All changesets

Changeset [b76135082d50626d247376119050329a41f1b0c6] by Colin

Revision b76135082d50626d247376119050329a41f1b0c6, committed by Colin · June 23rd, 2014 @ 09:10 AM

582 changed files

• M server/Apollo/src/org/bbop/apollo/config/Configuration.java
• M server/Apollo/src/org/bbop/apollo/editor/AbstractAnnotationSession.java
• M server/Apollo/src/org/bbop/apollo/editor/AnnotationEditor.java
• M server/Apollo/src/org/bbop/apollo/editor/session/AnnotationSession.java
• M server/Apollo/src/org/bbop/apollo/editor/session/DataStore.java
• M server/Apollo/src/org/bbop/apollo/editor/session/MemoryDataStore.java
• M server/Apollo/src/org/bbop/apollo/tests/AnnotationEditorTest.java
• M server/Apollo/src/org/bbop/apollo/tests/AnnotationSessionTest.java
• M server/Apollo/src/org/bbop/apollo/tests/BlastAlignmentTest.java
• M server/Apollo/src/org/bbop/apollo/tests/BlatCommandLineTest.java
• M server/Apollo/src/org/bbop/apollo/tools/seq/search/Alignment.java
• M server/Apollo/src/org/bbop/apollo/tools/seq/search/AlignmentParsingException.java
• M server/Apollo/src/org/bbop/apollo/tools/seq/search/SequenceSearchTool.java
• M server/Apollo/src/org/bbop/apollo/tools/seq/search/SequenceSearchToolException.java
• M server/Apollo/src/org/bbop/apollo/tools/seq/search/blast/BlastAlignment.java
• M server/Apollo/src/org/bbop/apollo/tools/seq/search/blast/TabDelimittedAlignment.java
• M server/Apollo/src/org/bbop/apollo/tools/seq/search/blat/BlatCommandLine.java
• M server/Apollo/src/org/bbop/apollo/tools/seq/search/blat/BlatCommandLineProteinToNucleotide.java
• M server/GBOL/generated/org/gmod/gbol/simpleObject/generated/AbstractAcquisition.java
• M server/GBOL/generated/org/gmod/gbol/simpleObject/generated/AbstractAcquisitionProperty.java
• M server/GBOL/generated/org/gmod/gbol/simpleObject/generated/AbstractAcquisitionRelationship.java
• M server/GBOL/generated/org/gmod/gbol/simpleObject/generated/AbstractAnalysis.java
• M server/GBOL/generated/org/gmod/gbol/simpleObject/generated/AbstractAnalysisFeature.java
• M server/GBOL/generated/org/gmod/gbol/simpleObject/generated/AbstractAnalysisProperty.java
• M server/GBOL/generated/org/gmod/gbol/simpleObject/generated/AbstractArrayDesign.java
• M server/GBOL/generated/org/gmod/gbol/simpleObject/generated/AbstractArrayDesignProperty.java
• M server/GBOL/generated/org/gmod/gbol/simpleObject/generated/AbstractAssay.java
• M server/GBOL/generated/org/gmod/gbol/simpleObject/generated/AbstractAssayBiomaterial.java
• M server/GBOL/generated/org/gmod/gbol/simpleObject/generated/AbstractAssayProject.java
• M server/GBOL/generated/org/gmod/gbol/simpleObject/generated/AbstractAssayProperty.java
• M server/GBOL/generated/org/gmod/gbol/simpleObject/generated/AbstractBiomaterial.java
• M server/GBOL/generated/org/gmod/gbol/simpleObject/generated/AbstractBiomaterialDBXref.java
• M server/GBOL/generated/org/gmod/gbol/simpleObject/generated/AbstractBiomaterialProperty.java
• M server/GBOL/generated/org/gmod/gbol/simpleObject/generated/AbstractBiomaterialRelationship.java
• M server/GBOL/generated/org/gmod/gbol/simpleObject/generated/AbstractBiomaterialTreatment.java
• M server/GBOL/generated/org/gmod/gbol/simpleObject/generated/AbstractCV.java
• M server/GBOL/generated/org/gmod/gbol/simpleObject/generated/AbstractCVTerm.java
• M server/GBOL/generated/org/gmod/gbol/simpleObject/generated/AbstractCVTermDBXref.java
• M server/GBOL/generated/org/gmod/gbol/simpleObject/generated/AbstractCVTermPath.java
• M server/GBOL/generated/org/gmod/gbol/simpleObject/generated/AbstractCVTermProperty.java
• M server/GBOL/generated/org/gmod/gbol/simpleObject/generated/AbstractCVTermRelationship.java
• M server/GBOL/generated/org/gmod/gbol/simpleObject/generated/AbstractCVTermSynonym.java
• M server/GBOL/generated/org/gmod/gbol/simpleObject/generated/AbstractChannel.java
• M server/GBOL/generated/org/gmod/gbol/simpleObject/generated/AbstractContact.java
• M server/GBOL/generated/org/gmod/gbol/simpleObject/generated/AbstractContactRelationship.java
• M server/GBOL/generated/org/gmod/gbol/simpleObject/generated/AbstractControl.java
• M server/GBOL/generated/org/gmod/gbol/simpleObject/generated/AbstractDB.java
• M server/GBOL/generated/org/gmod/gbol/simpleObject/generated/AbstractDBXref.java
• M server/GBOL/generated/org/gmod/gbol/simpleObject/generated/AbstractDBXrefProperty.java
• M server/GBOL/generated/org/gmod/gbol/simpleObject/generated/AbstractEImage.java
• M server/GBOL/generated/org/gmod/gbol/simpleObject/generated/AbstractElement.java
• M server/GBOL/generated/org/gmod/gbol/simpleObject/generated/AbstractElementRelationship.java
• M server/GBOL/generated/org/gmod/gbol/simpleObject/generated/AbstractElementResult.java
• M server/GBOL/generated/org/gmod/gbol/simpleObject/generated/AbstractElementResultRelationship.java
• M server/GBOL/generated/org/gmod/gbol/simpleObject/generated/AbstractEnvironment.java
• M server/GBOL/generated/org/gmod/gbol/simpleObject/generated/AbstractEnvironmentCVTerm.java
• M server/GBOL/generated/org/gmod/gbol/simpleObject/generated/AbstractExpression.java
• M server/GBOL/generated/org/gmod/gbol/simpleObject/generated/AbstractExpressionCVTerm.java
• M server/GBOL/generated/org/gmod/gbol/simpleObject/generated/AbstractExpressionCVTermProperty.java
• M server/GBOL/generated/org/gmod/gbol/simpleObject/generated/AbstractExpressionImage.java
• M server/GBOL/generated/org/gmod/gbol/simpleObject/generated/AbstractExpressionProperty.java
• M server/GBOL/generated/org/gmod/gbol/simpleObject/generated/AbstractExpressionPublication.java
• M server/GBOL/generated/org/gmod/gbol/simpleObject/generated/AbstractFeature.java
• M server/GBOL/generated/org/gmod/gbol/simpleObject/generated/AbstractFeatureCVTerm.java
• M server/GBOL/generated/org/gmod/gbol/simpleObject/generated/AbstractFeatureCVTermDBXref.java
• M server/GBOL/generated/org/gmod/gbol/simpleObject/generated/AbstractFeatureCVTermProperty.java
• M server/GBOL/generated/org/gmod/gbol/simpleObject/generated/AbstractFeatureCVTermPublication.java
• M server/GBOL/generated/org/gmod/gbol/simpleObject/generated/AbstractFeatureDBXref.java
• M server/GBOL/generated/org/gmod/gbol/simpleObject/generated/AbstractFeatureExpression.java
• M server/GBOL/generated/org/gmod/gbol/simpleObject/generated/AbstractFeatureExpressionProperty.java
• M server/GBOL/generated/org/gmod/gbol/simpleObject/generated/AbstractFeatureGenotype.java
• M server/GBOL/generated/org/gmod/gbol/simpleObject/generated/AbstractFeatureLocation.java
• M server/GBOL/generated/org/gmod/gbol/simpleObject/generated/AbstractFeatureLocationPublication.java
• M server/GBOL/generated/org/gmod/gbol/simpleObject/generated/AbstractFeatureMap.java
• M server/GBOL/generated/org/gmod/gbol/simpleObject/generated/AbstractFeatureMapPublication.java
• M server/GBOL/generated/org/gmod/gbol/simpleObject/generated/AbstractFeaturePhenotype.java
• M server/GBOL/generated/org/gmod/gbol/simpleObject/generated/AbstractFeaturePosition.java
• M server/GBOL/generated/org/gmod/gbol/simpleObject/generated/AbstractFeatureProperty.java
• M server/GBOL/generated/org/gmod/gbol/simpleObject/generated/AbstractFeaturePropertyPublication.java
• M server/GBOL/generated/org/gmod/gbol/simpleObject/generated/AbstractFeaturePublication.java
• M server/GBOL/generated/org/gmod/gbol/simpleObject/generated/AbstractFeaturePublicationProperty.java
• M server/GBOL/generated/org/gmod/gbol/simpleObject/generated/AbstractFeatureRange.java
• M server/GBOL/generated/org/gmod/gbol/simpleObject/generated/AbstractFeatureRelationship.java
• M server/GBOL/generated/org/gmod/gbol/simpleObject/generated/AbstractFeatureRelationshipProperty.java
• M server/GBOL/generated/org/gmod/gbol/simpleObject/generated/AbstractFeatureRelationshipPropertyPublication.java
• M server/GBOL/generated/org/gmod/gbol/simpleObject/generated/AbstractFeatureRelationshipPublication.java
• M server/GBOL/generated/org/gmod/gbol/simpleObject/generated/AbstractFeatureSynonym.java
• M server/GBOL/generated/org/gmod/gbol/simpleObject/generated/AbstractGenotype.java
• M server/GBOL/generated/org/gmod/gbol/simpleObject/generated/AbstractLibrary.java
• M server/GBOL/generated/org/gmod/gbol/simpleObject/generated/AbstractLibraryCVTerm.java
• M server/GBOL/generated/org/gmod/gbol/simpleObject/generated/AbstractLibraryDBXref.java
• M server/GBOL/generated/org/gmod/gbol/simpleObject/generated/AbstractLibraryFeature.java
• M server/GBOL/generated/org/gmod/gbol/simpleObject/generated/AbstractLibraryProperty.java
• M server/GBOL/generated/org/gmod/gbol/simpleObject/generated/AbstractLibraryPropertyPublication.java
• M server/GBOL/generated/org/gmod/gbol/simpleObject/generated/AbstractLibraryPublication.java
• M server/GBOL/generated/org/gmod/gbol/simpleObject/generated/AbstractLibrarySynonym.java
• M server/GBOL/generated/org/gmod/gbol/simpleObject/generated/AbstractMAGEDocumentation.java
• M server/GBOL/generated/org/gmod/gbol/simpleObject/generated/AbstractMAGEML.java
• M server/GBOL/generated/org/gmod/gbol/simpleObject/generated/AbstractOrganism.java
• M server/GBOL/generated/org/gmod/gbol/simpleObject/generated/AbstractOrganismDBXref.java
• M server/GBOL/generated/org/gmod/gbol/simpleObject/generated/AbstractOrganismProperty.java
• M server/GBOL/generated/org/gmod/gbol/simpleObject/generated/AbstractPhenotype.java
• M server/GBOL/generated/org/gmod/gbol/simpleObject/generated/AbstractPhenotypeCVTerm.java
• M server/GBOL/generated/org/gmod/gbol/simpleObject/generated/AbstractPhenotypeComparison.java
• M server/GBOL/generated/org/gmod/gbol/simpleObject/generated/AbstractPhenotypeComparisonCVTerm.java
• M server/GBOL/generated/org/gmod/gbol/simpleObject/generated/AbstractPhenotypeDescription.java
• M server/GBOL/generated/org/gmod/gbol/simpleObject/generated/AbstractPhenotypeStatement.java
• M server/GBOL/generated/org/gmod/gbol/simpleObject/generated/AbstractPhylogeneticNode.java
• M server/GBOL/generated/org/gmod/gbol/simpleObject/generated/AbstractPhylogeneticNodeDBXref.java
• M server/GBOL/generated/org/gmod/gbol/simpleObject/generated/AbstractPhylogeneticNodeOrganism.java
• M server/GBOL/generated/org/gmod/gbol/simpleObject/generated/AbstractPhylogeneticNodeProperty.java
• M server/GBOL/generated/org/gmod/gbol/simpleObject/generated/AbstractPhylogeneticNodePublication.java
• M server/GBOL/generated/org/gmod/gbol/simpleObject/generated/AbstractPhylogeneticNodeRelationship.java
• M server/GBOL/generated/org/gmod/gbol/simpleObject/generated/AbstractPhylogeneticTree.java
• M server/GBOL/generated/org/gmod/gbol/simpleObject/generated/AbstractPhylogeneticTreePublication.java
• M server/GBOL/generated/org/gmod/gbol/simpleObject/generated/AbstractProject.java
• M server/GBOL/generated/org/gmod/gbol/simpleObject/generated/AbstractProtocol.java
• M server/GBOL/generated/org/gmod/gbol/simpleObject/generated/AbstractProtocolParameter.java
• M server/GBOL/generated/org/gmod/gbol/simpleObject/generated/AbstractPublication.java
• M server/GBOL/generated/org/gmod/gbol/simpleObject/generated/AbstractPublicationAuthor.java
• M server/GBOL/generated/org/gmod/gbol/simpleObject/generated/AbstractPublicationDBXref.java
• M server/GBOL/generated/org/gmod/gbol/simpleObject/generated/AbstractPublicationProperty.java
• M server/GBOL/generated/org/gmod/gbol/simpleObject/generated/AbstractPublicationRelationship.java
• M server/GBOL/generated/org/gmod/gbol/simpleObject/generated/AbstractQuantification.java
• M server/GBOL/generated/org/gmod/gbol/simpleObject/generated/AbstractQuantificationProperty.java
• M server/GBOL/generated/org/gmod/gbol/simpleObject/generated/AbstractQuantificationRelationship.java
• M server/GBOL/generated/org/gmod/gbol/simpleObject/generated/AbstractStock.java
• M server/GBOL/generated/org/gmod/gbol/simpleObject/generated/AbstractStockCVTerm.java
• M server/GBOL/generated/org/gmod/gbol/simpleObject/generated/AbstractStockCollection.java
• M server/GBOL/generated/org/gmod/gbol/simpleObject/generated/AbstractStockCollectionProperty.java
• M server/GBOL/generated/org/gmod/gbol/simpleObject/generated/AbstractStockCollectionStock.java
• M server/GBOL/generated/org/gmod/gbol/simpleObject/generated/AbstractStockDBXref.java
• M server/GBOL/generated/org/gmod/gbol/simpleObject/generated/AbstractStockGenotype.java
• M server/GBOL/generated/org/gmod/gbol/simpleObject/generated/AbstractStockProperty.java
• M server/GBOL/generated/org/gmod/gbol/simpleObject/generated/AbstractStockPropertyPublication.java
• M server/GBOL/generated/org/gmod/gbol/simpleObject/generated/AbstractStockPublication.java
• M server/GBOL/generated/org/gmod/gbol/simpleObject/generated/AbstractStockRelationship.java
• M server/GBOL/generated/org/gmod/gbol/simpleObject/generated/AbstractStockRelationshipPublication.java
• M server/GBOL/generated/org/gmod/gbol/simpleObject/generated/AbstractStudy.java
• M server/GBOL/generated/org/gmod/gbol/simpleObject/generated/AbstractStudyAssay.java
• M server/GBOL/generated/org/gmod/gbol/simpleObject/generated/AbstractStudyDesign.java
• M server/GBOL/generated/org/gmod/gbol/simpleObject/generated/AbstractStudyDesignProperty.java
• M server/GBOL/generated/org/gmod/gbol/simpleObject/generated/AbstractStudyFactor.java
• M server/GBOL/generated/org/gmod/gbol/simpleObject/generated/AbstractStudyFactorValue.java
• M server/GBOL/generated/org/gmod/gbol/simpleObject/generated/AbstractStudyProperty.java
• M server/GBOL/generated/org/gmod/gbol/simpleObject/generated/AbstractStudyPropertyFeature.java
• M server/GBOL/generated/org/gmod/gbol/simpleObject/generated/AbstractSynonym.java
• M server/GBOL/generated/org/gmod/gbol/simpleObject/generated/AbstractTableInfo.java
• M server/GBOL/generated/org/gmod/gbol/simpleObject/generated/AbstractTreatment.java
• M server/GBOL/src/org/gmod/gbol/bioObject/AbstractBioFeature.java
• M server/GBOL/src/org/gmod/gbol/bioObject/AbstractBioFeatureProperty.java
• M server/GBOL/src/org/gmod/gbol/bioObject/AbstractBioFeatureRelationship.java
• M server/GBOL/src/org/gmod/gbol/bioObject/AbstractBioObject.java
• M server/GBOL/src/org/gmod/gbol/bioObject/AbstractSimpleObjectIterator.java
• M server/GBOL/src/org/gmod/gbol/bioObject/AbstractSingleLocationBioFeature.java
• M server/GBOL/src/org/gmod/gbol/bioObject/AbstractSingleLocationBioObject.java
• M server/GBOL/src/org/gmod/gbol/bioObject/CDS.java
• M server/GBOL/src/org/gmod/gbol/bioObject/Chromosome.java
• M server/GBOL/src/org/gmod/gbol/bioObject/Comment.java
• M server/GBOL/src/org/gmod/gbol/bioObject/Contig.java
• M server/GBOL/src/org/gmod/gbol/bioObject/Deletion.java
• M server/GBOL/src/org/gmod/gbol/bioObject/Description.java
• M server/GBOL/src/org/gmod/gbol/bioObject/Exon.java
• M server/GBOL/src/org/gmod/gbol/bioObject/FeatureAttribute.java
• M server/GBOL/src/org/gmod/gbol/bioObject/FlankingRegion.java
• M server/GBOL/src/org/gmod/gbol/bioObject/Frameshift.java
• M server/GBOL/src/org/gmod/gbol/bioObject/Gene.java
• M server/GBOL/src/org/gmod/gbol/bioObject/GenericFeatureProperty.java
• M server/GBOL/src/org/gmod/gbol/bioObject/Insertion.java
• M server/GBOL/src/org/gmod/gbol/bioObject/Intron.java
• M server/GBOL/src/org/gmod/gbol/bioObject/MRNA.java
• M server/GBOL/src/org/gmod/gbol/bioObject/Match.java
• M server/GBOL/src/org/gmod/gbol/bioObject/MiRNA.java
• M server/GBOL/src/org/gmod/gbol/bioObject/Minus1Frameshift.java
• M server/GBOL/src/org/gmod/gbol/bioObject/Minus2Frameshift.java
• M server/GBOL/src/org/gmod/gbol/bioObject/NcRNA.java
• M server/GBOL/src/org/gmod/gbol/bioObject/NonCanonicalFivePrimeSpliceSite.java
• M server/GBOL/src/org/gmod/gbol/bioObject/NonCanonicalThreePrimeSpliceSite.java
• M server/GBOL/src/org/gmod/gbol/bioObject/Owner.java
• M server/GBOL/src/org/gmod/gbol/bioObject/PartOf.java
• M server/GBOL/src/org/gmod/gbol/bioObject/Plus1Frameshift.java
• M server/GBOL/src/org/gmod/gbol/bioObject/Plus2Frameshift.java
• M server/GBOL/src/org/gmod/gbol/bioObject/Pseudogene.java
• M server/GBOL/src/org/gmod/gbol/bioObject/RRNA.java
• M server/GBOL/src/org/gmod/gbol/bioObject/ReadthroughStopCodon.java
• M server/GBOL/src/org/gmod/gbol/bioObject/Region.java
• M server/GBOL/src/org/gmod/gbol/bioObject/RepeatRegion.java
• M server/GBOL/src/org/gmod/gbol/bioObject/Scaffold.java
• M server/GBOL/src/org/gmod/gbol/bioObject/SequenceAlteration.java
• M server/GBOL/src/org/gmod/gbol/bioObject/SequenceAttribute.java
• M server/GBOL/src/org/gmod/gbol/bioObject/SequenceFeature.java
• M server/GBOL/src/org/gmod/gbol/bioObject/SnRNA.java
• M server/GBOL/src/org/gmod/gbol/bioObject/SnoRNA.java
• M server/GBOL/src/org/gmod/gbol/bioObject/SpliceSite.java
• M server/GBOL/src/org/gmod/gbol/bioObject/Status.java
• M server/GBOL/src/org/gmod/gbol/bioObject/StopCodonReadThrough.java
• M server/GBOL/src/org/gmod/gbol/bioObject/Substitution.java
• M server/GBOL/src/org/gmod/gbol/bioObject/Symbol.java
• M server/GBOL/src/org/gmod/gbol/bioObject/TRNA.java
• M server/GBOL/src/org/gmod/gbol/bioObject/Transcript.java
• M server/GBOL/src/org/gmod/gbol/bioObject/TranscriptAttribute.java
• M server/GBOL/src/org/gmod/gbol/bioObject/TransposableElement.java
• M server/GBOL/src/org/gmod/gbol/bioObject/conf/BioObjectConfiguration.java
• M server/GBOL/src/org/gmod/gbol/bioObject/conf/BioObjectConfigurationException.java
• M server/GBOL/src/org/gmod/gbol/bioObject/io/BioObjectHandler.java
• M server/GBOL/src/org/gmod/gbol/bioObject/io/BioObjectIOInterface.java
• M server/GBOL/src/org/gmod/gbol/bioObject/io/FastaHandler.java
• M server/GBOL/src/org/gmod/gbol/bioObject/io/GFF3Handler.java
• M server/GBOL/src/org/gmod/gbol/bioObject/util/BioObjectUtil.java
• M server/GBOL/src/org/gmod/gbol/generator/HibernateConfigurationExporter.java
• M server/GBOL/src/org/gmod/gbol/generator/SimpleObjectFactoryExporter.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/AbstractSimpleObject.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/AbstractSimpleObjectIterator.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/Acquisition.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/AcquisitionProperty.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/AcquisitionRelationship.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/Analysis.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/AnalysisFeature.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/AnalysisProperty.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/ArrayDesign.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/ArrayDesignProperty.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/Assay.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/AssayBiomaterial.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/AssayProject.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/AssayProperty.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/Biomaterial.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/BiomaterialDBXref.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/BiomaterialProperty.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/BiomaterialRelationship.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/BiomaterialTreatment.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/CV.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/CVTerm.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/CVTermDBXref.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/CVTermPath.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/CVTermProperty.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/CVTermRelationship.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/CVTermSynonym.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/Channel.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/Contact.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/ContactRelationship.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/Control.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/DB.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/DBXref.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/DBXrefProperty.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/EImage.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/Element.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/ElementRelationship.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/ElementResult.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/ElementResultRelationship.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/Environment.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/EnvironmentCVTerm.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/Expression.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/ExpressionCVTerm.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/ExpressionCVTermProperty.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/ExpressionImage.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/ExpressionProperty.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/ExpressionPublication.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/Feature.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/FeatureCVTerm.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/FeatureCVTermDBXref.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/FeatureCVTermProperty.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/FeatureCVTermPublication.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/FeatureDBXref.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/FeatureExpression.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/FeatureExpressionProperty.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/FeatureGenotype.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/FeatureLocation.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/FeatureLocationPublication.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/FeatureMap.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/FeatureMapPublication.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/FeaturePhenotype.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/FeaturePosition.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/FeatureProperty.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/FeaturePropertyPublication.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/FeaturePublication.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/FeaturePublicationProperty.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/FeatureRange.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/FeatureRelationship.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/FeatureRelationshipProperty.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/FeatureRelationshipPropertyPublication.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/FeatureRelationshipPublication.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/FeatureSynonym.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/Genotype.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/Library.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/LibraryCVTerm.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/LibraryDBXref.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/LibraryFeature.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/LibraryProperty.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/LibraryPropertyPublication.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/LibraryPublication.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/LibrarySynonym.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/MAGEDocumentation.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/MAGEML.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/Organism.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/OrganismDBXref.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/OrganismProperty.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/Phenotype.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/PhenotypeCVTerm.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/PhenotypeComparison.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/PhenotypeComparisonCVTerm.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/PhenotypeDescription.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/PhenotypeStatement.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/PhylogeneticNode.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/PhylogeneticNodeDBXref.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/PhylogeneticNodeOrganism.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/PhylogeneticNodeProperty.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/PhylogeneticNodePublication.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/PhylogeneticNodeRelationship.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/PhylogeneticTree.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/PhylogeneticTreePublication.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/Project.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/Protocol.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/ProtocolParameter.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/Publication.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/PublicationAuthor.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/PublicationDBXref.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/PublicationProperty.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/PublicationRelationship.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/Quantification.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/QuantificationProperty.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/QuantificationRelationship.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/SimpleObjectIteratorInterface.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/Stock.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/StockCVTerm.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/StockCollection.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/StockCollectionProperty.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/StockCollectionStock.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/StockDBXref.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/StockGenotype.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/StockProperty.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/StockPropertyPublication.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/StockPublication.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/StockRelationship.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/StockRelationshipPublication.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/Study.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/StudyAssay.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/StudyDesign.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/StudyDesignProperty.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/StudyFactor.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/StudyFactorValue.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/StudyProperty.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/StudyPropertyFeature.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/Synonym.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/TableInfo.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/Treatment.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/generated/AbstractAcquisition.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/generated/AbstractAcquisitionProperty.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/generated/AbstractAcquisitionRelationship.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/generated/AbstractAnalysis.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/generated/AbstractAnalysisFeature.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/generated/AbstractAnalysisProperty.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/generated/AbstractArrayDesign.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/generated/AbstractArrayDesignProperty.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/generated/AbstractAssay.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/generated/AbstractAssayBiomaterial.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/generated/AbstractAssayProject.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/generated/AbstractAssayProperty.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/generated/AbstractBiomaterial.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/generated/AbstractBiomaterialDBXref.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/generated/AbstractBiomaterialProperty.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/generated/AbstractBiomaterialRelationship.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/generated/AbstractBiomaterialTreatment.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/generated/AbstractCV.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/generated/AbstractCVTerm.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/generated/AbstractCVTermDBXref.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/generated/AbstractCVTermPath.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/generated/AbstractCVTermProperty.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/generated/AbstractCVTermRelationship.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/generated/AbstractCVTermSynonym.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/generated/AbstractChannel.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/generated/AbstractContact.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/generated/AbstractContactRelationship.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/generated/AbstractControl.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/generated/AbstractDB.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/generated/AbstractDBXref.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/generated/AbstractDBXrefProperty.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/generated/AbstractEImage.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/generated/AbstractElement.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/generated/AbstractElementRelationship.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/generated/AbstractElementResult.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/generated/AbstractElementResultRelationship.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/generated/AbstractEnvironment.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/generated/AbstractEnvironmentCVTerm.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/generated/AbstractExpression.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/generated/AbstractExpressionCVTerm.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/generated/AbstractExpressionCVTermProperty.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/generated/AbstractExpressionImage.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/generated/AbstractExpressionProperty.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/generated/AbstractExpressionPublication.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/generated/AbstractFeature.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/generated/AbstractFeatureCVTerm.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/generated/AbstractFeatureCVTermDBXref.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/generated/AbstractFeatureCVTermProperty.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/generated/AbstractFeatureCVTermPublication.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/generated/AbstractFeatureDBXref.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/generated/AbstractFeatureExpression.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/generated/AbstractFeatureExpressionProperty.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/generated/AbstractFeatureGenotype.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/generated/AbstractFeatureLocation.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/generated/AbstractFeatureLocationPublication.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/generated/AbstractFeatureMap.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/generated/AbstractFeatureMapPublication.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/generated/AbstractFeaturePhenotype.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/generated/AbstractFeaturePosition.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/generated/AbstractFeatureProperty.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/generated/AbstractFeaturePropertyPublication.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/generated/AbstractFeaturePublication.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/generated/AbstractFeaturePublicationProperty.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/generated/AbstractFeatureRange.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/generated/AbstractFeatureRelationship.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/generated/AbstractFeatureRelationshipProperty.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/generated/AbstractFeatureRelationshipPropertyPublication.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/generated/AbstractFeatureRelationshipPublication.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/generated/AbstractFeatureSynonym.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/generated/AbstractGenotype.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/generated/AbstractLibrary.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/generated/AbstractLibraryCVTerm.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/generated/AbstractLibraryDBXref.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/generated/AbstractLibraryFeature.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/generated/AbstractLibraryProperty.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/generated/AbstractLibraryPropertyPublication.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/generated/AbstractLibraryPublication.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/generated/AbstractLibrarySynonym.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/generated/AbstractMAGEDocumentation.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/generated/AbstractMAGEML.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/generated/AbstractOrganism.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/generated/AbstractOrganismDBXref.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/generated/AbstractOrganismProperty.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/generated/AbstractPhenotype.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/generated/AbstractPhenotypeCVTerm.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/generated/AbstractPhenotypeComparison.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/generated/AbstractPhenotypeComparisonCVTerm.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/generated/AbstractPhenotypeDescription.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/generated/AbstractPhenotypeStatement.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/generated/AbstractPhylogeneticNode.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/generated/AbstractPhylogeneticNodeDBXref.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/generated/AbstractPhylogeneticNodeOrganism.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/generated/AbstractPhylogeneticNodeProperty.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/generated/AbstractPhylogeneticNodePublication.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/generated/AbstractPhylogeneticNodeRelationship.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/generated/AbstractPhylogeneticTree.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/generated/AbstractPhylogeneticTreePublication.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/generated/AbstractProject.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/generated/AbstractProtocol.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/generated/AbstractProtocolParameter.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/generated/AbstractPublication.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/generated/AbstractPublicationAuthor.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/generated/AbstractPublicationDBXref.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/generated/AbstractPublicationProperty.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/generated/AbstractPublicationRelationship.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/generated/AbstractQuantification.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/generated/AbstractQuantificationProperty.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/generated/AbstractQuantificationRelationship.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/generated/AbstractStock.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/generated/AbstractStockCVTerm.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/generated/AbstractStockCollection.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/generated/AbstractStockCollectionProperty.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/generated/AbstractStockCollectionStock.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/generated/AbstractStockDBXref.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/generated/AbstractStockGenotype.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/generated/AbstractStockProperty.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/generated/AbstractStockPropertyPublication.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/generated/AbstractStockPublication.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/generated/AbstractStockRelationship.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/generated/AbstractStockRelationshipPublication.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/generated/AbstractStudy.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/generated/AbstractStudyAssay.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/generated/AbstractStudyDesign.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/generated/AbstractStudyDesignProperty.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/generated/AbstractStudyFactor.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/generated/AbstractStudyFactorValue.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/generated/AbstractStudyProperty.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/generated/AbstractStudyPropertyFeature.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/generated/AbstractSynonym.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/generated/AbstractTableInfo.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/generated/AbstractTreatment.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/io/AbstractSimpleIO.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/io/FileHandler.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/io/SimpleObjectIOException.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/io/SimpleObjectIOInterface.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/io/impl/GFF3Handler.java
• M server/GBOL/src/org/gmod/gbol/simpleObject/io/impl/HibernateHandler.java
• M server/GBOL/src/org/gmod/gbol/test/AbstractGBOLHibernateTest.java
• M server/GBOL/src/org/gmod/gbol/test/BioFeatureTest.java
• M server/GBOL/src/org/gmod/gbol/test/BioObjectConfigurationTest.java
• M server/GBOL/src/org/gmod/gbol/test/BioObjectHandlerTest.java
• M server/GBOL/src/org/gmod/gbol/test/BioObjectHandlerTestGeneDB.java
• M server/GBOL/src/org/gmod/gbol/test/FileHandlerTest.java
• M server/GBOL/src/org/gmod/gbol/test/FlybaseConfigurationTest.java
• M server/GBOL/src/org/gmod/gbol/test/FlybaseGenotypeTest.java
• M server/GBOL/src/org/gmod/gbol/test/GFF3HandlerTest.java
• M server/GBOL/src/org/gmod/gbol/test/HibernateHandlerTest.java
• M server/GBOL/src/org/gmod/gbol/test/HibernateHandlerTestAmel.java
• M server/GBOL/src/org/gmod/gbol/test/HibernateHandlerTestGeneDB.java
• M server/GBOL/src/org/gmod/gbol/test/SequenceUtilTest.java
• M server/GBOL/src/org/gmod/gbol/util/GBOLUtilException.java
• M server/GBOL/src/org/gmod/gbol/util/HashComparator.java
• M server/GBOL/src/org/gmod/gbol/util/HibernateUtil.java
• M server/GBOL/src/org/gmod/gbol/util/SequenceUtil.java
• M server/WebApollo/src/org/bbop/apollo/web/AnnotationChangeNotificationService.java
• M server/WebApollo/src/org/bbop/apollo/web/AnnotationEditorService.java
• M server/WebApollo/src/org/bbop/apollo/web/ErrorReportValve.java
• M server/WebApollo/src/org/bbop/apollo/web/Login.java
• M server/WebApollo/src/org/bbop/apollo/web/ProxyService.java
• M server/WebApollo/src/org/bbop/apollo/web/UserManagerService.java
• M server/WebApollo/src/org/bbop/apollo/web/config/CannedComments.java
• M server/WebApollo/src/org/bbop/apollo/web/config/ServerConfiguration.java
• M server/WebApollo/src/org/bbop/apollo/web/data/FeatureLazyResidues.java
• M server/WebApollo/src/org/bbop/apollo/web/data/FeatureSequenceChunkManager.java
• M server/WebApollo/src/org/bbop/apollo/web/dataadapter/DataAdapter.java
• M server/WebApollo/src/org/bbop/apollo/web/dataadapter/IOService.java
• M server/WebApollo/src/org/bbop/apollo/web/dataadapter/chado/ChadoDataAdapter.java
• M server/WebApollo/src/org/bbop/apollo/web/dataadapter/chado/ChadoIO.java
• M server/WebApollo/src/org/bbop/apollo/web/dataadapter/chado/ChadoJEDatabaseIO.java
• M server/WebApollo/src/org/bbop/apollo/web/dataadapter/fasta/FastaDataAdapter.java
• M server/WebApollo/src/org/bbop/apollo/web/dataadapter/fasta/FastaIO.java
• M server/WebApollo/src/org/bbop/apollo/web/dataadapter/fasta/FastaJEDatabaseIO.java
• M server/WebApollo/src/org/bbop/apollo/web/dataadapter/gff3/Gff3DataAdapter.java
• M server/WebApollo/src/org/bbop/apollo/web/dataadapter/gff3/Gff3IO.java
• M server/WebApollo/src/org/bbop/apollo/web/dataadapter/gff3/Gff3JEDatabaseIO.java
• M server/WebApollo/src/org/bbop/apollo/web/datastore/AbstractDataStore.java
• M server/WebApollo/src/org/bbop/apollo/web/datastore/AbstractDataStoreManager.java
• M server/WebApollo/src/org/bbop/apollo/web/datastore/DataStoreChangeEvent.java
• M server/WebApollo/src/org/bbop/apollo/web/datastore/DataStoreChangeListener.java
• M server/WebApollo/src/org/bbop/apollo/web/datastore/JEDatabase.java
• M server/WebApollo/src/org/bbop/apollo/web/datastore/JEDatabaseIterator.java
• M server/WebApollo/src/org/bbop/apollo/web/datastore/JESerializedDatabase.java
• M server/WebApollo/src/org/bbop/apollo/web/datastore/history/AbstractHistoryStore.java
• M server/WebApollo/src/org/bbop/apollo/web/datastore/history/AbstractHistoryStoreManager.java
• M server/WebApollo/src/org/bbop/apollo/web/datastore/history/CompoundTransaction.java
• M server/WebApollo/src/org/bbop/apollo/web/datastore/history/JEHistoryDatabase.java
• M server/WebApollo/src/org/bbop/apollo/web/datastore/history/Transaction.java
• M server/WebApollo/src/org/bbop/apollo/web/datastore/history/TransactionList.java
• M server/WebApollo/src/org/bbop/apollo/web/datastore/session/JEDatabaseSessionHybridArrayDataStore.java
• M server/WebApollo/src/org/bbop/apollo/web/datastore/session/JEDatabaseSessionHybridBetterDataStore.java
• M server/WebApollo/src/org/bbop/apollo/web/datastore/session/JEDatabaseSessionHybridDataStore.java
• M server/WebApollo/src/org/bbop/apollo/web/datastore/session/JEDatabaseSessionHybridWithTreeDataStore.java
• M server/WebApollo/src/org/bbop/apollo/web/datastore/session/JEDatabaseSessionMemoryDataStore.java
• M server/WebApollo/src/org/bbop/apollo/web/name/AbstractNameAdapter.java
• M server/WebApollo/src/org/bbop/apollo/web/name/FeatureNameAdapter.java
• M server/WebApollo/src/org/bbop/apollo/web/name/HttpSessionNameAdapter.java
• M server/WebApollo/src/org/bbop/apollo/web/name/HttpSessionTimeStampNameAdapter.java
• M server/WebApollo/src/org/bbop/apollo/web/name/PreDefinedNameAdapter.java
• M server/WebApollo/src/org/bbop/apollo/web/name/TemplateNameAdapter.java
• M server/WebApollo/src/org/bbop/apollo/web/overlap/NoOverlapper.java
• M server/WebApollo/src/org/bbop/apollo/web/overlap/OrfOverlapper.java
• M server/WebApollo/src/org/bbop/apollo/web/overlap/Overlapper.java
• M server/WebApollo/src/org/bbop/apollo/web/overlap/SimpleOverlapper.java
• M server/WebApollo/src/org/bbop/apollo/web/proxy/AbstractProxy.java
• M server/WebApollo/src/org/bbop/apollo/web/proxy/EUtilsProxy.java
• M server/WebApollo/src/org/bbop/apollo/web/test/AnnotationEditorServiceTest.java
• M server/WebApollo/src/org/bbop/apollo/web/test/AnnotationEditorServiceWithPersistentStorageTest.java
• M server/WebApollo/src/org/bbop/apollo/web/test/FeatureLazyResiduesTest.java
• M server/WebApollo/src/org/bbop/apollo/web/test/FormatUtilTest.java
• M server/WebApollo/src/org/bbop/apollo/web/test/JEDatabasePrintValues.java
• M server/WebApollo/src/org/bbop/apollo/web/test/JEDatabaseTest.java
• M server/WebApollo/src/org/bbop/apollo/web/test/JEHistoryDatabasePrintValues.java
• M server/WebApollo/src/org/bbop/apollo/web/test/JSONUtilTest.java
• M server/WebApollo/src/org/bbop/apollo/web/tools/FixGeneBoundaries.java
• M server/WebApollo/src/org/bbop/apollo/web/tools/JEDatabaseMerger.java
• M server/WebApollo/src/org/bbop/apollo/web/tools/RemoveIsoforms.java
• M server/WebApollo/src/org/bbop/apollo/web/tools/RemoveOrphanFeatures.java
• M server/WebApollo/src/org/bbop/apollo/web/tools/RemoveTopLevelFeaturesById.java
• M server/WebApollo/src/org/bbop/apollo/web/tools/UpdateSequenceAlterations.java
• M server/WebApollo/src/org/bbop/apollo/web/tools/UpdateTranscriptToMrna.java
• M server/WebApollo/src/org/bbop/apollo/web/track/AmelTrackNameComparator.java
• M server/WebApollo/src/org/bbop/apollo/web/track/BtauTrackNameComparator.java
• M server/WebApollo/src/org/bbop/apollo/web/track/DecreasingLengthTrackNameComparator.java
• M server/WebApollo/src/org/bbop/apollo/web/track/DefaultTrackNameComparator.java
• M server/WebApollo/src/org/bbop/apollo/web/track/IncreasingLengthTrackNameComparator.java
• M server/WebApollo/src/org/bbop/apollo/web/track/TrackNameComparator.java
• M server/WebApollo/src/org/bbop/apollo/web/user/Permission.java
• M server/WebApollo/src/org/bbop/apollo/web/user/UserAuthentication.java
• M server/WebApollo/src/org/bbop/apollo/web/user/UserAuthenticationException.java
• M server/WebApollo/src/org/bbop/apollo/web/user/UserManager.java
• M server/WebApollo/src/org/bbop/apollo/web/user/browserid/BrowserIdUserAuthentication.java
• M server/WebApollo/src/org/bbop/apollo/web/user/encryptedlocaldb/EncryptedLocalDbUserAuthentication.java
• M server/WebApollo/src/org/bbop/apollo/web/user/localdb/LocalDbUserAuthentication.java
• M server/WebApollo/src/org/bbop/apollo/web/util/FeatureIterator.java
• M server/WebApollo/src/org/bbop/apollo/web/util/FormatUtil.java
• M server/WebApollo/src/org/bbop/apollo/web/util/JSONUtil.java
• M server/WebApollo/src/org/bbop/apollo/web/util/Pair.java