-ws/src/main/java/org/biojava3/ws/hmmer/RemoteHmmerScan.java

biojava3-aa-prop/pom.xml

biojava3-alignment/pom.xml

biojava3-alignment/src/main/java/org/biojava3/alignment/GuideTree.java

biojava3-alignment/src/main/java/org/biojava3/alignment/SimpleProfile.java

biojava3-alignment/src/test/java/org/biojava3/alignment/GuideTreeTest.java

biojava3-core/pom.xml

biojava3-core/src/main/java/org/biojava3/core/sequence/BasicSequence.java

biojava3-core/src/main/java/org/biojava3/core/sequence/DataSource.java

biojava3-core/src/main/java/org/biojava3/core/sequence/compound/NucleotideCompound.java

biojava3-core/src/main/java/org/biojava3/core/sequence/io/GenericFastaHeaderParser.java

biojava3-core/src/main/java/org/biojava3/core/sequence/template/AbstractNucleotideCompoundSet.java

biojava3-core/src/main/java/org/biojava3/core/sequence/template/AbstractSequence.java

biojava3-core/src/main/java/org/biojava3/core/util/UncompressInputStream.java

biojava3-forester/src/main/java/org/forester/application/confadd.java

biojava3-forester/src/main/java/org/forester/application/count_support.java

biojava3-forester/src/main/java/org/forester/application/decorator.java

biojava3-forester/src/main/java/org/forester/application/goac.java

biojava3-forester/src/main/java/org/forester/application/meta_ontologizer.java

biojava3-forester/src/main/java/org/forester/application/nhx_too.java

biojava3-forester/src/main/java/org/forester/application/nj.java

biojava3-forester/src/main/java/org/forester/application/obo_tool.java

biojava3-forester/src/main/java/org/forester/application/pccx.java

biojava3-forester/src/main/java/org/forester/application/pfam2go_extractor.java

biojava3-forester/src/main/java/org/forester/application/pfam_go.java

biojava3-forester/src/main/java/org/forester/application/phyloxml_converter.java

biojava3-forester/src/main/java/org/forester/application/printAllSpecies.java

biojava3-forester/src/main/java/org/forester/application/printSameOrder.java

biojava3-forester/src/main/java/org/forester/application/rio.java

biojava3-forester/src/main/java/org/forester/application/sdi_r.java

biojava3-forester/src/main/java/org/forester/application/strip.java

biojava3-forester/src/main/java/org/forester/application/support_statistics.java

biojava3-forester/src/main/java/org/forester/application/support_transfer.java

biojava3-forester/src/main/java/org/forester/application/surf_paup.java

biojava3-forester/src/main/java/org/forester/application/surfacing.java

biojava3-forester/src/main/java/org/forester/archaeopteryx/Archaeopteryx.java

biojava3-forester/src/main/java/org/forester/archaeopteryx/ArchaeopteryxA.java

biojava3-forester/src/main/java/org/forester/archaeopteryx/ArchaeopteryxE.java

biojava3-forester/src/main/java/org/forester/archaeopteryx/ColorSchemeChooser.java

biojava3-forester/src/main/java/org/forester/archaeopteryx/Configuration.java

biojava3-forester/src/main/java/org/forester/archaeopteryx/Constants.java

biojava3-forester/src/main/java/org/forester/archaeopteryx/ControlPanel.java

biojava3-forester/src/main/java/org/forester/archaeopteryx/FontChooser.java

biojava3-forester/src/main/java/org/forester/archaeopteryx/MainFrame.java

biojava3-forester/src/main/java/org/forester/archaeopteryx/MainFrameApplet.java

biojava3-forester/src/main/java/org/forester/archaeopteryx/MainFrameApplication.java

biojava3-forester/src/main/java/org/forester/archaeopteryx/MainPanel.java

biojava3-forester/src/main/java/org/forester/archaeopteryx/MainPanelApplets.java

biojava3-forester/src/main/java/org/forester/archaeopteryx/MouseListener.java

biojava3-forester/src/main/java/org/forester/archaeopteryx/NodeEditPanel.java

biojava3-forester/src/main/java/org/forester/archaeopteryx/NodeFrame.java

biojava3-forester/src/main/java/org/forester/archaeopteryx/NodePanel.java

biojava3-forester/src/main/java/org/forester/archaeopteryx/Options.java

biojava3-forester/src/main/java/org/forester/archaeopteryx/PdfExporter.java

biojava3-forester/src/main/java/org/forester/archaeopteryx/Printer.java

biojava3-forester/src/main/java/org/forester/archaeopteryx/TextFrame.java

biojava3-forester/src/main/java/org/forester/archaeopteryx/TreeColorSet.java

biojava3-forester/src/main/java/org/forester/archaeopteryx/TreeFontSet.java

biojava3-forester/src/main/java/org/forester/archaeopteryx/TreePanel.java

biojava3-forester/src/main/java/org/forester/archaeopteryx/UrlTreeReader.java

biojava3-forester/src/main/java/org/forester/archaeopteryx/WebLink.java

biojava3-forester/src/main/java/org/forester/archaeopteryx/phylogeny/data/RenderableDomainArchitecture.java

biojava3-forester/src/main/java/org/forester/archaeopteryx/phylogeny/data/RenderablePhylogenyData.java

biojava3-forester/src/main/java/org/forester/archaeopteryx/webservices/BasicPhylogeniesWebserviceClient.java

biojava3-forester/src/main/java/org/forester/archaeopteryx/webservices/PhylogeniesWebserviceClient.java

biojava3-forester/src/main/java/org/forester/archaeopteryx/webservices/WebserviceUtil.java

biojava3-forester/src/main/java/org/forester/archaeopteryx/webservices/WebservicesManager.java

biojava3-forester/src/main/java/org/forester/datastructures/Queue.java

biojava3-forester/src/main/java/org/forester/development/DevelopmentTools.java

biojava3-forester/src/main/java/org/forester/development/Test.java

biojava3-forester/src/main/java/org/forester/go/BasicGoRelationship.java

biojava3-forester/src/main/java/org/forester/go/BasicGoSubset.java

biojava3-forester/src/main/java/org/forester/go/BasicGoTerm.java

biojava3-forester/src/main/java/org/forester/go/BasicGoXRef.java

biojava3-forester/src/main/java/org/forester/go/GoId.java

biojava3-forester/src/main/java/org/forester/go/GoNameSpace.java

biojava3-forester/src/main/java/org/forester/go/GoRelationship.java

biojava3-forester/src/main/java/org/forester/go/GoSubset.java

biojava3-forester/src/main/java/org/forester/go/GoTerm.java

biojava3-forester/src/main/java/org/forester/go/GoUtils.java

biojava3-forester/src/main/java/org/forester/go/GoXRef.java

biojava3-forester/src/main/java/org/forester/go/Mapping.java

biojava3-forester/src/main/java/org/forester/go/OBOparser.java

biojava3-forester/src/main/java/org/forester/go/PfamToGoMapping.java

biojava3-forester/src/main/java/org/forester/go/PfamToGoParser.java

biojava3-forester/src/main/java/org/forester/go/TestGo.java

biojava3-forester/src/main/java/org/forester/go/etc/MetaOntologizer.java

biojava3-forester/src/main/java/org/forester/go/etc/OntologizerResult.java

biojava3-forester/src/main/java/org/forester/io/parsers/HmmPfamOutputParser.java

biojava3-forester/src/main/java/org/forester/io/parsers/HmmscanPerDomainTableParser.java

biojava3-forester/src/main/java/org/forester/io/parsers/PhylogenyParser.java

biojava3-forester/src/main/java/org/forester/io/parsers/nexus/NexusBinaryStatesMatrixParser.java

biojava3-forester/src/main/java/org/forester/io/parsers/nexus/NexusCharactersParser.java

biojava3-forester/src/main/java/org/forester/io/parsers/nexus/NexusConstants.java

biojava3-forester/src/main/java/org/forester/io/parsers/nexus/NexusFormatException.java

biojava3-forester/src/main/java/org/forester/io/parsers/nexus/NexusPhylogeniesParser.java

biojava3-forester/src/main/java/org/forester/io/parsers/nexus/PaupLogParser.java

biojava3-forester/src/main/java/org/forester/io/parsers/nhx/NHXFormatException.java

biojava3-forester/src/main/java/org/forester/io/parsers/nhx/NHXParser.java

biojava3-forester/src/main/java/org/forester/io/parsers/nhx/NHXtags.java

biojava3-forester/src/main/java/org/forester/io/parsers/phyloxml/PhyloXmlDataFormatException.java

biojava3-forester/src/main/java/org/forester/io/parsers/phyloxml/PhyloXmlException.java

biojava3-forester/src/main/java/org/forester/io/parsers/phyloxml/PhyloXmlHandler.java

biojava3-forester/src/main/java/org/forester/io/parsers/phyloxml/PhyloXmlMapping.java

biojava3-forester/src/main/java/org/forester/io/parsers/phyloxml/PhyloXmlParser.java

biojava3-forester/src/main/java/org/forester/io/parsers/phyloxml/PhyloXmlUtil.java

biojava3-forester/src/main/java/org/forester/io/parsers/phyloxml/XmlElement.java

biojava3-forester/src/main/java/org/forester/io/parsers/tol/TolParser.java

biojava3-forester/src/main/java/org/forester/io/parsers/tol/TolXmlHandler.java

biojava3-forester/src/main/java/org/forester/io/parsers/tol/TolXmlMapping.java

biojava3-forester/src/main/java/org/forester/io/writers/PhyloXmlNodeWriter.java

biojava3-forester/src/main/java/org/forester/io/writers/PhylogenyWriter.java

biojava3-forester/src/main/java/org/forester/pccx/BasicExternalNodeBasedCoverageExtender.java

biojava3-forester/src/main/java/org/forester/pccx/BranchCountingBasedScoringMethod.java

biojava3-forester/src/main/java/org/forester/pccx/BranchLengthBasedScoringMethod.java

biojava3-forester/src/main/java/org/forester/pccx/Coverage.java

biojava3-forester/src/main/java/org/forester/pccx/CoverageCalculationMethod.java

biojava3-forester/src/main/java/org/forester/pccx/CoverageCalculationOptions.java

biojava3-forester/src/main/java/org/forester/pccx/CoverageCalculator.java

biojava3-forester/src/main/java/org/forester/pccx/CoverageExtender.java

biojava3-forester/src/main/java/org/forester/pccx/ExternalNodeBasedCoverage.java

biojava3-forester/src/main/java/org/forester/pccx/ExternalNodeBasedCoverageMethod.java

biojava3-forester/src/main/java/org/forester/pccx/ExternalNodeBasedCoverageMethodOptions.java

biojava3-forester/src/main/java/org/forester/pccx/LogBranchLengthBasedScoringMethod.java

biojava3-forester/src/main/java/org/forester/pccx/ModelingUtils.java

biojava3-forester/src/main/java/org/forester/pccx/ScoringMethodForExternalNode.java

biojava3-forester/src/main/java/org/forester/pccx/TestPccx.java

biojava3-forester/src/main/java/org/forester/phylogeny/Edge.java

biojava3-forester/src/main/java/org/forester/phylogeny/Phylogeny.java

biojava3-forester/src/main/java/org/forester/phylogeny/PhylogenyBranch.java

biojava3-forester/src/main/java/org/forester/phylogeny/PhylogenyMethods.java

biojava3-forester/src/main/java/org/forester/phylogeny/PhylogenyNode.java

biojava3-forester/src/main/java/org/forester/phylogeny/PhylogenyNodeI.java

biojava3-forester/src/main/java/org/forester/phylogeny/data/Accession.java

biojava3-forester/src/main/java/org/forester/phylogeny/data/Annotation.java

biojava3-forester/src/main/java/org/forester/phylogeny/data/BinaryCharacters.java

biojava3-forester/src/main/java/org/forester/phylogeny/data/BranchColor.java

biojava3-forester/src/main/java/org/forester/phylogeny/data/BranchData.java

biojava3-forester/src/main/java/org/forester/phylogeny/data/BranchWidth.java

biojava3-forester/src/main/java/org/forester/phylogeny/data/Confidence.java

biojava3-forester/src/main/java/org/forester/phylogeny/data/Date.java

biojava3-forester/src/main/java/org/forester/phylogeny/data/Distribution.java

biojava3-forester/src/main/java/org/forester/phylogeny/data/DomainArchitecture.java

biojava3-forester/src/main/java/org/forester/phylogeny/data/Event.java

biojava3-forester/src/main/java/org/forester/phylogeny/data/Identifier.java

biojava3-forester/src/main/java/org/forester/phylogeny/data/NodeData.java

biojava3-forester/src/main/java/org/forester/phylogeny/data/PhylogenyData.java

biojava3-forester/src/main/java/org/forester/phylogeny/data/PhylogenyDataUtil.java

biojava3-forester/src/main/java/org/forester/phylogeny/data/Point.java

biojava3-forester/src/main/java/org/forester/phylogeny/data/PropertiesMap.java

biojava3-forester/src/main/java/org/forester/phylogeny/data/Property.java

biojava3-forester/src/main/java/org/forester/phylogeny/data/ProteinDomain.java

biojava3-forester/src/main/java/org/forester/phylogeny/data/Reference.java

biojava3-forester/src/main/java/org/forester/phylogeny/data/Sequence.java

biojava3-forester/src/main/java/org/forester/phylogeny/data/SequenceRelation.java

biojava3-forester/src/main/java/org/forester/phylogeny/data/Taxonomy.java

biojava3-forester/src/main/java/org/forester/phylogeny/data/Uri.java

biojava3-forester/src/main/java/org/forester/phylogeny/factories/BasicPhylogenyFactory.java

biojava3-forester/src/main/java/org/forester/phylogeny/factories/ParserBasedPhylogenyFactory.java

biojava3-forester/src/main/java/org/forester/phylogeny/factories/PhylogenyFactory.java

biojava3-forester/src/main/java/org/forester/phylogeny/iterators/ExternalForwardIterator.java

biojava3-forester/src/main/java/org/forester/phylogeny/iterators/LevelOrderTreeIterator.java

biojava3-forester/src/main/java/org/forester/phylogeny/iterators/PhylogenyNodeIterator.java

biojava3-forester/src/main/java/org/forester/phylogeny/iterators/PostOrderStackObject.java

biojava3-forester/src/main/java/org/forester/phylogeny/iterators/PostorderTreeIterator.java

biojava3-forester/src/main/java/org/forester/phylogeny/iterators/PreorderTreeIterator.java

biojava3-forester/src/main/java/org/forester/sdi/DistanceCalculator.java

biojava3-forester/src/main/java/org/forester/sdi/GSDI.java

biojava3-forester/src/main/java/org/forester/sdi/ORcount.java

biojava3-forester/src/main/java/org/forester/sdi/RIO.java

biojava3-forester/src/main/java/org/forester/sdi/RIOn.java

biojava3-forester/src/main/java/org/forester/sdi/SDI.java

biojava3-forester/src/main/java/org/forester/sdi/SDIR.java

biojava3-forester/src/main/java/org/forester/sdi/SDIse.java

biojava3-forester/src/main/java/org/forester/sdi/TestGSDI.java

biojava3-forester/src/main/java/org/forester/sdi/Tuplet.java

biojava3-forester/src/main/java/org/forester/surfacing/AdjactantDirectedBinaryDomainCombination.java

biojava3-forester/src/main/java/org/forester/surfacing/AdjactantDirectedCombinableDomains.java

biojava3-forester/src/main/java/org/forester/surfacing/BasicBinaryDomainCombination.java

biojava3-forester/src/main/java/org/forester/surfacing/BasicCombinableDomains.java

biojava3-forester/src/main/java/org/forester/surfacing/BasicDomainSimilarityCalculator.java

biojava3-forester/src/main/java/org/forester/surfacing/BasicGenomeWideCombinableDomains.java

biojava3-forester/src/main/java/org/forester/surfacing/CombinableDomains.java

biojava3-forester/src/main/java/org/forester/surfacing/CombinationsBasedPairwiseDomainSimilarity.java

biojava3-forester/src/main/java/org/forester/surfacing/CombinationsBasedPairwiseDomainSimilarityCalculator.java

biojava3-forester/src/main/java/org/forester/surfacing/CountsBasedPairwiseDomainSimilarity.java

biojava3-forester/src/main/java/org/forester/surfacing/DirectedBinaryDomainCombination.java

biojava3-forester/src/main/java/org/forester/surfacing/DirectedCombinableDomains.java

biojava3-forester/src/main/java/org/forester/surfacing/DomainArchitectureBasedGenomeSimilarityCalculator.java

biojava3-forester/src/main/java/org/forester/surfacing/DomainCountsBasedPairwiseSimilarityCalculator.java

biojava3-forester/src/main/java/org/forester/surfacing/DomainCountsDifferenceUtil.java

biojava3-forester/src/main/java/org/forester/surfacing/DomainLengths.java

biojava3-forester/src/main/java/org/forester/surfacing/DomainLengthsTable.java

biojava3-forester/src/main/java/org/forester/surfacing/DomainParsimonyCalculator.java

biojava3-forester/src/main/java/org/forester/surfacing/DomainSimilarity.java

biojava3-forester/src/main/java/org/forester/surfacing/DomainSimilarityCalculator.java

biojava3-forester/src/main/java/org/forester/surfacing/GenomeWideCombinableDomains.java

biojava3-forester/src/main/java/org/forester/surfacing/MappingResults.java

biojava3-forester/src/main/java/org/forester/surfacing/PairwiseDomainSimilarity.java

biojava3-forester/src/main/java/org/forester/surfacing/PairwiseDomainSimilarityCalculator.java

biojava3-forester/src/main/java/org/forester/surfacing/PairwiseGenomeComparator.java

biojava3-forester/src/main/java/org/forester/surfacing/PrintableDomainSimilarity.java

biojava3-forester/src/main/java/org/forester/surfacing/PrintableSpeciesSpecificDomainSimilariyData.java

biojava3-forester/src/main/java/org/forester/surfacing/ProteinCountsBasedPairwiseDomainSimilarityCalculator.java

biojava3-forester/src/main/java/org/forester/surfacing/SimpleDomain.java

biojava3-forester/src/main/java/org/forester/surfacing/SpeciesSpecificDomainSimilariyData.java

biojava3-forester/src/main/java/org/forester/surfacing/SurfacingConstants.java

biojava3-forester/src/main/java/org/forester/surfacing/SurfacingUtil.java

biojava3-forester/src/main/java/org/forester/surfacing/TestSurfacing.java

biojava3-forester/src/main/java/org/forester/test/Test.java

biojava3-forester/src/main/java/org/forester/tools/ConfidenceAssessor.java

biojava3-forester/src/main/java/org/forester/tools/PhylogenyDecorator.java

biojava3-forester/src/main/java/org/forester/tools/TreeSplitMatrix.java

biojava3-forester/src/main/java/org/forester/util/AsciiHistogram.java

biojava3-forester/src/main/java/org/forester/util/BasicDescriptiveStatistics.java

biojava3-forester/src/main/java/org/forester/util/BasicTable.java

biojava3-forester/src/main/java/org/forester/util/BasicTableParser.java

biojava3-forester/src/main/java/org/forester/util/CommandLineArguments.java

biojava3-forester/src/main/java/org/forester/util/DescriptiveStatistics.java

biojava3-forester/src/main/java/org/forester/util/ForesterConstants.java

biojava3-forester/src/main/java/org/forester/util/ForesterUtil.java

biojava3-forester/src/main/java/org/forester/util/GeneralTable.java

biojava3-forester/src/main/java/org/forester/util/WindowsUtils.java

biojava3-genome/pom.xml

biojava3-genome/src/main/java/org/biojava3/genome/parsers/gff/Feature.java

biojava3-genome/src/main/java/org/biojava3/genome/parsers/gff/FeatureI.java

biojava3-genome/src/main/java/org/biojava3/genome/parsers/gff/FeatureList.java

biojava3-genome/src/main/java/org/biojava3/genome/parsers/gff/GFF3Reader.java

biojava3-genome/src/test/java/org/biojava3/genome/GeneFeatureHelperTest.java

biojava3-modfinder/pom.xml

biojava3-phylo/pom.xml

biojava3-phylo/src/main/java/org/biojava3/phylo/CheckTreeAccuracy.java

biojava3-phylo/src/main/java/org/biojava3/phylo/TreeConstructor.java

biojava3-protein-disorder/pom.xml

biojava3-protein-disorder/src/main/java/org/biojava3/data/sequence/SequenceUtil.java

biojava3-protein-disorder/src/main/java/org/biojava3/ronn/Jronn.java

biojava3-protein-disorder/src/main/java/org/biojava3/ronn/ORonn.java

biojava3-sequencing/pom.xml

biojava3-structure-gui/pom.xml

biojava3-structure-gui/src/main/java/org/biojava/bio/structure/align/gui/AlignmentCalcDB.java

biojava3-structure-gui/src/main/java/org/biojava/bio/structure/align/gui/AlignmentGui.java

biojava3-structure-gui/src/main/java/org/biojava/bio/structure/align/gui/DBResultTable.java

biojava3-structure-gui/src/main/java/org/biojava/bio/structure/align/gui/DBSearchGUI.java

biojava3-structure-gui/src/main/java/org/biojava/bio/structure/align/gui/MenuCreator.java

biojava3-structure-gui/src/main/java/org/biojava/bio/structure/align/gui/ShowPDBIDListener.java

biojava3-structure-gui/src/main/java/org/biojava/bio/structure/align/gui/autosuggest/JAutoSuggest.java

biojava3-structure-gui/src/main/java/org/biojava/bio/structure/align/gui/jmol/JmolPanel.java

biojava3-structure-gui/src/main/java/org/biojava/bio/structure/align/gui/jmol/StructureAlignmentJmol.java

biojava3-structure-gui/src/main/java/org/biojava/bio/structure/align/webstart/AligUIManager.java

biojava3-structure-gui/src/main/java/org/biojava/bio/structure/gui/util/ScopSelectPanel.java

biojava3-structure/pom.xml

biojava3-structure/src/main/java/demo/DemoAtomCache.java

biojava3-structure/src/main/java/demo/DemoSCOP.java

biojava3-structure/src/main/java/org/biojava/bio/structure/Chain.java

biojava3-structure/src/main/java/org/biojava/bio/structure/ChainImpl.java

biojava3-structure/src/main/java/org/biojava/bio/structure/DBRef.java

biojava3-structure/src/main/java/org/biojava/bio/structure/HetatomImpl.java

biojava3-structure/src/main/java/org/biojava/bio/structure/PDBCrystallographicInfo.java

biojava3-structure/src/main/java/org/biojava/bio/structure/PDBHeader.java

biojava3-structure/src/main/java/org/biojava/bio/structure/PDBStatus.java

biojava3-structure/src/main/java/org/biojava/bio/structure/ResidueNumber.java

biojava3-structure/src/main/java/org/biojava/bio/structure/Site.java

biojava3-structure/src/main/java/org/biojava/bio/structure/StructureImpl.java

biojava3-structure/src/main/java/org/biojava/bio/structure/StructureTools.java

biojava3-structure/src/main/java/org/biojava/bio/structure/align/ce/AbstractUserArgumentProcessor.java

biojava3-structure/src/main/java/org/biojava/bio/structure/align/ce/CeUserArgumentProcessor.java

biojava3-structure/src/main/java/org/biojava/bio/structure/align/ce/GuiWrapper.java

biojava3-structure/src/main/java/org/biojava/bio/structure/align/client/FarmJobRunnable.java

biojava3-structure/src/main/java/org/biojava/bio/structure/align/client/StructureName.java

biojava3-structure/src/main/java/org/biojava/bio/structure/align/fatcat/FatCatUserArgumentProcessor.java

biojava3-structure/src/main/java/org/biojava/bio/structure/align/util/AlignmentTools.java

biojava3-structure/src/main/java/org/biojava/bio/structure/align/util/AtomCache.java

biojava3-structure/src/main/java/org/biojava/bio/structure/align/util/SynchronizedOutFile.java

biojava3-structure/src/main/java/org/biojava/bio/structure/io/FileParsingParameters.java

biojava3-structure/src/main/java/org/biojava/bio/structure/io/LocalCacheStructureProvider.java

biojava3-structure/src/main/java/org/biojava/bio/structure/io/MMCIFFileReader.java

biojava3-structure/src/main/java/org/biojava/bio/structure/io/PDBFileParser.java

biojava3-structure/src/main/java/org/biojava/bio/structure/io/PDBFileReader.java

biojava3-structure/src/main/java/org/biojava/bio/structure/io/SeqRes2AtomAligner.java

biojava3-structure/src/main/java/org/biojava/bio/structure/io/StructureIO.java

biojava3-structure/src/main/java/org/biojava/bio/structure/io/mmcif/ChemCompConsumer.java

biojava3-structure/src/main/java/org/biojava/bio/structure/io/mmcif/MMcifConsumer.java

biojava3-structure/src/main/java/org/biojava/bio/structure/io/mmcif/SimpleMMcifConsumer.java

biojava3-structure/src/main/java/org/biojava/bio/structure/io/mmcif/SimpleMMcifParser.java

biojava3-structure/src/main/java/org/biojava/bio/structure/io/mmcif/model/Refine.java

biojava3-structure/src/main/java/org/biojava/bio/structure/scop/ScopDomain.java

biojava3-structure/src/main/java/org/biojava/bio/structure/scop/ScopInstallation.java

biojava3-structure/src/main/java/org/biojava/bio/structure/secstruc/SecStruc.java

biojava3-structure/src/main/java/org/biojava/bio/structure/secstruc/SecStrucState.java

biojava3-structure/src/main/resources/ce.properties

biojava3-structure/src/test/java/org/biojava/bio/structure/ResidueNumberTest.java

biojava3-structure/src/test/java/org/biojava/bio/structure/TestNucleotides.java

biojava3-structure/src/test/java/org/biojava/bio/structure/align/util/AlignmentToolsTest.java

biojava3-ws/pom.xml

biojava3-ws/src/main/java/org/biojava3/ws/hmmer/HmmerDomain.java

biojava3-ws/src/main/java/org/biojava3/ws/hmmer/HmmerResult.java

biojava3-ws/src/main/java/org/biojava3/ws/hmmer/RemoteHmmerScan.java

debian/build.xml

debian/changelog

debian/control

debian/get-orig-source

debian/patches/series

debian/patches/use_simple_json

debian/rules

pom.xml

Show diffs side-by-side

added added

removed removed

.pc/applied-patches

.pc/fix_ascii_character_issue/

.pc/fix_ascii_character_issue/biojava3-forester/

.pc/fix_ascii_character_issue/biojava3-forester/src/

.pc/fix_ascii_character_issue/biojava3-forester/src/main/

.pc/fix_ascii_character_issue/biojava3-forester/src/main/java/

.pc/fix_ascii_character_issue/biojava3-forester/src/main/java/org/

.pc/fix_ascii_character_issue/biojava3-forester/src/main/java/org/forester/

.pc/fix_ascii_character_issue/biojava3-forester/src/main/java/org/forester/archaeopteryx/

.pc/fix_ascii_character_issue/biojava3-forester/src/main/java/org/forester/archaeopteryx/Blast.java

.pc/fix_ascii_characters_mapping/

.pc/fix_ascii_characters_mapping/biojava3-forester/

.pc/fix_ascii_characters_mapping/biojava3-forester/src/

.pc/fix_ascii_characters_mapping/biojava3-forester/src/main/

.pc/fix_ascii_characters_mapping/biojava3-forester/src/main/java/

.pc/fix_ascii_characters_mapping/biojava3-forester/src/main/java/org/

.pc/fix_ascii_characters_mapping/biojava3-forester/src/main/java/org/forester/

.pc/fix_ascii_characters_mapping/biojava3-forester/src/main/java/org/forester/test/

.pc/fix_ascii_characters_mapping/biojava3-forester/src/main/java/org/forester/test/Test.java

.pc/use_simple_json/biojava3-ws/src/main/java/org/biojava3/ws/hmmer/RemoteHmmerScan.java

biojava3-aa-prop/pom.xml

biojava3-aa-prop/src/main/assembly/

biojava3-aa-prop/src/main/assembly/assembly.xml

biojava3-alignment/pom.xml

biojava3-alignment/src/main/java/demo/

biojava3-alignment/src/main/java/demo/CookbookMSA.java

biojava3-alignment/src/main/java/demo/DemoLoadSubstMax.java

biojava3-alignment/src/main/java/demo/TestDNANeedlemanWunsch.java

biojava3-alignment/src/main/java/org/biojava3/alignment/GuideTree.java

biojava3-alignment/src/main/java/org/biojava3/alignment/SimpleProfile.java

biojava3-alignment/src/main/java/org/biojava3/alignment/io/

biojava3-alignment/src/main/java/org/biojava3/alignment/io/StockholmConsensusAnnotation.java

biojava3-alignment/src/main/java/org/biojava3/alignment/io/StockholmFileAnnotation.java

biojava3-alignment/src/main/java/org/biojava3/alignment/io/StockholmFileParser.java

biojava3-alignment/src/main/java/org/biojava3/alignment/io/StockholmResidueAnnotation.java

biojava3-alignment/src/main/java/org/biojava3/alignment/io/StockholmSequenceAnnotation.java

biojava3-alignment/src/main/java/org/biojava3/alignment/io/StockholmStructure.java

biojava3-alignment/src/test/java/org/biojava3/alignment/GuideTreeTest.java

biojava3-alignment/src/test/java/org/biojava3/alignment/io/

biojava3-alignment/src/test/java/org/biojava3/alignment/io/TestStockholmParser.java

biojava3-alignment/src/test/resources/longTest(Ankyrin repeat).sto

biojava3-alignment/src/test/resources/piwi.sth.gz

biojava3-alignment/src/test/resources/pkinase.sto

biojava3-alignment/src/test/resources/rrm.sto

biojava3-alignment/src/test/resources/test.sth

biojava3-alignment/src/test/resources/test1.sth

biojava3-core/pom.xml

biojava3-core/src/main/java/org/biojava3/core/sequence/BasicSequence.java

biojava3-core/src/main/java/org/biojava3/core/sequence/DataSource.java

biojava3-core/src/main/java/org/biojava3/core/sequence/compound/NucleotideCompound.java

biojava3-core/src/main/java/org/biojava3/core/sequence/io/GenericFastaHeaderParser.java

biojava3-core/src/main/java/org/biojava3/core/sequence/template/AbstractNucleotideCompoundSet.java

biojava3-core/src/main/java/org/biojava3/core/sequence/template/AbstractSequence.java

biojava3-core/src/main/java/org/biojava3/core/util/UncompressInputStream.java

biojava3-forester/src/main/java/.classpath

biojava3-forester/src/main/java/.project

biojava3-forester/src/main/java/META-INF/

biojava3-forester/src/main/java/META-INF/MANIFEST.MF

biojava3-forester/src/main/java/build.xml

biojava3-forester/src/main/java/classes/

biojava3-forester/src/main/java/classes/org/

biojava3-forester/src/main/java/classes/org/forester/

biojava3-forester/src/main/java/classes/org/forester/analysis/

biojava3-forester/src/main/java/classes/org/forester/application/

biojava3-forester/src/main/java/classes/org/forester/archaeopteryx/

biojava3-forester/src/main/java/classes/org/forester/archaeopteryx/phylogeny/

biojava3-forester/src/main/java/classes/org/forester/archaeopteryx/phylogeny/data/

biojava3-forester/src/main/java/classes/org/forester/archaeopteryx/tools/

biojava3-forester/src/main/java/classes/org/forester/archaeopteryx/webservices/

biojava3-forester/src/main/java/classes/org/forester/datastructures/

biojava3-forester/src/main/java/classes/org/forester/development/

biojava3-forester/src/main/java/classes/org/forester/evoinference/

biojava3-forester/src/main/java/classes/org/forester/evoinference/distance/

biojava3-forester/src/main/java/classes/org/forester/evoinference/matrix/

biojava3-forester/src/main/java/classes/org/forester/evoinference/matrix/character/

biojava3-forester/src/main/java/classes/org/forester/evoinference/matrix/distance/

biojava3-forester/src/main/java/classes/org/forester/evoinference/parsimony/

biojava3-forester/src/main/java/classes/org/forester/evoinference/tools/

biojava3-forester/src/main/java/classes/org/forester/go/

biojava3-forester/src/main/java/classes/org/forester/go/etc/

biojava3-forester/src/main/java/classes/org/forester/io/

biojava3-forester/src/main/java/classes/org/forester/io/parsers/

biojava3-forester/src/main/java/classes/org/forester/io/parsers/nexus/

biojava3-forester/src/main/java/classes/org/forester/io/parsers/nhx/

biojava3-forester/src/main/java/classes/org/forester/io/parsers/phyloxml/

biojava3-forester/src/main/java/classes/org/forester/io/parsers/phyloxml/data/

biojava3-forester/src/main/java/classes/org/forester/io/parsers/tol/

biojava3-forester/src/main/java/classes/org/forester/io/parsers/util/

biojava3-forester/src/main/java/classes/org/forester/io/writers/

biojava3-forester/src/main/java/classes/org/forester/msa/

biojava3-forester/src/main/java/classes/org/forester/pccx/

biojava3-forester/src/main/java/classes/org/forester/phylogeny/

biojava3-forester/src/main/java/classes/org/forester/phylogeny/data/

biojava3-forester/src/main/java/classes/org/forester/phylogeny/factories/

biojava3-forester/src/main/java/classes/org/forester/phylogeny/iterators/

biojava3-forester/src/main/java/classes/org/forester/protein/

biojava3-forester/src/main/java/classes/org/forester/sdi/

biojava3-forester/src/main/java/classes/org/forester/sequence/

biojava3-forester/src/main/java/classes/org/forester/species/

biojava3-forester/src/main/java/classes/org/forester/surfacing/

biojava3-forester/src/main/java/classes/org/forester/test/

biojava3-forester/src/main/java/classes/org/forester/test/examples/

biojava3-forester/src/main/java/classes/org/forester/tools/

biojava3-forester/src/main/java/classes/org/forester/util/

biojava3-forester/src/main/java/classes/org/forester/ws/

biojava3-forester/src/main/java/classes/org/forester/ws/hmmer/

biojava3-forester/src/main/java/classes/org/forester/ws/seqdb/

biojava3-forester/src/main/java/classes/org/forester/ws/uniprot/

biojava3-forester/src/main/java/classes/org/forester/ws/wabi/

biojava3-forester/src/main/java/forester-0.955-sources.jar

biojava3-forester/src/main/java/forester-1.005-sources-1.005.jar

biojava3-forester/src/main/java/org/forester/analysis/

biojava3-forester/src/main/java/org/forester/analysis/AncestralTaxonomyInference.java

biojava3-forester/src/main/java/org/forester/analysis/AncestralTaxonomyInferenceException.java

biojava3-forester/src/main/java/org/forester/analysis/TaxonomyDataManager.java

biojava3-forester/src/main/java/org/forester/application/CheckTreeAccuracy.java

biojava3-forester/src/main/java/org/forester/application/confadd.java

biojava3-forester/src/main/java/org/forester/application/count_support.java

biojava3-forester/src/main/java/org/forester/application/decorator.java

biojava3-forester/src/main/java/org/forester/application/gene_tree_preprocess.java

biojava3-forester/src/main/java/org/forester/application/get_distances.java

biojava3-forester/src/main/java/org/forester/application/goac.java

biojava3-forester/src/main/java/org/forester/application/gsdi.java

biojava3-forester/src/main/java/org/forester/application/mcc.java

biojava3-forester/src/main/java/org/forester/application/meta_ontologizer.java

biojava3-forester/src/main/java/org/forester/application/nhx_too.java

biojava3-forester/src/main/java/org/forester/application/nj.java

biojava3-forester/src/main/java/org/forester/application/obo_tool.java

biojava3-forester/src/main/java/org/forester/application/pccx.java

biojava3-forester/src/main/java/org/forester/application/perfume.java

biojava3-forester/src/main/java/org/forester/application/pfam2go_extractor.java

biojava3-forester/src/main/java/org/forester/application/pfam_go.java

biojava3-forester/src/main/java/org/forester/application/pfamacc2go.java

biojava3-forester/src/main/java/org/forester/application/pfamacc2pfamid.java

biojava3-forester/src/main/java/org/forester/application/phyloxml_converter.java

biojava3-forester/src/main/java/org/forester/application/printAllSpecies.java

biojava3-forester/src/main/java/org/forester/application/printSameOrder.java

biojava3-forester/src/main/java/org/forester/application/rio.java

biojava3-forester/src/main/java/org/forester/application/sdi.java

biojava3-forester/src/main/java/org/forester/application/sdi_dir.java

biojava3-forester/src/main/java/org/forester/application/sdi_r.java

biojava3-forester/src/main/java/org/forester/application/shin.java

biojava3-forester/src/main/java/org/forester/application/strip.java

biojava3-forester/src/main/java/org/forester/application/support_statistics.java

biojava3-forester/src/main/java/org/forester/application/support_transfer.java

biojava3-forester/src/main/java/org/forester/application/surf_paup.java

biojava3-forester/src/main/java/org/forester/application/surfacing.java

biojava3-forester/src/main/java/org/forester/application/surfacing_old.java

biojava3-forester/src/main/java/org/forester/application/ta.java

biojava3-forester/src/main/java/org/forester/archaeopteryx/AptxUtil.java

biojava3-forester/src/main/java/org/forester/archaeopteryx/Archaeopteryx.java

biojava3-forester/src/main/java/org/forester/archaeopteryx/ArchaeopteryxA.java

biojava3-forester/src/main/java/org/forester/archaeopteryx/ArchaeopteryxE.java

biojava3-forester/src/main/java/org/forester/archaeopteryx/Blast.java

biojava3-forester/src/main/java/org/forester/archaeopteryx/ColorSchemeChooser.java

biojava3-forester/src/main/java/org/forester/archaeopteryx/Configuration.java

biojava3-forester/src/main/java/org/forester/archaeopteryx/Constants.java

biojava3-forester/src/main/java/org/forester/archaeopteryx/ControlPanel.java

biojava3-forester/src/main/java/org/forester/archaeopteryx/FontChooser.java

biojava3-forester/src/main/java/org/forester/archaeopteryx/MainFrame.java

biojava3-forester/src/main/java/org/forester/archaeopteryx/MainFrameApplet.java

biojava3-forester/src/main/java/org/forester/archaeopteryx/MainFrameApplication.java

biojava3-forester/src/main/java/org/forester/archaeopteryx/MainPanel.java

biojava3-forester/src/main/java/org/forester/archaeopteryx/MainPanelApplets.java

biojava3-forester/src/main/java/org/forester/archaeopteryx/MouseListener.java

biojava3-forester/src/main/java/org/forester/archaeopteryx/NodeEditPanel.java

biojava3-forester/src/main/java/org/forester/archaeopteryx/NodeFrame.java

biojava3-forester/src/main/java/org/forester/archaeopteryx/NodePanel.java

biojava3-forester/src/main/java/org/forester/archaeopteryx/Options.java

biojava3-forester/src/main/java/org/forester/archaeopteryx/PdfExporter.java

biojava3-forester/src/main/java/org/forester/archaeopteryx/PdfWriter.java

biojava3-forester/src/main/java/org/forester/archaeopteryx/Printer.java

biojava3-forester/src/main/java/org/forester/archaeopteryx/TextFrame.java

biojava3-forester/src/main/java/org/forester/archaeopteryx/TreeColorSet.java

biojava3-forester/src/main/java/org/forester/archaeopteryx/TreeFontSet.java

biojava3-forester/src/main/java/org/forester/archaeopteryx/TreePanel.java

biojava3-forester/src/main/java/org/forester/archaeopteryx/UrlTreeReader.java

biojava3-forester/src/main/java/org/forester/archaeopteryx/Util.java

biojava3-forester/src/main/java/org/forester/archaeopteryx/WebLink.java

biojava3-forester/src/main/java/org/forester/archaeopteryx/phylogeny/data/RenderableDomainArchitecture.java

biojava3-forester/src/main/java/org/forester/archaeopteryx/phylogeny/data/RenderablePhylogenyData.java

biojava3-forester/src/main/java/org/forester/archaeopteryx/phylogeny/data/RenderableVector.java

biojava3-forester/src/main/java/org/forester/archaeopteryx/tools/

biojava3-forester/src/main/java/org/forester/archaeopteryx/tools/AncestralTaxonomyInferrer.java

biojava3-forester/src/main/java/org/forester/archaeopteryx/tools/Blast.java

biojava3-forester/src/main/java/org/forester/archaeopteryx/tools/GoAnnotation.java

biojava3-forester/src/main/java/org/forester/archaeopteryx/tools/ImageLoader.java

biojava3-forester/src/main/java/org/forester/archaeopteryx/tools/InferenceManager.java

biojava3-forester/src/main/java/org/forester/archaeopteryx/tools/PhyloInferenceDialog.java

biojava3-forester/src/main/java/org/forester/archaeopteryx/tools/PhylogeneticInferenceOptions.java

biojava3-forester/src/main/java/org/forester/archaeopteryx/tools/PhylogeneticInferrer.java

biojava3-forester/src/main/java/org/forester/archaeopteryx/tools/ProcessPool.java

biojava3-forester/src/main/java/org/forester/archaeopteryx/tools/ProcessRunning.java

biojava3-forester/src/main/java/org/forester/archaeopteryx/tools/RunnableProcess.java

biojava3-forester/src/main/java/org/forester/archaeopteryx/tools/SequenceDataRetriver.java

biojava3-forester/src/main/java/org/forester/archaeopteryx/webservices/BasicPhylogeniesWebserviceClient.java

biojava3-forester/src/main/java/org/forester/archaeopteryx/webservices/PhylogeniesWebserviceClient.java

biojava3-forester/src/main/java/org/forester/archaeopteryx/webservices/WebserviceUtil.java

biojava3-forester/src/main/java/org/forester/archaeopteryx/webservices/WebservicesManager.java

biojava3-forester/src/main/java/org/forester/datastructures/Queue.java

biojava3-forester/src/main/java/org/forester/development/AbstractRenderer.java

biojava3-forester/src/main/java/org/forester/development/AminoAcid.java

biojava3-forester/src/main/java/org/forester/development/AminoAcidSequence.java

biojava3-forester/src/main/java/org/forester/development/BasicMsa.java

biojava3-forester/src/main/java/org/forester/development/DevelopmentTools.java

biojava3-forester/src/main/java/org/forester/development/Factory.java

biojava3-forester/src/main/java/org/forester/development/Hello3d.java

biojava3-forester/src/main/java/org/forester/development/HmmerRest.java

biojava3-forester/src/main/java/org/forester/development/Msa.java

biojava3-forester/src/main/java/org/forester/development/MsaFactory.java

biojava3-forester/src/main/java/org/forester/development/MsaRenderer.java

biojava3-forester/src/main/java/org/forester/development/RandomThing.java

biojava3-forester/src/main/java/org/forester/development/ResidueRenderer.java

biojava3-forester/src/main/java/org/forester/development/Sequence.java

biojava3-forester/src/main/java/org/forester/development/SimpleMutableMsa.java

biojava3-forester/src/main/java/org/forester/development/StreamBasedMsaFactory.java

biojava3-forester/src/main/java/org/forester/development/SupportCount.java

biojava3-forester/src/main/java/org/forester/development/Test.java

biojava3-forester/src/main/java/org/forester/development/Time.java

biojava3-forester/src/main/java/org/forester/development/neTest.java

biojava3-forester/src/main/java/org/forester/evoinference/

biojava3-forester/src/main/java/org/forester/evoinference/TestPhylogenyReconstruction.java

biojava3-forester/src/main/java/org/forester/evoinference/distance/

biojava3-forester/src/main/java/org/forester/evoinference/distance/NeighborJoining.java

biojava3-forester/src/main/java/org/forester/evoinference/distance/PairwiseDistanceCalculator.java

biojava3-forester/src/main/java/org/forester/evoinference/matrix/

biojava3-forester/src/main/java/org/forester/evoinference/matrix/character/

biojava3-forester/src/main/java/org/forester/evoinference/matrix/character/BasicCharacterStateMatrix.java

biojava3-forester/src/main/java/org/forester/evoinference/matrix/character/CharacterStateMatrix.java

biojava3-forester/src/main/java/org/forester/evoinference/matrix/character/DiscreteState.java

biojava3-forester/src/main/java/org/forester/evoinference/matrix/distance/

biojava3-forester/src/main/java/org/forester/evoinference/matrix/distance/BasicSymmetricalDistanceMatrix.java

biojava3-forester/src/main/java/org/forester/evoinference/matrix/distance/DistanceMatrix.java

biojava3-forester/src/main/java/org/forester/evoinference/parsimony/

biojava3-forester/src/main/java/org/forester/evoinference/parsimony/DolloParsimony.java

biojava3-forester/src/main/java/org/forester/evoinference/parsimony/FitchParsimony.java

biojava3-forester/src/main/java/org/forester/evoinference/parsimony/SankoffParsimony.java

biojava3-forester/src/main/java/org/forester/evoinference/tools/

biojava3-forester/src/main/java/org/forester/evoinference/tools/BootstrapResampler.java

biojava3-forester/src/main/java/org/forester/go/BasicGoRelationship.java

biojava3-forester/src/main/java/org/forester/go/BasicGoSubset.java

biojava3-forester/src/main/java/org/forester/go/BasicGoTerm.java

biojava3-forester/src/main/java/org/forester/go/BasicGoXRef.java

biojava3-forester/src/main/java/org/forester/go/GoId.java

biojava3-forester/src/main/java/org/forester/go/GoNameSpace.java

biojava3-forester/src/main/java/org/forester/go/GoRelationship.java

biojava3-forester/src/main/java/org/forester/go/GoSubset.java

biojava3-forester/src/main/java/org/forester/go/GoTerm.java

biojava3-forester/src/main/java/org/forester/go/GoUtils.java

biojava3-forester/src/main/java/org/forester/go/GoXRef.java

biojava3-forester/src/main/java/org/forester/go/Mapping.java

biojava3-forester/src/main/java/org/forester/go/OBOparser.java

biojava3-forester/src/main/java/org/forester/go/PfamToGoMapping.java

biojava3-forester/src/main/java/org/forester/go/PfamToGoParser.java

biojava3-forester/src/main/java/org/forester/go/TestGo.java

biojava3-forester/src/main/java/org/forester/go/etc/MetaOntologizer.java

biojava3-forester/src/main/java/org/forester/go/etc/OntologizerResult.java

biojava3-forester/src/main/java/org/forester/io/parsers/FastaParser.java

biojava3-forester/src/main/java/org/forester/io/parsers/GeneralMsaParser.java

biojava3-forester/src/main/java/org/forester/io/parsers/HmmPfamOutputParser.java

biojava3-forester/src/main/java/org/forester/io/parsers/HmmscanPerDomainTableParser.java

biojava3-forester/src/main/java/org/forester/io/parsers/ParserUtils.java

biojava3-forester/src/main/java/org/forester/io/parsers/PhylogenyParser.java

biojava3-forester/src/main/java/org/forester/io/parsers/PhylogenyParserException.java

biojava3-forester/src/main/java/org/forester/io/parsers/SymmetricalDistanceMatrixParser.java

biojava3-forester/src/main/java/org/forester/io/parsers/nexus/NexusBinaryStatesMatrixParser.java

biojava3-forester/src/main/java/org/forester/io/parsers/nexus/NexusCharactersParser.java

biojava3-forester/src/main/java/org/forester/io/parsers/nexus/NexusConstants.java

biojava3-forester/src/main/java/org/forester/io/parsers/nexus/NexusFormatException.java

biojava3-forester/src/main/java/org/forester/io/parsers/nexus/NexusPhylogeniesParser.java

biojava3-forester/src/main/java/org/forester/io/parsers/nexus/PaupLogParser.java

biojava3-forester/src/main/java/org/forester/io/parsers/nhx/NHXFormatException.java

biojava3-forester/src/main/java/org/forester/io/parsers/nhx/NHXParser.java

biojava3-forester/src/main/java/org/forester/io/parsers/nhx/NHXtags.java

biojava3-forester/src/main/java/org/forester/io/parsers/phyloxml/PhyloXmlDataFormatException.java

biojava3-forester/src/main/java/org/forester/io/parsers/phyloxml/PhyloXmlException.java

biojava3-forester/src/main/java/org/forester/io/parsers/phyloxml/PhyloXmlHandler.java

biojava3-forester/src/main/java/org/forester/io/parsers/phyloxml/PhyloXmlMapping.java

biojava3-forester/src/main/java/org/forester/io/parsers/phyloxml/PhyloXmlParser.java

biojava3-forester/src/main/java/org/forester/io/parsers/phyloxml/PhyloXmlUtil.java

biojava3-forester/src/main/java/org/forester/io/parsers/phyloxml/XmlElement.java

biojava3-forester/src/main/java/org/forester/io/parsers/phyloxml/data/

biojava3-forester/src/main/java/org/forester/io/parsers/phyloxml/data/AccessionParser.java

biojava3-forester/src/main/java/org/forester/io/parsers/phyloxml/data/AnnotationParser.java

biojava3-forester/src/main/java/org/forester/io/parsers/phyloxml/data/BinaryCharactersParser.java

biojava3-forester/src/main/java/org/forester/io/parsers/phyloxml/data/BranchWidthParser.java

biojava3-forester/src/main/java/org/forester/io/parsers/phyloxml/data/ColorParser.java

biojava3-forester/src/main/java/org/forester/io/parsers/phyloxml/data/ConfidenceParser.java

biojava3-forester/src/main/java/org/forester/io/parsers/phyloxml/data/DateParser.java

biojava3-forester/src/main/java/org/forester/io/parsers/phyloxml/data/DistributionParser.java

biojava3-forester/src/main/java/org/forester/io/parsers/phyloxml/data/DomainArchitectureParser.java

biojava3-forester/src/main/java/org/forester/io/parsers/phyloxml/data/EventParser.java

biojava3-forester/src/main/java/org/forester/io/parsers/phyloxml/data/IdentifierParser.java

biojava3-forester/src/main/java/org/forester/io/parsers/phyloxml/data/PhylogenyDataPhyloXmlParser.java

biojava3-forester/src/main/java/org/forester/io/parsers/phyloxml/data/PointParser.java

biojava3-forester/src/main/java/org/forester/io/parsers/phyloxml/data/PolygonParser.java

biojava3-forester/src/main/java/org/forester/io/parsers/phyloxml/data/PropertyParser.java

biojava3-forester/src/main/java/org/forester/io/parsers/phyloxml/data/ProteinDomainParser.java

biojava3-forester/src/main/java/org/forester/io/parsers/phyloxml/data/ReferenceParser.java

biojava3-forester/src/main/java/org/forester/io/parsers/phyloxml/data/SequenceParser.java

biojava3-forester/src/main/java/org/forester/io/parsers/phyloxml/data/SequenceRelationParser.java

biojava3-forester/src/main/java/org/forester/io/parsers/phyloxml/data/TaxonomyParser.java

biojava3-forester/src/main/java/org/forester/io/parsers/phyloxml/data/UriParser.java

biojava3-forester/src/main/java/org/forester/io/parsers/phyloxml/phylogenydata/

biojava3-forester/src/main/java/org/forester/io/parsers/phyloxml/phylogenydata/AccessionParser.java

biojava3-forester/src/main/java/org/forester/io/parsers/phyloxml/phylogenydata/AnnotationParser.java

biojava3-forester/src/main/java/org/forester/io/parsers/phyloxml/phylogenydata/BinaryCharactersParser.java

biojava3-forester/src/main/java/org/forester/io/parsers/phyloxml/phylogenydata/BranchWidthParser.java

biojava3-forester/src/main/java/org/forester/io/parsers/phyloxml/phylogenydata/ColorParser.java

biojava3-forester/src/main/java/org/forester/io/parsers/phyloxml/phylogenydata/ConfidenceParser.java

biojava3-forester/src/main/java/org/forester/io/parsers/phyloxml/phylogenydata/DateParser.java

biojava3-forester/src/main/java/org/forester/io/parsers/phyloxml/phylogenydata/DistributionParser.java

biojava3-forester/src/main/java/org/forester/io/parsers/phyloxml/phylogenydata/DomainArchitectureParser.java

biojava3-forester/src/main/java/org/forester/io/parsers/phyloxml/phylogenydata/EventParser.java

biojava3-forester/src/main/java/org/forester/io/parsers/phyloxml/phylogenydata/IdentifierParser.java

biojava3-forester/src/main/java/org/forester/io/parsers/phyloxml/phylogenydata/PhylogenyDataPhyloXmlParser.java

biojava3-forester/src/main/java/org/forester/io/parsers/phyloxml/phylogenydata/PointParser.java

biojava3-forester/src/main/java/org/forester/io/parsers/phyloxml/phylogenydata/PropertyParser.java

biojava3-forester/src/main/java/org/forester/io/parsers/phyloxml/phylogenydata/ProteinDomainParser.java

biojava3-forester/src/main/java/org/forester/io/parsers/phyloxml/phylogenydata/ReferenceParser.java

biojava3-forester/src/main/java/org/forester/io/parsers/phyloxml/phylogenydata/SequenceParser.java

biojava3-forester/src/main/java/org/forester/io/parsers/phyloxml/phylogenydata/SequenceRelationParser.java

biojava3-forester/src/main/java/org/forester/io/parsers/phyloxml/phylogenydata/TaxonomyParser.java

biojava3-forester/src/main/java/org/forester/io/parsers/phyloxml/phylogenydata/UriParser.java

biojava3-forester/src/main/java/org/forester/io/parsers/tol/TolParser.java

biojava3-forester/src/main/java/org/forester/io/parsers/tol/TolXmlHandler.java

biojava3-forester/src/main/java/org/forester/io/parsers/tol/TolXmlMapping.java

biojava3-forester/src/main/java/org/forester/io/parsers/util/

biojava3-forester/src/main/java/org/forester/io/parsers/util/ParserUtils.java

biojava3-forester/src/main/java/org/forester/io/parsers/util/PhylogenyParserException.java

biojava3-forester/src/main/java/org/forester/io/writers/PhyloXmlNodeWriter.java

biojava3-forester/src/main/java/org/forester/io/writers/PhylogenyWriter.java

biojava3-forester/src/main/java/org/forester/io/writers/SequenceWriter.java

biojava3-forester/src/main/java/org/forester/msa/

biojava3-forester/src/main/java/org/forester/msa/BasicMsa.java

biojava3-forester/src/main/java/org/forester/msa/Mafft.java

biojava3-forester/src/main/java/org/forester/msa/MafftOLD.java

biojava3-forester/src/main/java/org/forester/msa/Msa.java

biojava3-forester/src/main/java/org/forester/msa/MsaFormatException.java

biojava3-forester/src/main/java/org/forester/msa/MsaInferrer.java

biojava3-forester/src/main/java/org/forester/msa/MsaMethods.java

biojava3-forester/src/main/java/org/forester/msa/ResampleableMsa.java

biojava3-forester/src/main/java/org/forester/pccx/BasicExternalNodeBasedCoverageExtender.java

biojava3-forester/src/main/java/org/forester/pccx/BranchCountingBasedScoringMethod.java

biojava3-forester/src/main/java/org/forester/pccx/BranchLengthBasedScoringMethod.java

biojava3-forester/src/main/java/org/forester/pccx/Coverage.java

biojava3-forester/src/main/java/org/forester/pccx/CoverageCalculationMethod.java

biojava3-forester/src/main/java/org/forester/pccx/CoverageCalculationOptions.java

biojava3-forester/src/main/java/org/forester/pccx/CoverageCalculator.java

biojava3-forester/src/main/java/org/forester/pccx/CoverageExtender.java

biojava3-forester/src/main/java/org/forester/pccx/ExternalNodeBasedCoverage.java

biojava3-forester/src/main/java/org/forester/pccx/ExternalNodeBasedCoverageMethod.java

biojava3-forester/src/main/java/org/forester/pccx/ExternalNodeBasedCoverageMethodOptions.java

biojava3-forester/src/main/java/org/forester/pccx/LogBranchLengthBasedScoringMethod.java

biojava3-forester/src/main/java/org/forester/pccx/ModelingUtils.java

biojava3-forester/src/main/java/org/forester/pccx/ScoringMethodForExternalNode.java

biojava3-forester/src/main/java/org/forester/pccx/TestPccx.java

biojava3-forester/src/main/java/org/forester/phylogeny/Edge.java

biojava3-forester/src/main/java/org/forester/phylogeny/Phylogeny.java

biojava3-forester/src/main/java/org/forester/phylogeny/PhylogenyBranch.java

biojava3-forester/src/main/java/org/forester/phylogeny/PhylogenyMethods.java

biojava3-forester/src/main/java/org/forester/phylogeny/PhylogenyNode.java

biojava3-forester/src/main/java/org/forester/phylogeny/PhylogenyNodeI.java

biojava3-forester/src/main/java/org/forester/phylogeny/data/Accession.java

biojava3-forester/src/main/java/org/forester/phylogeny/data/Annotation.java

biojava3-forester/src/main/java/org/forester/phylogeny/data/BinaryCharacters.java

biojava3-forester/src/main/java/org/forester/phylogeny/data/BranchColor.java

biojava3-forester/src/main/java/org/forester/phylogeny/data/BranchData.java

biojava3-forester/src/main/java/org/forester/phylogeny/data/BranchWidth.java

biojava3-forester/src/main/java/org/forester/phylogeny/data/Confidence.java

biojava3-forester/src/main/java/org/forester/phylogeny/data/Date.java

biojava3-forester/src/main/java/org/forester/phylogeny/data/Distribution.java

biojava3-forester/src/main/java/org/forester/phylogeny/data/DomainArchitecture.java

biojava3-forester/src/main/java/org/forester/phylogeny/data/Event.java

biojava3-forester/src/main/java/org/forester/phylogeny/data/Identifier.java

biojava3-forester/src/main/java/org/forester/phylogeny/data/MultipleUris.java

biojava3-forester/src/main/java/org/forester/phylogeny/data/NodeData.java

biojava3-forester/src/main/java/org/forester/phylogeny/data/NodeVisualization.java

biojava3-forester/src/main/java/org/forester/phylogeny/data/PhylogenyData.java

biojava3-forester/src/main/java/org/forester/phylogeny/data/PhylogenyDataUtil.java

biojava3-forester/src/main/java/org/forester/phylogeny/data/Point.java

biojava3-forester/src/main/java/org/forester/phylogeny/data/Polygon.java

biojava3-forester/src/main/java/org/forester/phylogeny/data/PropertiesMap.java

biojava3-forester/src/main/java/org/forester/phylogeny/data/Property.java

biojava3-forester/src/main/java/org/forester/phylogeny/data/ProteinDomain.java

biojava3-forester/src/main/java/org/forester/phylogeny/data/Reference.java

biojava3-forester/src/main/java/org/forester/phylogeny/data/Sequence.java

biojava3-forester/src/main/java/org/forester/phylogeny/data/SequenceRelation.java

biojava3-forester/src/main/java/org/forester/phylogeny/data/Taxonomy.java

biojava3-forester/src/main/java/org/forester/phylogeny/data/Uri.java

biojava3-forester/src/main/java/org/forester/phylogeny/factories/BasicPhylogenyFactory.java

biojava3-forester/src/main/java/org/forester/phylogeny/factories/ParserBasedPhylogenyFactory.java

biojava3-forester/src/main/java/org/forester/phylogeny/factories/PhylogenyFactory.java

biojava3-forester/src/main/java/org/forester/phylogeny/iterators/ChildNodeIteratorForward.java

biojava3-forester/src/main/java/org/forester/phylogeny/iterators/ExternalForwardIterator.java

biojava3-forester/src/main/java/org/forester/phylogeny/iterators/LevelOrderTreeIterator.java

biojava3-forester/src/main/java/org/forester/phylogeny/iterators/PhylogenyNodeIterator.java

biojava3-forester/src/main/java/org/forester/phylogeny/iterators/PostOrderStackObject.java

biojava3-forester/src/main/java/org/forester/phylogeny/iterators/PostorderTreeIterator.java

biojava3-forester/src/main/java/org/forester/phylogeny/iterators/PreorderTreeIterator.java

biojava3-forester/src/main/java/org/forester/phylogenyinference/

biojava3-forester/src/main/java/org/forester/phylogenyinference/BasicCharacterStateMatrix.java

biojava3-forester/src/main/java/org/forester/phylogenyinference/BasicSymmetricalDistanceMatrix.java

biojava3-forester/src/main/java/org/forester/phylogenyinference/CharacterStateMatrix.java

biojava3-forester/src/main/java/org/forester/phylogenyinference/DiscreteState.java

biojava3-forester/src/main/java/org/forester/phylogenyinference/DistanceMatrix.java

biojava3-forester/src/main/java/org/forester/phylogenyinference/DistanceMatrixParser.java

biojava3-forester/src/main/java/org/forester/phylogenyinference/DistanceMethod.java

biojava3-forester/src/main/java/org/forester/phylogenyinference/DolloParsimony.java

biojava3-forester/src/main/java/org/forester/phylogenyinference/FitchParsimony.java

biojava3-forester/src/main/java/org/forester/phylogenyinference/NeighborJoining.java

biojava3-forester/src/main/java/org/forester/phylogenyinference/SankoffParsimony.java

biojava3-forester/src/main/java/org/forester/phylogenyinference/SymmetricalDistanceMatrixParser.java

biojava3-forester/src/main/java/org/forester/phylogenyinference/TestPhylogenyReconstruction.java

biojava3-forester/src/main/java/org/forester/protein/

biojava3-forester/src/main/java/org/forester/protein/BasicDomain.java

biojava3-forester/src/main/java/org/forester/protein/BasicProtein.java

biojava3-forester/src/main/java/org/forester/protein/BinaryDomainCombination.java

biojava3-forester/src/main/java/org/forester/protein/Domain.java

biojava3-forester/src/main/java/org/forester/protein/DomainId.java

biojava3-forester/src/main/java/org/forester/protein/Protein.java

biojava3-forester/src/main/java/org/forester/protein/ProteinId.java

biojava3-forester/src/main/java/org/forester/sdi/DistanceCalculator.java

biojava3-forester/src/main/java/org/forester/sdi/GSDI.java

biojava3-forester/src/main/java/org/forester/sdi/ORcount.java

biojava3-forester/src/main/java/org/forester/sdi/RIO.java

biojava3-forester/src/main/java/org/forester/sdi/RIOn.java

biojava3-forester/src/main/java/org/forester/sdi/SDI.java

biojava3-forester/src/main/java/org/forester/sdi/SDIException.java

biojava3-forester/src/main/java/org/forester/sdi/SDIR.java

biojava3-forester/src/main/java/org/forester/sdi/SDIdirectory.java

biojava3-forester/src/main/java/org/forester/sdi/SDIse.java

biojava3-forester/src/main/java/org/forester/sdi/Shin.java

biojava3-forester/src/main/java/org/forester/sdi/TaxonomyAssigner.java

biojava3-forester/src/main/java/org/forester/sdi/TestGSDI.java

biojava3-forester/src/main/java/org/forester/sdi/Tuplet.java

biojava3-forester/src/main/java/org/forester/sequence/

biojava3-forester/src/main/java/org/forester/sequence/BasicSequence.java

biojava3-forester/src/main/java/org/forester/sequence/Sequence.java

biojava3-forester/src/main/java/org/forester/species/

biojava3-forester/src/main/java/org/forester/species/BasicSpecies.java

biojava3-forester/src/main/java/org/forester/species/Species.java

biojava3-forester/src/main/java/org/forester/surfacing/AdjactantDirectedBinaryDomainCombination.java

biojava3-forester/src/main/java/org/forester/surfacing/AdjactantDirectedCombinableDomains.java

biojava3-forester/src/main/java/org/forester/surfacing/BasicBinaryDomainCombination.java

biojava3-forester/src/main/java/org/forester/surfacing/BasicCombinableDomains.java

biojava3-forester/src/main/java/org/forester/surfacing/BasicDomain.java

biojava3-forester/src/main/java/org/forester/surfacing/BasicDomainSimilarityCalculator.java

biojava3-forester/src/main/java/org/forester/surfacing/BasicGenomeWideCombinableDomains.java

biojava3-forester/src/main/java/org/forester/surfacing/BasicProtein.java

biojava3-forester/src/main/java/org/forester/surfacing/BasicSpecies.java

biojava3-forester/src/main/java/org/forester/surfacing/BinaryDomainCombination.java

biojava3-forester/src/main/java/org/forester/surfacing/CombinableDomains.java

biojava3-forester/src/main/java/org/forester/surfacing/CombinationsBasedPairwiseDomainSimilarity.java

biojava3-forester/src/main/java/org/forester/surfacing/CombinationsBasedPairwiseDomainSimilarityCalculator.java

biojava3-forester/src/main/java/org/forester/surfacing/CountsBasedPairwiseDomainSimilarity.java

biojava3-forester/src/main/java/org/forester/surfacing/DirectedBinaryDomainCombination.java

biojava3-forester/src/main/java/org/forester/surfacing/DirectedCombinableDomains.java

biojava3-forester/src/main/java/org/forester/surfacing/Domain.java

biojava3-forester/src/main/java/org/forester/surfacing/DomainArchitectureBasedGenomeSimilarityCalculator.java

biojava3-forester/src/main/java/org/forester/surfacing/DomainCountsBasedPairwiseSimilarityCalculator.java

biojava3-forester/src/main/java/org/forester/surfacing/DomainCountsDifferenceUtil.java

biojava3-forester/src/main/java/org/forester/surfacing/DomainId.java

biojava3-forester/src/main/java/org/forester/surfacing/DomainLengths.java

biojava3-forester/src/main/java/org/forester/surfacing/DomainLengthsTable.java

biojava3-forester/src/main/java/org/forester/surfacing/DomainParsimonyCalculator.java

biojava3-forester/src/main/java/org/forester/surfacing/DomainSimilarity.java

biojava3-forester/src/main/java/org/forester/surfacing/DomainSimilarityCalculator.java

biojava3-forester/src/main/java/org/forester/surfacing/GenomeWideCombinableDomains.java

biojava3-forester/src/main/java/org/forester/surfacing/MappingResults.java

biojava3-forester/src/main/java/org/forester/surfacing/PairwiseDomainSimilarity.java

biojava3-forester/src/main/java/org/forester/surfacing/PairwiseDomainSimilarityCalculator.java

biojava3-forester/src/main/java/org/forester/surfacing/PairwiseGenomeComparator.java

biojava3-forester/src/main/java/org/forester/surfacing/PrintableDomainSimilarity.java

biojava3-forester/src/main/java/org/forester/surfacing/PrintableSpeciesSpecificDomainSimilariyData.java

biojava3-forester/src/main/java/org/forester/surfacing/Protein.java

biojava3-forester/src/main/java/org/forester/surfacing/ProteinCountsBasedPairwiseDomainSimilarityCalculator.java

biojava3-forester/src/main/java/org/forester/surfacing/ProteinId.java

biojava3-forester/src/main/java/org/forester/surfacing/SimpleDomain.java

biojava3-forester/src/main/java/org/forester/surfacing/Species.java

biojava3-forester/src/main/java/org/forester/surfacing/SpeciesSpecificDomainSimilariyData.java

biojava3-forester/src/main/java/org/forester/surfacing/SurfacingConstants.java

biojava3-forester/src/main/java/org/forester/surfacing/SurfacingUtil.java

biojava3-forester/src/main/java/org/forester/surfacing/TestSurfacing.java

biojava3-forester/src/main/java/org/forester/test/Test.java

biojava3-forester/src/main/java/org/forester/test/examples/

biojava3-forester/src/main/java/org/forester/test/examples/Example1.java

biojava3-forester/src/main/java/org/forester/test/examples/Example2.java

biojava3-forester/src/main/java/org/forester/test/examples/Example3.java

biojava3-forester/src/main/java/org/forester/test/examples/Example4.java

biojava3-forester/src/main/java/org/forester/test/examples/Example5.java

biojava3-forester/src/main/java/org/forester/tools/ConfidenceAssessor.java

biojava3-forester/src/main/java/org/forester/tools/PhylogenyDecorator.java

biojava3-forester/src/main/java/org/forester/tools/SupportCount.java

biojava3-forester/src/main/java/org/forester/tools/TreeSplitMatrix.java

biojava3-forester/src/main/java/org/forester/util/AsciiHistogram.java

biojava3-forester/src/main/java/org/forester/util/BasicDescriptiveStatistics.java

biojava3-forester/src/main/java/org/forester/util/BasicTable.java

biojava3-forester/src/main/java/org/forester/util/BasicTableParser.java

biojava3-forester/src/main/java/org/forester/util/CommandLineArguments.java

biojava3-forester/src/main/java/org/forester/util/CommandProcessBuilder.java

biojava3-forester/src/main/java/org/forester/util/DescriptiveStatistics.java

biojava3-forester/src/main/java/org/forester/util/EasyWriter.java

biojava3-forester/src/main/java/org/forester/util/ExternalProgram.java

biojava3-forester/src/main/java/org/forester/util/FailedConditionCheckException.java

biojava3-forester/src/main/java/org/forester/util/ForesterConstants.java

biojava3-forester/src/main/java/org/forester/util/ForesterUtil.java

biojava3-forester/src/main/java/org/forester/util/GeneralTable.java

biojava3-forester/src/main/java/org/forester/util/IllegalFormatUseException.java

biojava3-forester/src/main/java/org/forester/util/SequenceIdParser.java

biojava3-forester/src/main/java/org/forester/util/SystemCommandExecutor.java

biojava3-forester/src/main/java/org/forester/util/ThreadedStreamHandler.java

biojava3-forester/src/main/java/org/forester/util/WindowsUtils.java

biojava3-forester/src/main/java/org/forester/ws/

biojava3-forester/src/main/java/org/forester/ws/hmmer/

biojava3-forester/src/main/java/org/forester/ws/hmmer/Test.java

biojava3-forester/src/main/java/org/forester/ws/seqdb/

biojava3-forester/src/main/java/org/forester/ws/seqdb/DatabaseTools.java

biojava3-forester/src/main/java/org/forester/ws/seqdb/EbiDbEntry.java

biojava3-forester/src/main/java/org/forester/ws/seqdb/SequenceDatabaseEntry.java

biojava3-forester/src/main/java/org/forester/ws/seqdb/SequenceDbWsTools.java

biojava3-forester/src/main/java/org/forester/ws/seqdb/UniProtEntry.java

biojava3-forester/src/main/java/org/forester/ws/seqdb/UniProtTaxonomy.java

biojava3-forester/src/main/java/org/forester/ws/uniprot/

biojava3-forester/src/main/java/org/forester/ws/uniprot/DatabaseTools.java

biojava3-forester/src/main/java/org/forester/ws/uniprot/EbiDbEntry.java

biojava3-forester/src/main/java/org/forester/ws/uniprot/SequenceDatabaseEntry.java

biojava3-forester/src/main/java/org/forester/ws/uniprot/SequenceDbWsTools.java

biojava3-forester/src/main/java/org/forester/ws/uniprot/UniProtEntry.java

biojava3-forester/src/main/java/org/forester/ws/uniprot/UniProtTaxonomy.java

biojava3-forester/src/main/java/org/forester/ws/wabi/

biojava3-forester/src/main/java/org/forester/ws/wabi/RestUtil.java

biojava3-forester/src/main/java/org/forester/ws/wabi/TxSearch.java

biojava3-forester/src/main/java/org/forester/ws/wabi/WabiTools.java

biojava3-forester/src/main/java/resources/

biojava3-forester/src/main/java/resources/NOTICE.txt

biojava3-forester/src/main/java/resources/commons-codec-1.5.jar

biojava3-forester/src/main/java/resources/itextpdf-5.1.0.jar

biojava3-genome/pom.xml

biojava3-genome/src/main/java/org/biojava3/genome/parsers/gff/Feature.java

biojava3-genome/src/main/java/org/biojava3/genome/parsers/gff/FeatureI.java

biojava3-genome/src/main/java/org/biojava3/genome/parsers/gff/FeatureList.java

biojava3-genome/src/main/java/org/biojava3/genome/parsers/gff/GFF3Reader.java

biojava3-genome/src/test/java/org/biojava3/genome/GeneFeatureHelperTest.java

biojava3-genome/src/test/resources/testoutput/volvox_all.faa

biojava3-genome/src/test/resources/testoutput/volvox_all_genes_exon_uppercase.gff3

biojava3-genome/src/test/resources/testoutput/volvox_length.gff3

biojava3-modfinder/pom.xml

biojava3-phylo/pom.xml

biojava3-phylo/src/main/java/org/biojava3/phylo/CheckTreeAccuracy.java

biojava3-phylo/src/main/java/org/biojava3/phylo/TreeConstructor.java

biojava3-protein-disorder/pom.xml

biojava3-protein-disorder/src/main/java/demo/

biojava3-protein-disorder/src/main/java/demo/PredictDisorder.java

biojava3-protein-disorder/src/main/java/org/biojava3/data/sequence/SequenceUtil.java

biojava3-protein-disorder/src/main/java/org/biojava3/ronn/Jronn.java

biojava3-protein-disorder/src/main/java/org/biojava3/ronn/ORonn.java

biojava3-protein-disorder/src/test/java/org/biojava3/ronn/NonstandardProteinCompoundTest.java

biojava3-sequencing/pom.xml

biojava3-structure-gui/pom.xml

biojava3-structure-gui/src/main/java/demo/DemoShowBiolAssembly.java

biojava3-structure-gui/src/main/java/org/biojava/bio/structure/align/gui/AlignmentCalcDB.java

biojava3-structure-gui/src/main/java/org/biojava/bio/structure/align/gui/AlignmentGui.java

biojava3-structure-gui/src/main/java/org/biojava/bio/structure/align/gui/DBResultTable.java

biojava3-structure-gui/src/main/java/org/biojava/bio/structure/align/gui/DBSearchGUI.java

biojava3-structure-gui/src/main/java/org/biojava/bio/structure/align/gui/MemoryMonitor.java

biojava3-structure-gui/src/main/java/org/biojava/bio/structure/align/gui/MenuCreator.java

biojava3-structure-gui/src/main/java/org/biojava/bio/structure/align/gui/ShowPDBIDListener.java

biojava3-structure-gui/src/main/java/org/biojava/bio/structure/align/gui/StructureLoaderThread.java

biojava3-structure-gui/src/main/java/org/biojava/bio/structure/align/gui/autosuggest/JAutoSuggest.java

biojava3-structure-gui/src/main/java/org/biojava/bio/structure/align/gui/jmol/JmolPanel.java

biojava3-structure-gui/src/main/java/org/biojava/bio/structure/align/gui/jmol/StructureAlignmentJmol.java

biojava3-structure-gui/src/main/java/org/biojava/bio/structure/align/webstart/AligUIManager.java

biojava3-structure-gui/src/main/java/org/biojava/bio/structure/gui/util/ScopSelectPanel.java

biojava3-structure/pom.xml

biojava3-structure/src/main/java/demo/DemoAtomCache.java

biojava3-structure/src/main/java/demo/DemoBerkeleyScop.java

biojava3-structure/src/main/java/demo/DemoCATH.java

biojava3-structure/src/main/java/demo/DemoSCOP.java

biojava3-structure/src/main/java/org/biojava/bio/structure/Chain.java

biojava3-structure/src/main/java/org/biojava/bio/structure/ChainImpl.java

biojava3-structure/src/main/java/org/biojava/bio/structure/DBRef.java

biojava3-structure/src/main/java/org/biojava/bio/structure/HetatomImpl.java

biojava3-structure/src/main/java/org/biojava/bio/structure/PDBCrystallographicInfo.java

biojava3-structure/src/main/java/org/biojava/bio/structure/PDBHeader.java

biojava3-structure/src/main/java/org/biojava/bio/structure/PDBStatus.java

biojava3-structure/src/main/java/org/biojava/bio/structure/ResidueNumber.java

biojava3-structure/src/main/java/org/biojava/bio/structure/Site.java

biojava3-structure/src/main/java/org/biojava/bio/structure/StructureImpl.java

biojava3-structure/src/main/java/org/biojava/bio/structure/StructureTools.java

biojava3-structure/src/main/java/org/biojava/bio/structure/align/ce/AbstractUserArgumentProcessor.java

biojava3-structure/src/main/java/org/biojava/bio/structure/align/ce/CeUserArgumentProcessor.java

biojava3-structure/src/main/java/org/biojava/bio/structure/align/ce/GuiWrapper.java

biojava3-structure/src/main/java/org/biojava/bio/structure/align/client/FarmJobRunnable.java

biojava3-structure/src/main/java/org/biojava/bio/structure/align/client/StructureName.java

biojava3-structure/src/main/java/org/biojava/bio/structure/align/fatcat/FatCatUserArgumentProcessor.java

biojava3-structure/src/main/java/org/biojava/bio/structure/align/util/AlignmentTools.java

biojava3-structure/src/main/java/org/biojava/bio/structure/align/util/AtomCache.java

biojava3-structure/src/main/java/org/biojava/bio/structure/align/util/SynchronizedOutFile.java

biojava3-structure/src/main/java/org/biojava/bio/structure/cath/

biojava3-structure/src/main/java/org/biojava/bio/structure/cath/CathCategory.java

biojava3-structure/src/main/java/org/biojava/bio/structure/cath/CathDatabase.java

biojava3-structure/src/main/java/org/biojava/bio/structure/cath/CathDomain.java

biojava3-structure/src/main/java/org/biojava/bio/structure/cath/CathFragment.java

biojava3-structure/src/main/java/org/biojava/bio/structure/cath/CathInstallation.java

biojava3-structure/src/main/java/org/biojava/bio/structure/cath/CathNode.java

biojava3-structure/src/main/java/org/biojava/bio/structure/cath/CathSegment.java

biojava3-structure/src/main/java/org/biojava/bio/structure/domain/PDBDomainProvider.java

biojava3-structure/src/main/java/org/biojava/bio/structure/io/FileParsingParameters.java

biojava3-structure/src/main/java/org/biojava/bio/structure/io/LocalCacheStructureProvider.java

biojava3-structure/src/main/java/org/biojava/bio/structure/io/MMCIFFileReader.java

biojava3-structure/src/main/java/org/biojava/bio/structure/io/PDBBioAssemblyParser.java

biojava3-structure/src/main/java/org/biojava/bio/structure/io/PDBFileParser.java

biojava3-structure/src/main/java/org/biojava/bio/structure/io/PDBFileReader.java

biojava3-structure/src/main/java/org/biojava/bio/structure/io/SeqRes2AtomAligner.java

biojava3-structure/src/main/java/org/biojava/bio/structure/io/StructureIO.java

biojava3-structure/src/main/java/org/biojava/bio/structure/io/mmcif/ChemCompConsumer.java

biojava3-structure/src/main/java/org/biojava/bio/structure/io/mmcif/MMcifConsumer.java

biojava3-structure/src/main/java/org/biojava/bio/structure/io/mmcif/SimpleMMcifConsumer.java

biojava3-structure/src/main/java/org/biojava/bio/structure/io/mmcif/SimpleMMcifParser.java

biojava3-structure/src/main/java/org/biojava/bio/structure/io/mmcif/model/PdbxStructAssembly.java

biojava3-structure/src/main/java/org/biojava/bio/structure/io/mmcif/model/PdbxStructAssemblyGen.java

biojava3-structure/src/main/java/org/biojava/bio/structure/io/mmcif/model/PdbxStructAssemblyGenXMLContainer.java

biojava3-structure/src/main/java/org/biojava/bio/structure/io/mmcif/model/PdbxStructAssemblyXMLContainer.java

biojava3-structure/src/main/java/org/biojava/bio/structure/io/mmcif/model/PdbxStructOperList.java

biojava3-structure/src/main/java/org/biojava/bio/structure/io/mmcif/model/PdbxStructOperListXMLContainer.java

biojava3-structure/src/main/java/org/biojava/bio/structure/io/mmcif/model/Refine.java

biojava3-structure/src/main/java/org/biojava/bio/structure/quaternary/

biojava3-structure/src/main/java/org/biojava/bio/structure/quaternary/BioAssemblyTools.java

biojava3-structure/src/main/java/org/biojava/bio/structure/quaternary/BiologicalAssemblyBuilder.java

biojava3-structure/src/main/java/org/biojava/bio/structure/quaternary/CartesianProduct.java

biojava3-structure/src/main/java/org/biojava/bio/structure/quaternary/ModelTransformationMatrix.java

biojava3-structure/src/main/java/org/biojava/bio/structure/quaternary/OperatorResolver.java

biojava3-structure/src/main/java/org/biojava/bio/structure/quaternary/OrderedPair.java

biojava3-structure/src/main/java/org/biojava/bio/structure/quaternary/io/

biojava3-structure/src/main/java/org/biojava/bio/structure/quaternary/io/BioUnitDataProvider.java

biojava3-structure/src/main/java/org/biojava/bio/structure/quaternary/io/BioUnitDataProviderFactory.java

biojava3-structure/src/main/java/org/biojava/bio/structure/quaternary/io/FileBasedPDBBioUnitDataProvider.java

biojava3-structure/src/main/java/org/biojava/bio/structure/quaternary/io/MmCifBiolAssemblyProvider.java

biojava3-structure/src/main/java/org/biojava/bio/structure/quaternary/io/MmCifPDBBiolAssemblyProvider.java

biojava3-structure/src/main/java/org/biojava/bio/structure/quaternary/io/PDBBioUnitDataProvider.java

biojava3-structure/src/main/java/org/biojava/bio/structure/quaternary/io/RawBioUnitDataProvider.java

biojava3-structure/src/main/java/org/biojava/bio/structure/quaternary/io/RemoteBioUnitDataProvider.java

biojava3-structure/src/main/java/org/biojava/bio/structure/quaternary/io/RemoteRawBioUnitDataProvider.java

biojava3-structure/src/main/java/org/biojava/bio/structure/scop/ScopDomain.java

biojava3-structure/src/main/java/org/biojava/bio/structure/scop/ScopInstallation.java

biojava3-structure/src/main/java/org/biojava/bio/structure/secstruc/BridgeType.java

biojava3-structure/src/main/java/org/biojava/bio/structure/secstruc/Ladder.java

biojava3-structure/src/main/java/org/biojava/bio/structure/secstruc/SecStruc.java

biojava3-structure/src/main/java/org/biojava/bio/structure/secstruc/SecStrucState.java

biojava3-structure/src/main/java/org/biojava/bio/structure/secstruc/SecStrucType.java

biojava3-structure/src/main/java/org/biojava3/

biojava3-structure/src/main/java/org/biojava3/structure/

biojava3-structure/src/main/java/org/biojava3/structure/StructureIO.java

biojava3-structure/src/main/resources/about.properties

biojava3-structure/src/main/resources/ce.properties

biojava3-structure/src/test/java/org/biojava/bio/structure/HeaderOnlyTest.java

biojava3-structure/src/test/java/org/biojava/bio/structure/MMcifTest.java

biojava3-structure/src/test/java/org/biojava/bio/structure/PDBFileParserTest.java

biojava3-structure/src/test/java/org/biojava/bio/structure/ResidueNumberTest.java

biojava3-structure/src/test/java/org/biojava/bio/structure/StructureIOTest.java

biojava3-structure/src/test/java/org/biojava/bio/structure/StructurePairAlignerTest.java

biojava3-structure/src/test/java/org/biojava/bio/structure/StructureTest.java

biojava3-structure/src/test/java/org/biojava/bio/structure/StructureToolsTest.java

biojava3-structure/src/test/java/org/biojava/bio/structure/Test1a4w.java

biojava3-structure/src/test/java/org/biojava/bio/structure/TestCloning.java

biojava3-structure/src/test/java/org/biojava/bio/structure/TestNucleotides.java

biojava3-structure/src/test/java/org/biojava/bio/structure/TestSECalignment.java

biojava3-structure/src/test/java/org/biojava/bio/structure/align/FlipAFPChainTest.java

biojava3-structure/src/test/java/org/biojava/bio/structure/align/ce/OptimalCECPMainTest.java

biojava3-structure/src/test/java/org/biojava/bio/structure/align/fatcat/

biojava3-structure/src/test/java/org/biojava/bio/structure/align/fatcat/AFPChainSerialisationTest.java

biojava3-structure/src/test/java/org/biojava/bio/structure/align/fatcat/FlipAFPChainTest.java

biojava3-structure/src/test/java/org/biojava/bio/structure/align/fatcat/MyTestHelper.java

biojava3-structure/src/test/java/org/biojava/bio/structure/align/fatcat/TestFlexibleRotationMatrices.java

biojava3-structure/src/test/java/org/biojava/bio/structure/align/fatcat/TestOutputStrings.java

biojava3-structure/src/test/java/org/biojava/bio/structure/align/util/AlignmentToolsTest.java

biojava3-structure/src/test/java/org/biojava/bio/structure/cath/

biojava3-structure/src/test/java/org/biojava/bio/structure/io/TestHardBioUnits.java

biojava3-structure/src/test/java/org/biojava/bio/structure/io/TestQuaternaryStructureProviders.java

biojava3-structure/src/test/java/org/biojava/bio/structure/scop/ScopTest.java

biojava3-structure/src/test/java/org/biojava/bio/structure/util/StringManipulationTestsHelper.java

biojava3-structure/src/test/resources/1a4w.cif

biojava3-structure/src/test/resources/1a4w.pdb

biojava3-structure/src/test/resources/1fdo.cif

biojava3-structure/src/test/resources/1fdo.pdb

biojava3-structure/src/test/resources/1j59.cif

biojava3-structure/src/test/resources/1j59.pdb

biojava3-structure/src/test/resources/1lnl.pdb

biojava3-structure/src/test/resources/1tap.pdb

biojava3-structure/src/test/resources/2kc9.cif

biojava3-structure/src/test/resources/2kc9.pdb

biojava3-structure/src/test/resources/5pti.cif

biojava3-structure/src/test/resources/5pti.pdb

biojava3-structure/src/test/resources/5pti_old.pdb

biojava3-structure/src/test/resources/ce_1fdo.A_2iv2.X.out

biojava3-ws/pom.xml

biojava3-ws/src/main/java/org/biojava3/ws/hmmer/HmmerDomain.java

biojava3-ws/src/main/java/org/biojava3/ws/hmmer/HmmerResult.java

biojava3-ws/src/main/java/org/biojava3/ws/hmmer/RemoteHmmerScan.java

debian/build.xml

debian/changelog

debian/get-orig-source

debian/patches/fix_ascii_character_issue

debian/patches/fix_ascii_characters_mapping

debian/patches/series

debian/patches/use_simple_json

integrationtest/

integrationtest/pom.xml

integrationtest/src/

integrationtest/src/main/

integrationtest/src/main/java/

integrationtest/src/test/

integrationtest/src/test/java/

integrationtest/src/test/java/org/

integrationtest/src/test/java/org/biojava/

integrationtest/src/test/java/org/biojava/bio/

integrationtest/src/test/java/org/biojava/bio/structure/

integrationtest/src/test/java/org/biojava/bio/structure/HeaderOnlyTest.java

integrationtest/src/test/java/org/biojava/bio/structure/MMcifTest.java

integrationtest/src/test/java/org/biojava/bio/structure/PDBFileParserTest.java

integrationtest/src/test/java/org/biojava/bio/structure/StructurePairAlignerTest.java

integrationtest/src/test/java/org/biojava/bio/structure/StructureTest.java

integrationtest/src/test/java/org/biojava/bio/structure/StructureToolsTest.java

integrationtest/src/test/java/org/biojava/bio/structure/Test1a4w.java

integrationtest/src/test/java/org/biojava/bio/structure/TestSECalignment.java

integrationtest/src/test/java/org/biojava/bio/structure/align/

integrationtest/src/test/java/org/biojava/bio/structure/align/FlipAFPChainTest.java

integrationtest/src/test/java/org/biojava/bio/structure/align/ce/

integrationtest/src/test/java/org/biojava/bio/structure/align/ce/OptimalCECPMainTest.java

integrationtest/src/test/java/org/biojava/bio/structure/align/fatcat/

integrationtest/src/test/java/org/biojava/bio/structure/align/fatcat/AFPChainSerialisationTest.java

integrationtest/src/test/java/org/biojava/bio/structure/align/fatcat/FlipAFPChainTest.java

integrationtest/src/test/java/org/biojava/bio/structure/align/fatcat/MyTestHelper.java

integrationtest/src/test/java/org/biojava/bio/structure/align/fatcat/TestFlexibleRotationMatrices.java

integrationtest/src/test/java/org/biojava/bio/structure/align/fatcat/TestOutputStrings.java

integrationtest/src/test/java/org/biojava/bio/structure/cath/

integrationtest/src/test/java/org/biojava/bio/structure/cath/CathTest.java

integrationtest/src/test/java/org/biojava/bio/structure/scop/

integrationtest/src/test/java/org/biojava/bio/structure/scop/ScopTest.java

integrationtest/src/test/java/org/biojava/bio/structure/util/

integrationtest/src/test/java/org/biojava/bio/structure/util/StringManipulationTestsHelper.java

integrationtest/src/test/java/org/integrationtest/

integrationtest/src/test/java/org/integrationtest/AppTest.java

integrationtest/src/test/resources/

integrationtest/src/test/resources/1a4w.cif

integrationtest/src/test/resources/1a4w.pdb

integrationtest/src/test/resources/1fdo.cif

integrationtest/src/test/resources/1fdo.pdb

integrationtest/src/test/resources/1j59.cif

integrationtest/src/test/resources/1j59.pdb

integrationtest/src/test/resources/1lnl.pdb

integrationtest/src/test/resources/1tap.pdb

integrationtest/src/test/resources/2kc9.cif

integrationtest/src/test/resources/2kc9.pdb

integrationtest/src/test/resources/5pti.cif

integrationtest/src/test/resources/5pti.pdb

integrationtest/src/test/resources/5pti_old.pdb

integrationtest/src/test/resources/ce_1fdo.A_2iv2.X.out

integrationtest/target/

integrationtest/target/failsafe-reports/

integrationtest/target/failsafe-reports/failsafe-summary.xml

integrationtest/target/generated-site/

integrationtest/target/generated-site/xdoc/

integrationtest/target/generated-site/xdoc/statscm/

integrationtest/target/generated-test-sources/

integrationtest/target/generated-test-sources/test-annotations/

integrationtest/target/integrationtest-3.0.5.jar

integrationtest/target/javadoc-bundle-options/

integrationtest/target/javadoc-bundle-options/javadoc-options-javadoc-resources.xml

integrationtest/target/maven-archiver/

integrationtest/target/maven-archiver/pom.properties

integrationtest/target/site/

integrationtest/target/site/css/

integrationtest/target/site/css/maven-base.css

integrationtest/target/site/css/maven-theme.css

integrationtest/target/site/css/print.css

integrationtest/target/site/css/site.css

integrationtest/target/site/dependencies.html

integrationtest/target/site/dependency-convergence.html

integrationtest/target/site/dependency-info.html

integrationtest/target/site/dependency-management.html

integrationtest/target/site/distribution-management.html

integrationtest/target/site/images/

integrationtest/target/site/images/close.gif

integrationtest/target/site/images/collapsed.gif

integrationtest/target/site/images/expanded.gif

integrationtest/target/site/images/external.png

integrationtest/target/site/images/icon_error_sml.gif

integrationtest/target/site/images/icon_info_sml.gif

integrationtest/target/site/images/icon_success_sml.gif

integrationtest/target/site/images/icon_warning_sml.gif

integrationtest/target/site/images/logos/

integrationtest/target/site/images/logos/build-by-maven-black.png

integrationtest/target/site/images/logos/build-by-maven-white.png

integrationtest/target/site/images/logos/maven-feather.png

integrationtest/target/site/images/newwindow.png

integrationtest/target/site/index.html

integrationtest/target/site/integration.html

integrationtest/target/site/issue-tracking.html

integrationtest/target/site/license.html

integrationtest/target/site/mail-lists.html

integrationtest/target/site/plugin-management.html

integrationtest/target/site/plugins.html

integrationtest/target/site/project-info.html

integrationtest/target/site/project-reports.html

integrationtest/target/site/project-summary.html

integrationtest/target/site/source-repository.html

integrationtest/target/site/statscm/

integrationtest/target/site/statscm/statscm.html

integrationtest/target/site/team-list.html

integrationtest/target/surefire-reports/

integrationtest/target/surefire-reports/TEST-org.biojava.bio.structure.HeaderOnlyTest.xml

integrationtest/target/surefire-reports/TEST-org.biojava.bio.structure.MMcifTest.xml

integrationtest/target/surefire-reports/TEST-org.biojava.bio.structure.PDBFileParserTest.xml

integrationtest/target/surefire-reports/TEST-org.biojava.bio.structure.StructurePairAlignerTest.xml

integrationtest/target/surefire-reports/TEST-org.biojava.bio.structure.StructureTest.xml

integrationtest/target/surefire-reports/TEST-org.biojava.bio.structure.StructureToolsTest.xml

integrationtest/target/surefire-reports/TEST-org.biojava.bio.structure.Test1a4w.xml

integrationtest/target/surefire-reports/TEST-org.biojava.bio.structure.TestSECalignment.xml

integrationtest/target/surefire-reports/TEST-org.biojava.bio.structure.align.FlipAFPChainTest.xml

integrationtest/target/surefire-reports/TEST-org.biojava.bio.structure.align.ce.OptimalCECPMainTest.xml

integrationtest/target/surefire-reports/TEST-org.biojava.bio.structure.align.fatcat.AFPChainSerialisationTest.xml

integrationtest/target/surefire-reports/TEST-org.biojava.bio.structure.align.fatcat.FlipAFPChainTest.xml

integrationtest/target/surefire-reports/TEST-org.biojava.bio.structure.align.fatcat.TestFlexibleRotationMatrices.xml

integrationtest/target/surefire-reports/TEST-org.biojava.bio.structure.align.fatcat.TestOutputStrings.xml

integrationtest/target/surefire-reports/TEST-org.biojava.bio.structure.cath.CathTest.xml

integrationtest/target/surefire-reports/TEST-org.biojava.bio.structure.scop.ScopTest.xml

integrationtest/target/surefire-reports/TEST-org.integrationtest.AppTest.xml

integrationtest/target/surefire-reports/org.biojava.bio.structure.HeaderOnlyTest.txt

integrationtest/target/surefire-reports/org.biojava.bio.structure.MMcifTest.txt

integrationtest/target/surefire-reports/org.biojava.bio.structure.PDBFileParserTest.txt

integrationtest/target/surefire-reports/org.biojava.bio.structure.StructurePairAlignerTest.txt

integrationtest/target/surefire-reports/org.biojava.bio.structure.StructureTest.txt

integrationtest/target/surefire-reports/org.biojava.bio.structure.StructureToolsTest.txt

integrationtest/target/surefire-reports/org.biojava.bio.structure.Test1a4w.txt

integrationtest/target/surefire-reports/org.biojava.bio.structure.TestSECalignment.txt

integrationtest/target/surefire-reports/org.biojava.bio.structure.align.FlipAFPChainTest.txt

integrationtest/target/surefire-reports/org.biojava.bio.structure.align.ce.OptimalCECPMainTest.txt

integrationtest/target/surefire-reports/org.biojava.bio.structure.align.fatcat.AFPChainSerialisationTest.txt

integrationtest/target/surefire-reports/org.biojava.bio.structure.align.fatcat.FlipAFPChainTest.txt

integrationtest/target/surefire-reports/org.biojava.bio.structure.align.fatcat.TestFlexibleRotationMatrices.txt

integrationtest/target/surefire-reports/org.biojava.bio.structure.align.fatcat.TestOutputStrings.txt

integrationtest/target/surefire-reports/org.biojava.bio.structure.cath.CathTest.txt

integrationtest/target/surefire-reports/org.biojava.bio.structure.scop.ScopTest.txt

integrationtest/target/surefire-reports/org.integrationtest.AppTest.txt

integrationtest/target/surefire/

integrationtest/target/test-classes/

integrationtest/target/test-classes/1a4w.cif

integrationtest/target/test-classes/1a4w.pdb

integrationtest/target/test-classes/1fdo.cif

integrationtest/target/test-classes/1fdo.pdb

integrationtest/target/test-classes/1j59.cif

integrationtest/target/test-classes/1j59.pdb

integrationtest/target/test-classes/1lnl.pdb

integrationtest/target/test-classes/1tap.pdb

integrationtest/target/test-classes/2kc9.cif

integrationtest/target/test-classes/2kc9.pdb

integrationtest/target/test-classes/5pti.cif

integrationtest/target/test-classes/5pti.pdb

integrationtest/target/test-classes/5pti_old.pdb

integrationtest/target/test-classes/ce_1fdo.A_2iv2.X.out

integrationtest/target/test-classes/org/

integrationtest/target/test-classes/org/biojava/

integrationtest/target/test-classes/org/biojava/bio/

integrationtest/target/test-classes/org/biojava/bio/structure/

integrationtest/target/test-classes/org/biojava/bio/structure/HeaderOnlyTest.class

integrationtest/target/test-classes/org/biojava/bio/structure/MMcifTest.class

integrationtest/target/test-classes/org/biojava/bio/structure/PDBFileParserTest.class

integrationtest/target/test-classes/org/biojava/bio/structure/StructurePairAlignerTest.class

integrationtest/target/test-classes/org/biojava/bio/structure/StructureTest.class

integrationtest/target/test-classes/org/biojava/bio/structure/StructureToolsTest.class

integrationtest/target/test-classes/org/biojava/bio/structure/Test1a4w.class

integrationtest/target/test-classes/org/biojava/bio/structure/TestSECalignment.class

integrationtest/target/test-classes/org/biojava/bio/structure/align/

integrationtest/target/test-classes/org/biojava/bio/structure/align/FlipAFPChainTest.class

integrationtest/target/test-classes/org/biojava/bio/structure/align/ce/

integrationtest/target/test-classes/org/biojava/bio/structure/align/ce/OptimalCECPMainTest.class

integrationtest/target/test-classes/org/biojava/bio/structure/align/fatcat/

integrationtest/target/test-classes/org/biojava/bio/structure/align/fatcat/AFPChainSerialisationTest.class

integrationtest/target/test-classes/org/biojava/bio/structure/align/fatcat/FlipAFPChainTest.class

integrationtest/target/test-classes/org/biojava/bio/structure/align/fatcat/MyTestHelper.class

integrationtest/target/test-classes/org/biojava/bio/structure/align/fatcat/TestFlexibleRotationMatrices.class

integrationtest/target/test-classes/org/biojava/bio/structure/align/fatcat/TestOutputStrings.class

integrationtest/target/test-classes/org/biojava/bio/structure/cath/

integrationtest/target/test-classes/org/biojava/bio/structure/cath/CathTest.class

integrationtest/target/test-classes/org/biojava/bio/structure/scop/

integrationtest/target/test-classes/org/biojava/bio/structure/scop/ScopTest.class

integrationtest/target/test-classes/org/biojava/bio/structure/util/

integrationtest/target/test-classes/org/biojava/bio/structure/util/StringManipulationTestsHelper.class

integrationtest/target/test-classes/org/integrationtest/

integrationtest/target/test-classes/org/integrationtest/AppTest.class

protein-comparison-tool/

protein-comparison-tool/pom.xml

protein-comparison-tool/src/

protein-comparison-tool/src/main/

protein-comparison-tool/src/main/assembly/

protein-comparison-tool/src/main/assembly/LICENSE

protein-comparison-tool/src/main/assembly/assembly.xml

protein-comparison-tool/src/main/assembly/db.out

protein-comparison-tool/src/main/assembly/example.lst

protein-comparison-tool/src/main/assembly/runCE.sh

protein-comparison-tool/src/main/assembly/runFATCAT.sh

protein-comparison-tool/src/main/assembly/startFarmJob.sh

protein-comparison-tool/target/

protein-comparison-tool/target/archive-tmp/

protein-comparison-tool/target/generated-site/

protein-comparison-tool/target/generated-site/xdoc/

protein-comparison-tool/target/generated-site/xdoc/statscm/

protein-comparison-tool/target/javadoc-bundle-options/

protein-comparison-tool/target/javadoc-bundle-options/javadoc-options-javadoc-resources.xml

protein-comparison-tool/target/maven-archiver/

protein-comparison-tool/target/maven-archiver/pom.properties

protein-comparison-tool/target/protein-comparison-tool-3.0.5-bundle.tar.gz

protein-comparison-tool/target/protein-comparison-tool-3.0.5.jar

protein-comparison-tool/target/site/

protein-comparison-tool/target/site/css/

protein-comparison-tool/target/site/css/maven-base.css

protein-comparison-tool/target/site/css/maven-theme.css

protein-comparison-tool/target/site/css/print.css

protein-comparison-tool/target/site/css/site.css

protein-comparison-tool/target/site/dependencies.html

protein-comparison-tool/target/site/dependency-convergence.html

protein-comparison-tool/target/site/dependency-info.html

protein-comparison-tool/target/site/dependency-management.html

protein-comparison-tool/target/site/distribution-management.html

protein-comparison-tool/target/site/images/

protein-comparison-tool/target/site/images/close.gif

protein-comparison-tool/target/site/images/collapsed.gif

protein-comparison-tool/target/site/images/expanded.gif

protein-comparison-tool/target/site/images/external.png

protein-comparison-tool/target/site/images/icon_error_sml.gif

protein-comparison-tool/target/site/images/icon_info_sml.gif

protein-comparison-tool/target/site/images/icon_success_sml.gif

protein-comparison-tool/target/site/images/icon_warning_sml.gif

protein-comparison-tool/target/site/images/logos/

protein-comparison-tool/target/site/images/logos/build-by-maven-black.png

protein-comparison-tool/target/site/images/logos/build-by-maven-white.png

protein-comparison-tool/target/site/images/logos/maven-feather.png

protein-comparison-tool/target/site/images/newwindow.png

protein-comparison-tool/target/site/index.html

protein-comparison-tool/target/site/integration.html

protein-comparison-tool/target/site/issue-tracking.html

protein-comparison-tool/target/site/license.html

protein-comparison-tool/target/site/mail-lists.html

protein-comparison-tool/target/site/plugin-management.html

protein-comparison-tool/target/site/plugins.html

protein-comparison-tool/target/site/project-info.html

protein-comparison-tool/target/site/project-reports.html

protein-comparison-tool/target/site/project-summary.html

protein-comparison-tool/target/site/source-repository.html

protein-comparison-tool/target/site/statscm/

protein-comparison-tool/target/site/statscm/statscm.html

protein-comparison-tool/target/site/team-list.html

protein-comparison-tool/target/surefire/

Older »