A B C D E F G H I J L M N O P Q R S T U V Y
All Classes All Packages

A

abbreviation - Variable in class org.intermine.model.bio.OrthologueEvidenceCodeShadow

abstractText - Variable in class org.intermine.model.bio.PublicationShadow

addAdjacentGenes(Gene) - Method in interface org.intermine.model.bio.IntergenicRegion

addAdjacentGenes(Gene) - Method in class org.intermine.model.bio.IntergenicRegionShadow

addAuthors(Author) - Method in interface org.intermine.model.bio.Publication

addAuthors(Author) - Method in class org.intermine.model.bio.PublicationShadow

addBioEntities(BioEntity) - Method in interface org.intermine.model.bio.DataSet

addBioEntities(BioEntity) - Method in class org.intermine.model.bio.DataSetShadow

addcDSs(CDS) - Method in interface org.intermine.model.bio.Gene

addcDSs(CDS) - Method in class org.intermine.model.bio.GeneShadow

addcDSs(CDS) - Method in interface org.intermine.model.bio.Protein

addcDSs(CDS) - Method in class org.intermine.model.bio.ProteinShadow

addChildFeatures(SequenceFeature) - Method in class org.intermine.model.bio.CDSShadow

addChildFeatures(SequenceFeature) - Method in class org.intermine.model.bio.ChromosomeShadow

addChildFeatures(SequenceFeature) - Method in class org.intermine.model.bio.ExonShadow

addChildFeatures(SequenceFeature) - Method in class org.intermine.model.bio.GeneFlankingRegionShadow

addChildFeatures(SequenceFeature) - Method in class org.intermine.model.bio.GeneShadow

addChildFeatures(SequenceFeature) - Method in class org.intermine.model.bio.IntergenicRegionShadow

addChildFeatures(SequenceFeature) - Method in class org.intermine.model.bio.IntronShadow

addChildFeatures(SequenceFeature) - Method in interface org.intermine.model.bio.SequenceFeature

addChildFeatures(SequenceFeature) - Method in class org.intermine.model.bio.SequenceFeatureShadow

addChildFeatures(SequenceFeature) - Method in class org.intermine.model.bio.SyntenicRegionShadow

addChildFeatures(SequenceFeature) - Method in class org.intermine.model.bio.TranscriptShadow

addChildFeatures(SequenceFeature) - Method in class org.intermine.model.bio.UTRShadow

addCollectionElement(String, InterMineObject) - Method in class org.intermine.model.bio.AnnotatableShadow

addCollectionElement(String, InterMineObject) - Method in class org.intermine.model.bio.AuthorShadow

addCollectionElement(String, InterMineObject) - Method in class org.intermine.model.bio.BioEntityShadow

addCollectionElement(String, InterMineObject) - Method in class org.intermine.model.bio.CDSShadow

addCollectionElement(String, InterMineObject) - Method in class org.intermine.model.bio.ChromosomeShadow

addCollectionElement(String, InterMineObject) - Method in class org.intermine.model.bio.CommentShadow

addCollectionElement(String, InterMineObject) - Method in class org.intermine.model.bio.CrossReferenceShadow

addCollectionElement(String, InterMineObject) - Method in class org.intermine.model.bio.DataSetShadow

addCollectionElement(String, InterMineObject) - Method in class org.intermine.model.bio.DataSourceShadow

addCollectionElement(String, InterMineObject) - Method in class org.intermine.model.bio.ExonShadow

addCollectionElement(String, InterMineObject) - Method in class org.intermine.model.bio.GeneFlankingRegionShadow

addCollectionElement(String, InterMineObject) - Method in class org.intermine.model.bio.GeneShadow

addCollectionElement(String, InterMineObject) - Method in class org.intermine.model.bio.HomologueShadow

addCollectionElement(String, InterMineObject) - Method in class org.intermine.model.bio.IntergenicRegionShadow

addCollectionElement(String, InterMineObject) - Method in class org.intermine.model.bio.IntronShadow

addCollectionElement(String, InterMineObject) - Method in class org.intermine.model.bio.LocationShadow

addCollectionElement(String, InterMineObject) - Method in class org.intermine.model.bio.MeshTermShadow

addCollectionElement(String, InterMineObject) - Method in class org.intermine.model.bio.OntologyAnnotationEvidenceCodeShadow

addCollectionElement(String, InterMineObject) - Method in class org.intermine.model.bio.OntologyAnnotationShadow

addCollectionElement(String, InterMineObject) - Method in class org.intermine.model.bio.OntologyEvidenceShadow

addCollectionElement(String, InterMineObject) - Method in class org.intermine.model.bio.OntologyRelationShadow

addCollectionElement(String, InterMineObject) - Method in class org.intermine.model.bio.OntologyShadow

addCollectionElement(String, InterMineObject) - Method in class org.intermine.model.bio.OntologyTermShadow

addCollectionElement(String, InterMineObject) - Method in class org.intermine.model.bio.OntologyTermSynonymShadow

addCollectionElement(String, InterMineObject) - Method in class org.intermine.model.bio.OrganismShadow

addCollectionElement(String, InterMineObject) - Method in class org.intermine.model.bio.OrthologueEvidenceCodeShadow

addCollectionElement(String, InterMineObject) - Method in class org.intermine.model.bio.OrthologueEvidenceShadow

addCollectionElement(String, InterMineObject) - Method in class org.intermine.model.bio.ProteinShadow

addCollectionElement(String, InterMineObject) - Method in class org.intermine.model.bio.PublicationShadow

addCollectionElement(String, InterMineObject) - Method in class org.intermine.model.bio.SequenceCollectionShadow

addCollectionElement(String, InterMineObject) - Method in class org.intermine.model.bio.SequenceFeatureShadow

addCollectionElement(String, InterMineObject) - Method in class org.intermine.model.bio.SequenceShadow

addCollectionElement(String, InterMineObject) - Method in class org.intermine.model.bio.SequenceVariantShadow

addCollectionElement(String, InterMineObject) - Method in class org.intermine.model.bio.SOTermShadow

addCollectionElement(String, InterMineObject) - Method in class org.intermine.model.bio.StrainShadow

addCollectionElement(String, InterMineObject) - Method in class org.intermine.model.bio.SynonymShadow

addCollectionElement(String, InterMineObject) - Method in class org.intermine.model.bio.SyntenicRegionShadow

addCollectionElement(String, InterMineObject) - Method in class org.intermine.model.bio.SyntenyBlockShadow

addCollectionElement(String, InterMineObject) - Method in class org.intermine.model.bio.TranscriptShadow

addCollectionElement(String, InterMineObject) - Method in class org.intermine.model.bio.UTRShadow

addCrossReferences(CrossReference) - Method in interface org.intermine.model.bio.BioEntity

addCrossReferences(CrossReference) - Method in class org.intermine.model.bio.BioEntityShadow

addCrossReferences(CrossReference) - Method in class org.intermine.model.bio.CDSShadow

addCrossReferences(CrossReference) - Method in class org.intermine.model.bio.ChromosomeShadow

addCrossReferences(CrossReference) - Method in class org.intermine.model.bio.ExonShadow

addCrossReferences(CrossReference) - Method in class org.intermine.model.bio.GeneFlankingRegionShadow

addCrossReferences(CrossReference) - Method in class org.intermine.model.bio.GeneShadow

addCrossReferences(CrossReference) - Method in interface org.intermine.model.bio.Homologue

addCrossReferences(CrossReference) - Method in class org.intermine.model.bio.HomologueShadow

addCrossReferences(CrossReference) - Method in class org.intermine.model.bio.IntergenicRegionShadow

addCrossReferences(CrossReference) - Method in class org.intermine.model.bio.IntronShadow

addCrossReferences(CrossReference) - Method in class org.intermine.model.bio.ProteinShadow

addCrossReferences(CrossReference) - Method in class org.intermine.model.bio.SequenceCollectionShadow

addCrossReferences(CrossReference) - Method in class org.intermine.model.bio.SequenceFeatureShadow

addCrossReferences(CrossReference) - Method in class org.intermine.model.bio.StrainShadow

addCrossReferences(CrossReference) - Method in class org.intermine.model.bio.SyntenicRegionShadow

addCrossReferences(CrossReference) - Method in class org.intermine.model.bio.TranscriptShadow

addCrossReferences(CrossReference) - Method in class org.intermine.model.bio.UTRShadow

addCrossReferences(OntologyTerm) - Method in interface org.intermine.model.bio.OntologyTerm

addCrossReferences(OntologyTerm) - Method in class org.intermine.model.bio.OntologyTermShadow

addCrossReferences(OntologyTerm) - Method in class org.intermine.model.bio.SOTermShadow

addDataSets(DataSet) - Method in interface org.intermine.model.bio.BioEntity

addDataSets(DataSet) - Method in class org.intermine.model.bio.BioEntityShadow

addDataSets(DataSet) - Method in class org.intermine.model.bio.CDSShadow

addDataSets(DataSet) - Method in class org.intermine.model.bio.ChromosomeShadow

addDataSets(DataSet) - Method in interface org.intermine.model.bio.DataSource

addDataSets(DataSet) - Method in class org.intermine.model.bio.DataSourceShadow

addDataSets(DataSet) - Method in class org.intermine.model.bio.ExonShadow

addDataSets(DataSet) - Method in class org.intermine.model.bio.GeneFlankingRegionShadow

addDataSets(DataSet) - Method in class org.intermine.model.bio.GeneShadow

addDataSets(DataSet) - Method in interface org.intermine.model.bio.Homologue

addDataSets(DataSet) - Method in class org.intermine.model.bio.HomologueShadow

addDataSets(DataSet) - Method in class org.intermine.model.bio.IntergenicRegionShadow

addDataSets(DataSet) - Method in class org.intermine.model.bio.IntronShadow

addDataSets(DataSet) - Method in interface org.intermine.model.bio.Location

addDataSets(DataSet) - Method in class org.intermine.model.bio.LocationShadow

addDataSets(DataSet) - Method in interface org.intermine.model.bio.Ontology

addDataSets(DataSet) - Method in interface org.intermine.model.bio.OntologyAnnotation

addDataSets(DataSet) - Method in class org.intermine.model.bio.OntologyAnnotationShadow

addDataSets(DataSet) - Method in class org.intermine.model.bio.OntologyShadow

addDataSets(DataSet) - Method in interface org.intermine.model.bio.OntologyTerm

addDataSets(DataSet) - Method in class org.intermine.model.bio.OntologyTermShadow

addDataSets(DataSet) - Method in class org.intermine.model.bio.ProteinShadow

addDataSets(DataSet) - Method in class org.intermine.model.bio.SequenceCollectionShadow

addDataSets(DataSet) - Method in class org.intermine.model.bio.SequenceFeatureShadow

addDataSets(DataSet) - Method in class org.intermine.model.bio.SOTermShadow

addDataSets(DataSet) - Method in class org.intermine.model.bio.StrainShadow

addDataSets(DataSet) - Method in interface org.intermine.model.bio.Synonym

addDataSets(DataSet) - Method in class org.intermine.model.bio.SynonymShadow

addDataSets(DataSet) - Method in class org.intermine.model.bio.SyntenicRegionShadow

addDataSets(DataSet) - Method in interface org.intermine.model.bio.SyntenyBlock

addDataSets(DataSet) - Method in class org.intermine.model.bio.SyntenyBlockShadow

addDataSets(DataSet) - Method in class org.intermine.model.bio.TranscriptShadow

addDataSets(DataSet) - Method in class org.intermine.model.bio.UTRShadow

addEntities(Annotatable) - Method in interface org.intermine.model.bio.Publication

addEntities(Annotatable) - Method in class org.intermine.model.bio.PublicationShadow

addEvidence(OntologyEvidence) - Method in interface org.intermine.model.bio.OntologyAnnotation

addEvidence(OntologyEvidence) - Method in class org.intermine.model.bio.OntologyAnnotationShadow

addEvidence(OrthologueEvidence) - Method in interface org.intermine.model.bio.Homologue

addEvidence(OrthologueEvidence) - Method in class org.intermine.model.bio.HomologueShadow

addExons(Exon) - Method in interface org.intermine.model.bio.Gene

addExons(Exon) - Method in class org.intermine.model.bio.GeneShadow

addFeatures(SequenceFeature) - Method in interface org.intermine.model.bio.Strain

addFeatures(SequenceFeature) - Method in class org.intermine.model.bio.StrainShadow

addFlankingRegions(GeneFlankingRegion) - Method in interface org.intermine.model.bio.Gene

addFlankingRegions(GeneFlankingRegion) - Method in class org.intermine.model.bio.GeneShadow

addGenes(Gene) - Method in interface org.intermine.model.bio.Intron

addGenes(Gene) - Method in class org.intermine.model.bio.IntronShadow

addGenes(Gene) - Method in interface org.intermine.model.bio.Protein

addGenes(Gene) - Method in class org.intermine.model.bio.ProteinShadow

addGenes(Gene) - Method in interface org.intermine.model.bio.SequenceVariant

addGenes(Gene) - Method in class org.intermine.model.bio.SequenceVariantShadow

addHomologues(Homologue) - Method in interface org.intermine.model.bio.Gene

addHomologues(Homologue) - Method in class org.intermine.model.bio.GeneShadow

addIntrons(Intron) - Method in interface org.intermine.model.bio.Gene

addIntrons(Intron) - Method in class org.intermine.model.bio.GeneShadow

addLocatedFeatures(Location) - Method in interface org.intermine.model.bio.BioEntity

addLocatedFeatures(Location) - Method in class org.intermine.model.bio.BioEntityShadow

addLocatedFeatures(Location) - Method in class org.intermine.model.bio.CDSShadow

addLocatedFeatures(Location) - Method in class org.intermine.model.bio.ChromosomeShadow

addLocatedFeatures(Location) - Method in class org.intermine.model.bio.ExonShadow

addLocatedFeatures(Location) - Method in class org.intermine.model.bio.GeneFlankingRegionShadow

addLocatedFeatures(Location) - Method in class org.intermine.model.bio.GeneShadow

addLocatedFeatures(Location) - Method in class org.intermine.model.bio.IntergenicRegionShadow

addLocatedFeatures(Location) - Method in class org.intermine.model.bio.IntronShadow

addLocatedFeatures(Location) - Method in class org.intermine.model.bio.ProteinShadow

addLocatedFeatures(Location) - Method in class org.intermine.model.bio.SequenceCollectionShadow

addLocatedFeatures(Location) - Method in class org.intermine.model.bio.SequenceFeatureShadow

addLocatedFeatures(Location) - Method in class org.intermine.model.bio.StrainShadow

addLocatedFeatures(Location) - Method in class org.intermine.model.bio.SyntenicRegionShadow

addLocatedFeatures(Location) - Method in class org.intermine.model.bio.TranscriptShadow

addLocatedFeatures(Location) - Method in class org.intermine.model.bio.UTRShadow

addLocations(Location) - Method in interface org.intermine.model.bio.BioEntity

addLocations(Location) - Method in class org.intermine.model.bio.BioEntityShadow

addLocations(Location) - Method in class org.intermine.model.bio.CDSShadow

addLocations(Location) - Method in class org.intermine.model.bio.ChromosomeShadow

addLocations(Location) - Method in class org.intermine.model.bio.ExonShadow

addLocations(Location) - Method in class org.intermine.model.bio.GeneFlankingRegionShadow

addLocations(Location) - Method in class org.intermine.model.bio.GeneShadow

addLocations(Location) - Method in class org.intermine.model.bio.IntergenicRegionShadow

addLocations(Location) - Method in class org.intermine.model.bio.IntronShadow

addLocations(Location) - Method in class org.intermine.model.bio.ProteinShadow

addLocations(Location) - Method in class org.intermine.model.bio.SequenceCollectionShadow

addLocations(Location) - Method in class org.intermine.model.bio.SequenceFeatureShadow

addLocations(Location) - Method in class org.intermine.model.bio.StrainShadow

addLocations(Location) - Method in class org.intermine.model.bio.SyntenicRegionShadow

addLocations(Location) - Method in class org.intermine.model.bio.TranscriptShadow

addLocations(Location) - Method in class org.intermine.model.bio.UTRShadow

addMeshTerms(MeshTerm) - Method in interface org.intermine.model.bio.Publication

addMeshTerms(MeshTerm) - Method in class org.intermine.model.bio.PublicationShadow

addOntologyAnnotations(OntologyAnnotation) - Method in interface org.intermine.model.bio.Annotatable

addOntologyAnnotations(OntologyAnnotation) - Method in class org.intermine.model.bio.AnnotatableShadow

addOntologyAnnotations(OntologyAnnotation) - Method in class org.intermine.model.bio.BioEntityShadow

addOntologyAnnotations(OntologyAnnotation) - Method in class org.intermine.model.bio.CDSShadow

addOntologyAnnotations(OntologyAnnotation) - Method in class org.intermine.model.bio.ChromosomeShadow

addOntologyAnnotations(OntologyAnnotation) - Method in class org.intermine.model.bio.ExonShadow

addOntologyAnnotations(OntologyAnnotation) - Method in class org.intermine.model.bio.GeneFlankingRegionShadow

addOntologyAnnotations(OntologyAnnotation) - Method in class org.intermine.model.bio.GeneShadow

addOntologyAnnotations(OntologyAnnotation) - Method in class org.intermine.model.bio.IntergenicRegionShadow

addOntologyAnnotations(OntologyAnnotation) - Method in class org.intermine.model.bio.IntronShadow

addOntologyAnnotations(OntologyAnnotation) - Method in interface org.intermine.model.bio.OntologyTerm

addOntologyAnnotations(OntologyAnnotation) - Method in class org.intermine.model.bio.OntologyTermShadow

addOntologyAnnotations(OntologyAnnotation) - Method in class org.intermine.model.bio.ProteinShadow

addOntologyAnnotations(OntologyAnnotation) - Method in class org.intermine.model.bio.SequenceCollectionShadow

addOntologyAnnotations(OntologyAnnotation) - Method in class org.intermine.model.bio.SequenceFeatureShadow

addOntologyAnnotations(OntologyAnnotation) - Method in class org.intermine.model.bio.SOTermShadow

addOntologyAnnotations(OntologyAnnotation) - Method in class org.intermine.model.bio.StrainShadow

addOntologyAnnotations(OntologyAnnotation) - Method in class org.intermine.model.bio.SyntenicRegionShadow

addOntologyAnnotations(OntologyAnnotation) - Method in class org.intermine.model.bio.TranscriptShadow

addOntologyAnnotations(OntologyAnnotation) - Method in class org.intermine.model.bio.UTRShadow

addOverlappingFeatures(SequenceFeature) - Method in class org.intermine.model.bio.CDSShadow

addOverlappingFeatures(SequenceFeature) - Method in class org.intermine.model.bio.ChromosomeShadow

addOverlappingFeatures(SequenceFeature) - Method in class org.intermine.model.bio.ExonShadow

addOverlappingFeatures(SequenceFeature) - Method in class org.intermine.model.bio.GeneFlankingRegionShadow

addOverlappingFeatures(SequenceFeature) - Method in class org.intermine.model.bio.GeneShadow

addOverlappingFeatures(SequenceFeature) - Method in class org.intermine.model.bio.IntergenicRegionShadow

addOverlappingFeatures(SequenceFeature) - Method in class org.intermine.model.bio.IntronShadow

addOverlappingFeatures(SequenceFeature) - Method in interface org.intermine.model.bio.SequenceFeature

addOverlappingFeatures(SequenceFeature) - Method in class org.intermine.model.bio.SequenceFeatureShadow

addOverlappingFeatures(SequenceFeature) - Method in class org.intermine.model.bio.SyntenicRegionShadow

addOverlappingFeatures(SequenceFeature) - Method in class org.intermine.model.bio.TranscriptShadow

addOverlappingFeatures(SequenceFeature) - Method in class org.intermine.model.bio.UTRShadow

addParents(OntologyTerm) - Method in interface org.intermine.model.bio.OntologyTerm

addParents(OntologyTerm) - Method in class org.intermine.model.bio.OntologyTermShadow

addParents(OntologyTerm) - Method in class org.intermine.model.bio.SOTermShadow

addProteins(Protein) - Method in interface org.intermine.model.bio.Gene

addProteins(Protein) - Method in class org.intermine.model.bio.GeneShadow

addPublications(Publication) - Method in interface org.intermine.model.bio.Annotatable

addPublications(Publication) - Method in class org.intermine.model.bio.AnnotatableShadow

addPublications(Publication) - Method in interface org.intermine.model.bio.Author

addPublications(Publication) - Method in class org.intermine.model.bio.AuthorShadow

addPublications(Publication) - Method in class org.intermine.model.bio.BioEntityShadow

addPublications(Publication) - Method in class org.intermine.model.bio.CDSShadow

addPublications(Publication) - Method in class org.intermine.model.bio.ChromosomeShadow

addPublications(Publication) - Method in interface org.intermine.model.bio.DataSource

addPublications(Publication) - Method in class org.intermine.model.bio.DataSourceShadow

addPublications(Publication) - Method in class org.intermine.model.bio.ExonShadow

addPublications(Publication) - Method in class org.intermine.model.bio.GeneFlankingRegionShadow

addPublications(Publication) - Method in class org.intermine.model.bio.GeneShadow

addPublications(Publication) - Method in class org.intermine.model.bio.IntergenicRegionShadow

addPublications(Publication) - Method in class org.intermine.model.bio.IntronShadow

addPublications(Publication) - Method in interface org.intermine.model.bio.MeshTerm

addPublications(Publication) - Method in class org.intermine.model.bio.MeshTermShadow

addPublications(Publication) - Method in interface org.intermine.model.bio.OntologyEvidence

addPublications(Publication) - Method in class org.intermine.model.bio.OntologyEvidenceShadow

addPublications(Publication) - Method in interface org.intermine.model.bio.OrthologueEvidence

addPublications(Publication) - Method in class org.intermine.model.bio.OrthologueEvidenceShadow

addPublications(Publication) - Method in class org.intermine.model.bio.ProteinShadow

addPublications(Publication) - Method in class org.intermine.model.bio.SequenceCollectionShadow

addPublications(Publication) - Method in class org.intermine.model.bio.SequenceFeatureShadow

addPublications(Publication) - Method in class org.intermine.model.bio.StrainShadow

addPublications(Publication) - Method in class org.intermine.model.bio.SyntenicRegionShadow

addPublications(Publication) - Method in interface org.intermine.model.bio.SyntenyBlock

addPublications(Publication) - Method in class org.intermine.model.bio.SyntenyBlockShadow

addPublications(Publication) - Method in class org.intermine.model.bio.TranscriptShadow

addPublications(Publication) - Method in class org.intermine.model.bio.UTRShadow

addRelations(OntologyRelation) - Method in interface org.intermine.model.bio.OntologyTerm

addRelations(OntologyRelation) - Method in class org.intermine.model.bio.OntologyTermShadow

addRelations(OntologyRelation) - Method in class org.intermine.model.bio.SOTermShadow

addStrains(Strain) - Method in interface org.intermine.model.bio.Organism

addStrains(Strain) - Method in class org.intermine.model.bio.OrganismShadow

addSynonyms(OntologyTermSynonym) - Method in interface org.intermine.model.bio.OntologyTerm

addSynonyms(OntologyTermSynonym) - Method in class org.intermine.model.bio.OntologyTermShadow

addSynonyms(OntologyTermSynonym) - Method in class org.intermine.model.bio.SOTermShadow

addSynonyms(Synonym) - Method in interface org.intermine.model.bio.BioEntity

addSynonyms(Synonym) - Method in class org.intermine.model.bio.BioEntityShadow

addSynonyms(Synonym) - Method in class org.intermine.model.bio.CDSShadow

addSynonyms(Synonym) - Method in class org.intermine.model.bio.ChromosomeShadow

addSynonyms(Synonym) - Method in class org.intermine.model.bio.ExonShadow

addSynonyms(Synonym) - Method in class org.intermine.model.bio.GeneFlankingRegionShadow

addSynonyms(Synonym) - Method in class org.intermine.model.bio.GeneShadow

addSynonyms(Synonym) - Method in class org.intermine.model.bio.IntergenicRegionShadow

addSynonyms(Synonym) - Method in class org.intermine.model.bio.IntronShadow

addSynonyms(Synonym) - Method in class org.intermine.model.bio.ProteinShadow

addSynonyms(Synonym) - Method in class org.intermine.model.bio.SequenceCollectionShadow

addSynonyms(Synonym) - Method in class org.intermine.model.bio.SequenceFeatureShadow

addSynonyms(Synonym) - Method in class org.intermine.model.bio.StrainShadow

addSynonyms(Synonym) - Method in class org.intermine.model.bio.SyntenicRegionShadow

addSynonyms(Synonym) - Method in class org.intermine.model.bio.TranscriptShadow

addSynonyms(Synonym) - Method in class org.intermine.model.bio.UTRShadow

addSyntenicRegions(SyntenicRegion) - Method in interface org.intermine.model.bio.SyntenyBlock

addSyntenicRegions(SyntenicRegion) - Method in class org.intermine.model.bio.SyntenyBlockShadow

addTranscripts(Transcript) - Method in interface org.intermine.model.bio.Protein

addTranscripts(Transcript) - Method in class org.intermine.model.bio.ProteinShadow

adduTRs(UTR) - Method in interface org.intermine.model.bio.Gene

adduTRs(UTR) - Method in class org.intermine.model.bio.GeneShadow

adjacentGenes - Variable in class org.intermine.model.bio.IntergenicRegionShadow

Annotatable - Interface in org.intermine.model.bio

AnnotatableShadow - Class in org.intermine.model.bio

AnnotatableShadow() - Constructor for class org.intermine.model.bio.AnnotatableShadow

annotationVersion - Variable in class org.intermine.model.bio.StrainShadow

assemblyVersion - Variable in class org.intermine.model.bio.StrainShadow

Author - Interface in org.intermine.model.bio

authors - Variable in class org.intermine.model.bio.PublicationShadow

AuthorShadow - Class in org.intermine.model.bio

AuthorShadow() - Constructor for class org.intermine.model.bio.AuthorShadow

B

bioEntities - Variable in class org.intermine.model.bio.DataSetShadow

BioEntity - Interface in org.intermine.model.bio

BioEntityShadow - Class in org.intermine.model.bio

BioEntityShadow() - Constructor for class org.intermine.model.bio.BioEntityShadow

briefDescription - Variable in class org.intermine.model.bio.GeneShadow

C

CDS - Interface in org.intermine.model.bio

CDSs - Variable in class org.intermine.model.bio.GeneShadow

CDSs - Variable in class org.intermine.model.bio.ProteinShadow

CDSShadow - Class in org.intermine.model.bio

CDSShadow() - Constructor for class org.intermine.model.bio.CDSShadow

childFeatures - Variable in class org.intermine.model.bio.CDSShadow

childFeatures - Variable in class org.intermine.model.bio.ChromosomeShadow

childFeatures - Variable in class org.intermine.model.bio.ExonShadow

childFeatures - Variable in class org.intermine.model.bio.GeneFlankingRegionShadow

childFeatures - Variable in class org.intermine.model.bio.GeneShadow

childFeatures - Variable in class org.intermine.model.bio.IntergenicRegionShadow

childFeatures - Variable in class org.intermine.model.bio.IntronShadow

childFeatures - Variable in class org.intermine.model.bio.SequenceFeatureShadow

childFeatures - Variable in class org.intermine.model.bio.SyntenicRegionShadow

childFeatures - Variable in class org.intermine.model.bio.TranscriptShadow

childFeatures - Variable in class org.intermine.model.bio.UTRShadow

childTerm - Variable in class org.intermine.model.bio.OntologyRelationShadow

chromosome - Variable in class org.intermine.model.bio.CDSShadow

chromosome - Variable in class org.intermine.model.bio.ChromosomeShadow

chromosome - Variable in class org.intermine.model.bio.ExonShadow

chromosome - Variable in class org.intermine.model.bio.GeneFlankingRegionShadow

chromosome - Variable in class org.intermine.model.bio.GeneShadow

chromosome - Variable in class org.intermine.model.bio.IntergenicRegionShadow

chromosome - Variable in class org.intermine.model.bio.IntronShadow

chromosome - Variable in class org.intermine.model.bio.SequenceFeatureShadow

chromosome - Variable in class org.intermine.model.bio.SyntenicRegionShadow

chromosome - Variable in class org.intermine.model.bio.TranscriptShadow

chromosome - Variable in class org.intermine.model.bio.UTRShadow

Chromosome - Interface in org.intermine.model.bio

chromosomeLocation - Variable in class org.intermine.model.bio.CDSShadow

chromosomeLocation - Variable in class org.intermine.model.bio.ChromosomeShadow

chromosomeLocation - Variable in class org.intermine.model.bio.ExonShadow

chromosomeLocation - Variable in class org.intermine.model.bio.GeneFlankingRegionShadow

chromosomeLocation - Variable in class org.intermine.model.bio.GeneShadow

chromosomeLocation - Variable in class org.intermine.model.bio.IntergenicRegionShadow

chromosomeLocation - Variable in class org.intermine.model.bio.IntronShadow

chromosomeLocation - Variable in class org.intermine.model.bio.SequenceFeatureShadow

chromosomeLocation - Variable in class org.intermine.model.bio.SyntenicRegionShadow

chromosomeLocation - Variable in class org.intermine.model.bio.TranscriptShadow

chromosomeLocation - Variable in class org.intermine.model.bio.UTRShadow

ChromosomeShadow - Class in org.intermine.model.bio

ChromosomeShadow() - Constructor for class org.intermine.model.bio.ChromosomeShadow

code - Variable in class org.intermine.model.bio.OntologyAnnotationEvidenceCodeShadow

code - Variable in class org.intermine.model.bio.OntologyEvidenceShadow

Comment - Interface in org.intermine.model.bio

CommentShadow - Class in org.intermine.model.bio

CommentShadow() - Constructor for class org.intermine.model.bio.CommentShadow

commonName - Variable in class org.intermine.model.bio.OrganismShadow

CrossReference - Interface in org.intermine.model.bio

crossReferences - Variable in class org.intermine.model.bio.BioEntityShadow

crossReferences - Variable in class org.intermine.model.bio.CDSShadow

crossReferences - Variable in class org.intermine.model.bio.ChromosomeShadow

crossReferences - Variable in class org.intermine.model.bio.ExonShadow

crossReferences - Variable in class org.intermine.model.bio.GeneFlankingRegionShadow

crossReferences - Variable in class org.intermine.model.bio.GeneShadow

crossReferences - Variable in class org.intermine.model.bio.HomologueShadow

crossReferences - Variable in class org.intermine.model.bio.IntergenicRegionShadow

crossReferences - Variable in class org.intermine.model.bio.IntronShadow

crossReferences - Variable in class org.intermine.model.bio.OntologyTermShadow

crossReferences - Variable in class org.intermine.model.bio.ProteinShadow

crossReferences - Variable in class org.intermine.model.bio.SequenceCollectionShadow

crossReferences - Variable in class org.intermine.model.bio.SequenceFeatureShadow

crossReferences - Variable in class org.intermine.model.bio.SOTermShadow

crossReferences - Variable in class org.intermine.model.bio.StrainShadow

crossReferences - Variable in class org.intermine.model.bio.SyntenicRegionShadow

crossReferences - Variable in class org.intermine.model.bio.TranscriptShadow

crossReferences - Variable in class org.intermine.model.bio.UTRShadow

CrossReferenceShadow - Class in org.intermine.model.bio

CrossReferenceShadow() - Constructor for class org.intermine.model.bio.CrossReferenceShadow

D

DataSet - Interface in org.intermine.model.bio

dataSets - Variable in class org.intermine.model.bio.BioEntityShadow

dataSets - Variable in class org.intermine.model.bio.CDSShadow

dataSets - Variable in class org.intermine.model.bio.ChromosomeShadow

dataSets - Variable in class org.intermine.model.bio.DataSourceShadow

dataSets - Variable in class org.intermine.model.bio.ExonShadow

dataSets - Variable in class org.intermine.model.bio.GeneFlankingRegionShadow

dataSets - Variable in class org.intermine.model.bio.GeneShadow

dataSets - Variable in class org.intermine.model.bio.HomologueShadow

dataSets - Variable in class org.intermine.model.bio.IntergenicRegionShadow

dataSets - Variable in class org.intermine.model.bio.IntronShadow

dataSets - Variable in class org.intermine.model.bio.LocationShadow

dataSets - Variable in class org.intermine.model.bio.OntologyAnnotationShadow

dataSets - Variable in class org.intermine.model.bio.OntologyShadow

dataSets - Variable in class org.intermine.model.bio.OntologyTermShadow

dataSets - Variable in class org.intermine.model.bio.ProteinShadow

dataSets - Variable in class org.intermine.model.bio.SequenceCollectionShadow

dataSets - Variable in class org.intermine.model.bio.SequenceFeatureShadow

dataSets - Variable in class org.intermine.model.bio.SOTermShadow

dataSets - Variable in class org.intermine.model.bio.StrainShadow

dataSets - Variable in class org.intermine.model.bio.SynonymShadow

dataSets - Variable in class org.intermine.model.bio.SyntenicRegionShadow

dataSets - Variable in class org.intermine.model.bio.SyntenyBlockShadow

dataSets - Variable in class org.intermine.model.bio.TranscriptShadow

dataSets - Variable in class org.intermine.model.bio.UTRShadow

DataSetShadow - Class in org.intermine.model.bio

DataSetShadow() - Constructor for class org.intermine.model.bio.DataSetShadow

dataSource - Variable in class org.intermine.model.bio.DataSetShadow

DataSource - Interface in org.intermine.model.bio

DataSourceShadow - Class in org.intermine.model.bio

DataSourceShadow() - Constructor for class org.intermine.model.bio.DataSourceShadow

description - Variable in class org.intermine.model.bio.CommentShadow

description - Variable in class org.intermine.model.bio.DataSetShadow

description - Variable in class org.intermine.model.bio.DataSourceShadow

description - Variable in class org.intermine.model.bio.GeneShadow

description - Variable in class org.intermine.model.bio.OntologyTermShadow

description - Variable in class org.intermine.model.bio.SOTermShadow

direct - Variable in class org.intermine.model.bio.OntologyRelationShadow

direction - Variable in class org.intermine.model.bio.GeneFlankingRegionShadow

distance - Variable in class org.intermine.model.bio.GeneFlankingRegionShadow

doi - Variable in class org.intermine.model.bio.PublicationShadow

downstreamIntergenicRegion - Variable in class org.intermine.model.bio.GeneShadow

E

end - Variable in class org.intermine.model.bio.LocationShadow

entities - Variable in class org.intermine.model.bio.PublicationShadow

equals(Object) - Method in class org.intermine.model.bio.AnnotatableShadow

equals(Object) - Method in class org.intermine.model.bio.AuthorShadow

equals(Object) - Method in class org.intermine.model.bio.BioEntityShadow

equals(Object) - Method in class org.intermine.model.bio.CDSShadow

equals(Object) - Method in class org.intermine.model.bio.ChromosomeShadow

equals(Object) - Method in class org.intermine.model.bio.CommentShadow

equals(Object) - Method in class org.intermine.model.bio.CrossReferenceShadow

equals(Object) - Method in class org.intermine.model.bio.DataSetShadow

equals(Object) - Method in class org.intermine.model.bio.DataSourceShadow

equals(Object) - Method in class org.intermine.model.bio.ExonShadow

equals(Object) - Method in class org.intermine.model.bio.GeneFlankingRegionShadow

equals(Object) - Method in class org.intermine.model.bio.GeneShadow

equals(Object) - Method in class org.intermine.model.bio.HomologueShadow

equals(Object) - Method in class org.intermine.model.bio.IntergenicRegionShadow

equals(Object) - Method in class org.intermine.model.bio.IntronShadow

equals(Object) - Method in class org.intermine.model.bio.LocationShadow

equals(Object) - Method in class org.intermine.model.bio.MeshTermShadow

equals(Object) - Method in class org.intermine.model.bio.OntologyAnnotationEvidenceCodeShadow

equals(Object) - Method in class org.intermine.model.bio.OntologyAnnotationShadow

equals(Object) - Method in class org.intermine.model.bio.OntologyEvidenceShadow

equals(Object) - Method in class org.intermine.model.bio.OntologyRelationShadow

equals(Object) - Method in class org.intermine.model.bio.OntologyShadow

equals(Object) - Method in class org.intermine.model.bio.OntologyTermShadow

equals(Object) - Method in class org.intermine.model.bio.OntologyTermSynonymShadow

equals(Object) - Method in class org.intermine.model.bio.OrganismShadow

equals(Object) - Method in class org.intermine.model.bio.OrthologueEvidenceCodeShadow

equals(Object) - Method in class org.intermine.model.bio.OrthologueEvidenceShadow

equals(Object) - Method in class org.intermine.model.bio.ProteinShadow

equals(Object) - Method in class org.intermine.model.bio.PublicationShadow

equals(Object) - Method in class org.intermine.model.bio.SequenceCollectionShadow

equals(Object) - Method in class org.intermine.model.bio.SequenceFeatureShadow

equals(Object) - Method in class org.intermine.model.bio.SequenceShadow

equals(Object) - Method in class org.intermine.model.bio.SequenceVariantShadow

equals(Object) - Method in class org.intermine.model.bio.SOTermShadow

equals(Object) - Method in class org.intermine.model.bio.StrainShadow

equals(Object) - Method in class org.intermine.model.bio.SynonymShadow

equals(Object) - Method in class org.intermine.model.bio.SyntenicRegionShadow

equals(Object) - Method in class org.intermine.model.bio.SyntenyBlockShadow

equals(Object) - Method in class org.intermine.model.bio.TranscriptShadow

equals(Object) - Method in class org.intermine.model.bio.UTRShadow

evidence - Variable in class org.intermine.model.bio.HomologueShadow

evidence - Variable in class org.intermine.model.bio.OntologyAnnotationShadow

evidenceCode - Variable in class org.intermine.model.bio.OrthologueEvidenceShadow

Exon - Interface in org.intermine.model.bio

exons - Variable in class org.intermine.model.bio.GeneShadow

ExonShadow - Class in org.intermine.model.bio

ExonShadow() - Constructor for class org.intermine.model.bio.ExonShadow

F

feature - Variable in class org.intermine.model.bio.LocationShadow

features - Variable in class org.intermine.model.bio.StrainShadow

firstAuthor - Variable in class org.intermine.model.bio.PublicationShadow

firstName - Variable in class org.intermine.model.bio.AuthorShadow

flankingRegions - Variable in class org.intermine.model.bio.GeneShadow

G

gene - Variable in class org.intermine.model.bio.CDSShadow

gene - Variable in class org.intermine.model.bio.ExonShadow

gene - Variable in class org.intermine.model.bio.GeneFlankingRegionShadow

gene - Variable in class org.intermine.model.bio.HomologueShadow

gene - Variable in class org.intermine.model.bio.UTRShadow

Gene - Interface in org.intermine.model.bio

GeneFlankingRegion - Interface in org.intermine.model.bio

GeneFlankingRegionShadow - Class in org.intermine.model.bio

GeneFlankingRegionShadow() - Constructor for class org.intermine.model.bio.GeneFlankingRegionShadow

GeneRecord(String, String) - Constructor for class org.intermine.bio.dataconversion.HomologeneConverter.GeneRecord

geneRefId - Variable in class org.intermine.bio.dataconversion.HomologeneConverter.GeneRecord

genes - Variable in class org.intermine.model.bio.IntronShadow

genes - Variable in class org.intermine.model.bio.ProteinShadow

genes - Variable in class org.intermine.model.bio.SequenceVariantShadow

GeneShadow - Class in org.intermine.model.bio

GeneShadow() - Constructor for class org.intermine.model.bio.GeneShadow

genus - Variable in class org.intermine.model.bio.OrganismShadow

getAbbreviation() - Method in interface org.intermine.model.bio.OrthologueEvidenceCode

getAbbreviation() - Method in class org.intermine.model.bio.OrthologueEvidenceCodeShadow

getAbstractText() - Method in interface org.intermine.model.bio.Publication

getAbstractText() - Method in class org.intermine.model.bio.PublicationShadow

getAdjacentGenes() - Method in interface org.intermine.model.bio.IntergenicRegion

getAdjacentGenes() - Method in class org.intermine.model.bio.IntergenicRegionShadow

getAnnotationVersion() - Method in interface org.intermine.model.bio.Strain

getAnnotationVersion() - Method in class org.intermine.model.bio.StrainShadow

getAssemblyVersion() - Method in interface org.intermine.model.bio.Strain

getAssemblyVersion() - Method in class org.intermine.model.bio.StrainShadow

getAuthors() - Method in interface org.intermine.model.bio.Publication

getAuthors() - Method in class org.intermine.model.bio.PublicationShadow

getBioEntities() - Method in interface org.intermine.model.bio.DataSet

getBioEntities() - Method in class org.intermine.model.bio.DataSetShadow

getBriefDescription() - Method in interface org.intermine.model.bio.Gene

getBriefDescription() - Method in class org.intermine.model.bio.GeneShadow

getcDSs() - Method in interface org.intermine.model.bio.Gene

getcDSs() - Method in class org.intermine.model.bio.GeneShadow

getcDSs() - Method in interface org.intermine.model.bio.Protein

getcDSs() - Method in class org.intermine.model.bio.ProteinShadow

getChildFeatures() - Method in class org.intermine.model.bio.CDSShadow

getChildFeatures() - Method in class org.intermine.model.bio.ChromosomeShadow

getChildFeatures() - Method in class org.intermine.model.bio.ExonShadow

getChildFeatures() - Method in class org.intermine.model.bio.GeneFlankingRegionShadow

getChildFeatures() - Method in class org.intermine.model.bio.GeneShadow

getChildFeatures() - Method in class org.intermine.model.bio.IntergenicRegionShadow

getChildFeatures() - Method in class org.intermine.model.bio.IntronShadow

getChildFeatures() - Method in interface org.intermine.model.bio.SequenceFeature

getChildFeatures() - Method in class org.intermine.model.bio.SequenceFeatureShadow

getChildFeatures() - Method in class org.intermine.model.bio.SyntenicRegionShadow

getChildFeatures() - Method in class org.intermine.model.bio.TranscriptShadow

getChildFeatures() - Method in class org.intermine.model.bio.UTRShadow

getChildTerm() - Method in interface org.intermine.model.bio.OntologyRelation

getChildTerm() - Method in class org.intermine.model.bio.OntologyRelationShadow

getChromosome() - Method in class org.intermine.model.bio.CDSShadow

getChromosome() - Method in class org.intermine.model.bio.ChromosomeShadow

getChromosome() - Method in class org.intermine.model.bio.ExonShadow

getChromosome() - Method in class org.intermine.model.bio.GeneFlankingRegionShadow

getChromosome() - Method in class org.intermine.model.bio.GeneShadow

getChromosome() - Method in class org.intermine.model.bio.IntergenicRegionShadow

getChromosome() - Method in class org.intermine.model.bio.IntronShadow

getChromosome() - Method in interface org.intermine.model.bio.SequenceFeature

getChromosome() - Method in class org.intermine.model.bio.SequenceFeatureShadow

getChromosome() - Method in class org.intermine.model.bio.SyntenicRegionShadow

getChromosome() - Method in class org.intermine.model.bio.TranscriptShadow

getChromosome() - Method in class org.intermine.model.bio.UTRShadow

getChromosomeLocation() - Method in class org.intermine.model.bio.CDSShadow

getChromosomeLocation() - Method in class org.intermine.model.bio.ChromosomeShadow

getChromosomeLocation() - Method in class org.intermine.model.bio.ExonShadow

getChromosomeLocation() - Method in class org.intermine.model.bio.GeneFlankingRegionShadow

getChromosomeLocation() - Method in class org.intermine.model.bio.GeneShadow

getChromosomeLocation() - Method in class org.intermine.model.bio.IntergenicRegionShadow

getChromosomeLocation() - Method in class org.intermine.model.bio.IntronShadow

getChromosomeLocation() - Method in interface org.intermine.model.bio.SequenceFeature

getChromosomeLocation() - Method in class org.intermine.model.bio.SequenceFeatureShadow

getChromosomeLocation() - Method in class org.intermine.model.bio.SyntenicRegionShadow

getChromosomeLocation() - Method in class org.intermine.model.bio.TranscriptShadow

getChromosomeLocation() - Method in class org.intermine.model.bio.UTRShadow

getCode() - Method in interface org.intermine.model.bio.OntologyAnnotationEvidenceCode

getCode() - Method in class org.intermine.model.bio.OntologyAnnotationEvidenceCodeShadow

getCode() - Method in interface org.intermine.model.bio.OntologyEvidence

getCode() - Method in class org.intermine.model.bio.OntologyEvidenceShadow

getCommonName() - Method in interface org.intermine.model.bio.Organism

getCommonName() - Method in class org.intermine.model.bio.OrganismShadow

getCrossReferences() - Method in interface org.intermine.model.bio.BioEntity

getCrossReferences() - Method in class org.intermine.model.bio.BioEntityShadow

getCrossReferences() - Method in class org.intermine.model.bio.CDSShadow

getCrossReferences() - Method in class org.intermine.model.bio.ChromosomeShadow

getCrossReferences() - Method in class org.intermine.model.bio.ExonShadow

getCrossReferences() - Method in class org.intermine.model.bio.GeneFlankingRegionShadow

getCrossReferences() - Method in class org.intermine.model.bio.GeneShadow

getCrossReferences() - Method in interface org.intermine.model.bio.Homologue

getCrossReferences() - Method in class org.intermine.model.bio.HomologueShadow

getCrossReferences() - Method in class org.intermine.model.bio.IntergenicRegionShadow

getCrossReferences() - Method in class org.intermine.model.bio.IntronShadow

getCrossReferences() - Method in interface org.intermine.model.bio.OntologyTerm

getCrossReferences() - Method in class org.intermine.model.bio.OntologyTermShadow

getCrossReferences() - Method in class org.intermine.model.bio.ProteinShadow

getCrossReferences() - Method in class org.intermine.model.bio.SequenceCollectionShadow

getCrossReferences() - Method in class org.intermine.model.bio.SequenceFeatureShadow

getCrossReferences() - Method in class org.intermine.model.bio.SOTermShadow

getCrossReferences() - Method in class org.intermine.model.bio.StrainShadow

getCrossReferences() - Method in class org.intermine.model.bio.SyntenicRegionShadow

getCrossReferences() - Method in class org.intermine.model.bio.TranscriptShadow

getCrossReferences() - Method in class org.intermine.model.bio.UTRShadow

getDataSets() - Method in interface org.intermine.model.bio.BioEntity

getDataSets() - Method in class org.intermine.model.bio.BioEntityShadow

getDataSets() - Method in class org.intermine.model.bio.CDSShadow

getDataSets() - Method in class org.intermine.model.bio.ChromosomeShadow

getDataSets() - Method in interface org.intermine.model.bio.DataSource

getDataSets() - Method in class org.intermine.model.bio.DataSourceShadow

getDataSets() - Method in class org.intermine.model.bio.ExonShadow

getDataSets() - Method in class org.intermine.model.bio.GeneFlankingRegionShadow

getDataSets() - Method in class org.intermine.model.bio.GeneShadow

getDataSets() - Method in interface org.intermine.model.bio.Homologue

getDataSets() - Method in class org.intermine.model.bio.HomologueShadow

getDataSets() - Method in class org.intermine.model.bio.IntergenicRegionShadow

getDataSets() - Method in class org.intermine.model.bio.IntronShadow

getDataSets() - Method in interface org.intermine.model.bio.Location

getDataSets() - Method in class org.intermine.model.bio.LocationShadow

getDataSets() - Method in interface org.intermine.model.bio.Ontology

getDataSets() - Method in interface org.intermine.model.bio.OntologyAnnotation

getDataSets() - Method in class org.intermine.model.bio.OntologyAnnotationShadow

getDataSets() - Method in class org.intermine.model.bio.OntologyShadow

getDataSets() - Method in interface org.intermine.model.bio.OntologyTerm

getDataSets() - Method in class org.intermine.model.bio.OntologyTermShadow

getDataSets() - Method in class org.intermine.model.bio.ProteinShadow

getDataSets() - Method in class org.intermine.model.bio.SequenceCollectionShadow

getDataSets() - Method in class org.intermine.model.bio.SequenceFeatureShadow

getDataSets() - Method in class org.intermine.model.bio.SOTermShadow

getDataSets() - Method in class org.intermine.model.bio.StrainShadow

getDataSets() - Method in interface org.intermine.model.bio.Synonym

getDataSets() - Method in class org.intermine.model.bio.SynonymShadow

getDataSets() - Method in class org.intermine.model.bio.SyntenicRegionShadow

getDataSets() - Method in interface org.intermine.model.bio.SyntenyBlock

getDataSets() - Method in class org.intermine.model.bio.SyntenyBlockShadow

getDataSets() - Method in class org.intermine.model.bio.TranscriptShadow

getDataSets() - Method in class org.intermine.model.bio.UTRShadow

getDataSource() - Method in interface org.intermine.model.bio.DataSet

getDataSource() - Method in class org.intermine.model.bio.DataSetShadow

getDescription() - Method in interface org.intermine.model.bio.Comment

getDescription() - Method in class org.intermine.model.bio.CommentShadow

getDescription() - Method in interface org.intermine.model.bio.DataSet

getDescription() - Method in class org.intermine.model.bio.DataSetShadow

getDescription() - Method in interface org.intermine.model.bio.DataSource

getDescription() - Method in class org.intermine.model.bio.DataSourceShadow

getDescription() - Method in interface org.intermine.model.bio.Gene

getDescription() - Method in class org.intermine.model.bio.GeneShadow

getDescription() - Method in interface org.intermine.model.bio.OntologyTerm

getDescription() - Method in class org.intermine.model.bio.OntologyTermShadow

getDescription() - Method in class org.intermine.model.bio.SOTermShadow

getDirect() - Method in interface org.intermine.model.bio.OntologyRelation

getDirect() - Method in class org.intermine.model.bio.OntologyRelationShadow

getDirection() - Method in interface org.intermine.model.bio.GeneFlankingRegion

getDirection() - Method in class org.intermine.model.bio.GeneFlankingRegionShadow

getDistance() - Method in interface org.intermine.model.bio.GeneFlankingRegion

getDistance() - Method in class org.intermine.model.bio.GeneFlankingRegionShadow

getDoi() - Method in interface org.intermine.model.bio.Publication

getDoi() - Method in class org.intermine.model.bio.PublicationShadow

getDownstreamIntergenicRegion() - Method in interface org.intermine.model.bio.Gene

getDownstreamIntergenicRegion() - Method in class org.intermine.model.bio.GeneShadow

getElementType(String) - Method in class org.intermine.model.bio.AnnotatableShadow

getElementType(String) - Method in class org.intermine.model.bio.AuthorShadow

getElementType(String) - Method in class org.intermine.model.bio.BioEntityShadow

getElementType(String) - Method in class org.intermine.model.bio.CDSShadow

getElementType(String) - Method in class org.intermine.model.bio.ChromosomeShadow

getElementType(String) - Method in class org.intermine.model.bio.CommentShadow

getElementType(String) - Method in class org.intermine.model.bio.CrossReferenceShadow

getElementType(String) - Method in class org.intermine.model.bio.DataSetShadow

getElementType(String) - Method in class org.intermine.model.bio.DataSourceShadow

getElementType(String) - Method in class org.intermine.model.bio.ExonShadow

getElementType(String) - Method in class org.intermine.model.bio.GeneFlankingRegionShadow

getElementType(String) - Method in class org.intermine.model.bio.GeneShadow

getElementType(String) - Method in class org.intermine.model.bio.HomologueShadow

getElementType(String) - Method in class org.intermine.model.bio.IntergenicRegionShadow

getElementType(String) - Method in class org.intermine.model.bio.IntronShadow

getElementType(String) - Method in class org.intermine.model.bio.LocationShadow

getElementType(String) - Method in class org.intermine.model.bio.MeshTermShadow

getElementType(String) - Method in class org.intermine.model.bio.OntologyAnnotationEvidenceCodeShadow

getElementType(String) - Method in class org.intermine.model.bio.OntologyAnnotationShadow

getElementType(String) - Method in class org.intermine.model.bio.OntologyEvidenceShadow

getElementType(String) - Method in class org.intermine.model.bio.OntologyRelationShadow

getElementType(String) - Method in class org.intermine.model.bio.OntologyShadow

getElementType(String) - Method in class org.intermine.model.bio.OntologyTermShadow

getElementType(String) - Method in class org.intermine.model.bio.OntologyTermSynonymShadow

getElementType(String) - Method in class org.intermine.model.bio.OrganismShadow

getElementType(String) - Method in class org.intermine.model.bio.OrthologueEvidenceCodeShadow

getElementType(String) - Method in class org.intermine.model.bio.OrthologueEvidenceShadow

getElementType(String) - Method in class org.intermine.model.bio.ProteinShadow

getElementType(String) - Method in class org.intermine.model.bio.PublicationShadow

getElementType(String) - Method in class org.intermine.model.bio.SequenceCollectionShadow

getElementType(String) - Method in class org.intermine.model.bio.SequenceFeatureShadow

getElementType(String) - Method in class org.intermine.model.bio.SequenceShadow

getElementType(String) - Method in class org.intermine.model.bio.SequenceVariantShadow

getElementType(String) - Method in class org.intermine.model.bio.SOTermShadow

getElementType(String) - Method in class org.intermine.model.bio.StrainShadow

getElementType(String) - Method in class org.intermine.model.bio.SynonymShadow

getElementType(String) - Method in class org.intermine.model.bio.SyntenicRegionShadow

getElementType(String) - Method in class org.intermine.model.bio.SyntenyBlockShadow

getElementType(String) - Method in class org.intermine.model.bio.TranscriptShadow

getElementType(String) - Method in class org.intermine.model.bio.UTRShadow

getEnd() - Method in interface org.intermine.model.bio.Location

getEnd() - Method in class org.intermine.model.bio.LocationShadow

getEntities() - Method in interface org.intermine.model.bio.Publication

getEntities() - Method in class org.intermine.model.bio.PublicationShadow

getEvidence() - Method in interface org.intermine.model.bio.Homologue

getEvidence() - Method in class org.intermine.model.bio.HomologueShadow

getEvidence() - Method in interface org.intermine.model.bio.OntologyAnnotation

getEvidence() - Method in class org.intermine.model.bio.OntologyAnnotationShadow

getEvidenceCode() - Method in interface org.intermine.model.bio.OrthologueEvidence

getEvidenceCode() - Method in class org.intermine.model.bio.OrthologueEvidenceShadow

getExons() - Method in interface org.intermine.model.bio.Gene

getExons() - Method in class org.intermine.model.bio.GeneShadow

getFeature() - Method in interface org.intermine.model.bio.Location

getFeature() - Method in class org.intermine.model.bio.LocationShadow

getFeatures() - Method in interface org.intermine.model.bio.Strain

getFeatures() - Method in class org.intermine.model.bio.StrainShadow

getFieldProxy(String) - Method in class org.intermine.model.bio.AnnotatableShadow

getFieldProxy(String) - Method in class org.intermine.model.bio.AuthorShadow

getFieldProxy(String) - Method in class org.intermine.model.bio.BioEntityShadow

getFieldProxy(String) - Method in class org.intermine.model.bio.CDSShadow

getFieldProxy(String) - Method in class org.intermine.model.bio.ChromosomeShadow

getFieldProxy(String) - Method in class org.intermine.model.bio.CommentShadow

getFieldProxy(String) - Method in class org.intermine.model.bio.CrossReferenceShadow

getFieldProxy(String) - Method in class org.intermine.model.bio.DataSetShadow

getFieldProxy(String) - Method in class org.intermine.model.bio.DataSourceShadow

getFieldProxy(String) - Method in class org.intermine.model.bio.ExonShadow

getFieldProxy(String) - Method in class org.intermine.model.bio.GeneFlankingRegionShadow

getFieldProxy(String) - Method in class org.intermine.model.bio.GeneShadow

getFieldProxy(String) - Method in class org.intermine.model.bio.HomologueShadow

getFieldProxy(String) - Method in class org.intermine.model.bio.IntergenicRegionShadow

getFieldProxy(String) - Method in class org.intermine.model.bio.IntronShadow

getFieldProxy(String) - Method in class org.intermine.model.bio.LocationShadow

getFieldProxy(String) - Method in class org.intermine.model.bio.MeshTermShadow

getFieldProxy(String) - Method in class org.intermine.model.bio.OntologyAnnotationEvidenceCodeShadow

getFieldProxy(String) - Method in class org.intermine.model.bio.OntologyAnnotationShadow

getFieldProxy(String) - Method in class org.intermine.model.bio.OntologyEvidenceShadow

getFieldProxy(String) - Method in class org.intermine.model.bio.OntologyRelationShadow

getFieldProxy(String) - Method in class org.intermine.model.bio.OntologyShadow

getFieldProxy(String) - Method in class org.intermine.model.bio.OntologyTermShadow

getFieldProxy(String) - Method in class org.intermine.model.bio.OntologyTermSynonymShadow

getFieldProxy(String) - Method in class org.intermine.model.bio.OrganismShadow

getFieldProxy(String) - Method in class org.intermine.model.bio.OrthologueEvidenceCodeShadow

getFieldProxy(String) - Method in class org.intermine.model.bio.OrthologueEvidenceShadow

getFieldProxy(String) - Method in class org.intermine.model.bio.ProteinShadow

getFieldProxy(String) - Method in class org.intermine.model.bio.PublicationShadow

getFieldProxy(String) - Method in class org.intermine.model.bio.SequenceCollectionShadow

getFieldProxy(String) - Method in class org.intermine.model.bio.SequenceFeatureShadow

getFieldProxy(String) - Method in class org.intermine.model.bio.SequenceShadow

getFieldProxy(String) - Method in class org.intermine.model.bio.SequenceVariantShadow

getFieldProxy(String) - Method in class org.intermine.model.bio.SOTermShadow

getFieldProxy(String) - Method in class org.intermine.model.bio.StrainShadow

getFieldProxy(String) - Method in class org.intermine.model.bio.SynonymShadow

getFieldProxy(String) - Method in class org.intermine.model.bio.SyntenicRegionShadow

getFieldProxy(String) - Method in class org.intermine.model.bio.SyntenyBlockShadow

getFieldProxy(String) - Method in class org.intermine.model.bio.TranscriptShadow

getFieldProxy(String) - Method in class org.intermine.model.bio.UTRShadow

getFieldType(String) - Method in class org.intermine.model.bio.AnnotatableShadow

getFieldType(String) - Method in class org.intermine.model.bio.AuthorShadow

getFieldType(String) - Method in class org.intermine.model.bio.BioEntityShadow

getFieldType(String) - Method in class org.intermine.model.bio.CDSShadow

getFieldType(String) - Method in class org.intermine.model.bio.ChromosomeShadow

getFieldType(String) - Method in class org.intermine.model.bio.CommentShadow

getFieldType(String) - Method in class org.intermine.model.bio.CrossReferenceShadow

getFieldType(String) - Method in class org.intermine.model.bio.DataSetShadow

getFieldType(String) - Method in class org.intermine.model.bio.DataSourceShadow

getFieldType(String) - Method in class org.intermine.model.bio.ExonShadow

getFieldType(String) - Method in class org.intermine.model.bio.GeneFlankingRegionShadow

getFieldType(String) - Method in class org.intermine.model.bio.GeneShadow

getFieldType(String) - Method in class org.intermine.model.bio.HomologueShadow

getFieldType(String) - Method in class org.intermine.model.bio.IntergenicRegionShadow

getFieldType(String) - Method in class org.intermine.model.bio.IntronShadow

getFieldType(String) - Method in class org.intermine.model.bio.LocationShadow

getFieldType(String) - Method in class org.intermine.model.bio.MeshTermShadow

getFieldType(String) - Method in class org.intermine.model.bio.OntologyAnnotationEvidenceCodeShadow

getFieldType(String) - Method in class org.intermine.model.bio.OntologyAnnotationShadow

getFieldType(String) - Method in class org.intermine.model.bio.OntologyEvidenceShadow

getFieldType(String) - Method in class org.intermine.model.bio.OntologyRelationShadow

getFieldType(String) - Method in class org.intermine.model.bio.OntologyShadow

getFieldType(String) - Method in class org.intermine.model.bio.OntologyTermShadow

getFieldType(String) - Method in class org.intermine.model.bio.OntologyTermSynonymShadow

getFieldType(String) - Method in class org.intermine.model.bio.OrganismShadow

getFieldType(String) - Method in class org.intermine.model.bio.OrthologueEvidenceCodeShadow

getFieldType(String) - Method in class org.intermine.model.bio.OrthologueEvidenceShadow

getFieldType(String) - Method in class org.intermine.model.bio.ProteinShadow

getFieldType(String) - Method in class org.intermine.model.bio.PublicationShadow

getFieldType(String) - Method in class org.intermine.model.bio.SequenceCollectionShadow

getFieldType(String) - Method in class org.intermine.model.bio.SequenceFeatureShadow

getFieldType(String) - Method in class org.intermine.model.bio.SequenceShadow

getFieldType(String) - Method in class org.intermine.model.bio.SequenceVariantShadow

getFieldType(String) - Method in class org.intermine.model.bio.SOTermShadow

getFieldType(String) - Method in class org.intermine.model.bio.StrainShadow

getFieldType(String) - Method in class org.intermine.model.bio.SynonymShadow

getFieldType(String) - Method in class org.intermine.model.bio.SyntenicRegionShadow

getFieldType(String) - Method in class org.intermine.model.bio.SyntenyBlockShadow

getFieldType(String) - Method in class org.intermine.model.bio.TranscriptShadow

getFieldType(String) - Method in class org.intermine.model.bio.UTRShadow

getFieldValue(String) - Method in class org.intermine.model.bio.AnnotatableShadow

getFieldValue(String) - Method in class org.intermine.model.bio.AuthorShadow

getFieldValue(String) - Method in class org.intermine.model.bio.BioEntityShadow

getFieldValue(String) - Method in class org.intermine.model.bio.CDSShadow

getFieldValue(String) - Method in class org.intermine.model.bio.ChromosomeShadow

getFieldValue(String) - Method in class org.intermine.model.bio.CommentShadow

getFieldValue(String) - Method in class org.intermine.model.bio.CrossReferenceShadow

getFieldValue(String) - Method in class org.intermine.model.bio.DataSetShadow

getFieldValue(String) - Method in class org.intermine.model.bio.DataSourceShadow

getFieldValue(String) - Method in class org.intermine.model.bio.ExonShadow

getFieldValue(String) - Method in class org.intermine.model.bio.GeneFlankingRegionShadow

getFieldValue(String) - Method in class org.intermine.model.bio.GeneShadow

getFieldValue(String) - Method in class org.intermine.model.bio.HomologueShadow

getFieldValue(String) - Method in class org.intermine.model.bio.IntergenicRegionShadow

getFieldValue(String) - Method in class org.intermine.model.bio.IntronShadow

getFieldValue(String) - Method in class org.intermine.model.bio.LocationShadow

getFieldValue(String) - Method in class org.intermine.model.bio.MeshTermShadow

getFieldValue(String) - Method in class org.intermine.model.bio.OntologyAnnotationEvidenceCodeShadow

getFieldValue(String) - Method in class org.intermine.model.bio.OntologyAnnotationShadow

getFieldValue(String) - Method in class org.intermine.model.bio.OntologyEvidenceShadow

getFieldValue(String) - Method in class org.intermine.model.bio.OntologyRelationShadow

getFieldValue(String) - Method in class org.intermine.model.bio.OntologyShadow

getFieldValue(String) - Method in class org.intermine.model.bio.OntologyTermShadow

getFieldValue(String) - Method in class org.intermine.model.bio.OntologyTermSynonymShadow

getFieldValue(String) - Method in class org.intermine.model.bio.OrganismShadow

getFieldValue(String) - Method in class org.intermine.model.bio.OrthologueEvidenceCodeShadow

getFieldValue(String) - Method in class org.intermine.model.bio.OrthologueEvidenceShadow

getFieldValue(String) - Method in class org.intermine.model.bio.ProteinShadow

getFieldValue(String) - Method in class org.intermine.model.bio.PublicationShadow

getFieldValue(String) - Method in class org.intermine.model.bio.SequenceCollectionShadow

getFieldValue(String) - Method in class org.intermine.model.bio.SequenceFeatureShadow

getFieldValue(String) - Method in class org.intermine.model.bio.SequenceShadow

getFieldValue(String) - Method in class org.intermine.model.bio.SequenceVariantShadow

getFieldValue(String) - Method in class org.intermine.model.bio.SOTermShadow

getFieldValue(String) - Method in class org.intermine.model.bio.StrainShadow

getFieldValue(String) - Method in class org.intermine.model.bio.SynonymShadow

getFieldValue(String) - Method in class org.intermine.model.bio.SyntenicRegionShadow

getFieldValue(String) - Method in class org.intermine.model.bio.SyntenyBlockShadow

getFieldValue(String) - Method in class org.intermine.model.bio.TranscriptShadow

getFieldValue(String) - Method in class org.intermine.model.bio.UTRShadow

getFirstAuthor() - Method in interface org.intermine.model.bio.Publication

getFirstAuthor() - Method in class org.intermine.model.bio.PublicationShadow

getFirstName() - Method in interface org.intermine.model.bio.Author

getFirstName() - Method in class org.intermine.model.bio.AuthorShadow

getFlankingRegions() - Method in interface org.intermine.model.bio.Gene

getFlankingRegions() - Method in class org.intermine.model.bio.GeneShadow

getGene() - Method in interface org.intermine.model.bio.CDS

getGene() - Method in class org.intermine.model.bio.CDSShadow

getGene() - Method in interface org.intermine.model.bio.Exon

getGene() - Method in class org.intermine.model.bio.ExonShadow

getGene() - Method in interface org.intermine.model.bio.GeneFlankingRegion

getGene() - Method in class org.intermine.model.bio.GeneFlankingRegionShadow

getGene() - Method in interface org.intermine.model.bio.Homologue

getGene() - Method in class org.intermine.model.bio.HomologueShadow

getGene() - Method in interface org.intermine.model.bio.UTR

getGene() - Method in class org.intermine.model.bio.UTRShadow

getGenes() - Method in interface org.intermine.model.bio.Intron

getGenes() - Method in class org.intermine.model.bio.IntronShadow

getGenes() - Method in interface org.intermine.model.bio.Protein

getGenes() - Method in class org.intermine.model.bio.ProteinShadow

getGenes() - Method in interface org.intermine.model.bio.SequenceVariant

getGenes() - Method in class org.intermine.model.bio.SequenceVariantShadow

getGenus() - Method in interface org.intermine.model.bio.Organism

getGenus() - Method in class org.intermine.model.bio.OrganismShadow

getHomologue() - Method in interface org.intermine.model.bio.Homologue

getHomologue() - Method in class org.intermine.model.bio.HomologueShadow

getHomologues() - Method in interface org.intermine.model.bio.Gene

getHomologues() - Method in class org.intermine.model.bio.GeneShadow

getId() - Method in class org.intermine.model.bio.AnnotatableShadow

getId() - Method in class org.intermine.model.bio.AuthorShadow

getId() - Method in class org.intermine.model.bio.BioEntityShadow

getId() - Method in class org.intermine.model.bio.CDSShadow

getId() - Method in class org.intermine.model.bio.ChromosomeShadow

getId() - Method in class org.intermine.model.bio.CommentShadow

getId() - Method in class org.intermine.model.bio.CrossReferenceShadow

getId() - Method in class org.intermine.model.bio.DataSetShadow

getId() - Method in class org.intermine.model.bio.DataSourceShadow

getId() - Method in class org.intermine.model.bio.ExonShadow

getId() - Method in class org.intermine.model.bio.GeneFlankingRegionShadow

getId() - Method in class org.intermine.model.bio.GeneShadow

getId() - Method in class org.intermine.model.bio.HomologueShadow

getId() - Method in class org.intermine.model.bio.IntergenicRegionShadow

getId() - Method in class org.intermine.model.bio.IntronShadow

getId() - Method in class org.intermine.model.bio.LocationShadow

getId() - Method in class org.intermine.model.bio.MeshTermShadow

getId() - Method in class org.intermine.model.bio.OntologyAnnotationEvidenceCodeShadow

getId() - Method in class org.intermine.model.bio.OntologyAnnotationShadow

getId() - Method in class org.intermine.model.bio.OntologyEvidenceShadow

getId() - Method in class org.intermine.model.bio.OntologyRelationShadow

getId() - Method in class org.intermine.model.bio.OntologyShadow

getId() - Method in class org.intermine.model.bio.OntologyTermShadow

getId() - Method in class org.intermine.model.bio.OntologyTermSynonymShadow

getId() - Method in class org.intermine.model.bio.OrganismShadow

getId() - Method in class org.intermine.model.bio.OrthologueEvidenceCodeShadow

getId() - Method in class org.intermine.model.bio.OrthologueEvidenceShadow

getId() - Method in class org.intermine.model.bio.ProteinShadow

getId() - Method in class org.intermine.model.bio.PublicationShadow

getId() - Method in class org.intermine.model.bio.SequenceCollectionShadow

getId() - Method in class org.intermine.model.bio.SequenceFeatureShadow

getId() - Method in class org.intermine.model.bio.SequenceShadow

getId() - Method in class org.intermine.model.bio.SequenceVariantShadow

getId() - Method in class org.intermine.model.bio.SOTermShadow

getId() - Method in class org.intermine.model.bio.StrainShadow

getId() - Method in class org.intermine.model.bio.SynonymShadow

getId() - Method in class org.intermine.model.bio.SyntenicRegionShadow

getId() - Method in class org.intermine.model.bio.SyntenyBlockShadow

getId() - Method in class org.intermine.model.bio.TranscriptShadow

getId() - Method in class org.intermine.model.bio.UTRShadow

getIdentifier() - Method in interface org.intermine.model.bio.CrossReference

getIdentifier() - Method in class org.intermine.model.bio.CrossReferenceShadow

getIdentifier() - Method in interface org.intermine.model.bio.OntologyTerm

getIdentifier() - Method in class org.intermine.model.bio.OntologyTermShadow

getIdentifier() - Method in class org.intermine.model.bio.SOTermShadow

getIncludeGene() - Method in interface org.intermine.model.bio.GeneFlankingRegion

getIncludeGene() - Method in class org.intermine.model.bio.GeneFlankingRegionShadow

getInitials() - Method in interface org.intermine.model.bio.Author

getInitials() - Method in class org.intermine.model.bio.AuthorShadow

getIntrons() - Method in interface org.intermine.model.bio.Gene

getIntrons() - Method in class org.intermine.model.bio.GeneShadow

getIssue() - Method in interface org.intermine.model.bio.Publication

getIssue() - Method in class org.intermine.model.bio.PublicationShadow

getJournal() - Method in interface org.intermine.model.bio.Publication

getJournal() - Method in class org.intermine.model.bio.PublicationShadow

getLastName() - Method in interface org.intermine.model.bio.Author

getLastName() - Method in class org.intermine.model.bio.AuthorShadow

getLength() - Method in class org.intermine.model.bio.CDSShadow

getLength() - Method in class org.intermine.model.bio.ChromosomeShadow

getLength() - Method in class org.intermine.model.bio.ExonShadow

getLength() - Method in class org.intermine.model.bio.GeneFlankingRegionShadow

getLength() - Method in class org.intermine.model.bio.GeneShadow

getLength() - Method in class org.intermine.model.bio.IntergenicRegionShadow

getLength() - Method in class org.intermine.model.bio.IntronShadow

getLength() - Method in interface org.intermine.model.bio.Protein

getLength() - Method in class org.intermine.model.bio.ProteinShadow

getLength() - Method in interface org.intermine.model.bio.Sequence

getLength() - Method in interface org.intermine.model.bio.SequenceFeature

getLength() - Method in class org.intermine.model.bio.SequenceFeatureShadow

getLength() - Method in class org.intermine.model.bio.SequenceShadow

getLength() - Method in class org.intermine.model.bio.SyntenicRegionShadow

getLength() - Method in class org.intermine.model.bio.TranscriptShadow

getLength() - Method in class org.intermine.model.bio.UTRShadow

getLicence() - Method in interface org.intermine.model.bio.DataSet

getLicence() - Method in class org.intermine.model.bio.DataSetShadow

getLocatedFeatures() - Method in interface org.intermine.model.bio.BioEntity

getLocatedFeatures() - Method in class org.intermine.model.bio.BioEntityShadow

getLocatedFeatures() - Method in class org.intermine.model.bio.CDSShadow

getLocatedFeatures() - Method in class org.intermine.model.bio.ChromosomeShadow

getLocatedFeatures() - Method in class org.intermine.model.bio.ExonShadow

getLocatedFeatures() - Method in class org.intermine.model.bio.GeneFlankingRegionShadow

getLocatedFeatures() - Method in class org.intermine.model.bio.GeneShadow

getLocatedFeatures() - Method in class org.intermine.model.bio.IntergenicRegionShadow

getLocatedFeatures() - Method in class org.intermine.model.bio.IntronShadow

getLocatedFeatures() - Method in class org.intermine.model.bio.ProteinShadow

getLocatedFeatures() - Method in class org.intermine.model.bio.SequenceCollectionShadow

getLocatedFeatures() - Method in class org.intermine.model.bio.SequenceFeatureShadow

getLocatedFeatures() - Method in class org.intermine.model.bio.StrainShadow

getLocatedFeatures() - Method in class org.intermine.model.bio.SyntenicRegionShadow

getLocatedFeatures() - Method in class org.intermine.model.bio.TranscriptShadow

getLocatedFeatures() - Method in class org.intermine.model.bio.UTRShadow

getLocatedOn() - Method in interface org.intermine.model.bio.Location

getLocatedOn() - Method in class org.intermine.model.bio.LocationShadow

getLocations() - Method in interface org.intermine.model.bio.BioEntity

getLocations() - Method in class org.intermine.model.bio.BioEntityShadow

getLocations() - Method in class org.intermine.model.bio.CDSShadow

getLocations() - Method in class org.intermine.model.bio.ChromosomeShadow

getLocations() - Method in class org.intermine.model.bio.ExonShadow

getLocations() - Method in class org.intermine.model.bio.GeneFlankingRegionShadow

getLocations() - Method in class org.intermine.model.bio.GeneShadow

getLocations() - Method in class org.intermine.model.bio.IntergenicRegionShadow

getLocations() - Method in class org.intermine.model.bio.IntronShadow

getLocations() - Method in class org.intermine.model.bio.ProteinShadow

getLocations() - Method in class org.intermine.model.bio.SequenceCollectionShadow

getLocations() - Method in class org.intermine.model.bio.SequenceFeatureShadow

getLocations() - Method in class org.intermine.model.bio.StrainShadow

getLocations() - Method in class org.intermine.model.bio.SyntenicRegionShadow

getLocations() - Method in class org.intermine.model.bio.TranscriptShadow

getLocations() - Method in class org.intermine.model.bio.UTRShadow

getMd5checksum() - Method in interface org.intermine.model.bio.Protein

getMd5checksum() - Method in class org.intermine.model.bio.ProteinShadow

getMd5checksum() - Method in interface org.intermine.model.bio.Sequence

getMd5checksum() - Method in class org.intermine.model.bio.SequenceShadow

getMeshTerms() - Method in interface org.intermine.model.bio.Publication

getMeshTerms() - Method in class org.intermine.model.bio.PublicationShadow

getMolecularWeight() - Method in interface org.intermine.model.bio.Protein

getMolecularWeight() - Method in class org.intermine.model.bio.ProteinShadow

getMonth() - Method in interface org.intermine.model.bio.Publication

getMonth() - Method in class org.intermine.model.bio.PublicationShadow

getName() - Method in interface org.intermine.model.bio.Author

getName() - Method in class org.intermine.model.bio.AuthorShadow

getName() - Method in interface org.intermine.model.bio.BioEntity

getName() - Method in class org.intermine.model.bio.BioEntityShadow

getName() - Method in class org.intermine.model.bio.CDSShadow

getName() - Method in class org.intermine.model.bio.ChromosomeShadow

getName() - Method in interface org.intermine.model.bio.DataSet

getName() - Method in class org.intermine.model.bio.DataSetShadow

getName() - Method in interface org.intermine.model.bio.DataSource

getName() - Method in class org.intermine.model.bio.DataSourceShadow

getName() - Method in class org.intermine.model.bio.ExonShadow

getName() - Method in class org.intermine.model.bio.GeneFlankingRegionShadow

getName() - Method in class org.intermine.model.bio.GeneShadow

getName() - Method in class org.intermine.model.bio.IntergenicRegionShadow

getName() - Method in class org.intermine.model.bio.IntronShadow

getName() - Method in interface org.intermine.model.bio.MeshTerm

getName() - Method in class org.intermine.model.bio.MeshTermShadow

getName() - Method in interface org.intermine.model.bio.Ontology

getName() - Method in interface org.intermine.model.bio.OntologyAnnotationEvidenceCode

getName() - Method in class org.intermine.model.bio.OntologyAnnotationEvidenceCodeShadow

getName() - Method in class org.intermine.model.bio.OntologyShadow

getName() - Method in interface org.intermine.model.bio.OntologyTerm

getName() - Method in class org.intermine.model.bio.OntologyTermShadow

getName() - Method in interface org.intermine.model.bio.OntologyTermSynonym

getName() - Method in class org.intermine.model.bio.OntologyTermSynonymShadow

getName() - Method in interface org.intermine.model.bio.Organism

getName() - Method in class org.intermine.model.bio.OrganismShadow

getName() - Method in interface org.intermine.model.bio.OrthologueEvidenceCode

getName() - Method in class org.intermine.model.bio.OrthologueEvidenceCodeShadow

getName() - Method in class org.intermine.model.bio.ProteinShadow

getName() - Method in class org.intermine.model.bio.SequenceCollectionShadow

getName() - Method in class org.intermine.model.bio.SequenceFeatureShadow

getName() - Method in class org.intermine.model.bio.SOTermShadow

getName() - Method in class org.intermine.model.bio.StrainShadow

getName() - Method in class org.intermine.model.bio.SyntenicRegionShadow

getName() - Method in class org.intermine.model.bio.TranscriptShadow

getName() - Method in class org.intermine.model.bio.UTRShadow

getNamespace() - Method in interface org.intermine.model.bio.OntologyTerm

getNamespace() - Method in class org.intermine.model.bio.OntologyTermShadow

getNamespace() - Method in class org.intermine.model.bio.SOTermShadow

getoBJECT() - Method in class org.intermine.model.bio.AnnotatableShadow

getoBJECT() - Method in class org.intermine.model.bio.AuthorShadow

getoBJECT() - Method in class org.intermine.model.bio.BioEntityShadow

getoBJECT() - Method in class org.intermine.model.bio.CDSShadow

getoBJECT() - Method in class org.intermine.model.bio.ChromosomeShadow

getoBJECT() - Method in class org.intermine.model.bio.CommentShadow

getoBJECT() - Method in class org.intermine.model.bio.CrossReferenceShadow

getoBJECT() - Method in class org.intermine.model.bio.DataSetShadow

getoBJECT() - Method in class org.intermine.model.bio.DataSourceShadow

getoBJECT() - Method in class org.intermine.model.bio.ExonShadow

getoBJECT() - Method in class org.intermine.model.bio.GeneFlankingRegionShadow

getoBJECT() - Method in class org.intermine.model.bio.GeneShadow

getoBJECT() - Method in class org.intermine.model.bio.HomologueShadow

getoBJECT() - Method in class org.intermine.model.bio.IntergenicRegionShadow

getoBJECT() - Method in class org.intermine.model.bio.IntronShadow

getoBJECT() - Method in class org.intermine.model.bio.LocationShadow

getoBJECT() - Method in class org.intermine.model.bio.MeshTermShadow

getoBJECT() - Method in class org.intermine.model.bio.OntologyAnnotationEvidenceCodeShadow

getoBJECT() - Method in class org.intermine.model.bio.OntologyAnnotationShadow

getoBJECT() - Method in class org.intermine.model.bio.OntologyEvidenceShadow

getoBJECT() - Method in class org.intermine.model.bio.OntologyRelationShadow

getoBJECT() - Method in class org.intermine.model.bio.OntologyShadow

getoBJECT() - Method in class org.intermine.model.bio.OntologyTermShadow

getoBJECT() - Method in class org.intermine.model.bio.OntologyTermSynonymShadow

getoBJECT() - Method in class org.intermine.model.bio.OrganismShadow

getoBJECT() - Method in class org.intermine.model.bio.OrthologueEvidenceCodeShadow

getoBJECT() - Method in class org.intermine.model.bio.OrthologueEvidenceShadow

getoBJECT() - Method in class org.intermine.model.bio.ProteinShadow

getoBJECT() - Method in class org.intermine.model.bio.PublicationShadow

getoBJECT() - Method in class org.intermine.model.bio.SequenceCollectionShadow

getoBJECT() - Method in class org.intermine.model.bio.SequenceFeatureShadow

getoBJECT() - Method in class org.intermine.model.bio.SequenceShadow

getoBJECT() - Method in class org.intermine.model.bio.SequenceVariantShadow

getoBJECT() - Method in class org.intermine.model.bio.SOTermShadow

getoBJECT() - Method in class org.intermine.model.bio.StrainShadow

getoBJECT() - Method in class org.intermine.model.bio.SynonymShadow

getoBJECT() - Method in class org.intermine.model.bio.SyntenicRegionShadow

getoBJECT() - Method in class org.intermine.model.bio.SyntenyBlockShadow

getoBJECT() - Method in class org.intermine.model.bio.TranscriptShadow

getoBJECT() - Method in class org.intermine.model.bio.UTRShadow

getObsolete() - Method in interface org.intermine.model.bio.OntologyTerm

getObsolete() - Method in class org.intermine.model.bio.OntologyTermShadow

getObsolete() - Method in class org.intermine.model.bio.SOTermShadow

getOntology() - Method in interface org.intermine.model.bio.OntologyTerm

getOntology() - Method in class org.intermine.model.bio.OntologyTermShadow

getOntology() - Method in class org.intermine.model.bio.SOTermShadow

getOntologyAnnotations() - Method in interface org.intermine.model.bio.Annotatable

getOntologyAnnotations() - Method in class org.intermine.model.bio.AnnotatableShadow

getOntologyAnnotations() - Method in class org.intermine.model.bio.BioEntityShadow

getOntologyAnnotations() - Method in class org.intermine.model.bio.CDSShadow

getOntologyAnnotations() - Method in class org.intermine.model.bio.ChromosomeShadow

getOntologyAnnotations() - Method in class org.intermine.model.bio.ExonShadow

getOntologyAnnotations() - Method in class org.intermine.model.bio.GeneFlankingRegionShadow

getOntologyAnnotations() - Method in class org.intermine.model.bio.GeneShadow

getOntologyAnnotations() - Method in class org.intermine.model.bio.IntergenicRegionShadow

getOntologyAnnotations() - Method in class org.intermine.model.bio.IntronShadow

getOntologyAnnotations() - Method in interface org.intermine.model.bio.OntologyTerm

getOntologyAnnotations() - Method in class org.intermine.model.bio.OntologyTermShadow

getOntologyAnnotations() - Method in class org.intermine.model.bio.ProteinShadow

getOntologyAnnotations() - Method in class org.intermine.model.bio.SequenceCollectionShadow

getOntologyAnnotations() - Method in class org.intermine.model.bio.SequenceFeatureShadow

getOntologyAnnotations() - Method in class org.intermine.model.bio.SOTermShadow

getOntologyAnnotations() - Method in class org.intermine.model.bio.StrainShadow

getOntologyAnnotations() - Method in class org.intermine.model.bio.SyntenicRegionShadow

getOntologyAnnotations() - Method in class org.intermine.model.bio.TranscriptShadow

getOntologyAnnotations() - Method in class org.intermine.model.bio.UTRShadow

getOntologyTerm() - Method in interface org.intermine.model.bio.OntologyAnnotation

getOntologyTerm() - Method in class org.intermine.model.bio.OntologyAnnotationShadow

getOrganism() - Method in interface org.intermine.model.bio.BioEntity

getOrganism() - Method in class org.intermine.model.bio.BioEntityShadow

getOrganism() - Method in class org.intermine.model.bio.CDSShadow

getOrganism() - Method in class org.intermine.model.bio.ChromosomeShadow

getOrganism() - Method in class org.intermine.model.bio.ExonShadow

getOrganism() - Method in class org.intermine.model.bio.GeneFlankingRegionShadow

getOrganism() - Method in class org.intermine.model.bio.GeneShadow

getOrganism() - Method in class org.intermine.model.bio.IntergenicRegionShadow

getOrganism() - Method in class org.intermine.model.bio.IntronShadow

getOrganism() - Method in class org.intermine.model.bio.ProteinShadow

getOrganism() - Method in class org.intermine.model.bio.SequenceCollectionShadow

getOrganism() - Method in class org.intermine.model.bio.SequenceFeatureShadow

getOrganism() - Method in class org.intermine.model.bio.StrainShadow

getOrganism() - Method in class org.intermine.model.bio.SyntenicRegionShadow

getOrganism() - Method in class org.intermine.model.bio.TranscriptShadow

getOrganism() - Method in class org.intermine.model.bio.UTRShadow

getOverlappingFeatures() - Method in class org.intermine.model.bio.CDSShadow

getOverlappingFeatures() - Method in class org.intermine.model.bio.ChromosomeShadow

getOverlappingFeatures() - Method in class org.intermine.model.bio.ExonShadow

getOverlappingFeatures() - Method in class org.intermine.model.bio.GeneFlankingRegionShadow

getOverlappingFeatures() - Method in class org.intermine.model.bio.GeneShadow

getOverlappingFeatures() - Method in class org.intermine.model.bio.IntergenicRegionShadow

getOverlappingFeatures() - Method in class org.intermine.model.bio.IntronShadow

getOverlappingFeatures() - Method in interface org.intermine.model.bio.SequenceFeature

getOverlappingFeatures() - Method in class org.intermine.model.bio.SequenceFeatureShadow

getOverlappingFeatures() - Method in class org.intermine.model.bio.SyntenicRegionShadow

getOverlappingFeatures() - Method in class org.intermine.model.bio.TranscriptShadow

getOverlappingFeatures() - Method in class org.intermine.model.bio.UTRShadow

getPages() - Method in interface org.intermine.model.bio.Publication

getPages() - Method in class org.intermine.model.bio.PublicationShadow

getParents() - Method in interface org.intermine.model.bio.OntologyTerm

getParents() - Method in class org.intermine.model.bio.OntologyTermShadow

getParents() - Method in class org.intermine.model.bio.SOTermShadow

getParentTerm() - Method in interface org.intermine.model.bio.OntologyRelation

getParentTerm() - Method in class org.intermine.model.bio.OntologyRelationShadow

getPrimaryAccession() - Method in interface org.intermine.model.bio.Protein

getPrimaryAccession() - Method in class org.intermine.model.bio.ProteinShadow

getPrimaryIdentifier() - Method in interface org.intermine.model.bio.Annotatable

getPrimaryIdentifier() - Method in class org.intermine.model.bio.AnnotatableShadow

getPrimaryIdentifier() - Method in class org.intermine.model.bio.BioEntityShadow

getPrimaryIdentifier() - Method in class org.intermine.model.bio.CDSShadow

getPrimaryIdentifier() - Method in class org.intermine.model.bio.ChromosomeShadow

getPrimaryIdentifier() - Method in class org.intermine.model.bio.ExonShadow

getPrimaryIdentifier() - Method in class org.intermine.model.bio.GeneFlankingRegionShadow

getPrimaryIdentifier() - Method in class org.intermine.model.bio.GeneShadow

getPrimaryIdentifier() - Method in class org.intermine.model.bio.IntergenicRegionShadow

getPrimaryIdentifier() - Method in class org.intermine.model.bio.IntronShadow

getPrimaryIdentifier() - Method in class org.intermine.model.bio.ProteinShadow

getPrimaryIdentifier() - Method in class org.intermine.model.bio.SequenceCollectionShadow

getPrimaryIdentifier() - Method in class org.intermine.model.bio.SequenceFeatureShadow

getPrimaryIdentifier() - Method in class org.intermine.model.bio.StrainShadow

getPrimaryIdentifier() - Method in class org.intermine.model.bio.SyntenicRegionShadow

getPrimaryIdentifier() - Method in class org.intermine.model.bio.TranscriptShadow

getPrimaryIdentifier() - Method in class org.intermine.model.bio.UTRShadow

getProtein() - Method in interface org.intermine.model.bio.CDS

getProtein() - Method in class org.intermine.model.bio.CDSShadow

getProtein() - Method in interface org.intermine.model.bio.Transcript

getProtein() - Method in class org.intermine.model.bio.TranscriptShadow

getProteins() - Method in interface org.intermine.model.bio.Gene

getProteins() - Method in class org.intermine.model.bio.GeneShadow

getPublication() - Method in interface org.intermine.model.bio.DataSet

getPublication() - Method in class org.intermine.model.bio.DataSetShadow

getPublications() - Method in interface org.intermine.model.bio.Annotatable

getPublications() - Method in class org.intermine.model.bio.AnnotatableShadow

getPublications() - Method in interface org.intermine.model.bio.Author

getPublications() - Method in class org.intermine.model.bio.AuthorShadow

getPublications() - Method in class org.intermine.model.bio.BioEntityShadow

getPublications() - Method in class org.intermine.model.bio.CDSShadow

getPublications() - Method in class org.intermine.model.bio.ChromosomeShadow

getPublications() - Method in interface org.intermine.model.bio.DataSource

getPublications() - Method in class org.intermine.model.bio.DataSourceShadow

getPublications() - Method in class org.intermine.model.bio.ExonShadow

getPublications() - Method in class org.intermine.model.bio.GeneFlankingRegionShadow

getPublications() - Method in class org.intermine.model.bio.GeneShadow

getPublications() - Method in class org.intermine.model.bio.IntergenicRegionShadow

getPublications() - Method in class org.intermine.model.bio.IntronShadow

getPublications() - Method in interface org.intermine.model.bio.MeshTerm

getPublications() - Method in class org.intermine.model.bio.MeshTermShadow

getPublications() - Method in interface org.intermine.model.bio.OntologyEvidence

getPublications() - Method in class org.intermine.model.bio.OntologyEvidenceShadow

getPublications() - Method in interface org.intermine.model.bio.OrthologueEvidence

getPublications() - Method in class org.intermine.model.bio.OrthologueEvidenceShadow

getPublications() - Method in class org.intermine.model.bio.ProteinShadow

getPublications() - Method in class org.intermine.model.bio.SequenceCollectionShadow

getPublications() - Method in class org.intermine.model.bio.SequenceFeatureShadow

getPublications() - Method in class org.intermine.model.bio.StrainShadow

getPublications() - Method in class org.intermine.model.bio.SyntenicRegionShadow

getPublications() - Method in interface org.intermine.model.bio.SyntenyBlock

getPublications() - Method in class org.intermine.model.bio.SyntenyBlockShadow

getPublications() - Method in class org.intermine.model.bio.TranscriptShadow

getPublications() - Method in class org.intermine.model.bio.UTRShadow

getPubMedId() - Method in interface org.intermine.model.bio.Publication

getPubMedId() - Method in class org.intermine.model.bio.PublicationShadow

getQualifier() - Method in interface org.intermine.model.bio.OntologyAnnotation

getQualifier() - Method in class org.intermine.model.bio.OntologyAnnotationShadow

getRedundant() - Method in interface org.intermine.model.bio.OntologyRelation

getRedundant() - Method in class org.intermine.model.bio.OntologyRelationShadow

getRelations() - Method in interface org.intermine.model.bio.OntologyTerm

getRelations() - Method in class org.intermine.model.bio.OntologyTermShadow

getRelations() - Method in class org.intermine.model.bio.SOTermShadow

getRelationship() - Method in interface org.intermine.model.bio.OntologyRelation

getRelationship() - Method in class org.intermine.model.bio.OntologyRelationShadow

getResidues() - Method in interface org.intermine.model.bio.Sequence

getResidues() - Method in class org.intermine.model.bio.SequenceShadow

getScore() - Method in class org.intermine.model.bio.CDSShadow

getScore() - Method in class org.intermine.model.bio.ChromosomeShadow

getScore() - Method in class org.intermine.model.bio.ExonShadow

getScore() - Method in class org.intermine.model.bio.GeneFlankingRegionShadow

getScore() - Method in class org.intermine.model.bio.GeneShadow

getScore() - Method in class org.intermine.model.bio.IntergenicRegionShadow

getScore() - Method in class org.intermine.model.bio.IntronShadow

getScore() - Method in interface org.intermine.model.bio.SequenceFeature

getScore() - Method in class org.intermine.model.bio.SequenceFeatureShadow

getScore() - Method in class org.intermine.model.bio.SyntenicRegionShadow

getScore() - Method in class org.intermine.model.bio.TranscriptShadow

getScore() - Method in class org.intermine.model.bio.UTRShadow

getScoreType() - Method in class org.intermine.model.bio.CDSShadow

getScoreType() - Method in class org.intermine.model.bio.ChromosomeShadow

getScoreType() - Method in class org.intermine.model.bio.ExonShadow

getScoreType() - Method in class org.intermine.model.bio.GeneFlankingRegionShadow

getScoreType() - Method in class org.intermine.model.bio.GeneShadow

getScoreType() - Method in class org.intermine.model.bio.IntergenicRegionShadow

getScoreType() - Method in class org.intermine.model.bio.IntronShadow

getScoreType() - Method in interface org.intermine.model.bio.SequenceFeature

getScoreType() - Method in class org.intermine.model.bio.SequenceFeatureShadow

getScoreType() - Method in class org.intermine.model.bio.SyntenicRegionShadow

getScoreType() - Method in class org.intermine.model.bio.TranscriptShadow

getScoreType() - Method in class org.intermine.model.bio.UTRShadow

getSecondaryIdentifier() - Method in interface org.intermine.model.bio.BioEntity

getSecondaryIdentifier() - Method in class org.intermine.model.bio.BioEntityShadow

getSecondaryIdentifier() - Method in class org.intermine.model.bio.CDSShadow

getSecondaryIdentifier() - Method in class org.intermine.model.bio.ChromosomeShadow

getSecondaryIdentifier() - Method in class org.intermine.model.bio.ExonShadow

getSecondaryIdentifier() - Method in class org.intermine.model.bio.GeneFlankingRegionShadow

getSecondaryIdentifier() - Method in class org.intermine.model.bio.GeneShadow

getSecondaryIdentifier() - Method in class org.intermine.model.bio.IntergenicRegionShadow

getSecondaryIdentifier() - Method in class org.intermine.model.bio.IntronShadow

getSecondaryIdentifier() - Method in class org.intermine.model.bio.ProteinShadow

getSecondaryIdentifier() - Method in class org.intermine.model.bio.SequenceCollectionShadow

getSecondaryIdentifier() - Method in class org.intermine.model.bio.SequenceFeatureShadow

getSecondaryIdentifier() - Method in class org.intermine.model.bio.StrainShadow

getSecondaryIdentifier() - Method in class org.intermine.model.bio.SyntenicRegionShadow

getSecondaryIdentifier() - Method in class org.intermine.model.bio.TranscriptShadow

getSecondaryIdentifier() - Method in class org.intermine.model.bio.UTRShadow

getSequence() - Method in class org.intermine.model.bio.CDSShadow

getSequence() - Method in class org.intermine.model.bio.ChromosomeShadow

getSequence() - Method in class org.intermine.model.bio.ExonShadow

getSequence() - Method in class org.intermine.model.bio.GeneFlankingRegionShadow

getSequence() - Method in class org.intermine.model.bio.GeneShadow

getSequence() - Method in class org.intermine.model.bio.IntergenicRegionShadow

getSequence() - Method in class org.intermine.model.bio.IntronShadow

getSequence() - Method in interface org.intermine.model.bio.Protein

getSequence() - Method in class org.intermine.model.bio.ProteinShadow

getSequence() - Method in interface org.intermine.model.bio.SequenceFeature

getSequence() - Method in class org.intermine.model.bio.SequenceFeatureShadow

getSequence() - Method in class org.intermine.model.bio.SyntenicRegionShadow

getSequence() - Method in class org.intermine.model.bio.TranscriptShadow

getSequence() - Method in class org.intermine.model.bio.UTRShadow

getSequenceOntologyTerm() - Method in class org.intermine.model.bio.CDSShadow

getSequenceOntologyTerm() - Method in class org.intermine.model.bio.ChromosomeShadow

getSequenceOntologyTerm() - Method in class org.intermine.model.bio.ExonShadow

getSequenceOntologyTerm() - Method in class org.intermine.model.bio.GeneFlankingRegionShadow

getSequenceOntologyTerm() - Method in class org.intermine.model.bio.GeneShadow

getSequenceOntologyTerm() - Method in class org.intermine.model.bio.IntergenicRegionShadow

getSequenceOntologyTerm() - Method in class org.intermine.model.bio.IntronShadow

getSequenceOntologyTerm() - Method in interface org.intermine.model.bio.SequenceCollection

getSequenceOntologyTerm() - Method in class org.intermine.model.bio.SequenceCollectionShadow

getSequenceOntologyTerm() - Method in interface org.intermine.model.bio.SequenceFeature

getSequenceOntologyTerm() - Method in class org.intermine.model.bio.SequenceFeatureShadow

getSequenceOntologyTerm() - Method in class org.intermine.model.bio.SyntenicRegionShadow

getSequenceOntologyTerm() - Method in class org.intermine.model.bio.TranscriptShadow

getSequenceOntologyTerm() - Method in class org.intermine.model.bio.UTRShadow

getShortName() - Method in interface org.intermine.model.bio.Organism

getShortName() - Method in class org.intermine.model.bio.OrganismShadow

getSource() - Method in interface org.intermine.model.bio.CrossReference

getSource() - Method in class org.intermine.model.bio.CrossReferenceShadow

getSpecies() - Method in interface org.intermine.model.bio.Organism

getSpecies() - Method in class org.intermine.model.bio.OrganismShadow

getStart() - Method in interface org.intermine.model.bio.Location

getStart() - Method in class org.intermine.model.bio.LocationShadow

getStrain() - Method in class org.intermine.model.bio.CDSShadow

getStrain() - Method in class org.intermine.model.bio.ChromosomeShadow

getStrain() - Method in class org.intermine.model.bio.ExonShadow

getStrain() - Method in class org.intermine.model.bio.GeneFlankingRegionShadow

getStrain() - Method in class org.intermine.model.bio.GeneShadow

getStrain() - Method in class org.intermine.model.bio.IntergenicRegionShadow

getStrain() - Method in class org.intermine.model.bio.IntronShadow

getStrain() - Method in interface org.intermine.model.bio.SequenceFeature

getStrain() - Method in class org.intermine.model.bio.SequenceFeatureShadow

getStrain() - Method in class org.intermine.model.bio.SyntenicRegionShadow

getStrain() - Method in class org.intermine.model.bio.TranscriptShadow

getStrain() - Method in class org.intermine.model.bio.UTRShadow

getStrains() - Method in interface org.intermine.model.bio.Organism

getStrains() - Method in class org.intermine.model.bio.OrganismShadow

getStrand() - Method in interface org.intermine.model.bio.Location

getStrand() - Method in class org.intermine.model.bio.LocationShadow

getSubject() - Method in interface org.intermine.model.bio.CrossReference

getSubject() - Method in class org.intermine.model.bio.CrossReferenceShadow

getSubject() - Method in interface org.intermine.model.bio.OntologyAnnotation

getSubject() - Method in class org.intermine.model.bio.OntologyAnnotationShadow

getSubject() - Method in interface org.intermine.model.bio.Synonym

getSubject() - Method in class org.intermine.model.bio.SynonymShadow

getSymbol() - Method in interface org.intermine.model.bio.BioEntity

getSymbol() - Method in class org.intermine.model.bio.BioEntityShadow

getSymbol() - Method in class org.intermine.model.bio.CDSShadow

getSymbol() - Method in class org.intermine.model.bio.ChromosomeShadow

getSymbol() - Method in class org.intermine.model.bio.ExonShadow

getSymbol() - Method in class org.intermine.model.bio.GeneFlankingRegionShadow

getSymbol() - Method in class org.intermine.model.bio.GeneShadow

getSymbol() - Method in class org.intermine.model.bio.IntergenicRegionShadow

getSymbol() - Method in class org.intermine.model.bio.IntronShadow

getSymbol() - Method in class org.intermine.model.bio.ProteinShadow

getSymbol() - Method in class org.intermine.model.bio.SequenceCollectionShadow

getSymbol() - Method in class org.intermine.model.bio.SequenceFeatureShadow

getSymbol() - Method in class org.intermine.model.bio.StrainShadow

getSymbol() - Method in class org.intermine.model.bio.SyntenicRegionShadow

getSymbol() - Method in class org.intermine.model.bio.TranscriptShadow

getSymbol() - Method in class org.intermine.model.bio.UTRShadow

getSynonyms() - Method in interface org.intermine.model.bio.BioEntity

getSynonyms() - Method in class org.intermine.model.bio.BioEntityShadow

getSynonyms() - Method in class org.intermine.model.bio.CDSShadow

getSynonyms() - Method in class org.intermine.model.bio.ChromosomeShadow

getSynonyms() - Method in class org.intermine.model.bio.ExonShadow

getSynonyms() - Method in class org.intermine.model.bio.GeneFlankingRegionShadow

getSynonyms() - Method in class org.intermine.model.bio.GeneShadow

getSynonyms() - Method in class org.intermine.model.bio.IntergenicRegionShadow

getSynonyms() - Method in class org.intermine.model.bio.IntronShadow

getSynonyms() - Method in interface org.intermine.model.bio.OntologyTerm

getSynonyms() - Method in class org.intermine.model.bio.OntologyTermShadow

getSynonyms() - Method in class org.intermine.model.bio.ProteinShadow

getSynonyms() - Method in class org.intermine.model.bio.SequenceCollectionShadow

getSynonyms() - Method in class org.intermine.model.bio.SequenceFeatureShadow

getSynonyms() - Method in class org.intermine.model.bio.SOTermShadow

getSynonyms() - Method in class org.intermine.model.bio.StrainShadow

getSynonyms() - Method in class org.intermine.model.bio.SyntenicRegionShadow

getSynonyms() - Method in class org.intermine.model.bio.TranscriptShadow

getSynonyms() - Method in class org.intermine.model.bio.UTRShadow

getSyntenicRegions() - Method in interface org.intermine.model.bio.SyntenyBlock

getSyntenicRegions() - Method in class org.intermine.model.bio.SyntenyBlockShadow

getSyntenyBlock() - Method in interface org.intermine.model.bio.SyntenicRegion

getSyntenyBlock() - Method in class org.intermine.model.bio.SyntenicRegionShadow

getTaxonId() - Method in interface org.intermine.model.bio.Organism

getTaxonId() - Method in class org.intermine.model.bio.OrganismShadow

getTitle() - Method in interface org.intermine.model.bio.Publication

getTitle() - Method in class org.intermine.model.bio.PublicationShadow

getTranscripts() - Method in interface org.intermine.model.bio.Protein

getTranscripts() - Method in class org.intermine.model.bio.ProteinShadow

getType() - Method in interface org.intermine.model.bio.Comment

getType() - Method in class org.intermine.model.bio.CommentShadow

getType() - Method in interface org.intermine.model.bio.Homologue

getType() - Method in class org.intermine.model.bio.HomologueShadow

getType() - Method in interface org.intermine.model.bio.OntologyTermSynonym

getType() - Method in class org.intermine.model.bio.OntologyTermSynonymShadow

getUpstreamIntergenicRegion() - Method in interface org.intermine.model.bio.Gene

getUpstreamIntergenicRegion() - Method in class org.intermine.model.bio.GeneShadow

getUrl() - Method in interface org.intermine.model.bio.DataSet

getUrl() - Method in class org.intermine.model.bio.DataSetShadow

getUrl() - Method in interface org.intermine.model.bio.DataSource

getUrl() - Method in class org.intermine.model.bio.DataSourceShadow

getUrl() - Method in interface org.intermine.model.bio.Ontology

getUrl() - Method in interface org.intermine.model.bio.OntologyAnnotationEvidenceCode

getUrl() - Method in class org.intermine.model.bio.OntologyAnnotationEvidenceCodeShadow

getUrl() - Method in class org.intermine.model.bio.OntologyShadow

getuTRs() - Method in interface org.intermine.model.bio.Gene

getuTRs() - Method in class org.intermine.model.bio.GeneShadow

getValue() - Method in interface org.intermine.model.bio.Synonym

getValue() - Method in class org.intermine.model.bio.SynonymShadow

getVersion() - Method in interface org.intermine.model.bio.DataSet

getVersion() - Method in class org.intermine.model.bio.DataSetShadow

getVolume() - Method in interface org.intermine.model.bio.Publication

getVolume() - Method in class org.intermine.model.bio.PublicationShadow

getYear() - Method in interface org.intermine.model.bio.Publication

getYear() - Method in class org.intermine.model.bio.PublicationShadow

H

hashCode() - Method in class org.intermine.model.bio.AnnotatableShadow

hashCode() - Method in class org.intermine.model.bio.AuthorShadow

hashCode() - Method in class org.intermine.model.bio.BioEntityShadow

hashCode() - Method in class org.intermine.model.bio.CDSShadow

hashCode() - Method in class org.intermine.model.bio.ChromosomeShadow

hashCode() - Method in class org.intermine.model.bio.CommentShadow

hashCode() - Method in class org.intermine.model.bio.CrossReferenceShadow

hashCode() - Method in class org.intermine.model.bio.DataSetShadow

hashCode() - Method in class org.intermine.model.bio.DataSourceShadow

hashCode() - Method in class org.intermine.model.bio.ExonShadow

hashCode() - Method in class org.intermine.model.bio.GeneFlankingRegionShadow

hashCode() - Method in class org.intermine.model.bio.GeneShadow

hashCode() - Method in class org.intermine.model.bio.HomologueShadow

hashCode() - Method in class org.intermine.model.bio.IntergenicRegionShadow

hashCode() - Method in class org.intermine.model.bio.IntronShadow

hashCode() - Method in class org.intermine.model.bio.LocationShadow

hashCode() - Method in class org.intermine.model.bio.MeshTermShadow

hashCode() - Method in class org.intermine.model.bio.OntologyAnnotationEvidenceCodeShadow

hashCode() - Method in class org.intermine.model.bio.OntologyAnnotationShadow

hashCode() - Method in class org.intermine.model.bio.OntologyEvidenceShadow

hashCode() - Method in class org.intermine.model.bio.OntologyRelationShadow

hashCode() - Method in class org.intermine.model.bio.OntologyShadow

hashCode() - Method in class org.intermine.model.bio.OntologyTermShadow

hashCode() - Method in class org.intermine.model.bio.OntologyTermSynonymShadow

hashCode() - Method in class org.intermine.model.bio.OrganismShadow

hashCode() - Method in class org.intermine.model.bio.OrthologueEvidenceCodeShadow

hashCode() - Method in class org.intermine.model.bio.OrthologueEvidenceShadow

hashCode() - Method in class org.intermine.model.bio.ProteinShadow

hashCode() - Method in class org.intermine.model.bio.PublicationShadow

hashCode() - Method in class org.intermine.model.bio.SequenceCollectionShadow

hashCode() - Method in class org.intermine.model.bio.SequenceFeatureShadow

hashCode() - Method in class org.intermine.model.bio.SequenceShadow

hashCode() - Method in class org.intermine.model.bio.SequenceVariantShadow

hashCode() - Method in class org.intermine.model.bio.SOTermShadow

hashCode() - Method in class org.intermine.model.bio.StrainShadow

hashCode() - Method in class org.intermine.model.bio.SynonymShadow

hashCode() - Method in class org.intermine.model.bio.SyntenicRegionShadow

hashCode() - Method in class org.intermine.model.bio.SyntenyBlockShadow

hashCode() - Method in class org.intermine.model.bio.TranscriptShadow

hashCode() - Method in class org.intermine.model.bio.UTRShadow

HomologeneConverter - Class in org.intermine.bio.dataconversion

HomoloGene data converter, to use symbol and organism to identify a gene

HomologeneConverter(ItemWriter, Model) - Constructor for class org.intermine.bio.dataconversion.HomologeneConverter

Constructor

HomologeneConverter.GeneRecord - Class in org.intermine.bio.dataconversion

represents a gene record in the data files

homologue - Variable in class org.intermine.model.bio.HomologueShadow

Homologue - Interface in org.intermine.model.bio

homologues - Variable in class org.intermine.model.bio.GeneShadow

HomologueShadow - Class in org.intermine.model.bio

HomologueShadow() - Constructor for class org.intermine.model.bio.HomologueShadow

I

id - Variable in class org.intermine.model.bio.AnnotatableShadow

id - Variable in class org.intermine.model.bio.AuthorShadow

id - Variable in class org.intermine.model.bio.BioEntityShadow

id - Variable in class org.intermine.model.bio.CDSShadow

id - Variable in class org.intermine.model.bio.ChromosomeShadow

id - Variable in class org.intermine.model.bio.CommentShadow

id - Variable in class org.intermine.model.bio.CrossReferenceShadow

id - Variable in class org.intermine.model.bio.DataSetShadow

id - Variable in class org.intermine.model.bio.DataSourceShadow

id - Variable in class org.intermine.model.bio.ExonShadow

id - Variable in class org.intermine.model.bio.GeneFlankingRegionShadow

id - Variable in class org.intermine.model.bio.GeneShadow

id - Variable in class org.intermine.model.bio.HomologueShadow

id - Variable in class org.intermine.model.bio.IntergenicRegionShadow

id - Variable in class org.intermine.model.bio.IntronShadow

id - Variable in class org.intermine.model.bio.LocationShadow

id - Variable in class org.intermine.model.bio.MeshTermShadow

id - Variable in class org.intermine.model.bio.OntologyAnnotationEvidenceCodeShadow

id - Variable in class org.intermine.model.bio.OntologyAnnotationShadow

id - Variable in class org.intermine.model.bio.OntologyEvidenceShadow

id - Variable in class org.intermine.model.bio.OntologyRelationShadow

id - Variable in class org.intermine.model.bio.OntologyShadow

id - Variable in class org.intermine.model.bio.OntologyTermShadow

id - Variable in class org.intermine.model.bio.OntologyTermSynonymShadow

id - Variable in class org.intermine.model.bio.OrganismShadow

id - Variable in class org.intermine.model.bio.OrthologueEvidenceCodeShadow

id - Variable in class org.intermine.model.bio.OrthologueEvidenceShadow

id - Variable in class org.intermine.model.bio.ProteinShadow

id - Variable in class org.intermine.model.bio.PublicationShadow

id - Variable in class org.intermine.model.bio.SequenceCollectionShadow

id - Variable in class org.intermine.model.bio.SequenceFeatureShadow

id - Variable in class org.intermine.model.bio.SequenceShadow

id - Variable in class org.intermine.model.bio.SequenceVariantShadow

id - Variable in class org.intermine.model.bio.SOTermShadow

id - Variable in class org.intermine.model.bio.StrainShadow

id - Variable in class org.intermine.model.bio.SynonymShadow

id - Variable in class org.intermine.model.bio.SyntenicRegionShadow

id - Variable in class org.intermine.model.bio.SyntenyBlockShadow

id - Variable in class org.intermine.model.bio.TranscriptShadow

id - Variable in class org.intermine.model.bio.UTRShadow

identifier - Variable in class org.intermine.model.bio.CrossReferenceShadow

identifier - Variable in class org.intermine.model.bio.OntologyTermShadow

identifier - Variable in class org.intermine.model.bio.SOTermShadow

includeGene - Variable in class org.intermine.model.bio.GeneFlankingRegionShadow

initials - Variable in class org.intermine.model.bio.AuthorShadow

IntergenicRegion - Interface in org.intermine.model.bio

IntergenicRegionShadow - Class in org.intermine.model.bio

IntergenicRegionShadow() - Constructor for class org.intermine.model.bio.IntergenicRegionShadow

Intron - Interface in org.intermine.model.bio

introns - Variable in class org.intermine.model.bio.GeneShadow

IntronShadow - Class in org.intermine.model.bio

IntronShadow() - Constructor for class org.intermine.model.bio.IntronShadow

issue - Variable in class org.intermine.model.bio.PublicationShadow

J

journal - Variable in class org.intermine.model.bio.PublicationShadow

L

lastName - Variable in class org.intermine.model.bio.AuthorShadow

length - Variable in class org.intermine.model.bio.CDSShadow

length - Variable in class org.intermine.model.bio.ChromosomeShadow

length - Variable in class org.intermine.model.bio.ExonShadow

length - Variable in class org.intermine.model.bio.GeneFlankingRegionShadow

length - Variable in class org.intermine.model.bio.GeneShadow

length - Variable in class org.intermine.model.bio.IntergenicRegionShadow

length - Variable in class org.intermine.model.bio.IntronShadow

length - Variable in class org.intermine.model.bio.ProteinShadow

length - Variable in class org.intermine.model.bio.SequenceFeatureShadow

length - Variable in class org.intermine.model.bio.SequenceShadow

length - Variable in class org.intermine.model.bio.SyntenicRegionShadow

length - Variable in class org.intermine.model.bio.TranscriptShadow

length - Variable in class org.intermine.model.bio.UTRShadow

licence - Variable in class org.intermine.model.bio.DataSetShadow

locatedFeatures - Variable in class org.intermine.model.bio.BioEntityShadow

locatedFeatures - Variable in class org.intermine.model.bio.CDSShadow

locatedFeatures - Variable in class org.intermine.model.bio.ChromosomeShadow

locatedFeatures - Variable in class org.intermine.model.bio.ExonShadow

locatedFeatures - Variable in class org.intermine.model.bio.GeneFlankingRegionShadow

locatedFeatures - Variable in class org.intermine.model.bio.GeneShadow

locatedFeatures - Variable in class org.intermine.model.bio.IntergenicRegionShadow

locatedFeatures - Variable in class org.intermine.model.bio.IntronShadow

locatedFeatures - Variable in class org.intermine.model.bio.ProteinShadow

locatedFeatures - Variable in class org.intermine.model.bio.SequenceCollectionShadow

locatedFeatures - Variable in class org.intermine.model.bio.SequenceFeatureShadow

locatedFeatures - Variable in class org.intermine.model.bio.StrainShadow

locatedFeatures - Variable in class org.intermine.model.bio.SyntenicRegionShadow

locatedFeatures - Variable in class org.intermine.model.bio.TranscriptShadow

locatedFeatures - Variable in class org.intermine.model.bio.UTRShadow

locatedOn - Variable in class org.intermine.model.bio.LocationShadow

Location - Interface in org.intermine.model.bio

locations - Variable in class org.intermine.model.bio.BioEntityShadow

locations - Variable in class org.intermine.model.bio.CDSShadow

locations - Variable in class org.intermine.model.bio.ChromosomeShadow

locations - Variable in class org.intermine.model.bio.ExonShadow

locations - Variable in class org.intermine.model.bio.GeneFlankingRegionShadow

locations - Variable in class org.intermine.model.bio.GeneShadow

locations - Variable in class org.intermine.model.bio.IntergenicRegionShadow

locations - Variable in class org.intermine.model.bio.IntronShadow

locations - Variable in class org.intermine.model.bio.ProteinShadow

locations - Variable in class org.intermine.model.bio.SequenceCollectionShadow

locations - Variable in class org.intermine.model.bio.SequenceFeatureShadow

locations - Variable in class org.intermine.model.bio.StrainShadow

locations - Variable in class org.intermine.model.bio.SyntenicRegionShadow

locations - Variable in class org.intermine.model.bio.TranscriptShadow

locations - Variable in class org.intermine.model.bio.UTRShadow

LocationShadow - Class in org.intermine.model.bio

LocationShadow() - Constructor for class org.intermine.model.bio.LocationShadow

M

md5checksum - Variable in class org.intermine.model.bio.ProteinShadow

md5checksum - Variable in class org.intermine.model.bio.SequenceShadow

MeshTerm - Interface in org.intermine.model.bio

meshTerms - Variable in class org.intermine.model.bio.PublicationShadow

MeshTermShadow - Class in org.intermine.model.bio

MeshTermShadow() - Constructor for class org.intermine.model.bio.MeshTermShadow

molecularWeight - Variable in class org.intermine.model.bio.ProteinShadow

month - Variable in class org.intermine.model.bio.PublicationShadow

N

name - Variable in class org.intermine.model.bio.AuthorShadow

name - Variable in class org.intermine.model.bio.BioEntityShadow

name - Variable in class org.intermine.model.bio.CDSShadow

name - Variable in class org.intermine.model.bio.ChromosomeShadow

name - Variable in class org.intermine.model.bio.DataSetShadow

name - Variable in class org.intermine.model.bio.DataSourceShadow

name - Variable in class org.intermine.model.bio.ExonShadow

name - Variable in class org.intermine.model.bio.GeneFlankingRegionShadow

name - Variable in class org.intermine.model.bio.GeneShadow

name - Variable in class org.intermine.model.bio.IntergenicRegionShadow

name - Variable in class org.intermine.model.bio.IntronShadow

name - Variable in class org.intermine.model.bio.MeshTermShadow

name - Variable in class org.intermine.model.bio.OntologyAnnotationEvidenceCodeShadow

name - Variable in class org.intermine.model.bio.OntologyShadow

name - Variable in class org.intermine.model.bio.OntologyTermShadow

name - Variable in class org.intermine.model.bio.OntologyTermSynonymShadow

name - Variable in class org.intermine.model.bio.OrganismShadow

name - Variable in class org.intermine.model.bio.OrthologueEvidenceCodeShadow

name - Variable in class org.intermine.model.bio.ProteinShadow

name - Variable in class org.intermine.model.bio.SequenceCollectionShadow

name - Variable in class org.intermine.model.bio.SequenceFeatureShadow

name - Variable in class org.intermine.model.bio.SOTermShadow

name - Variable in class org.intermine.model.bio.StrainShadow

name - Variable in class org.intermine.model.bio.SyntenicRegionShadow

name - Variable in class org.intermine.model.bio.TranscriptShadow

name - Variable in class org.intermine.model.bio.UTRShadow

namespace - Variable in class org.intermine.model.bio.OntologyTermShadow

namespace - Variable in class org.intermine.model.bio.SOTermShadow

O

obsolete - Variable in class org.intermine.model.bio.OntologyTermShadow

obsolete - Variable in class org.intermine.model.bio.SOTermShadow

ontology - Variable in class org.intermine.model.bio.OntologyTermShadow

ontology - Variable in class org.intermine.model.bio.SOTermShadow

Ontology - Interface in org.intermine.model.bio

OntologyAnnotation - Interface in org.intermine.model.bio

OntologyAnnotationEvidenceCode - Interface in org.intermine.model.bio

OntologyAnnotationEvidenceCodeShadow - Class in org.intermine.model.bio

OntologyAnnotationEvidenceCodeShadow() - Constructor for class org.intermine.model.bio.OntologyAnnotationEvidenceCodeShadow

ontologyAnnotations - Variable in class org.intermine.model.bio.AnnotatableShadow

ontologyAnnotations - Variable in class org.intermine.model.bio.BioEntityShadow

ontologyAnnotations - Variable in class org.intermine.model.bio.CDSShadow

ontologyAnnotations - Variable in class org.intermine.model.bio.ChromosomeShadow

ontologyAnnotations - Variable in class org.intermine.model.bio.ExonShadow

ontologyAnnotations - Variable in class org.intermine.model.bio.GeneFlankingRegionShadow

ontologyAnnotations - Variable in class org.intermine.model.bio.GeneShadow

ontologyAnnotations - Variable in class org.intermine.model.bio.IntergenicRegionShadow

ontologyAnnotations - Variable in class org.intermine.model.bio.IntronShadow

ontologyAnnotations - Variable in class org.intermine.model.bio.OntologyTermShadow

ontologyAnnotations - Variable in class org.intermine.model.bio.ProteinShadow

ontologyAnnotations - Variable in class org.intermine.model.bio.SequenceCollectionShadow

ontologyAnnotations - Variable in class org.intermine.model.bio.SequenceFeatureShadow

ontologyAnnotations - Variable in class org.intermine.model.bio.SOTermShadow

ontologyAnnotations - Variable in class org.intermine.model.bio.StrainShadow

ontologyAnnotations - Variable in class org.intermine.model.bio.SyntenicRegionShadow

ontologyAnnotations - Variable in class org.intermine.model.bio.TranscriptShadow

ontologyAnnotations - Variable in class org.intermine.model.bio.UTRShadow

OntologyAnnotationShadow - Class in org.intermine.model.bio

OntologyAnnotationShadow() - Constructor for class org.intermine.model.bio.OntologyAnnotationShadow

OntologyEvidence - Interface in org.intermine.model.bio

OntologyEvidenceShadow - Class in org.intermine.model.bio

OntologyEvidenceShadow() - Constructor for class org.intermine.model.bio.OntologyEvidenceShadow

OntologyRelation - Interface in org.intermine.model.bio

OntologyRelationShadow - Class in org.intermine.model.bio

OntologyRelationShadow() - Constructor for class org.intermine.model.bio.OntologyRelationShadow

OntologyShadow - Class in org.intermine.model.bio

OntologyShadow() - Constructor for class org.intermine.model.bio.OntologyShadow

ontologyTerm - Variable in class org.intermine.model.bio.OntologyAnnotationShadow

OntologyTerm - Interface in org.intermine.model.bio

OntologyTermShadow - Class in org.intermine.model.bio

OntologyTermShadow() - Constructor for class org.intermine.model.bio.OntologyTermShadow

OntologyTermSynonym - Interface in org.intermine.model.bio

OntologyTermSynonymShadow - Class in org.intermine.model.bio

OntologyTermSynonymShadow() - Constructor for class org.intermine.model.bio.OntologyTermSynonymShadow

org.intermine.bio.dataconversion - package org.intermine.bio.dataconversion

org.intermine.model.bio - package org.intermine.model.bio

organism - Variable in class org.intermine.model.bio.BioEntityShadow

organism - Variable in class org.intermine.model.bio.CDSShadow

organism - Variable in class org.intermine.model.bio.ChromosomeShadow

organism - Variable in class org.intermine.model.bio.ExonShadow

organism - Variable in class org.intermine.model.bio.GeneFlankingRegionShadow

organism - Variable in class org.intermine.model.bio.GeneShadow

organism - Variable in class org.intermine.model.bio.IntergenicRegionShadow

organism - Variable in class org.intermine.model.bio.IntronShadow

organism - Variable in class org.intermine.model.bio.ProteinShadow

organism - Variable in class org.intermine.model.bio.SequenceCollectionShadow

organism - Variable in class org.intermine.model.bio.SequenceFeatureShadow

organism - Variable in class org.intermine.model.bio.StrainShadow

organism - Variable in class org.intermine.model.bio.SyntenicRegionShadow

organism - Variable in class org.intermine.model.bio.TranscriptShadow

organism - Variable in class org.intermine.model.bio.UTRShadow

Organism - Interface in org.intermine.model.bio

OrganismShadow - Class in org.intermine.model.bio

OrganismShadow() - Constructor for class org.intermine.model.bio.OrganismShadow

OrthologueEvidence - Interface in org.intermine.model.bio

OrthologueEvidenceCode - Interface in org.intermine.model.bio

OrthologueEvidenceCodeShadow - Class in org.intermine.model.bio

OrthologueEvidenceCodeShadow() - Constructor for class org.intermine.model.bio.OrthologueEvidenceCodeShadow

OrthologueEvidenceShadow - Class in org.intermine.model.bio

OrthologueEvidenceShadow() - Constructor for class org.intermine.model.bio.OrthologueEvidenceShadow

overlappingFeatures - Variable in class org.intermine.model.bio.CDSShadow

overlappingFeatures - Variable in class org.intermine.model.bio.ChromosomeShadow

overlappingFeatures - Variable in class org.intermine.model.bio.ExonShadow

overlappingFeatures - Variable in class org.intermine.model.bio.GeneFlankingRegionShadow

overlappingFeatures - Variable in class org.intermine.model.bio.GeneShadow

overlappingFeatures - Variable in class org.intermine.model.bio.IntergenicRegionShadow

overlappingFeatures - Variable in class org.intermine.model.bio.IntronShadow

overlappingFeatures - Variable in class org.intermine.model.bio.SequenceFeatureShadow

overlappingFeatures - Variable in class org.intermine.model.bio.SyntenicRegionShadow

overlappingFeatures - Variable in class org.intermine.model.bio.TranscriptShadow

overlappingFeatures - Variable in class org.intermine.model.bio.UTRShadow

P

pages - Variable in class org.intermine.model.bio.PublicationShadow

parents - Variable in class org.intermine.model.bio.OntologyTermShadow

parents - Variable in class org.intermine.model.bio.SOTermShadow

parentTerm - Variable in class org.intermine.model.bio.OntologyRelationShadow

primaryAccession - Variable in class org.intermine.model.bio.ProteinShadow

primaryIdentifier - Variable in class org.intermine.model.bio.AnnotatableShadow

primaryIdentifier - Variable in class org.intermine.model.bio.BioEntityShadow

primaryIdentifier - Variable in class org.intermine.model.bio.CDSShadow

primaryIdentifier - Variable in class org.intermine.model.bio.ChromosomeShadow

primaryIdentifier - Variable in class org.intermine.model.bio.ExonShadow

primaryIdentifier - Variable in class org.intermine.model.bio.GeneFlankingRegionShadow

primaryIdentifier - Variable in class org.intermine.model.bio.GeneShadow

primaryIdentifier - Variable in class org.intermine.model.bio.IntergenicRegionShadow

primaryIdentifier - Variable in class org.intermine.model.bio.IntronShadow

primaryIdentifier - Variable in class org.intermine.model.bio.ProteinShadow

primaryIdentifier - Variable in class org.intermine.model.bio.SequenceCollectionShadow

primaryIdentifier - Variable in class org.intermine.model.bio.SequenceFeatureShadow

primaryIdentifier - Variable in class org.intermine.model.bio.StrainShadow

primaryIdentifier - Variable in class org.intermine.model.bio.SyntenicRegionShadow

primaryIdentifier - Variable in class org.intermine.model.bio.TranscriptShadow

primaryIdentifier - Variable in class org.intermine.model.bio.UTRShadow

process(Reader) - Method in class org.intermine.bio.dataconversion.HomologeneConverter

protein - Variable in class org.intermine.model.bio.CDSShadow

protein - Variable in class org.intermine.model.bio.TranscriptShadow

Protein - Interface in org.intermine.model.bio

proteins - Variable in class org.intermine.model.bio.GeneShadow

ProteinShadow - Class in org.intermine.model.bio

ProteinShadow() - Constructor for class org.intermine.model.bio.ProteinShadow

proxGetChildTerm() - Method in interface org.intermine.model.bio.OntologyRelation

proxGetChildTerm() - Method in class org.intermine.model.bio.OntologyRelationShadow

proxGetChromosome() - Method in class org.intermine.model.bio.CDSShadow

proxGetChromosome() - Method in class org.intermine.model.bio.ChromosomeShadow

proxGetChromosome() - Method in class org.intermine.model.bio.ExonShadow

proxGetChromosome() - Method in class org.intermine.model.bio.GeneFlankingRegionShadow

proxGetChromosome() - Method in class org.intermine.model.bio.GeneShadow

proxGetChromosome() - Method in class org.intermine.model.bio.IntergenicRegionShadow

proxGetChromosome() - Method in class org.intermine.model.bio.IntronShadow

proxGetChromosome() - Method in interface org.intermine.model.bio.SequenceFeature

proxGetChromosome() - Method in class org.intermine.model.bio.SequenceFeatureShadow

proxGetChromosome() - Method in class org.intermine.model.bio.SyntenicRegionShadow

proxGetChromosome() - Method in class org.intermine.model.bio.TranscriptShadow

proxGetChromosome() - Method in class org.intermine.model.bio.UTRShadow

proxGetChromosomeLocation() - Method in class org.intermine.model.bio.CDSShadow

proxGetChromosomeLocation() - Method in class org.intermine.model.bio.ChromosomeShadow

proxGetChromosomeLocation() - Method in class org.intermine.model.bio.ExonShadow

proxGetChromosomeLocation() - Method in class org.intermine.model.bio.GeneFlankingRegionShadow

proxGetChromosomeLocation() - Method in class org.intermine.model.bio.GeneShadow

proxGetChromosomeLocation() - Method in class org.intermine.model.bio.IntergenicRegionShadow

proxGetChromosomeLocation() - Method in class org.intermine.model.bio.IntronShadow

proxGetChromosomeLocation() - Method in interface org.intermine.model.bio.SequenceFeature

proxGetChromosomeLocation() - Method in class org.intermine.model.bio.SequenceFeatureShadow

proxGetChromosomeLocation() - Method in class org.intermine.model.bio.SyntenicRegionShadow

proxGetChromosomeLocation() - Method in class org.intermine.model.bio.TranscriptShadow

proxGetChromosomeLocation() - Method in class org.intermine.model.bio.UTRShadow

proxGetCode() - Method in interface org.intermine.model.bio.OntologyEvidence

proxGetCode() - Method in class org.intermine.model.bio.OntologyEvidenceShadow

proxGetDataSource() - Method in interface org.intermine.model.bio.DataSet

proxGetDataSource() - Method in class org.intermine.model.bio.DataSetShadow

proxGetDownstreamIntergenicRegion() - Method in interface org.intermine.model.bio.Gene

proxGetDownstreamIntergenicRegion() - Method in class org.intermine.model.bio.GeneShadow

proxGetEvidenceCode() - Method in interface org.intermine.model.bio.OrthologueEvidence

proxGetEvidenceCode() - Method in class org.intermine.model.bio.OrthologueEvidenceShadow

proxGetFeature() - Method in interface org.intermine.model.bio.Location

proxGetFeature() - Method in class org.intermine.model.bio.LocationShadow

proxGetGene() - Method in interface org.intermine.model.bio.CDS

proxGetGene() - Method in class org.intermine.model.bio.CDSShadow

proxGetGene() - Method in interface org.intermine.model.bio.Exon

proxGetGene() - Method in class org.intermine.model.bio.ExonShadow

proxGetGene() - Method in interface org.intermine.model.bio.GeneFlankingRegion

proxGetGene() - Method in class org.intermine.model.bio.GeneFlankingRegionShadow

proxGetGene() - Method in interface org.intermine.model.bio.Homologue

proxGetGene() - Method in class org.intermine.model.bio.HomologueShadow

proxGetGene() - Method in interface org.intermine.model.bio.UTR

proxGetGene() - Method in class org.intermine.model.bio.UTRShadow

proxGetHomologue() - Method in interface org.intermine.model.bio.Homologue

proxGetHomologue() - Method in class org.intermine.model.bio.HomologueShadow

proxGetLocatedOn() - Method in interface org.intermine.model.bio.Location

proxGetLocatedOn() - Method in class org.intermine.model.bio.LocationShadow

proxGetOntology() - Method in interface org.intermine.model.bio.OntologyTerm

proxGetOntology() - Method in class org.intermine.model.bio.OntologyTermShadow

proxGetOntology() - Method in class org.intermine.model.bio.SOTermShadow

proxGetOntologyTerm() - Method in interface org.intermine.model.bio.OntologyAnnotation

proxGetOntologyTerm() - Method in class org.intermine.model.bio.OntologyAnnotationShadow

proxGetOrganism() - Method in interface org.intermine.model.bio.BioEntity

proxGetOrganism() - Method in class org.intermine.model.bio.BioEntityShadow

proxGetOrganism() - Method in class org.intermine.model.bio.CDSShadow

proxGetOrganism() - Method in class org.intermine.model.bio.ChromosomeShadow

proxGetOrganism() - Method in class org.intermine.model.bio.ExonShadow

proxGetOrganism() - Method in class org.intermine.model.bio.GeneFlankingRegionShadow

proxGetOrganism() - Method in class org.intermine.model.bio.GeneShadow

proxGetOrganism() - Method in class org.intermine.model.bio.IntergenicRegionShadow

proxGetOrganism() - Method in class org.intermine.model.bio.IntronShadow

proxGetOrganism() - Method in class org.intermine.model.bio.ProteinShadow

proxGetOrganism() - Method in class org.intermine.model.bio.SequenceCollectionShadow

proxGetOrganism() - Method in class org.intermine.model.bio.SequenceFeatureShadow

proxGetOrganism() - Method in class org.intermine.model.bio.StrainShadow

proxGetOrganism() - Method in class org.intermine.model.bio.SyntenicRegionShadow

proxGetOrganism() - Method in class org.intermine.model.bio.TranscriptShadow

proxGetOrganism() - Method in class org.intermine.model.bio.UTRShadow

proxGetParentTerm() - Method in interface org.intermine.model.bio.OntologyRelation

proxGetParentTerm() - Method in class org.intermine.model.bio.OntologyRelationShadow

proxGetProtein() - Method in interface org.intermine.model.bio.CDS

proxGetProtein() - Method in class org.intermine.model.bio.CDSShadow

proxGetProtein() - Method in interface org.intermine.model.bio.Transcript

proxGetProtein() - Method in class org.intermine.model.bio.TranscriptShadow

proxGetPublication() - Method in interface org.intermine.model.bio.DataSet

proxGetPublication() - Method in class org.intermine.model.bio.DataSetShadow

proxGetSequence() - Method in class org.intermine.model.bio.CDSShadow

proxGetSequence() - Method in class org.intermine.model.bio.ChromosomeShadow

proxGetSequence() - Method in class org.intermine.model.bio.ExonShadow

proxGetSequence() - Method in class org.intermine.model.bio.GeneFlankingRegionShadow

proxGetSequence() - Method in class org.intermine.model.bio.GeneShadow

proxGetSequence() - Method in class org.intermine.model.bio.IntergenicRegionShadow

proxGetSequence() - Method in class org.intermine.model.bio.IntronShadow

proxGetSequence() - Method in interface org.intermine.model.bio.Protein

proxGetSequence() - Method in class org.intermine.model.bio.ProteinShadow

proxGetSequence() - Method in interface org.intermine.model.bio.SequenceFeature

proxGetSequence() - Method in class org.intermine.model.bio.SequenceFeatureShadow

proxGetSequence() - Method in class org.intermine.model.bio.SyntenicRegionShadow

proxGetSequence() - Method in class org.intermine.model.bio.TranscriptShadow

proxGetSequence() - Method in class org.intermine.model.bio.UTRShadow

proxGetSequenceOntologyTerm() - Method in class org.intermine.model.bio.CDSShadow

proxGetSequenceOntologyTerm() - Method in class org.intermine.model.bio.ChromosomeShadow

proxGetSequenceOntologyTerm() - Method in class org.intermine.model.bio.ExonShadow

proxGetSequenceOntologyTerm() - Method in class org.intermine.model.bio.GeneFlankingRegionShadow

proxGetSequenceOntologyTerm() - Method in class org.intermine.model.bio.GeneShadow

proxGetSequenceOntologyTerm() - Method in class org.intermine.model.bio.IntergenicRegionShadow

proxGetSequenceOntologyTerm() - Method in class org.intermine.model.bio.IntronShadow

proxGetSequenceOntologyTerm() - Method in interface org.intermine.model.bio.SequenceCollection

proxGetSequenceOntologyTerm() - Method in class org.intermine.model.bio.SequenceCollectionShadow

proxGetSequenceOntologyTerm() - Method in interface org.intermine.model.bio.SequenceFeature

proxGetSequenceOntologyTerm() - Method in class org.intermine.model.bio.SequenceFeatureShadow

proxGetSequenceOntologyTerm() - Method in class org.intermine.model.bio.SyntenicRegionShadow

proxGetSequenceOntologyTerm() - Method in class org.intermine.model.bio.TranscriptShadow

proxGetSequenceOntologyTerm() - Method in class org.intermine.model.bio.UTRShadow

proxGetSource() - Method in interface org.intermine.model.bio.CrossReference

proxGetSource() - Method in class org.intermine.model.bio.CrossReferenceShadow

proxGetStrain() - Method in class org.intermine.model.bio.CDSShadow

proxGetStrain() - Method in class org.intermine.model.bio.ChromosomeShadow

proxGetStrain() - Method in class org.intermine.model.bio.ExonShadow

proxGetStrain() - Method in class org.intermine.model.bio.GeneFlankingRegionShadow

proxGetStrain() - Method in class org.intermine.model.bio.GeneShadow

proxGetStrain() - Method in class org.intermine.model.bio.IntergenicRegionShadow

proxGetStrain() - Method in class org.intermine.model.bio.IntronShadow

proxGetStrain() - Method in interface org.intermine.model.bio.SequenceFeature

proxGetStrain() - Method in class org.intermine.model.bio.SequenceFeatureShadow

proxGetStrain() - Method in class org.intermine.model.bio.SyntenicRegionShadow

proxGetStrain() - Method in class org.intermine.model.bio.TranscriptShadow

proxGetStrain() - Method in class org.intermine.model.bio.UTRShadow

proxGetSubject() - Method in interface org.intermine.model.bio.CrossReference

proxGetSubject() - Method in class org.intermine.model.bio.CrossReferenceShadow

proxGetSubject() - Method in interface org.intermine.model.bio.OntologyAnnotation

proxGetSubject() - Method in class org.intermine.model.bio.OntologyAnnotationShadow

proxGetSubject() - Method in interface org.intermine.model.bio.Synonym

proxGetSubject() - Method in class org.intermine.model.bio.SynonymShadow

proxGetSyntenyBlock() - Method in interface org.intermine.model.bio.SyntenicRegion

proxGetSyntenyBlock() - Method in class org.intermine.model.bio.SyntenicRegionShadow

proxGetUpstreamIntergenicRegion() - Method in interface org.intermine.model.bio.Gene

proxGetUpstreamIntergenicRegion() - Method in class org.intermine.model.bio.GeneShadow

proxyChildTerm(ProxyReference) - Method in interface org.intermine.model.bio.OntologyRelation

proxyChildTerm(ProxyReference) - Method in class org.intermine.model.bio.OntologyRelationShadow

proxyChromosome(ProxyReference) - Method in class org.intermine.model.bio.CDSShadow

proxyChromosome(ProxyReference) - Method in class org.intermine.model.bio.ChromosomeShadow

proxyChromosome(ProxyReference) - Method in class org.intermine.model.bio.ExonShadow

proxyChromosome(ProxyReference) - Method in class org.intermine.model.bio.GeneFlankingRegionShadow

proxyChromosome(ProxyReference) - Method in class org.intermine.model.bio.GeneShadow

proxyChromosome(ProxyReference) - Method in class org.intermine.model.bio.IntergenicRegionShadow

proxyChromosome(ProxyReference) - Method in class org.intermine.model.bio.IntronShadow

proxyChromosome(ProxyReference) - Method in interface org.intermine.model.bio.SequenceFeature

proxyChromosome(ProxyReference) - Method in class org.intermine.model.bio.SequenceFeatureShadow

proxyChromosome(ProxyReference) - Method in class org.intermine.model.bio.SyntenicRegionShadow

proxyChromosome(ProxyReference) - Method in class org.intermine.model.bio.TranscriptShadow

proxyChromosome(ProxyReference) - Method in class org.intermine.model.bio.UTRShadow

proxyChromosomeLocation(ProxyReference) - Method in class org.intermine.model.bio.CDSShadow

proxyChromosomeLocation(ProxyReference) - Method in class org.intermine.model.bio.ChromosomeShadow

proxyChromosomeLocation(ProxyReference) - Method in class org.intermine.model.bio.ExonShadow

proxyChromosomeLocation(ProxyReference) - Method in class org.intermine.model.bio.GeneFlankingRegionShadow

proxyChromosomeLocation(ProxyReference) - Method in class org.intermine.model.bio.GeneShadow

proxyChromosomeLocation(ProxyReference) - Method in class org.intermine.model.bio.IntergenicRegionShadow

proxyChromosomeLocation(ProxyReference) - Method in class org.intermine.model.bio.IntronShadow

proxyChromosomeLocation(ProxyReference) - Method in interface org.intermine.model.bio.SequenceFeature

proxyChromosomeLocation(ProxyReference) - Method in class org.intermine.model.bio.SequenceFeatureShadow

proxyChromosomeLocation(ProxyReference) - Method in class org.intermine.model.bio.SyntenicRegionShadow

proxyChromosomeLocation(ProxyReference) - Method in class org.intermine.model.bio.TranscriptShadow

proxyChromosomeLocation(ProxyReference) - Method in class org.intermine.model.bio.UTRShadow

proxyCode(ProxyReference) - Method in interface org.intermine.model.bio.OntologyEvidence

proxyCode(ProxyReference) - Method in class org.intermine.model.bio.OntologyEvidenceShadow

proxyDataSource(ProxyReference) - Method in interface org.intermine.model.bio.DataSet

proxyDataSource(ProxyReference) - Method in class org.intermine.model.bio.DataSetShadow

proxyDownstreamIntergenicRegion(ProxyReference) - Method in interface org.intermine.model.bio.Gene

proxyDownstreamIntergenicRegion(ProxyReference) - Method in class org.intermine.model.bio.GeneShadow

proxyEvidenceCode(ProxyReference) - Method in interface org.intermine.model.bio.OrthologueEvidence

proxyEvidenceCode(ProxyReference) - Method in class org.intermine.model.bio.OrthologueEvidenceShadow

proxyFeature(ProxyReference) - Method in interface org.intermine.model.bio.Location

proxyFeature(ProxyReference) - Method in class org.intermine.model.bio.LocationShadow

proxyGene(ProxyReference) - Method in interface org.intermine.model.bio.CDS

proxyGene(ProxyReference) - Method in class org.intermine.model.bio.CDSShadow

proxyGene(ProxyReference) - Method in interface org.intermine.model.bio.Exon

proxyGene(ProxyReference) - Method in class org.intermine.model.bio.ExonShadow

proxyGene(ProxyReference) - Method in interface org.intermine.model.bio.GeneFlankingRegion

proxyGene(ProxyReference) - Method in class org.intermine.model.bio.GeneFlankingRegionShadow

proxyGene(ProxyReference) - Method in interface org.intermine.model.bio.Homologue

proxyGene(ProxyReference) - Method in class org.intermine.model.bio.HomologueShadow

proxyGene(ProxyReference) - Method in interface org.intermine.model.bio.UTR

proxyGene(ProxyReference) - Method in class org.intermine.model.bio.UTRShadow

proxyHomologue(ProxyReference) - Method in interface org.intermine.model.bio.Homologue

proxyHomologue(ProxyReference) - Method in class org.intermine.model.bio.HomologueShadow

proxyLocatedOn(ProxyReference) - Method in interface org.intermine.model.bio.Location

proxyLocatedOn(ProxyReference) - Method in class org.intermine.model.bio.LocationShadow

proxyOntology(ProxyReference) - Method in interface org.intermine.model.bio.OntologyTerm

proxyOntology(ProxyReference) - Method in class org.intermine.model.bio.OntologyTermShadow

proxyOntology(ProxyReference) - Method in class org.intermine.model.bio.SOTermShadow

proxyOntologyTerm(ProxyReference) - Method in interface org.intermine.model.bio.OntologyAnnotation

proxyOntologyTerm(ProxyReference) - Method in class org.intermine.model.bio.OntologyAnnotationShadow

proxyOrganism(ProxyReference) - Method in interface org.intermine.model.bio.BioEntity

proxyOrganism(ProxyReference) - Method in class org.intermine.model.bio.BioEntityShadow

proxyOrganism(ProxyReference) - Method in class org.intermine.model.bio.CDSShadow

proxyOrganism(ProxyReference) - Method in class org.intermine.model.bio.ChromosomeShadow

proxyOrganism(ProxyReference) - Method in class org.intermine.model.bio.ExonShadow

proxyOrganism(ProxyReference) - Method in class org.intermine.model.bio.GeneFlankingRegionShadow

proxyOrganism(ProxyReference) - Method in class org.intermine.model.bio.GeneShadow

proxyOrganism(ProxyReference) - Method in class org.intermine.model.bio.IntergenicRegionShadow

proxyOrganism(ProxyReference) - Method in class org.intermine.model.bio.IntronShadow

proxyOrganism(ProxyReference) - Method in class org.intermine.model.bio.ProteinShadow

proxyOrganism(ProxyReference) - Method in class org.intermine.model.bio.SequenceCollectionShadow

proxyOrganism(ProxyReference) - Method in class org.intermine.model.bio.SequenceFeatureShadow

proxyOrganism(ProxyReference) - Method in class org.intermine.model.bio.StrainShadow

proxyOrganism(ProxyReference) - Method in class org.intermine.model.bio.SyntenicRegionShadow

proxyOrganism(ProxyReference) - Method in class org.intermine.model.bio.TranscriptShadow

proxyOrganism(ProxyReference) - Method in class org.intermine.model.bio.UTRShadow

proxyParentTerm(ProxyReference) - Method in interface org.intermine.model.bio.OntologyRelation

proxyParentTerm(ProxyReference) - Method in class org.intermine.model.bio.OntologyRelationShadow

proxyProtein(ProxyReference) - Method in interface org.intermine.model.bio.CDS

proxyProtein(ProxyReference) - Method in class org.intermine.model.bio.CDSShadow

proxyProtein(ProxyReference) - Method in interface org.intermine.model.bio.Transcript

proxyProtein(ProxyReference) - Method in class org.intermine.model.bio.TranscriptShadow

proxyPublication(ProxyReference) - Method in interface org.intermine.model.bio.DataSet

proxyPublication(ProxyReference) - Method in class org.intermine.model.bio.DataSetShadow

proxySequence(ProxyReference) - Method in class org.intermine.model.bio.CDSShadow

proxySequence(ProxyReference) - Method in class org.intermine.model.bio.ChromosomeShadow

proxySequence(ProxyReference) - Method in class org.intermine.model.bio.ExonShadow

proxySequence(ProxyReference) - Method in class org.intermine.model.bio.GeneFlankingRegionShadow

proxySequence(ProxyReference) - Method in class org.intermine.model.bio.GeneShadow

proxySequence(ProxyReference) - Method in class org.intermine.model.bio.IntergenicRegionShadow

proxySequence(ProxyReference) - Method in class org.intermine.model.bio.IntronShadow

proxySequence(ProxyReference) - Method in interface org.intermine.model.bio.Protein

proxySequence(ProxyReference) - Method in class org.intermine.model.bio.ProteinShadow

proxySequence(ProxyReference) - Method in interface org.intermine.model.bio.SequenceFeature

proxySequence(ProxyReference) - Method in class org.intermine.model.bio.SequenceFeatureShadow

proxySequence(ProxyReference) - Method in class org.intermine.model.bio.SyntenicRegionShadow

proxySequence(ProxyReference) - Method in class org.intermine.model.bio.TranscriptShadow

proxySequence(ProxyReference) - Method in class org.intermine.model.bio.UTRShadow

proxySequenceOntologyTerm(ProxyReference) - Method in class org.intermine.model.bio.CDSShadow

proxySequenceOntologyTerm(ProxyReference) - Method in class org.intermine.model.bio.ChromosomeShadow

proxySequenceOntologyTerm(ProxyReference) - Method in class org.intermine.model.bio.ExonShadow

proxySequenceOntologyTerm(ProxyReference) - Method in class org.intermine.model.bio.GeneFlankingRegionShadow

proxySequenceOntologyTerm(ProxyReference) - Method in class org.intermine.model.bio.GeneShadow

proxySequenceOntologyTerm(ProxyReference) - Method in class org.intermine.model.bio.IntergenicRegionShadow

proxySequenceOntologyTerm(ProxyReference) - Method in class org.intermine.model.bio.IntronShadow

proxySequenceOntologyTerm(ProxyReference) - Method in interface org.intermine.model.bio.SequenceCollection

proxySequenceOntologyTerm(ProxyReference) - Method in class org.intermine.model.bio.SequenceCollectionShadow

proxySequenceOntologyTerm(ProxyReference) - Method in interface org.intermine.model.bio.SequenceFeature

proxySequenceOntologyTerm(ProxyReference) - Method in class org.intermine.model.bio.SequenceFeatureShadow

proxySequenceOntologyTerm(ProxyReference) - Method in class org.intermine.model.bio.SyntenicRegionShadow

proxySequenceOntologyTerm(ProxyReference) - Method in class org.intermine.model.bio.TranscriptShadow

proxySequenceOntologyTerm(ProxyReference) - Method in class org.intermine.model.bio.UTRShadow

proxySource(ProxyReference) - Method in interface org.intermine.model.bio.CrossReference

proxySource(ProxyReference) - Method in class org.intermine.model.bio.CrossReferenceShadow

proxyStrain(ProxyReference) - Method in class org.intermine.model.bio.CDSShadow

proxyStrain(ProxyReference) - Method in class org.intermine.model.bio.ChromosomeShadow

proxyStrain(ProxyReference) - Method in class org.intermine.model.bio.ExonShadow

proxyStrain(ProxyReference) - Method in class org.intermine.model.bio.GeneFlankingRegionShadow

proxyStrain(ProxyReference) - Method in class org.intermine.model.bio.GeneShadow

proxyStrain(ProxyReference) - Method in class org.intermine.model.bio.IntergenicRegionShadow

proxyStrain(ProxyReference) - Method in class org.intermine.model.bio.IntronShadow

proxyStrain(ProxyReference) - Method in interface org.intermine.model.bio.SequenceFeature

proxyStrain(ProxyReference) - Method in class org.intermine.model.bio.SequenceFeatureShadow

proxyStrain(ProxyReference) - Method in class org.intermine.model.bio.SyntenicRegionShadow

proxyStrain(ProxyReference) - Method in class org.intermine.model.bio.TranscriptShadow

proxyStrain(ProxyReference) - Method in class org.intermine.model.bio.UTRShadow

proxySubject(ProxyReference) - Method in interface org.intermine.model.bio.CrossReference

proxySubject(ProxyReference) - Method in class org.intermine.model.bio.CrossReferenceShadow

proxySubject(ProxyReference) - Method in interface org.intermine.model.bio.OntologyAnnotation

proxySubject(ProxyReference) - Method in class org.intermine.model.bio.OntologyAnnotationShadow

proxySubject(ProxyReference) - Method in interface org.intermine.model.bio.Synonym

proxySubject(ProxyReference) - Method in class org.intermine.model.bio.SynonymShadow

proxySyntenyBlock(ProxyReference) - Method in interface org.intermine.model.bio.SyntenicRegion

proxySyntenyBlock(ProxyReference) - Method in class org.intermine.model.bio.SyntenicRegionShadow

proxyUpstreamIntergenicRegion(ProxyReference) - Method in interface org.intermine.model.bio.Gene

proxyUpstreamIntergenicRegion(ProxyReference) - Method in class org.intermine.model.bio.GeneShadow

publication - Variable in class org.intermine.model.bio.DataSetShadow

Publication - Interface in org.intermine.model.bio

publications - Variable in class org.intermine.model.bio.AnnotatableShadow

publications - Variable in class org.intermine.model.bio.AuthorShadow

publications - Variable in class org.intermine.model.bio.BioEntityShadow

publications - Variable in class org.intermine.model.bio.CDSShadow

publications - Variable in class org.intermine.model.bio.ChromosomeShadow

publications - Variable in class org.intermine.model.bio.DataSourceShadow

publications - Variable in class org.intermine.model.bio.ExonShadow

publications - Variable in class org.intermine.model.bio.GeneFlankingRegionShadow

publications - Variable in class org.intermine.model.bio.GeneShadow

publications - Variable in class org.intermine.model.bio.IntergenicRegionShadow

publications - Variable in class org.intermine.model.bio.IntronShadow

publications - Variable in class org.intermine.model.bio.MeshTermShadow

publications - Variable in class org.intermine.model.bio.OntologyEvidenceShadow

publications - Variable in class org.intermine.model.bio.OrthologueEvidenceShadow

publications - Variable in class org.intermine.model.bio.ProteinShadow

publications - Variable in class org.intermine.model.bio.SequenceCollectionShadow

publications - Variable in class org.intermine.model.bio.SequenceFeatureShadow

publications - Variable in class org.intermine.model.bio.StrainShadow

publications - Variable in class org.intermine.model.bio.SyntenicRegionShadow

publications - Variable in class org.intermine.model.bio.SyntenyBlockShadow

publications - Variable in class org.intermine.model.bio.TranscriptShadow

publications - Variable in class org.intermine.model.bio.UTRShadow

PublicationShadow - Class in org.intermine.model.bio

PublicationShadow() - Constructor for class org.intermine.model.bio.PublicationShadow

pubMedId - Variable in class org.intermine.model.bio.PublicationShadow

Q

qualifier - Variable in class org.intermine.model.bio.OntologyAnnotationShadow

R

redundant - Variable in class org.intermine.model.bio.OntologyRelationShadow

relations - Variable in class org.intermine.model.bio.OntologyTermShadow

relations - Variable in class org.intermine.model.bio.SOTermShadow

relationship - Variable in class org.intermine.model.bio.OntologyRelationShadow

residues - Variable in class org.intermine.model.bio.SequenceShadow

S

score - Variable in class org.intermine.model.bio.CDSShadow

score - Variable in class org.intermine.model.bio.ChromosomeShadow

score - Variable in class org.intermine.model.bio.ExonShadow

score - Variable in class org.intermine.model.bio.GeneFlankingRegionShadow

score - Variable in class org.intermine.model.bio.GeneShadow

score - Variable in class org.intermine.model.bio.IntergenicRegionShadow

score - Variable in class org.intermine.model.bio.IntronShadow

score - Variable in class org.intermine.model.bio.SequenceFeatureShadow

score - Variable in class org.intermine.model.bio.SyntenicRegionShadow

score - Variable in class org.intermine.model.bio.TranscriptShadow

score - Variable in class org.intermine.model.bio.UTRShadow

scoreType - Variable in class org.intermine.model.bio.CDSShadow

scoreType - Variable in class org.intermine.model.bio.ChromosomeShadow

scoreType - Variable in class org.intermine.model.bio.ExonShadow

scoreType - Variable in class org.intermine.model.bio.GeneFlankingRegionShadow

scoreType - Variable in class org.intermine.model.bio.GeneShadow

scoreType - Variable in class org.intermine.model.bio.IntergenicRegionShadow

scoreType - Variable in class org.intermine.model.bio.IntronShadow

scoreType - Variable in class org.intermine.model.bio.SequenceFeatureShadow

scoreType - Variable in class org.intermine.model.bio.SyntenicRegionShadow

scoreType - Variable in class org.intermine.model.bio.TranscriptShadow

scoreType - Variable in class org.intermine.model.bio.UTRShadow

secondaryIdentifier - Variable in class org.intermine.model.bio.BioEntityShadow

secondaryIdentifier - Variable in class org.intermine.model.bio.CDSShadow

secondaryIdentifier - Variable in class org.intermine.model.bio.ChromosomeShadow

secondaryIdentifier - Variable in class org.intermine.model.bio.ExonShadow

secondaryIdentifier - Variable in class org.intermine.model.bio.GeneFlankingRegionShadow

secondaryIdentifier - Variable in class org.intermine.model.bio.GeneShadow

secondaryIdentifier - Variable in class org.intermine.model.bio.IntergenicRegionShadow

secondaryIdentifier - Variable in class org.intermine.model.bio.IntronShadow

secondaryIdentifier - Variable in class org.intermine.model.bio.ProteinShadow

secondaryIdentifier - Variable in class org.intermine.model.bio.SequenceCollectionShadow

secondaryIdentifier - Variable in class org.intermine.model.bio.SequenceFeatureShadow

secondaryIdentifier - Variable in class org.intermine.model.bio.StrainShadow

secondaryIdentifier - Variable in class org.intermine.model.bio.SyntenicRegionShadow

secondaryIdentifier - Variable in class org.intermine.model.bio.TranscriptShadow

secondaryIdentifier - Variable in class org.intermine.model.bio.UTRShadow

sequence - Variable in class org.intermine.model.bio.CDSShadow

sequence - Variable in class org.intermine.model.bio.ChromosomeShadow

sequence - Variable in class org.intermine.model.bio.ExonShadow

sequence - Variable in class org.intermine.model.bio.GeneFlankingRegionShadow

sequence - Variable in class org.intermine.model.bio.GeneShadow

sequence - Variable in class org.intermine.model.bio.IntergenicRegionShadow

sequence - Variable in class org.intermine.model.bio.IntronShadow

sequence - Variable in class org.intermine.model.bio.ProteinShadow

sequence - Variable in class org.intermine.model.bio.SequenceFeatureShadow

sequence - Variable in class org.intermine.model.bio.SyntenicRegionShadow

sequence - Variable in class org.intermine.model.bio.TranscriptShadow

sequence - Variable in class org.intermine.model.bio.UTRShadow

Sequence - Interface in org.intermine.model.bio

SequenceCollection - Interface in org.intermine.model.bio

SequenceCollectionShadow - Class in org.intermine.model.bio

SequenceCollectionShadow() - Constructor for class org.intermine.model.bio.SequenceCollectionShadow

SequenceFeature - Interface in org.intermine.model.bio

SequenceFeatureShadow - Class in org.intermine.model.bio

SequenceFeatureShadow() - Constructor for class org.intermine.model.bio.SequenceFeatureShadow

sequenceOntologyTerm - Variable in class org.intermine.model.bio.CDSShadow

sequenceOntologyTerm - Variable in class org.intermine.model.bio.ChromosomeShadow

sequenceOntologyTerm - Variable in class org.intermine.model.bio.ExonShadow

sequenceOntologyTerm - Variable in class org.intermine.model.bio.GeneFlankingRegionShadow

sequenceOntologyTerm - Variable in class org.intermine.model.bio.GeneShadow

sequenceOntologyTerm - Variable in class org.intermine.model.bio.IntergenicRegionShadow

sequenceOntologyTerm - Variable in class org.intermine.model.bio.IntronShadow

sequenceOntologyTerm - Variable in class org.intermine.model.bio.SequenceCollectionShadow

sequenceOntologyTerm - Variable in class org.intermine.model.bio.SequenceFeatureShadow

sequenceOntologyTerm - Variable in class org.intermine.model.bio.SyntenicRegionShadow

sequenceOntologyTerm - Variable in class org.intermine.model.bio.TranscriptShadow

sequenceOntologyTerm - Variable in class org.intermine.model.bio.UTRShadow

SequenceShadow - Class in org.intermine.model.bio

SequenceShadow() - Constructor for class org.intermine.model.bio.SequenceShadow

SequenceVariant - Interface in org.intermine.model.bio

SequenceVariantShadow - Class in org.intermine.model.bio

SequenceVariantShadow() - Constructor for class org.intermine.model.bio.SequenceVariantShadow

setAbbreviation(String) - Method in interface org.intermine.model.bio.OrthologueEvidenceCode

setAbbreviation(String) - Method in class org.intermine.model.bio.OrthologueEvidenceCodeShadow

setAbstractText(String) - Method in interface org.intermine.model.bio.Publication

setAbstractText(String) - Method in class org.intermine.model.bio.PublicationShadow

setAdjacentGenes(Set<Gene>) - Method in interface org.intermine.model.bio.IntergenicRegion

setAdjacentGenes(Set<Gene>) - Method in class org.intermine.model.bio.IntergenicRegionShadow

setAnnotationVersion(String) - Method in interface org.intermine.model.bio.Strain

setAnnotationVersion(String) - Method in class org.intermine.model.bio.StrainShadow

setAssemblyVersion(String) - Method in interface org.intermine.model.bio.Strain

setAssemblyVersion(String) - Method in class org.intermine.model.bio.StrainShadow

setAuthors(Set<Author>) - Method in interface org.intermine.model.bio.Publication

setAuthors(Set<Author>) - Method in class org.intermine.model.bio.PublicationShadow

setBioEntities(Set<BioEntity>) - Method in interface org.intermine.model.bio.DataSet

setBioEntities(Set<BioEntity>) - Method in class org.intermine.model.bio.DataSetShadow

setBriefDescription(String) - Method in interface org.intermine.model.bio.Gene

setBriefDescription(String) - Method in class org.intermine.model.bio.GeneShadow

setcDSs(Set<CDS>) - Method in interface org.intermine.model.bio.Gene

setcDSs(Set<CDS>) - Method in class org.intermine.model.bio.GeneShadow

setcDSs(Set<CDS>) - Method in interface org.intermine.model.bio.Protein

setcDSs(Set<CDS>) - Method in class org.intermine.model.bio.ProteinShadow

setChildFeatures(Set<SequenceFeature>) - Method in class org.intermine.model.bio.CDSShadow

setChildFeatures(Set<SequenceFeature>) - Method in class org.intermine.model.bio.ChromosomeShadow

setChildFeatures(Set<SequenceFeature>) - Method in class org.intermine.model.bio.ExonShadow

setChildFeatures(Set<SequenceFeature>) - Method in class org.intermine.model.bio.GeneFlankingRegionShadow

setChildFeatures(Set<SequenceFeature>) - Method in class org.intermine.model.bio.GeneShadow

setChildFeatures(Set<SequenceFeature>) - Method in class org.intermine.model.bio.IntergenicRegionShadow

setChildFeatures(Set<SequenceFeature>) - Method in class org.intermine.model.bio.IntronShadow

setChildFeatures(Set<SequenceFeature>) - Method in interface org.intermine.model.bio.SequenceFeature

setChildFeatures(Set<SequenceFeature>) - Method in class org.intermine.model.bio.SequenceFeatureShadow

setChildFeatures(Set<SequenceFeature>) - Method in class org.intermine.model.bio.SyntenicRegionShadow

setChildFeatures(Set<SequenceFeature>) - Method in class org.intermine.model.bio.TranscriptShadow

setChildFeatures(Set<SequenceFeature>) - Method in class org.intermine.model.bio.UTRShadow

setChildTerm(OntologyTerm) - Method in interface org.intermine.model.bio.OntologyRelation

setChildTerm(OntologyTerm) - Method in class org.intermine.model.bio.OntologyRelationShadow

setChromosome(Chromosome) - Method in class org.intermine.model.bio.CDSShadow

setChromosome(Chromosome) - Method in class org.intermine.model.bio.ChromosomeShadow

setChromosome(Chromosome) - Method in class org.intermine.model.bio.ExonShadow

setChromosome(Chromosome) - Method in class org.intermine.model.bio.GeneFlankingRegionShadow

setChromosome(Chromosome) - Method in class org.intermine.model.bio.GeneShadow

setChromosome(Chromosome) - Method in class org.intermine.model.bio.IntergenicRegionShadow

setChromosome(Chromosome) - Method in class org.intermine.model.bio.IntronShadow

setChromosome(Chromosome) - Method in interface org.intermine.model.bio.SequenceFeature

setChromosome(Chromosome) - Method in class org.intermine.model.bio.SequenceFeatureShadow

setChromosome(Chromosome) - Method in class org.intermine.model.bio.SyntenicRegionShadow

setChromosome(Chromosome) - Method in class org.intermine.model.bio.TranscriptShadow

setChromosome(Chromosome) - Method in class org.intermine.model.bio.UTRShadow

setChromosomeLocation(Location) - Method in class org.intermine.model.bio.CDSShadow

setChromosomeLocation(Location) - Method in class org.intermine.model.bio.ChromosomeShadow

setChromosomeLocation(Location) - Method in class org.intermine.model.bio.ExonShadow

setChromosomeLocation(Location) - Method in class org.intermine.model.bio.GeneFlankingRegionShadow

setChromosomeLocation(Location) - Method in class org.intermine.model.bio.GeneShadow

setChromosomeLocation(Location) - Method in class org.intermine.model.bio.IntergenicRegionShadow

setChromosomeLocation(Location) - Method in class org.intermine.model.bio.IntronShadow

setChromosomeLocation(Location) - Method in interface org.intermine.model.bio.SequenceFeature

setChromosomeLocation(Location) - Method in class org.intermine.model.bio.SequenceFeatureShadow

setChromosomeLocation(Location) - Method in class org.intermine.model.bio.SyntenicRegionShadow

setChromosomeLocation(Location) - Method in class org.intermine.model.bio.TranscriptShadow

setChromosomeLocation(Location) - Method in class org.intermine.model.bio.UTRShadow

setCode(String) - Method in interface org.intermine.model.bio.OntologyAnnotationEvidenceCode

setCode(String) - Method in class org.intermine.model.bio.OntologyAnnotationEvidenceCodeShadow

setCode(OntologyAnnotationEvidenceCode) - Method in interface org.intermine.model.bio.OntologyEvidence

setCode(OntologyAnnotationEvidenceCode) - Method in class org.intermine.model.bio.OntologyEvidenceShadow

setCommonName(String) - Method in interface org.intermine.model.bio.Organism

setCommonName(String) - Method in class org.intermine.model.bio.OrganismShadow

setCrossReferences(Set<CrossReference>) - Method in interface org.intermine.model.bio.BioEntity

setCrossReferences(Set<CrossReference>) - Method in class org.intermine.model.bio.BioEntityShadow

setCrossReferences(Set<CrossReference>) - Method in class org.intermine.model.bio.CDSShadow

setCrossReferences(Set<CrossReference>) - Method in class org.intermine.model.bio.ChromosomeShadow

setCrossReferences(Set<CrossReference>) - Method in class org.intermine.model.bio.ExonShadow

setCrossReferences(Set<CrossReference>) - Method in class org.intermine.model.bio.GeneFlankingRegionShadow

setCrossReferences(Set<CrossReference>) - Method in class org.intermine.model.bio.GeneShadow

setCrossReferences(Set<CrossReference>) - Method in interface org.intermine.model.bio.Homologue

setCrossReferences(Set<CrossReference>) - Method in class org.intermine.model.bio.HomologueShadow

setCrossReferences(Set<CrossReference>) - Method in class org.intermine.model.bio.IntergenicRegionShadow

setCrossReferences(Set<CrossReference>) - Method in class org.intermine.model.bio.IntronShadow

setCrossReferences(Set<CrossReference>) - Method in class org.intermine.model.bio.ProteinShadow

setCrossReferences(Set<CrossReference>) - Method in class org.intermine.model.bio.SequenceCollectionShadow

setCrossReferences(Set<CrossReference>) - Method in class org.intermine.model.bio.SequenceFeatureShadow

setCrossReferences(Set<CrossReference>) - Method in class org.intermine.model.bio.StrainShadow

setCrossReferences(Set<CrossReference>) - Method in class org.intermine.model.bio.SyntenicRegionShadow

setCrossReferences(Set<CrossReference>) - Method in class org.intermine.model.bio.TranscriptShadow

setCrossReferences(Set<CrossReference>) - Method in class org.intermine.model.bio.UTRShadow

setCrossReferences(Set<OntologyTerm>) - Method in interface org.intermine.model.bio.OntologyTerm

setCrossReferences(Set<OntologyTerm>) - Method in class org.intermine.model.bio.OntologyTermShadow

setCrossReferences(Set<OntologyTerm>) - Method in class org.intermine.model.bio.SOTermShadow

setDataSets(Set<DataSet>) - Method in interface org.intermine.model.bio.BioEntity

setDataSets(Set<DataSet>) - Method in class org.intermine.model.bio.BioEntityShadow

setDataSets(Set<DataSet>) - Method in class org.intermine.model.bio.CDSShadow

setDataSets(Set<DataSet>) - Method in class org.intermine.model.bio.ChromosomeShadow

setDataSets(Set<DataSet>) - Method in interface org.intermine.model.bio.DataSource

setDataSets(Set<DataSet>) - Method in class org.intermine.model.bio.DataSourceShadow

setDataSets(Set<DataSet>) - Method in class org.intermine.model.bio.ExonShadow

setDataSets(Set<DataSet>) - Method in class org.intermine.model.bio.GeneFlankingRegionShadow

setDataSets(Set<DataSet>) - Method in class org.intermine.model.bio.GeneShadow

setDataSets(Set<DataSet>) - Method in interface org.intermine.model.bio.Homologue

setDataSets(Set<DataSet>) - Method in class org.intermine.model.bio.HomologueShadow

setDataSets(Set<DataSet>) - Method in class org.intermine.model.bio.IntergenicRegionShadow

setDataSets(Set<DataSet>) - Method in class org.intermine.model.bio.IntronShadow

setDataSets(Set<DataSet>) - Method in interface org.intermine.model.bio.Location

setDataSets(Set<DataSet>) - Method in class org.intermine.model.bio.LocationShadow

setDataSets(Set<DataSet>) - Method in interface org.intermine.model.bio.Ontology

setDataSets(Set<DataSet>) - Method in interface org.intermine.model.bio.OntologyAnnotation

setDataSets(Set<DataSet>) - Method in class org.intermine.model.bio.OntologyAnnotationShadow

setDataSets(Set<DataSet>) - Method in class org.intermine.model.bio.OntologyShadow

setDataSets(Set<DataSet>) - Method in interface org.intermine.model.bio.OntologyTerm

setDataSets(Set<DataSet>) - Method in class org.intermine.model.bio.OntologyTermShadow

setDataSets(Set<DataSet>) - Method in class org.intermine.model.bio.ProteinShadow

setDataSets(Set<DataSet>) - Method in class org.intermine.model.bio.SequenceCollectionShadow

setDataSets(Set<DataSet>) - Method in class org.intermine.model.bio.SequenceFeatureShadow

setDataSets(Set<DataSet>) - Method in class org.intermine.model.bio.SOTermShadow

setDataSets(Set<DataSet>) - Method in class org.intermine.model.bio.StrainShadow

setDataSets(Set<DataSet>) - Method in interface org.intermine.model.bio.Synonym

setDataSets(Set<DataSet>) - Method in class org.intermine.model.bio.SynonymShadow

setDataSets(Set<DataSet>) - Method in class org.intermine.model.bio.SyntenicRegionShadow

setDataSets(Set<DataSet>) - Method in interface org.intermine.model.bio.SyntenyBlock

setDataSets(Set<DataSet>) - Method in class org.intermine.model.bio.SyntenyBlockShadow

setDataSets(Set<DataSet>) - Method in class org.intermine.model.bio.TranscriptShadow

setDataSets(Set<DataSet>) - Method in class org.intermine.model.bio.UTRShadow

setDataSource(DataSource) - Method in interface org.intermine.model.bio.DataSet

setDataSource(DataSource) - Method in class org.intermine.model.bio.DataSetShadow

setDescription(String) - Method in interface org.intermine.model.bio.Comment

setDescription(String) - Method in class org.intermine.model.bio.CommentShadow

setDescription(String) - Method in interface org.intermine.model.bio.DataSet

setDescription(String) - Method in class org.intermine.model.bio.DataSetShadow

setDescription(String) - Method in interface org.intermine.model.bio.DataSource

setDescription(String) - Method in class org.intermine.model.bio.DataSourceShadow

setDescription(String) - Method in interface org.intermine.model.bio.Gene

setDescription(String) - Method in class org.intermine.model.bio.GeneShadow

setDescription(String) - Method in interface org.intermine.model.bio.OntologyTerm

setDescription(String) - Method in class org.intermine.model.bio.OntologyTermShadow

setDescription(String) - Method in class org.intermine.model.bio.SOTermShadow

setDirect(Boolean) - Method in interface org.intermine.model.bio.OntologyRelation

setDirect(Boolean) - Method in class org.intermine.model.bio.OntologyRelationShadow

setDirection(String) - Method in interface org.intermine.model.bio.GeneFlankingRegion

setDirection(String) - Method in class org.intermine.model.bio.GeneFlankingRegionShadow

setDistance(String) - Method in interface org.intermine.model.bio.GeneFlankingRegion

setDistance(String) - Method in class org.intermine.model.bio.GeneFlankingRegionShadow

setDoi(String) - Method in interface org.intermine.model.bio.Publication

setDoi(String) - Method in class org.intermine.model.bio.PublicationShadow

setDownstreamIntergenicRegion(IntergenicRegion) - Method in interface org.intermine.model.bio.Gene

setDownstreamIntergenicRegion(IntergenicRegion) - Method in class org.intermine.model.bio.GeneShadow

setEnd(Integer) - Method in interface org.intermine.model.bio.Location

setEnd(Integer) - Method in class org.intermine.model.bio.LocationShadow

setEntities(Set<Annotatable>) - Method in interface org.intermine.model.bio.Publication

setEntities(Set<Annotatable>) - Method in class org.intermine.model.bio.PublicationShadow

setEvidence(Set<OntologyEvidence>) - Method in interface org.intermine.model.bio.OntologyAnnotation

setEvidence(Set<OntologyEvidence>) - Method in class org.intermine.model.bio.OntologyAnnotationShadow

setEvidence(Set<OrthologueEvidence>) - Method in interface org.intermine.model.bio.Homologue

setEvidence(Set<OrthologueEvidence>) - Method in class org.intermine.model.bio.HomologueShadow

setEvidenceCode(OrthologueEvidenceCode) - Method in interface org.intermine.model.bio.OrthologueEvidence

setEvidenceCode(OrthologueEvidenceCode) - Method in class org.intermine.model.bio.OrthologueEvidenceShadow

setExons(Set<Exon>) - Method in interface org.intermine.model.bio.Gene

setExons(Set<Exon>) - Method in class org.intermine.model.bio.GeneShadow

setFeature(BioEntity) - Method in interface org.intermine.model.bio.Location

setFeature(BioEntity) - Method in class org.intermine.model.bio.LocationShadow

setFeatures(Set<SequenceFeature>) - Method in interface org.intermine.model.bio.Strain

setFeatures(Set<SequenceFeature>) - Method in class org.intermine.model.bio.StrainShadow

setFieldValue(String, Object) - Method in class org.intermine.model.bio.AnnotatableShadow

setFieldValue(String, Object) - Method in class org.intermine.model.bio.AuthorShadow

setFieldValue(String, Object) - Method in class org.intermine.model.bio.BioEntityShadow

setFieldValue(String, Object) - Method in class org.intermine.model.bio.CDSShadow

setFieldValue(String, Object) - Method in class org.intermine.model.bio.ChromosomeShadow

setFieldValue(String, Object) - Method in class org.intermine.model.bio.CommentShadow

setFieldValue(String, Object) - Method in class org.intermine.model.bio.CrossReferenceShadow

setFieldValue(String, Object) - Method in class org.intermine.model.bio.DataSetShadow

setFieldValue(String, Object) - Method in class org.intermine.model.bio.DataSourceShadow

setFieldValue(String, Object) - Method in class org.intermine.model.bio.ExonShadow

setFieldValue(String, Object) - Method in class org.intermine.model.bio.GeneFlankingRegionShadow

setFieldValue(String, Object) - Method in class org.intermine.model.bio.GeneShadow

setFieldValue(String, Object) - Method in class org.intermine.model.bio.HomologueShadow

setFieldValue(String, Object) - Method in class org.intermine.model.bio.IntergenicRegionShadow

setFieldValue(String, Object) - Method in class org.intermine.model.bio.IntronShadow

setFieldValue(String, Object) - Method in class org.intermine.model.bio.LocationShadow

setFieldValue(String, Object) - Method in class org.intermine.model.bio.MeshTermShadow

setFieldValue(String, Object) - Method in class org.intermine.model.bio.OntologyAnnotationEvidenceCodeShadow

setFieldValue(String, Object) - Method in class org.intermine.model.bio.OntologyAnnotationShadow

setFieldValue(String, Object) - Method in class org.intermine.model.bio.OntologyEvidenceShadow

setFieldValue(String, Object) - Method in class org.intermine.model.bio.OntologyRelationShadow

setFieldValue(String, Object) - Method in class org.intermine.model.bio.OntologyShadow

setFieldValue(String, Object) - Method in class org.intermine.model.bio.OntologyTermShadow

setFieldValue(String, Object) - Method in class org.intermine.model.bio.OntologyTermSynonymShadow

setFieldValue(String, Object) - Method in class org.intermine.model.bio.OrganismShadow

setFieldValue(String, Object) - Method in class org.intermine.model.bio.OrthologueEvidenceCodeShadow

setFieldValue(String, Object) - Method in class org.intermine.model.bio.OrthologueEvidenceShadow

setFieldValue(String, Object) - Method in class org.intermine.model.bio.ProteinShadow

setFieldValue(String, Object) - Method in class org.intermine.model.bio.PublicationShadow

setFieldValue(String, Object) - Method in class org.intermine.model.bio.SequenceCollectionShadow

setFieldValue(String, Object) - Method in class org.intermine.model.bio.SequenceFeatureShadow

setFieldValue(String, Object) - Method in class org.intermine.model.bio.SequenceShadow

setFieldValue(String, Object) - Method in class org.intermine.model.bio.SequenceVariantShadow

setFieldValue(String, Object) - Method in class org.intermine.model.bio.SOTermShadow

setFieldValue(String, Object) - Method in class org.intermine.model.bio.StrainShadow

setFieldValue(String, Object) - Method in class org.intermine.model.bio.SynonymShadow

setFieldValue(String, Object) - Method in class org.intermine.model.bio.SyntenicRegionShadow

setFieldValue(String, Object) - Method in class org.intermine.model.bio.SyntenyBlockShadow

setFieldValue(String, Object) - Method in class org.intermine.model.bio.TranscriptShadow

setFieldValue(String, Object) - Method in class org.intermine.model.bio.UTRShadow

setFirstAuthor(String) - Method in interface org.intermine.model.bio.Publication

setFirstAuthor(String) - Method in class org.intermine.model.bio.PublicationShadow

setFirstName(String) - Method in interface org.intermine.model.bio.Author

setFirstName(String) - Method in class org.intermine.model.bio.AuthorShadow

setFlankingRegions(Set<GeneFlankingRegion>) - Method in interface org.intermine.model.bio.Gene

setFlankingRegions(Set<GeneFlankingRegion>) - Method in class org.intermine.model.bio.GeneShadow

setGene(Gene) - Method in interface org.intermine.model.bio.CDS

setGene(Gene) - Method in class org.intermine.model.bio.CDSShadow

setGene(Gene) - Method in interface org.intermine.model.bio.Exon

setGene(Gene) - Method in class org.intermine.model.bio.ExonShadow

setGene(Gene) - Method in interface org.intermine.model.bio.GeneFlankingRegion

setGene(Gene) - Method in class org.intermine.model.bio.GeneFlankingRegionShadow

setGene(Gene) - Method in interface org.intermine.model.bio.Homologue

setGene(Gene) - Method in class org.intermine.model.bio.HomologueShadow

setGene(Gene) - Method in interface org.intermine.model.bio.UTR

setGene(Gene) - Method in class org.intermine.model.bio.UTRShadow

setGenes(Set<Gene>) - Method in interface org.intermine.model.bio.Intron

setGenes(Set<Gene>) - Method in class org.intermine.model.bio.IntronShadow

setGenes(Set<Gene>) - Method in interface org.intermine.model.bio.Protein

setGenes(Set<Gene>) - Method in class org.intermine.model.bio.ProteinShadow

setGenes(Set<Gene>) - Method in interface org.intermine.model.bio.SequenceVariant

setGenes(Set<Gene>) - Method in class org.intermine.model.bio.SequenceVariantShadow

setGenus(String) - Method in interface org.intermine.model.bio.Organism

setGenus(String) - Method in class org.intermine.model.bio.OrganismShadow

setHomologeneHomologues(String) - Method in class org.intermine.bio.dataconversion.HomologeneConverter

Sets the list of taxonIds of homologues that should be processed.

setHomologeneOrganisms(String) - Method in class org.intermine.bio.dataconversion.HomologeneConverter

Sets the list of taxonIds that should be processed.

setHomologue(Gene) - Method in interface org.intermine.model.bio.Homologue

setHomologue(Gene) - Method in class org.intermine.model.bio.HomologueShadow

setHomologues(Set<Homologue>) - Method in interface org.intermine.model.bio.Gene

setHomologues(Set<Homologue>) - Method in class org.intermine.model.bio.GeneShadow

setId(Integer) - Method in class org.intermine.model.bio.AnnotatableShadow

setId(Integer) - Method in class org.intermine.model.bio.AuthorShadow

setId(Integer) - Method in class org.intermine.model.bio.BioEntityShadow

setId(Integer) - Method in class org.intermine.model.bio.CDSShadow

setId(Integer) - Method in class org.intermine.model.bio.ChromosomeShadow

setId(Integer) - Method in class org.intermine.model.bio.CommentShadow

setId(Integer) - Method in class org.intermine.model.bio.CrossReferenceShadow

setId(Integer) - Method in class org.intermine.model.bio.DataSetShadow

setId(Integer) - Method in class org.intermine.model.bio.DataSourceShadow

setId(Integer) - Method in class org.intermine.model.bio.ExonShadow

setId(Integer) - Method in class org.intermine.model.bio.GeneFlankingRegionShadow

setId(Integer) - Method in class org.intermine.model.bio.GeneShadow

setId(Integer) - Method in class org.intermine.model.bio.HomologueShadow

setId(Integer) - Method in class org.intermine.model.bio.IntergenicRegionShadow

setId(Integer) - Method in class org.intermine.model.bio.IntronShadow

setId(Integer) - Method in class org.intermine.model.bio.LocationShadow

setId(Integer) - Method in class org.intermine.model.bio.MeshTermShadow

setId(Integer) - Method in class org.intermine.model.bio.OntologyAnnotationEvidenceCodeShadow

setId(Integer) - Method in class org.intermine.model.bio.OntologyAnnotationShadow

setId(Integer) - Method in class org.intermine.model.bio.OntologyEvidenceShadow

setId(Integer) - Method in class org.intermine.model.bio.OntologyRelationShadow

setId(Integer) - Method in class org.intermine.model.bio.OntologyShadow

setId(Integer) - Method in class org.intermine.model.bio.OntologyTermShadow

setId(Integer) - Method in class org.intermine.model.bio.OntologyTermSynonymShadow

setId(Integer) - Method in class org.intermine.model.bio.OrganismShadow

setId(Integer) - Method in class org.intermine.model.bio.OrthologueEvidenceCodeShadow

setId(Integer) - Method in class org.intermine.model.bio.OrthologueEvidenceShadow

setId(Integer) - Method in class org.intermine.model.bio.ProteinShadow

setId(Integer) - Method in class org.intermine.model.bio.PublicationShadow

setId(Integer) - Method in class org.intermine.model.bio.SequenceCollectionShadow

setId(Integer) - Method in class org.intermine.model.bio.SequenceFeatureShadow

setId(Integer) - Method in class org.intermine.model.bio.SequenceShadow

setId(Integer) - Method in class org.intermine.model.bio.SequenceVariantShadow

setId(Integer) - Method in class org.intermine.model.bio.SOTermShadow

setId(Integer) - Method in class org.intermine.model.bio.StrainShadow

setId(Integer) - Method in class org.intermine.model.bio.SynonymShadow

setId(Integer) - Method in class org.intermine.model.bio.SyntenicRegionShadow

setId(Integer) - Method in class org.intermine.model.bio.SyntenyBlockShadow

setId(Integer) - Method in class org.intermine.model.bio.TranscriptShadow

setId(Integer) - Method in class org.intermine.model.bio.UTRShadow

setIdentifier(String) - Method in interface org.intermine.model.bio.CrossReference

setIdentifier(String) - Method in class org.intermine.model.bio.CrossReferenceShadow

setIdentifier(String) - Method in interface org.intermine.model.bio.OntologyTerm

setIdentifier(String) - Method in class org.intermine.model.bio.OntologyTermShadow

setIdentifier(String) - Method in class org.intermine.model.bio.SOTermShadow

setIncludeGene(Boolean) - Method in interface org.intermine.model.bio.GeneFlankingRegion

setIncludeGene(Boolean) - Method in class org.intermine.model.bio.GeneFlankingRegionShadow

setInitials(String) - Method in interface org.intermine.model.bio.Author

setInitials(String) - Method in class org.intermine.model.bio.AuthorShadow

setIntrons(Set<Intron>) - Method in interface org.intermine.model.bio.Gene

setIntrons(Set<Intron>) - Method in class org.intermine.model.bio.GeneShadow

setIssue(String) - Method in interface org.intermine.model.bio.Publication

setIssue(String) - Method in class org.intermine.model.bio.PublicationShadow

setJournal(String) - Method in interface org.intermine.model.bio.Publication

setJournal(String) - Method in class org.intermine.model.bio.PublicationShadow

setLastName(String) - Method in interface org.intermine.model.bio.Author

setLastName(String) - Method in class org.intermine.model.bio.AuthorShadow

setLength(int) - Method in interface org.intermine.model.bio.Sequence

setLength(int) - Method in class org.intermine.model.bio.SequenceShadow

setLength(Integer) - Method in class org.intermine.model.bio.CDSShadow

setLength(Integer) - Method in class org.intermine.model.bio.ChromosomeShadow

setLength(Integer) - Method in class org.intermine.model.bio.ExonShadow

setLength(Integer) - Method in class org.intermine.model.bio.GeneFlankingRegionShadow

setLength(Integer) - Method in class org.intermine.model.bio.GeneShadow

setLength(Integer) - Method in class org.intermine.model.bio.IntergenicRegionShadow

setLength(Integer) - Method in class org.intermine.model.bio.IntronShadow

setLength(Integer) - Method in interface org.intermine.model.bio.Protein

setLength(Integer) - Method in class org.intermine.model.bio.ProteinShadow

setLength(Integer) - Method in interface org.intermine.model.bio.SequenceFeature

setLength(Integer) - Method in class org.intermine.model.bio.SequenceFeatureShadow

setLength(Integer) - Method in class org.intermine.model.bio.SyntenicRegionShadow

setLength(Integer) - Method in class org.intermine.model.bio.TranscriptShadow

setLength(Integer) - Method in class org.intermine.model.bio.UTRShadow

setLicence(String) - Method in interface org.intermine.model.bio.DataSet

setLicence(String) - Method in class org.intermine.model.bio.DataSetShadow

setLocatedFeatures(Set<Location>) - Method in interface org.intermine.model.bio.BioEntity

setLocatedFeatures(Set<Location>) - Method in class org.intermine.model.bio.BioEntityShadow

setLocatedFeatures(Set<Location>) - Method in class org.intermine.model.bio.CDSShadow

setLocatedFeatures(Set<Location>) - Method in class org.intermine.model.bio.ChromosomeShadow

setLocatedFeatures(Set<Location>) - Method in class org.intermine.model.bio.ExonShadow

setLocatedFeatures(Set<Location>) - Method in class org.intermine.model.bio.GeneFlankingRegionShadow

setLocatedFeatures(Set<Location>) - Method in class org.intermine.model.bio.GeneShadow

setLocatedFeatures(Set<Location>) - Method in class org.intermine.model.bio.IntergenicRegionShadow

setLocatedFeatures(Set<Location>) - Method in class org.intermine.model.bio.IntronShadow

setLocatedFeatures(Set<Location>) - Method in class org.intermine.model.bio.ProteinShadow

setLocatedFeatures(Set<Location>) - Method in class org.intermine.model.bio.SequenceCollectionShadow

setLocatedFeatures(Set<Location>) - Method in class org.intermine.model.bio.SequenceFeatureShadow

setLocatedFeatures(Set<Location>) - Method in class org.intermine.model.bio.StrainShadow

setLocatedFeatures(Set<Location>) - Method in class org.intermine.model.bio.SyntenicRegionShadow

setLocatedFeatures(Set<Location>) - Method in class org.intermine.model.bio.TranscriptShadow

setLocatedFeatures(Set<Location>) - Method in class org.intermine.model.bio.UTRShadow

setLocatedOn(BioEntity) - Method in interface org.intermine.model.bio.Location

setLocatedOn(BioEntity) - Method in class org.intermine.model.bio.LocationShadow

setLocations(Set<Location>) - Method in interface org.intermine.model.bio.BioEntity

setLocations(Set<Location>) - Method in class org.intermine.model.bio.BioEntityShadow

setLocations(Set<Location>) - Method in class org.intermine.model.bio.CDSShadow

setLocations(Set<Location>) - Method in class org.intermine.model.bio.ChromosomeShadow

setLocations(Set<Location>) - Method in class org.intermine.model.bio.ExonShadow

setLocations(Set<Location>) - Method in class org.intermine.model.bio.GeneFlankingRegionShadow

setLocations(Set<Location>) - Method in class org.intermine.model.bio.GeneShadow

setLocations(Set<Location>) - Method in class org.intermine.model.bio.IntergenicRegionShadow

setLocations(Set<Location>) - Method in class org.intermine.model.bio.IntronShadow

setLocations(Set<Location>) - Method in class org.intermine.model.bio.ProteinShadow

setLocations(Set<Location>) - Method in class org.intermine.model.bio.SequenceCollectionShadow

setLocations(Set<Location>) - Method in class org.intermine.model.bio.SequenceFeatureShadow

setLocations(Set<Location>) - Method in class org.intermine.model.bio.StrainShadow

setLocations(Set<Location>) - Method in class org.intermine.model.bio.SyntenicRegionShadow

setLocations(Set<Location>) - Method in class org.intermine.model.bio.TranscriptShadow

setLocations(Set<Location>) - Method in class org.intermine.model.bio.UTRShadow

setMd5checksum(String) - Method in interface org.intermine.model.bio.Protein

setMd5checksum(String) - Method in class org.intermine.model.bio.ProteinShadow

setMd5checksum(String) - Method in interface org.intermine.model.bio.Sequence

setMd5checksum(String) - Method in class org.intermine.model.bio.SequenceShadow

setMeshTerms(Set<MeshTerm>) - Method in interface org.intermine.model.bio.Publication

setMeshTerms(Set<MeshTerm>) - Method in class org.intermine.model.bio.PublicationShadow

setMolecularWeight(Double) - Method in interface org.intermine.model.bio.Protein

setMolecularWeight(Double) - Method in class org.intermine.model.bio.ProteinShadow

setMonth(String) - Method in interface org.intermine.model.bio.Publication

setMonth(String) - Method in class org.intermine.model.bio.PublicationShadow

setName(String) - Method in interface org.intermine.model.bio.Author

setName(String) - Method in class org.intermine.model.bio.AuthorShadow

setName(String) - Method in interface org.intermine.model.bio.BioEntity

setName(String) - Method in class org.intermine.model.bio.BioEntityShadow

setName(String) - Method in class org.intermine.model.bio.CDSShadow

setName(String) - Method in class org.intermine.model.bio.ChromosomeShadow

setName(String) - Method in interface org.intermine.model.bio.DataSet

setName(String) - Method in class org.intermine.model.bio.DataSetShadow

setName(String) - Method in interface org.intermine.model.bio.DataSource

setName(String) - Method in class org.intermine.model.bio.DataSourceShadow

setName(String) - Method in class org.intermine.model.bio.ExonShadow

setName(String) - Method in class org.intermine.model.bio.GeneFlankingRegionShadow

setName(String) - Method in class org.intermine.model.bio.GeneShadow

setName(String) - Method in class org.intermine.model.bio.IntergenicRegionShadow

setName(String) - Method in class org.intermine.model.bio.IntronShadow

setName(String) - Method in interface org.intermine.model.bio.MeshTerm

setName(String) - Method in class org.intermine.model.bio.MeshTermShadow

setName(String) - Method in interface org.intermine.model.bio.Ontology

setName(String) - Method in interface org.intermine.model.bio.OntologyAnnotationEvidenceCode

setName(String) - Method in class org.intermine.model.bio.OntologyAnnotationEvidenceCodeShadow

setName(String) - Method in class org.intermine.model.bio.OntologyShadow

setName(String) - Method in interface org.intermine.model.bio.OntologyTerm

setName(String) - Method in class org.intermine.model.bio.OntologyTermShadow

setName(String) - Method in interface org.intermine.model.bio.OntologyTermSynonym

setName(String) - Method in class org.intermine.model.bio.OntologyTermSynonymShadow

setName(String) - Method in interface org.intermine.model.bio.Organism

setName(String) - Method in class org.intermine.model.bio.OrganismShadow

setName(String) - Method in interface org.intermine.model.bio.OrthologueEvidenceCode

setName(String) - Method in class org.intermine.model.bio.OrthologueEvidenceCodeShadow

setName(String) - Method in class org.intermine.model.bio.ProteinShadow

setName(String) - Method in class org.intermine.model.bio.SequenceCollectionShadow

setName(String) - Method in class org.intermine.model.bio.SequenceFeatureShadow

setName(String) - Method in class org.intermine.model.bio.SOTermShadow

setName(String) - Method in class org.intermine.model.bio.StrainShadow

setName(String) - Method in class org.intermine.model.bio.SyntenicRegionShadow

setName(String) - Method in class org.intermine.model.bio.TranscriptShadow

setName(String) - Method in class org.intermine.model.bio.UTRShadow

setNamespace(String) - Method in interface org.intermine.model.bio.OntologyTerm

setNamespace(String) - Method in class org.intermine.model.bio.OntologyTermShadow

setNamespace(String) - Method in class org.intermine.model.bio.SOTermShadow

setoBJECT(String[], ObjectStore) - Method in class org.intermine.model.bio.AnnotatableShadow

setoBJECT(String[], ObjectStore) - Method in class org.intermine.model.bio.AuthorShadow

setoBJECT(String[], ObjectStore) - Method in class org.intermine.model.bio.BioEntityShadow

setoBJECT(String[], ObjectStore) - Method in class org.intermine.model.bio.CDSShadow

setoBJECT(String[], ObjectStore) - Method in class org.intermine.model.bio.ChromosomeShadow

setoBJECT(String[], ObjectStore) - Method in class org.intermine.model.bio.CommentShadow

setoBJECT(String[], ObjectStore) - Method in class org.intermine.model.bio.CrossReferenceShadow

setoBJECT(String[], ObjectStore) - Method in class org.intermine.model.bio.DataSetShadow

setoBJECT(String[], ObjectStore) - Method in class org.intermine.model.bio.DataSourceShadow

setoBJECT(String[], ObjectStore) - Method in class org.intermine.model.bio.ExonShadow

setoBJECT(String[], ObjectStore) - Method in class org.intermine.model.bio.GeneFlankingRegionShadow

setoBJECT(String[], ObjectStore) - Method in class org.intermine.model.bio.GeneShadow

setoBJECT(String[], ObjectStore) - Method in class org.intermine.model.bio.HomologueShadow

setoBJECT(String[], ObjectStore) - Method in class org.intermine.model.bio.IntergenicRegionShadow

setoBJECT(String[], ObjectStore) - Method in class org.intermine.model.bio.IntronShadow

setoBJECT(String[], ObjectStore) - Method in class org.intermine.model.bio.LocationShadow

setoBJECT(String[], ObjectStore) - Method in class org.intermine.model.bio.MeshTermShadow

setoBJECT(String[], ObjectStore) - Method in class org.intermine.model.bio.OntologyAnnotationEvidenceCodeShadow

setoBJECT(String[], ObjectStore) - Method in class org.intermine.model.bio.OntologyAnnotationShadow

setoBJECT(String[], ObjectStore) - Method in class org.intermine.model.bio.OntologyEvidenceShadow

setoBJECT(String[], ObjectStore) - Method in class org.intermine.model.bio.OntologyRelationShadow

setoBJECT(String[], ObjectStore) - Method in class org.intermine.model.bio.OntologyShadow

setoBJECT(String[], ObjectStore) - Method in class org.intermine.model.bio.OntologyTermShadow

setoBJECT(String[], ObjectStore) - Method in class org.intermine.model.bio.OntologyTermSynonymShadow

setoBJECT(String[], ObjectStore) - Method in class org.intermine.model.bio.OrganismShadow

setoBJECT(String[], ObjectStore) - Method in class org.intermine.model.bio.OrthologueEvidenceCodeShadow

setoBJECT(String[], ObjectStore) - Method in class org.intermine.model.bio.OrthologueEvidenceShadow

setoBJECT(String[], ObjectStore) - Method in class org.intermine.model.bio.ProteinShadow

setoBJECT(String[], ObjectStore) - Method in class org.intermine.model.bio.PublicationShadow

setoBJECT(String[], ObjectStore) - Method in class org.intermine.model.bio.SequenceCollectionShadow

setoBJECT(String[], ObjectStore) - Method in class org.intermine.model.bio.SequenceFeatureShadow

setoBJECT(String[], ObjectStore) - Method in class org.intermine.model.bio.SequenceShadow

setoBJECT(String[], ObjectStore) - Method in class org.intermine.model.bio.SequenceVariantShadow

setoBJECT(String[], ObjectStore) - Method in class org.intermine.model.bio.SOTermShadow

setoBJECT(String[], ObjectStore) - Method in class org.intermine.model.bio.StrainShadow

setoBJECT(String[], ObjectStore) - Method in class org.intermine.model.bio.SynonymShadow

setoBJECT(String[], ObjectStore) - Method in class org.intermine.model.bio.SyntenicRegionShadow

setoBJECT(String[], ObjectStore) - Method in class org.intermine.model.bio.SyntenyBlockShadow

setoBJECT(String[], ObjectStore) - Method in class org.intermine.model.bio.TranscriptShadow

setoBJECT(String[], ObjectStore) - Method in class org.intermine.model.bio.UTRShadow

setoBJECT(String, ObjectStore) - Method in class org.intermine.model.bio.AnnotatableShadow

setoBJECT(String, ObjectStore) - Method in class org.intermine.model.bio.AuthorShadow

setoBJECT(String, ObjectStore) - Method in class org.intermine.model.bio.BioEntityShadow

setoBJECT(String, ObjectStore) - Method in class org.intermine.model.bio.CDSShadow

setoBJECT(String, ObjectStore) - Method in class org.intermine.model.bio.ChromosomeShadow

setoBJECT(String, ObjectStore) - Method in class org.intermine.model.bio.CommentShadow

setoBJECT(String, ObjectStore) - Method in class org.intermine.model.bio.CrossReferenceShadow

setoBJECT(String, ObjectStore) - Method in class org.intermine.model.bio.DataSetShadow

setoBJECT(String, ObjectStore) - Method in class org.intermine.model.bio.DataSourceShadow

setoBJECT(String, ObjectStore) - Method in class org.intermine.model.bio.ExonShadow

setoBJECT(String, ObjectStore) - Method in class org.intermine.model.bio.GeneFlankingRegionShadow

setoBJECT(String, ObjectStore) - Method in class org.intermine.model.bio.GeneShadow

setoBJECT(String, ObjectStore) - Method in class org.intermine.model.bio.HomologueShadow

setoBJECT(String, ObjectStore) - Method in class org.intermine.model.bio.IntergenicRegionShadow

setoBJECT(String, ObjectStore) - Method in class org.intermine.model.bio.IntronShadow

setoBJECT(String, ObjectStore) - Method in class org.intermine.model.bio.LocationShadow

setoBJECT(String, ObjectStore) - Method in class org.intermine.model.bio.MeshTermShadow

setoBJECT(String, ObjectStore) - Method in class org.intermine.model.bio.OntologyAnnotationEvidenceCodeShadow

setoBJECT(String, ObjectStore) - Method in class org.intermine.model.bio.OntologyAnnotationShadow

setoBJECT(String, ObjectStore) - Method in class org.intermine.model.bio.OntologyEvidenceShadow

setoBJECT(String, ObjectStore) - Method in class org.intermine.model.bio.OntologyRelationShadow

setoBJECT(String, ObjectStore) - Method in class org.intermine.model.bio.OntologyShadow

setoBJECT(String, ObjectStore) - Method in class org.intermine.model.bio.OntologyTermShadow

setoBJECT(String, ObjectStore) - Method in class org.intermine.model.bio.OntologyTermSynonymShadow

setoBJECT(String, ObjectStore) - Method in class org.intermine.model.bio.OrganismShadow

setoBJECT(String, ObjectStore) - Method in class org.intermine.model.bio.OrthologueEvidenceCodeShadow

setoBJECT(String, ObjectStore) - Method in class org.intermine.model.bio.OrthologueEvidenceShadow

setoBJECT(String, ObjectStore) - Method in class org.intermine.model.bio.ProteinShadow

setoBJECT(String, ObjectStore) - Method in class org.intermine.model.bio.PublicationShadow

setoBJECT(String, ObjectStore) - Method in class org.intermine.model.bio.SequenceCollectionShadow

setoBJECT(String, ObjectStore) - Method in class org.intermine.model.bio.SequenceFeatureShadow

setoBJECT(String, ObjectStore) - Method in class org.intermine.model.bio.SequenceShadow

setoBJECT(String, ObjectStore) - Method in class org.intermine.model.bio.SequenceVariantShadow

setoBJECT(String, ObjectStore) - Method in class org.intermine.model.bio.SOTermShadow

setoBJECT(String, ObjectStore) - Method in class org.intermine.model.bio.StrainShadow

setoBJECT(String, ObjectStore) - Method in class org.intermine.model.bio.SynonymShadow

setoBJECT(String, ObjectStore) - Method in class org.intermine.model.bio.SyntenicRegionShadow

setoBJECT(String, ObjectStore) - Method in class org.intermine.model.bio.SyntenyBlockShadow

setoBJECT(String, ObjectStore) - Method in class org.intermine.model.bio.TranscriptShadow

setoBJECT(String, ObjectStore) - Method in class org.intermine.model.bio.UTRShadow

setObsolete(Boolean) - Method in interface org.intermine.model.bio.OntologyTerm

setObsolete(Boolean) - Method in class org.intermine.model.bio.OntologyTermShadow

setObsolete(Boolean) - Method in class org.intermine.model.bio.SOTermShadow

setOntology(Ontology) - Method in interface org.intermine.model.bio.OntologyTerm

setOntology(Ontology) - Method in class org.intermine.model.bio.OntologyTermShadow

setOntology(Ontology) - Method in class org.intermine.model.bio.SOTermShadow

setOntologyAnnotations(Set<OntologyAnnotation>) - Method in interface org.intermine.model.bio.Annotatable

setOntologyAnnotations(Set<OntologyAnnotation>) - Method in class org.intermine.model.bio.AnnotatableShadow

setOntologyAnnotations(Set<OntologyAnnotation>) - Method in class org.intermine.model.bio.BioEntityShadow

setOntologyAnnotations(Set<OntologyAnnotation>) - Method in class org.intermine.model.bio.CDSShadow

setOntologyAnnotations(Set<OntologyAnnotation>) - Method in class org.intermine.model.bio.ChromosomeShadow

setOntologyAnnotations(Set<OntologyAnnotation>) - Method in class org.intermine.model.bio.ExonShadow

setOntologyAnnotations(Set<OntologyAnnotation>) - Method in class org.intermine.model.bio.GeneFlankingRegionShadow

setOntologyAnnotations(Set<OntologyAnnotation>) - Method in class org.intermine.model.bio.GeneShadow

setOntologyAnnotations(Set<OntologyAnnotation>) - Method in class org.intermine.model.bio.IntergenicRegionShadow

setOntologyAnnotations(Set<OntologyAnnotation>) - Method in class org.intermine.model.bio.IntronShadow

setOntologyAnnotations(Set<OntologyAnnotation>) - Method in interface org.intermine.model.bio.OntologyTerm

setOntologyAnnotations(Set<OntologyAnnotation>) - Method in class org.intermine.model.bio.OntologyTermShadow

setOntologyAnnotations(Set<OntologyAnnotation>) - Method in class org.intermine.model.bio.ProteinShadow

setOntologyAnnotations(Set<OntologyAnnotation>) - Method in class org.intermine.model.bio.SequenceCollectionShadow

setOntologyAnnotations(Set<OntologyAnnotation>) - Method in class org.intermine.model.bio.SequenceFeatureShadow

setOntologyAnnotations(Set<OntologyAnnotation>) - Method in class org.intermine.model.bio.SOTermShadow

setOntologyAnnotations(Set<OntologyAnnotation>) - Method in class org.intermine.model.bio.StrainShadow

setOntologyAnnotations(Set<OntologyAnnotation>) - Method in class org.intermine.model.bio.SyntenicRegionShadow

setOntologyAnnotations(Set<OntologyAnnotation>) - Method in class org.intermine.model.bio.TranscriptShadow

setOntologyAnnotations(Set<OntologyAnnotation>) - Method in class org.intermine.model.bio.UTRShadow

setOntologyTerm(OntologyTerm) - Method in interface org.intermine.model.bio.OntologyAnnotation

setOntologyTerm(OntologyTerm) - Method in class org.intermine.model.bio.OntologyAnnotationShadow

setOrganism(Organism) - Method in interface org.intermine.model.bio.BioEntity

setOrganism(Organism) - Method in class org.intermine.model.bio.BioEntityShadow

setOrganism(Organism) - Method in class org.intermine.model.bio.CDSShadow

setOrganism(Organism) - Method in class org.intermine.model.bio.ChromosomeShadow

setOrganism(Organism) - Method in class org.intermine.model.bio.ExonShadow

setOrganism(Organism) - Method in class org.intermine.model.bio.GeneFlankingRegionShadow

setOrganism(Organism) - Method in class org.intermine.model.bio.GeneShadow

setOrganism(Organism) - Method in class org.intermine.model.bio.IntergenicRegionShadow

setOrganism(Organism) - Method in class org.intermine.model.bio.IntronShadow

setOrganism(Organism) - Method in class org.intermine.model.bio.ProteinShadow

setOrganism(Organism) - Method in class org.intermine.model.bio.SequenceCollectionShadow

setOrganism(Organism) - Method in class org.intermine.model.bio.SequenceFeatureShadow

setOrganism(Organism) - Method in class org.intermine.model.bio.StrainShadow

setOrganism(Organism) - Method in class org.intermine.model.bio.SyntenicRegionShadow

setOrganism(Organism) - Method in class org.intermine.model.bio.TranscriptShadow

setOrganism(Organism) - Method in class org.intermine.model.bio.UTRShadow

setOverlappingFeatures(Set<SequenceFeature>) - Method in class org.intermine.model.bio.CDSShadow

setOverlappingFeatures(Set<SequenceFeature>) - Method in class org.intermine.model.bio.ChromosomeShadow

setOverlappingFeatures(Set<SequenceFeature>) - Method in class org.intermine.model.bio.ExonShadow

setOverlappingFeatures(Set<SequenceFeature>) - Method in class org.intermine.model.bio.GeneFlankingRegionShadow

setOverlappingFeatures(Set<SequenceFeature>) - Method in class org.intermine.model.bio.GeneShadow

setOverlappingFeatures(Set<SequenceFeature>) - Method in class org.intermine.model.bio.IntergenicRegionShadow

setOverlappingFeatures(Set<SequenceFeature>) - Method in class org.intermine.model.bio.IntronShadow

setOverlappingFeatures(Set<SequenceFeature>) - Method in interface org.intermine.model.bio.SequenceFeature

setOverlappingFeatures(Set<SequenceFeature>) - Method in class org.intermine.model.bio.SequenceFeatureShadow

setOverlappingFeatures(Set<SequenceFeature>) - Method in class org.intermine.model.bio.SyntenicRegionShadow

setOverlappingFeatures(Set<SequenceFeature>) - Method in class org.intermine.model.bio.TranscriptShadow

setOverlappingFeatures(Set<SequenceFeature>) - Method in class org.intermine.model.bio.UTRShadow

setPages(String) - Method in interface org.intermine.model.bio.Publication

setPages(String) - Method in class org.intermine.model.bio.PublicationShadow

setParents(Set<OntologyTerm>) - Method in interface org.intermine.model.bio.OntologyTerm

setParents(Set<OntologyTerm>) - Method in class org.intermine.model.bio.OntologyTermShadow

setParents(Set<OntologyTerm>) - Method in class org.intermine.model.bio.SOTermShadow

setParentTerm(OntologyTerm) - Method in interface org.intermine.model.bio.OntologyRelation

setParentTerm(OntologyTerm) - Method in class org.intermine.model.bio.OntologyRelationShadow

setPrimaryAccession(String) - Method in interface org.intermine.model.bio.Protein

setPrimaryAccession(String) - Method in class org.intermine.model.bio.ProteinShadow

setPrimaryIdentifier(String) - Method in interface org.intermine.model.bio.Annotatable

setPrimaryIdentifier(String) - Method in class org.intermine.model.bio.AnnotatableShadow

setPrimaryIdentifier(String) - Method in class org.intermine.model.bio.BioEntityShadow

setPrimaryIdentifier(String) - Method in class org.intermine.model.bio.CDSShadow

setPrimaryIdentifier(String) - Method in class org.intermine.model.bio.ChromosomeShadow

setPrimaryIdentifier(String) - Method in class org.intermine.model.bio.ExonShadow

setPrimaryIdentifier(String) - Method in class org.intermine.model.bio.GeneFlankingRegionShadow

setPrimaryIdentifier(String) - Method in class org.intermine.model.bio.GeneShadow

setPrimaryIdentifier(String) - Method in class org.intermine.model.bio.IntergenicRegionShadow

setPrimaryIdentifier(String) - Method in class org.intermine.model.bio.IntronShadow

setPrimaryIdentifier(String) - Method in class org.intermine.model.bio.ProteinShadow

setPrimaryIdentifier(String) - Method in class org.intermine.model.bio.SequenceCollectionShadow

setPrimaryIdentifier(String) - Method in class org.intermine.model.bio.SequenceFeatureShadow

setPrimaryIdentifier(String) - Method in class org.intermine.model.bio.StrainShadow

setPrimaryIdentifier(String) - Method in class org.intermine.model.bio.SyntenicRegionShadow

setPrimaryIdentifier(String) - Method in class org.intermine.model.bio.TranscriptShadow

setPrimaryIdentifier(String) - Method in class org.intermine.model.bio.UTRShadow

setProtein(Protein) - Method in interface org.intermine.model.bio.CDS

setProtein(Protein) - Method in class org.intermine.model.bio.CDSShadow

setProtein(Protein) - Method in interface org.intermine.model.bio.Transcript

setProtein(Protein) - Method in class org.intermine.model.bio.TranscriptShadow

setProteins(Set<Protein>) - Method in interface org.intermine.model.bio.Gene

setProteins(Set<Protein>) - Method in class org.intermine.model.bio.GeneShadow

setPublication(Publication) - Method in interface org.intermine.model.bio.DataSet

setPublication(Publication) - Method in class org.intermine.model.bio.DataSetShadow

setPublications(Set<Publication>) - Method in interface org.intermine.model.bio.Annotatable

setPublications(Set<Publication>) - Method in class org.intermine.model.bio.AnnotatableShadow

setPublications(Set<Publication>) - Method in interface org.intermine.model.bio.Author

setPublications(Set<Publication>) - Method in class org.intermine.model.bio.AuthorShadow

setPublications(Set<Publication>) - Method in class org.intermine.model.bio.BioEntityShadow

setPublications(Set<Publication>) - Method in class org.intermine.model.bio.CDSShadow

setPublications(Set<Publication>) - Method in class org.intermine.model.bio.ChromosomeShadow

setPublications(Set<Publication>) - Method in interface org.intermine.model.bio.DataSource

setPublications(Set<Publication>) - Method in class org.intermine.model.bio.DataSourceShadow

setPublications(Set<Publication>) - Method in class org.intermine.model.bio.ExonShadow

setPublications(Set<Publication>) - Method in class org.intermine.model.bio.GeneFlankingRegionShadow

setPublications(Set<Publication>) - Method in class org.intermine.model.bio.GeneShadow

setPublications(Set<Publication>) - Method in class org.intermine.model.bio.IntergenicRegionShadow

setPublications(Set<Publication>) - Method in class org.intermine.model.bio.IntronShadow

setPublications(Set<Publication>) - Method in interface org.intermine.model.bio.MeshTerm

setPublications(Set<Publication>) - Method in class org.intermine.model.bio.MeshTermShadow

setPublications(Set<Publication>) - Method in interface org.intermine.model.bio.OntologyEvidence

setPublications(Set<Publication>) - Method in class org.intermine.model.bio.OntologyEvidenceShadow

setPublications(Set<Publication>) - Method in interface org.intermine.model.bio.OrthologueEvidence

setPublications(Set<Publication>) - Method in class org.intermine.model.bio.OrthologueEvidenceShadow

setPublications(Set<Publication>) - Method in class org.intermine.model.bio.ProteinShadow

setPublications(Set<Publication>) - Method in class org.intermine.model.bio.SequenceCollectionShadow

setPublications(Set<Publication>) - Method in class org.intermine.model.bio.SequenceFeatureShadow

setPublications(Set<Publication>) - Method in class org.intermine.model.bio.StrainShadow

setPublications(Set<Publication>) - Method in class org.intermine.model.bio.SyntenicRegionShadow

setPublications(Set<Publication>) - Method in interface org.intermine.model.bio.SyntenyBlock

setPublications(Set<Publication>) - Method in class org.intermine.model.bio.SyntenyBlockShadow

setPublications(Set<Publication>) - Method in class org.intermine.model.bio.TranscriptShadow

setPublications(Set<Publication>) - Method in class org.intermine.model.bio.UTRShadow

setPubMedId(String) - Method in interface org.intermine.model.bio.Publication

setPubMedId(String) - Method in class org.intermine.model.bio.PublicationShadow

setQualifier(String) - Method in interface org.intermine.model.bio.OntologyAnnotation

setQualifier(String) - Method in class org.intermine.model.bio.OntologyAnnotationShadow

setRedundant(Boolean) - Method in interface org.intermine.model.bio.OntologyRelation

setRedundant(Boolean) - Method in class org.intermine.model.bio.OntologyRelationShadow

setRelations(Set<OntologyRelation>) - Method in interface org.intermine.model.bio.OntologyTerm

setRelations(Set<OntologyRelation>) - Method in class org.intermine.model.bio.OntologyTermShadow

setRelations(Set<OntologyRelation>) - Method in class org.intermine.model.bio.SOTermShadow

setRelationship(String) - Method in interface org.intermine.model.bio.OntologyRelation

setRelationship(String) - Method in class org.intermine.model.bio.OntologyRelationShadow

setResidues(ClobAccess) - Method in interface org.intermine.model.bio.Sequence

setResidues(ClobAccess) - Method in class org.intermine.model.bio.SequenceShadow

setScore(Double) - Method in class org.intermine.model.bio.CDSShadow

setScore(Double) - Method in class org.intermine.model.bio.ChromosomeShadow

setScore(Double) - Method in class org.intermine.model.bio.ExonShadow

setScore(Double) - Method in class org.intermine.model.bio.GeneFlankingRegionShadow

setScore(Double) - Method in class org.intermine.model.bio.GeneShadow

setScore(Double) - Method in class org.intermine.model.bio.IntergenicRegionShadow

setScore(Double) - Method in class org.intermine.model.bio.IntronShadow

setScore(Double) - Method in interface org.intermine.model.bio.SequenceFeature

setScore(Double) - Method in class org.intermine.model.bio.SequenceFeatureShadow

setScore(Double) - Method in class org.intermine.model.bio.SyntenicRegionShadow

setScore(Double) - Method in class org.intermine.model.bio.TranscriptShadow

setScore(Double) - Method in class org.intermine.model.bio.UTRShadow

setScoreType(String) - Method in class org.intermine.model.bio.CDSShadow

setScoreType(String) - Method in class org.intermine.model.bio.ChromosomeShadow

setScoreType(String) - Method in class org.intermine.model.bio.ExonShadow

setScoreType(String) - Method in class org.intermine.model.bio.GeneFlankingRegionShadow

setScoreType(String) - Method in class org.intermine.model.bio.GeneShadow

setScoreType(String) - Method in class org.intermine.model.bio.IntergenicRegionShadow

setScoreType(String) - Method in class org.intermine.model.bio.IntronShadow

setScoreType(String) - Method in interface org.intermine.model.bio.SequenceFeature

setScoreType(String) - Method in class org.intermine.model.bio.SequenceFeatureShadow

setScoreType(String) - Method in class org.intermine.model.bio.SyntenicRegionShadow

setScoreType(String) - Method in class org.intermine.model.bio.TranscriptShadow

setScoreType(String) - Method in class org.intermine.model.bio.UTRShadow

setSecondaryIdentifier(String) - Method in interface org.intermine.model.bio.BioEntity

setSecondaryIdentifier(String) - Method in class org.intermine.model.bio.BioEntityShadow

setSecondaryIdentifier(String) - Method in class org.intermine.model.bio.CDSShadow

setSecondaryIdentifier(String) - Method in class org.intermine.model.bio.ChromosomeShadow

setSecondaryIdentifier(String) - Method in class org.intermine.model.bio.ExonShadow

setSecondaryIdentifier(String) - Method in class org.intermine.model.bio.GeneFlankingRegionShadow

setSecondaryIdentifier(String) - Method in class org.intermine.model.bio.GeneShadow

setSecondaryIdentifier(String) - Method in class org.intermine.model.bio.IntergenicRegionShadow

setSecondaryIdentifier(String) - Method in class org.intermine.model.bio.IntronShadow

setSecondaryIdentifier(String) - Method in class org.intermine.model.bio.ProteinShadow

setSecondaryIdentifier(String) - Method in class org.intermine.model.bio.SequenceCollectionShadow

setSecondaryIdentifier(String) - Method in class org.intermine.model.bio.SequenceFeatureShadow

setSecondaryIdentifier(String) - Method in class org.intermine.model.bio.StrainShadow

setSecondaryIdentifier(String) - Method in class org.intermine.model.bio.SyntenicRegionShadow

setSecondaryIdentifier(String) - Method in class org.intermine.model.bio.TranscriptShadow

setSecondaryIdentifier(String) - Method in class org.intermine.model.bio.UTRShadow

setSequence(Sequence) - Method in class org.intermine.model.bio.CDSShadow

setSequence(Sequence) - Method in class org.intermine.model.bio.ChromosomeShadow

setSequence(Sequence) - Method in class org.intermine.model.bio.ExonShadow

setSequence(Sequence) - Method in class org.intermine.model.bio.GeneFlankingRegionShadow

setSequence(Sequence) - Method in class org.intermine.model.bio.GeneShadow

setSequence(Sequence) - Method in class org.intermine.model.bio.IntergenicRegionShadow

setSequence(Sequence) - Method in class org.intermine.model.bio.IntronShadow

setSequence(Sequence) - Method in interface org.intermine.model.bio.Protein

setSequence(Sequence) - Method in class org.intermine.model.bio.ProteinShadow

setSequence(Sequence) - Method in interface org.intermine.model.bio.SequenceFeature

setSequence(Sequence) - Method in class org.intermine.model.bio.SequenceFeatureShadow

setSequence(Sequence) - Method in class org.intermine.model.bio.SyntenicRegionShadow

setSequence(Sequence) - Method in class org.intermine.model.bio.TranscriptShadow

setSequence(Sequence) - Method in class org.intermine.model.bio.UTRShadow

setSequenceOntologyTerm(SOTerm) - Method in class org.intermine.model.bio.CDSShadow

setSequenceOntologyTerm(SOTerm) - Method in class org.intermine.model.bio.ChromosomeShadow

setSequenceOntologyTerm(SOTerm) - Method in class org.intermine.model.bio.ExonShadow

setSequenceOntologyTerm(SOTerm) - Method in class org.intermine.model.bio.GeneFlankingRegionShadow

setSequenceOntologyTerm(SOTerm) - Method in class org.intermine.model.bio.GeneShadow

setSequenceOntologyTerm(SOTerm) - Method in class org.intermine.model.bio.IntergenicRegionShadow

setSequenceOntologyTerm(SOTerm) - Method in class org.intermine.model.bio.IntronShadow

setSequenceOntologyTerm(SOTerm) - Method in interface org.intermine.model.bio.SequenceCollection

setSequenceOntologyTerm(SOTerm) - Method in class org.intermine.model.bio.SequenceCollectionShadow

setSequenceOntologyTerm(SOTerm) - Method in interface org.intermine.model.bio.SequenceFeature

setSequenceOntologyTerm(SOTerm) - Method in class org.intermine.model.bio.SequenceFeatureShadow

setSequenceOntologyTerm(SOTerm) - Method in class org.intermine.model.bio.SyntenicRegionShadow

setSequenceOntologyTerm(SOTerm) - Method in class org.intermine.model.bio.TranscriptShadow

setSequenceOntologyTerm(SOTerm) - Method in class org.intermine.model.bio.UTRShadow

setShortName(String) - Method in interface org.intermine.model.bio.Organism

setShortName(String) - Method in class org.intermine.model.bio.OrganismShadow

setSource(DataSource) - Method in interface org.intermine.model.bio.CrossReference

setSource(DataSource) - Method in class org.intermine.model.bio.CrossReferenceShadow

setSpecies(String) - Method in interface org.intermine.model.bio.Organism

setSpecies(String) - Method in class org.intermine.model.bio.OrganismShadow

setStart(Integer) - Method in interface org.intermine.model.bio.Location

setStart(Integer) - Method in class org.intermine.model.bio.LocationShadow

setStrain(Strain) - Method in class org.intermine.model.bio.CDSShadow

setStrain(Strain) - Method in class org.intermine.model.bio.ChromosomeShadow

setStrain(Strain) - Method in class org.intermine.model.bio.ExonShadow

setStrain(Strain) - Method in class org.intermine.model.bio.GeneFlankingRegionShadow

setStrain(Strain) - Method in class org.intermine.model.bio.GeneShadow

setStrain(Strain) - Method in class org.intermine.model.bio.IntergenicRegionShadow

setStrain(Strain) - Method in class org.intermine.model.bio.IntronShadow

setStrain(Strain) - Method in interface org.intermine.model.bio.SequenceFeature

setStrain(Strain) - Method in class org.intermine.model.bio.SequenceFeatureShadow

setStrain(Strain) - Method in class org.intermine.model.bio.SyntenicRegionShadow

setStrain(Strain) - Method in class org.intermine.model.bio.TranscriptShadow

setStrain(Strain) - Method in class org.intermine.model.bio.UTRShadow

setStrains(Set<Strain>) - Method in interface org.intermine.model.bio.Organism

setStrains(Set<Strain>) - Method in class org.intermine.model.bio.OrganismShadow

setStrand(String) - Method in interface org.intermine.model.bio.Location

setStrand(String) - Method in class org.intermine.model.bio.LocationShadow

setSubject(Annotatable) - Method in interface org.intermine.model.bio.OntologyAnnotation

setSubject(Annotatable) - Method in class org.intermine.model.bio.OntologyAnnotationShadow

setSubject(BioEntity) - Method in interface org.intermine.model.bio.CrossReference

setSubject(BioEntity) - Method in class org.intermine.model.bio.CrossReferenceShadow

setSubject(BioEntity) - Method in interface org.intermine.model.bio.Synonym

setSubject(BioEntity) - Method in class org.intermine.model.bio.SynonymShadow

setSymbol(String) - Method in interface org.intermine.model.bio.BioEntity

setSymbol(String) - Method in class org.intermine.model.bio.BioEntityShadow

setSymbol(String) - Method in class org.intermine.model.bio.CDSShadow

setSymbol(String) - Method in class org.intermine.model.bio.ChromosomeShadow

setSymbol(String) - Method in class org.intermine.model.bio.ExonShadow

setSymbol(String) - Method in class org.intermine.model.bio.GeneFlankingRegionShadow

setSymbol(String) - Method in class org.intermine.model.bio.GeneShadow

setSymbol(String) - Method in class org.intermine.model.bio.IntergenicRegionShadow

setSymbol(String) - Method in class org.intermine.model.bio.IntronShadow

setSymbol(String) - Method in class org.intermine.model.bio.ProteinShadow

setSymbol(String) - Method in class org.intermine.model.bio.SequenceCollectionShadow

setSymbol(String) - Method in class org.intermine.model.bio.SequenceFeatureShadow

setSymbol(String) - Method in class org.intermine.model.bio.StrainShadow

setSymbol(String) - Method in class org.intermine.model.bio.SyntenicRegionShadow

setSymbol(String) - Method in class org.intermine.model.bio.TranscriptShadow

setSymbol(String) - Method in class org.intermine.model.bio.UTRShadow

setSynonyms(Set<OntologyTermSynonym>) - Method in interface org.intermine.model.bio.OntologyTerm

setSynonyms(Set<OntologyTermSynonym>) - Method in class org.intermine.model.bio.OntologyTermShadow

setSynonyms(Set<OntologyTermSynonym>) - Method in class org.intermine.model.bio.SOTermShadow

setSynonyms(Set<Synonym>) - Method in interface org.intermine.model.bio.BioEntity

setSynonyms(Set<Synonym>) - Method in class org.intermine.model.bio.BioEntityShadow

setSynonyms(Set<Synonym>) - Method in class org.intermine.model.bio.CDSShadow

setSynonyms(Set<Synonym>) - Method in class org.intermine.model.bio.ChromosomeShadow

setSynonyms(Set<Synonym>) - Method in class org.intermine.model.bio.ExonShadow

setSynonyms(Set<Synonym>) - Method in class org.intermine.model.bio.GeneFlankingRegionShadow

setSynonyms(Set<Synonym>) - Method in class org.intermine.model.bio.GeneShadow

setSynonyms(Set<Synonym>) - Method in class org.intermine.model.bio.IntergenicRegionShadow

setSynonyms(Set<Synonym>) - Method in class org.intermine.model.bio.IntronShadow

setSynonyms(Set<Synonym>) - Method in class org.intermine.model.bio.ProteinShadow

setSynonyms(Set<Synonym>) - Method in class org.intermine.model.bio.SequenceCollectionShadow

setSynonyms(Set<Synonym>) - Method in class org.intermine.model.bio.SequenceFeatureShadow

setSynonyms(Set<Synonym>) - Method in class org.intermine.model.bio.StrainShadow

setSynonyms(Set<Synonym>) - Method in class org.intermine.model.bio.SyntenicRegionShadow

setSynonyms(Set<Synonym>) - Method in class org.intermine.model.bio.TranscriptShadow

setSynonyms(Set<Synonym>) - Method in class org.intermine.model.bio.UTRShadow

setSyntenicRegions(Set<SyntenicRegion>) - Method in interface org.intermine.model.bio.SyntenyBlock

setSyntenicRegions(Set<SyntenicRegion>) - Method in class org.intermine.model.bio.SyntenyBlockShadow

setSyntenyBlock(SyntenyBlock) - Method in interface org.intermine.model.bio.SyntenicRegion

setSyntenyBlock(SyntenyBlock) - Method in class org.intermine.model.bio.SyntenicRegionShadow

setTaxonId(String) - Method in interface org.intermine.model.bio.Organism

setTaxonId(String) - Method in class org.intermine.model.bio.OrganismShadow

setTitle(String) - Method in interface org.intermine.model.bio.Publication

setTitle(String) - Method in class org.intermine.model.bio.PublicationShadow

setTranscripts(Set<Transcript>) - Method in interface org.intermine.model.bio.Protein

setTranscripts(Set<Transcript>) - Method in class org.intermine.model.bio.ProteinShadow

setType(String) - Method in interface org.intermine.model.bio.Comment

setType(String) - Method in class org.intermine.model.bio.CommentShadow

setType(String) - Method in interface org.intermine.model.bio.Homologue

setType(String) - Method in class org.intermine.model.bio.HomologueShadow

setType(String) - Method in interface org.intermine.model.bio.OntologyTermSynonym

setType(String) - Method in class org.intermine.model.bio.OntologyTermSynonymShadow

setUpstreamIntergenicRegion(IntergenicRegion) - Method in interface org.intermine.model.bio.Gene

setUpstreamIntergenicRegion(IntergenicRegion) - Method in class org.intermine.model.bio.GeneShadow

setUrl(String) - Method in interface org.intermine.model.bio.DataSet

setUrl(String) - Method in class org.intermine.model.bio.DataSetShadow

setUrl(String) - Method in interface org.intermine.model.bio.DataSource

setUrl(String) - Method in class org.intermine.model.bio.DataSourceShadow

setUrl(String) - Method in interface org.intermine.model.bio.Ontology

setUrl(String) - Method in interface org.intermine.model.bio.OntologyAnnotationEvidenceCode

setUrl(String) - Method in class org.intermine.model.bio.OntologyAnnotationEvidenceCodeShadow

setUrl(String) - Method in class org.intermine.model.bio.OntologyShadow

setuTRs(Set<UTR>) - Method in interface org.intermine.model.bio.Gene

setuTRs(Set<UTR>) - Method in class org.intermine.model.bio.GeneShadow

setValue(String) - Method in interface org.intermine.model.bio.Synonym

setValue(String) - Method in class org.intermine.model.bio.SynonymShadow

setVersion(String) - Method in interface org.intermine.model.bio.DataSet

setVersion(String) - Method in class org.intermine.model.bio.DataSetShadow

setVolume(String) - Method in interface org.intermine.model.bio.Publication

setVolume(String) - Method in class org.intermine.model.bio.PublicationShadow

setYear(Integer) - Method in interface org.intermine.model.bio.Publication

setYear(Integer) - Method in class org.intermine.model.bio.PublicationShadow

shadowOf - Static variable in class org.intermine.model.bio.AnnotatableShadow

shadowOf - Static variable in class org.intermine.model.bio.AuthorShadow

shadowOf - Static variable in class org.intermine.model.bio.BioEntityShadow

shadowOf - Static variable in class org.intermine.model.bio.CDSShadow

shadowOf - Static variable in class org.intermine.model.bio.ChromosomeShadow

shadowOf - Static variable in class org.intermine.model.bio.CommentShadow

shadowOf - Static variable in class org.intermine.model.bio.CrossReferenceShadow

shadowOf - Static variable in class org.intermine.model.bio.DataSetShadow

shadowOf - Static variable in class org.intermine.model.bio.DataSourceShadow

shadowOf - Static variable in class org.intermine.model.bio.ExonShadow

shadowOf - Static variable in class org.intermine.model.bio.GeneFlankingRegionShadow

shadowOf - Static variable in class org.intermine.model.bio.GeneShadow

shadowOf - Static variable in class org.intermine.model.bio.HomologueShadow

shadowOf - Static variable in class org.intermine.model.bio.IntergenicRegionShadow

shadowOf - Static variable in class org.intermine.model.bio.IntronShadow

shadowOf - Static variable in class org.intermine.model.bio.LocationShadow

shadowOf - Static variable in class org.intermine.model.bio.MeshTermShadow

shadowOf - Static variable in class org.intermine.model.bio.OntologyAnnotationEvidenceCodeShadow

shadowOf - Static variable in class org.intermine.model.bio.OntologyAnnotationShadow

shadowOf - Static variable in class org.intermine.model.bio.OntologyEvidenceShadow

shadowOf - Static variable in class org.intermine.model.bio.OntologyRelationShadow

shadowOf - Static variable in class org.intermine.model.bio.OntologyShadow

shadowOf - Static variable in class org.intermine.model.bio.OntologyTermShadow

shadowOf - Static variable in class org.intermine.model.bio.OntologyTermSynonymShadow

shadowOf - Static variable in class org.intermine.model.bio.OrganismShadow

shadowOf - Static variable in class org.intermine.model.bio.OrthologueEvidenceCodeShadow

shadowOf - Static variable in class org.intermine.model.bio.OrthologueEvidenceShadow

shadowOf - Static variable in class org.intermine.model.bio.ProteinShadow

shadowOf - Static variable in class org.intermine.model.bio.PublicationShadow

shadowOf - Static variable in class org.intermine.model.bio.SequenceCollectionShadow

shadowOf - Static variable in class org.intermine.model.bio.SequenceFeatureShadow

shadowOf - Static variable in class org.intermine.model.bio.SequenceShadow

shadowOf - Static variable in class org.intermine.model.bio.SequenceVariantShadow

shadowOf - Static variable in class org.intermine.model.bio.SOTermShadow

shadowOf - Static variable in class org.intermine.model.bio.StrainShadow

shadowOf - Static variable in class org.intermine.model.bio.SynonymShadow

shadowOf - Static variable in class org.intermine.model.bio.SyntenicRegionShadow

shadowOf - Static variable in class org.intermine.model.bio.SyntenyBlockShadow

shadowOf - Static variable in class org.intermine.model.bio.TranscriptShadow

shadowOf - Static variable in class org.intermine.model.bio.UTRShadow

shortName - Variable in class org.intermine.model.bio.OrganismShadow

SOTerm - Interface in org.intermine.model.bio

SOTermShadow - Class in org.intermine.model.bio

SOTermShadow() - Constructor for class org.intermine.model.bio.SOTermShadow

source - Variable in class org.intermine.model.bio.CrossReferenceShadow

species - Variable in class org.intermine.model.bio.OrganismShadow

start - Variable in class org.intermine.model.bio.LocationShadow

strain - Variable in class org.intermine.model.bio.CDSShadow

strain - Variable in class org.intermine.model.bio.ChromosomeShadow

strain - Variable in class org.intermine.model.bio.ExonShadow

strain - Variable in class org.intermine.model.bio.GeneFlankingRegionShadow

strain - Variable in class org.intermine.model.bio.GeneShadow

strain - Variable in class org.intermine.model.bio.IntergenicRegionShadow

strain - Variable in class org.intermine.model.bio.IntronShadow

strain - Variable in class org.intermine.model.bio.SequenceFeatureShadow

strain - Variable in class org.intermine.model.bio.SyntenicRegionShadow

strain - Variable in class org.intermine.model.bio.TranscriptShadow

strain - Variable in class org.intermine.model.bio.UTRShadow

Strain - Interface in org.intermine.model.bio

strains - Variable in class org.intermine.model.bio.OrganismShadow

StrainShadow - Class in org.intermine.model.bio

StrainShadow() - Constructor for class org.intermine.model.bio.StrainShadow

strand - Variable in class org.intermine.model.bio.LocationShadow

subject - Variable in class org.intermine.model.bio.CrossReferenceShadow

subject - Variable in class org.intermine.model.bio.OntologyAnnotationShadow

subject - Variable in class org.intermine.model.bio.SynonymShadow

symbol - Variable in class org.intermine.model.bio.BioEntityShadow

symbol - Variable in class org.intermine.model.bio.CDSShadow

symbol - Variable in class org.intermine.model.bio.ChromosomeShadow

symbol - Variable in class org.intermine.model.bio.ExonShadow

symbol - Variable in class org.intermine.model.bio.GeneFlankingRegionShadow

symbol - Variable in class org.intermine.model.bio.GeneShadow

symbol - Variable in class org.intermine.model.bio.IntergenicRegionShadow

symbol - Variable in class org.intermine.model.bio.IntronShadow

symbol - Variable in class org.intermine.model.bio.ProteinShadow

symbol - Variable in class org.intermine.model.bio.SequenceCollectionShadow

symbol - Variable in class org.intermine.model.bio.SequenceFeatureShadow

symbol - Variable in class org.intermine.model.bio.StrainShadow

symbol - Variable in class org.intermine.model.bio.SyntenicRegionShadow

symbol - Variable in class org.intermine.model.bio.TranscriptShadow

symbol - Variable in class org.intermine.model.bio.UTRShadow

Synonym - Interface in org.intermine.model.bio

synonyms - Variable in class org.intermine.model.bio.BioEntityShadow

synonyms - Variable in class org.intermine.model.bio.CDSShadow

synonyms - Variable in class org.intermine.model.bio.ChromosomeShadow

synonyms - Variable in class org.intermine.model.bio.ExonShadow

synonyms - Variable in class org.intermine.model.bio.GeneFlankingRegionShadow

synonyms - Variable in class org.intermine.model.bio.GeneShadow

synonyms - Variable in class org.intermine.model.bio.IntergenicRegionShadow

synonyms - Variable in class org.intermine.model.bio.IntronShadow

synonyms - Variable in class org.intermine.model.bio.OntologyTermShadow

synonyms - Variable in class org.intermine.model.bio.ProteinShadow

synonyms - Variable in class org.intermine.model.bio.SequenceCollectionShadow

synonyms - Variable in class org.intermine.model.bio.SequenceFeatureShadow

synonyms - Variable in class org.intermine.model.bio.SOTermShadow

synonyms - Variable in class org.intermine.model.bio.StrainShadow

synonyms - Variable in class org.intermine.model.bio.SyntenicRegionShadow

synonyms - Variable in class org.intermine.model.bio.TranscriptShadow

synonyms - Variable in class org.intermine.model.bio.UTRShadow

SynonymShadow - Class in org.intermine.model.bio

SynonymShadow() - Constructor for class org.intermine.model.bio.SynonymShadow

SyntenicRegion - Interface in org.intermine.model.bio

syntenicRegions - Variable in class org.intermine.model.bio.SyntenyBlockShadow

SyntenicRegionShadow - Class in org.intermine.model.bio

SyntenicRegionShadow() - Constructor for class org.intermine.model.bio.SyntenicRegionShadow

syntenyBlock - Variable in class org.intermine.model.bio.SyntenicRegionShadow

SyntenyBlock - Interface in org.intermine.model.bio

SyntenyBlockShadow - Class in org.intermine.model.bio

SyntenyBlockShadow() - Constructor for class org.intermine.model.bio.SyntenyBlockShadow

T

taxonId - Variable in class org.intermine.bio.dataconversion.HomologeneConverter.GeneRecord

taxonId - Variable in class org.intermine.model.bio.OrganismShadow

title - Variable in class org.intermine.model.bio.PublicationShadow

toString() - Method in class org.intermine.model.bio.AnnotatableShadow

toString() - Method in class org.intermine.model.bio.AuthorShadow

toString() - Method in class org.intermine.model.bio.BioEntityShadow

toString() - Method in class org.intermine.model.bio.CDSShadow

toString() - Method in class org.intermine.model.bio.ChromosomeShadow

toString() - Method in class org.intermine.model.bio.CommentShadow

toString() - Method in class org.intermine.model.bio.CrossReferenceShadow

toString() - Method in class org.intermine.model.bio.DataSetShadow

toString() - Method in class org.intermine.model.bio.DataSourceShadow

toString() - Method in class org.intermine.model.bio.ExonShadow

toString() - Method in class org.intermine.model.bio.GeneFlankingRegionShadow

toString() - Method in class org.intermine.model.bio.GeneShadow

toString() - Method in class org.intermine.model.bio.HomologueShadow

toString() - Method in class org.intermine.model.bio.IntergenicRegionShadow

toString() - Method in class org.intermine.model.bio.IntronShadow

toString() - Method in class org.intermine.model.bio.LocationShadow

toString() - Method in class org.intermine.model.bio.MeshTermShadow

toString() - Method in class org.intermine.model.bio.OntologyAnnotationEvidenceCodeShadow

toString() - Method in class org.intermine.model.bio.OntologyAnnotationShadow

toString() - Method in class org.intermine.model.bio.OntologyEvidenceShadow

toString() - Method in class org.intermine.model.bio.OntologyRelationShadow

toString() - Method in class org.intermine.model.bio.OntologyShadow

toString() - Method in class org.intermine.model.bio.OntologyTermShadow

toString() - Method in class org.intermine.model.bio.OntologyTermSynonymShadow

toString() - Method in class org.intermine.model.bio.OrganismShadow

toString() - Method in class org.intermine.model.bio.OrthologueEvidenceCodeShadow

toString() - Method in class org.intermine.model.bio.OrthologueEvidenceShadow

toString() - Method in class org.intermine.model.bio.ProteinShadow

toString() - Method in class org.intermine.model.bio.PublicationShadow

toString() - Method in class org.intermine.model.bio.SequenceCollectionShadow

toString() - Method in class org.intermine.model.bio.SequenceFeatureShadow

toString() - Method in class org.intermine.model.bio.SequenceShadow

toString() - Method in class org.intermine.model.bio.SequenceVariantShadow

toString() - Method in class org.intermine.model.bio.SOTermShadow

toString() - Method in class org.intermine.model.bio.StrainShadow

toString() - Method in class org.intermine.model.bio.SynonymShadow

toString() - Method in class org.intermine.model.bio.SyntenicRegionShadow

toString() - Method in class org.intermine.model.bio.SyntenyBlockShadow

toString() - Method in class org.intermine.model.bio.TranscriptShadow

toString() - Method in class org.intermine.model.bio.UTRShadow

Transcript - Interface in org.intermine.model.bio

transcripts - Variable in class org.intermine.model.bio.ProteinShadow

TranscriptShadow - Class in org.intermine.model.bio

TranscriptShadow() - Constructor for class org.intermine.model.bio.TranscriptShadow

type - Variable in class org.intermine.model.bio.CommentShadow

type - Variable in class org.intermine.model.bio.HomologueShadow

type - Variable in class org.intermine.model.bio.OntologyTermSynonymShadow

U

upstreamIntergenicRegion - Variable in class org.intermine.model.bio.GeneShadow

url - Variable in class org.intermine.model.bio.DataSetShadow

url - Variable in class org.intermine.model.bio.DataSourceShadow

url - Variable in class org.intermine.model.bio.OntologyAnnotationEvidenceCodeShadow

url - Variable in class org.intermine.model.bio.OntologyShadow

UTR - Interface in org.intermine.model.bio

UTRs - Variable in class org.intermine.model.bio.GeneShadow

UTRShadow - Class in org.intermine.model.bio

UTRShadow() - Constructor for class org.intermine.model.bio.UTRShadow

V

value - Variable in class org.intermine.model.bio.SynonymShadow

version - Variable in class org.intermine.model.bio.DataSetShadow

volume - Variable in class org.intermine.model.bio.PublicationShadow

Y

year - Variable in class org.intermine.model.bio.PublicationShadow

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