Ensembl Model v1.09
© Roslin Institute 2010. GNU General Public License, version3
Ensembl Model
v1.09
A B C D E F G H I K L M N O P Q R S T U V W X Z

A

addDatabase(Database) - Method in interface uk.ac.roslin.ensembl.model.core.Species
 
addDatabases(TreeSet<? extends CollectionDatabase>) - Method in interface uk.ac.roslin.ensembl.model.core.CollectionOfSpecies
 
addDatabases(TreeSet<? extends Database>) - Method in interface uk.ac.roslin.ensembl.model.core.Species
 
addFeatureCS(String, Integer, Integer, Species) - Method in interface uk.ac.roslin.ensembl.model.database.CollectionCoreDatabase
 
addFeatureCS(String, Integer, Integer) - Method in interface uk.ac.roslin.ensembl.model.database.SingleSpeciesCoreDatabase
 
addMappedObjectType(ObjectType) - Method in interface uk.ac.roslin.ensembl.model.core.Feature
 
addMapping(Mapping) - Method in interface uk.ac.roslin.ensembl.model.MappableObject
 
addReverseMapping(Mapping) - Static method in class uk.ac.roslin.ensembl.model.Mapping
 
addSessionAlias(String, String) - Method in interface uk.ac.roslin.ensembl.model.database.Registry
 
addSpecies(Collection<? extends CollectionSpecies>) - Method in interface uk.ac.roslin.ensembl.model.core.CollectionOfSpecies
 
addSpecies(CollectionSpecies) - Method in interface uk.ac.roslin.ensembl.model.core.CollectionOfSpecies
 
addSpecies(String, Species) - Method in interface uk.ac.roslin.ensembl.model.database.Registry
 
analysis - Static variable in class uk.ac.roslin.ensembl.config.EnsemblCoreObjectType
 
Analysis - Interface in uk.ac.roslin.ensembl.model.core
 
ancestral - Static variable in class uk.ac.roslin.ensembl.config.EnsemblDBType
A concrete instantiation of an DatabaseType object representing the ensembl ancestral database sType
APPARENT_ORTHOLOG_ONE2ONE - Static variable in class uk.ac.roslin.ensembl.model.compara.HomologyType
two homologous objects derived by speciation Ensembl pipeline annotates as apparent_ortholog_one2one see http://Nov2010.archive.ensembl.org/info/docs/compara/homology_method.html
AssembledDNASequence - Interface in uk.ac.roslin.ensembl.model.core
 
assembledSequence - Static variable in class uk.ac.roslin.ensembl.config.EnsemblCoreObjectType
 
assembly - Static variable in class uk.ac.roslin.ensembl.config.EnsemblCoreObjectType
 
Assembly - Interface in uk.ac.roslin.ensembl.model.core
 
assembly_exception - Static variable in class uk.ac.roslin.ensembl.config.FeatureType
 

B

BACTERIA - Static variable in class uk.ac.roslin.ensembl.config.EnsemblComparaDivision
 
BETWEEN_SPECIES_PARALOG - Static variable in class uk.ac.roslin.ensembl.model.compara.HomologyType
two homologous objects derived by duplication Ensembl pipeline annotates as between_species_paralog see http://Nov2010.archive.ensembl.org/info/docs/compara/homology_method.html
BinaryRelationship<CLAZZ extends IdentifiableObject> - Interface in uk.ac.roslin.ensembl.model.relationship
 

C

cdna - Static variable in class uk.ac.roslin.ensembl.config.EnsemblDBType
A concrete instantiation of an DatabaseType object representing the ensembl species cDNA database sType
chromosome - Static variable in class uk.ac.roslin.ensembl.config.EnsemblCoordSystemType
 
chromosome - Static variable in class uk.ac.roslin.ensembl.config.EnsemblCoreObjectType
 
Chromosome - Interface in uk.ac.roslin.ensembl.model.core
 
clearAllMappings() - Method in interface uk.ac.roslin.ensembl.model.MappableObject
 
clone - Static variable in class uk.ac.roslin.ensembl.config.EnsemblCoordSystemType
 
collection_core - Static variable in class uk.ac.roslin.ensembl.config.EnsemblDBType
A concrete instantiation of an DatabaseType object representing the ensemblgenomes collection core database sType
collection_funcgen - Static variable in class uk.ac.roslin.ensembl.config.EnsemblDBType
A concrete instantiation of an DatabaseType object representing the ensemblgenomes collection funcgen database sType
collection_variation - Static variable in class uk.ac.roslin.ensembl.config.EnsemblDBType
A concrete instantiation of an DatabaseType object representing the ensemblgenomes collection variation database sType
CollectionCoreDatabase - Interface in uk.ac.roslin.ensembl.model.database
 
CollectionDatabase - Interface in uk.ac.roslin.ensembl.model.database
 
CollectionOfSpecies - Interface in uk.ac.roslin.ensembl.model.core
 
CollectionSpecies - Interface in uk.ac.roslin.ensembl.model.core
 
compara - Static variable in class uk.ac.roslin.ensembl.config.EnsemblDBType
A concrete instantiation of an DatabaseType object representing the ensembl compara database sType
compareTo(EnsemblComparaDivision) - Method in class uk.ac.roslin.ensembl.config.EnsemblComparaDivision
 
compareTo(EnsemblDBType) - Method in class uk.ac.roslin.ensembl.config.EnsemblDBType
 
compareTo(Coordinate) - Method in class uk.ac.roslin.ensembl.model.Coordinate
 
ComparisonDatabase - Interface in uk.ac.roslin.ensembl.model.database
 
ConfigurationException - Exception in uk.ac.roslin.ensembl.exception
 
ConfigurationException() - Constructor for exception uk.ac.roslin.ensembl.exception.ConfigurationException
 
ConfigurationException(String) - Constructor for exception uk.ac.roslin.ensembl.exception.ConfigurationException
 
ConfigurationException(String, Exception) - Constructor for exception uk.ac.roslin.ensembl.exception.ConfigurationException
 
ConfigurationException(Exception) - Constructor for exception uk.ac.roslin.ensembl.exception.ConfigurationException
 
containsCoordinateWithoutGaps(Coordinate) - Method in class uk.ac.roslin.ensembl.model.CoordinateSet
 
contig - Static variable in class uk.ac.roslin.ensembl.config.EnsemblCoordSystemType
 
CONTIGUOUS_GENE_SPLIT - Static variable in class uk.ac.roslin.ensembl.model.compara.HomologyType
two homologous objects derived by duplication Ensembl pipeline annotates as contiguous_gene_split see http://Nov2010.archive.ensembl.org/info/docs/compara/homology_method.html
Coordinate - Class in uk.ac.roslin.ensembl.model
 
Coordinate() - Constructor for class uk.ac.roslin.ensembl.model.Coordinate
 
Coordinate(Integer, Integer) - Constructor for class uk.ac.roslin.ensembl.model.Coordinate
 
Coordinate(Integer, Integer, Integer) - Constructor for class uk.ac.roslin.ensembl.model.Coordinate
 
Coordinate(Integer, Integer, Coordinate.Strand) - Constructor for class uk.ac.roslin.ensembl.model.Coordinate
 
Coordinate.Strand - Enum in uk.ac.roslin.ensembl.model
 
CoordinateSet - Class in uk.ac.roslin.ensembl.model
 
CoordinateSet() - Constructor for class uk.ac.roslin.ensembl.model.CoordinateSet
 
CoordinateSystem - Interface in uk.ac.roslin.ensembl.model.core
 
CoordSystemType - Interface in uk.ac.roslin.ensembl.model.core
 
core - Static variable in class uk.ac.roslin.ensembl.config.EnsemblDBType
A concrete instantiation of an DatabaseType object representing the ensembl species core database sType
CoreDatabase - Interface in uk.ac.roslin.ensembl.model.database
 
coreexpressionest - Static variable in class uk.ac.roslin.ensembl.config.EnsemblDBType
A concrete instantiation of an DatabaseType object representing the ensembl species coreexpressioncdna database sType
coreexpressiongnf - Static variable in class uk.ac.roslin.ensembl.config.EnsemblDBType
A concrete instantiation of an DatabaseType object representing the ensembl species coreexpressiongnf database sType
CoreObject - Interface in uk.ac.roslin.ensembl.model.core
 
CoreObjectType - Interface in uk.ac.roslin.ensembl.model.core
 

D

DAOException - Exception in uk.ac.roslin.ensembl.exception
 
DAOException() - Constructor for exception uk.ac.roslin.ensembl.exception.DAOException
 
DAOException(String) - Constructor for exception uk.ac.roslin.ensembl.exception.DAOException
 
DAOException(String, Exception) - Constructor for exception uk.ac.roslin.ensembl.exception.DAOException
 
DAOException(Exception) - Constructor for exception uk.ac.roslin.ensembl.exception.DAOException
 
Database - Interface in uk.ac.roslin.ensembl.model.database
 
DatabaseType - Interface in uk.ac.roslin.ensembl.model.database
Interface for representing static DatabaseTypes
DBConnection - Class in uk.ac.roslin.ensembl.config
 
DBConnection(DBConnection.DataSource) - Constructor for class uk.ac.roslin.ensembl.config.DBConnection
 
DBConnection(DBConnection.DataSource, Properties) - Constructor for class uk.ac.roslin.ensembl.config.DBConnection
 
DBConnection.DataSource - Enum in uk.ac.roslin.ensembl.config
 
defaultVersion - Static variable in class uk.ac.roslin.ensembl.config.EnsemblCoordSystemType
 
density_feature - Static variable in class uk.ac.roslin.ensembl.config.FeatureType
 
ditag_feature - Static variable in class uk.ac.roslin.ensembl.config.FeatureType
 
dna_align_feature - Static variable in class uk.ac.roslin.ensembl.config.FeatureType
 
dna_peptide_align_feature - Static variable in class uk.ac.roslin.ensembl.config.FeatureType
 
DNASequence - Static variable in class uk.ac.roslin.ensembl.config.EnsemblCoreObjectType
 
DNASequence - Interface in uk.ac.roslin.ensembl.model.core
 

E

EnsemblComparaDivision - Class in uk.ac.roslin.ensembl.config
In 'ensembl.org' there is a single 'ensembl_compara' database which contains the pairwise comparison data on all the species in 'ensembl.org.
EnsemblCoordSystemType - Class in uk.ac.roslin.ensembl.config
 
EnsemblCoreObjectType - Class in uk.ac.roslin.ensembl.config
 
EnsemblCoreObjectType() - Constructor for class uk.ac.roslin.ensembl.config.EnsemblCoreObjectType
 
EnsemblDBType - Class in uk.ac.roslin.ensembl.config
Concrete implementation of DatabaseType interface for representing static Ensembl DatabaseTypes.
EnsemblDNACompoundSet - Class in uk.ac.roslin.ensembl.biojava3
 
EnsemblDNACompoundSet() - Constructor for class uk.ac.roslin.ensembl.biojava3.EnsemblDNACompoundSet
 
EnsemblDNASequenceReader - Interface in uk.ac.roslin.ensembl.biojava3
 
EnsemblException - Exception in uk.ac.roslin.ensembl.exception
 
EnsemblException() - Constructor for exception uk.ac.roslin.ensembl.exception.EnsemblException
 
EnsemblException(String) - Constructor for exception uk.ac.roslin.ensembl.exception.EnsemblException
 
EnsemblException(String, Exception) - Constructor for exception uk.ac.roslin.ensembl.exception.EnsemblException
 
EnsemblException(Exception) - Constructor for exception uk.ac.roslin.ensembl.exception.EnsemblException
 
EnsemblType - Class in uk.ac.roslin.ensembl.config
 
EnsemblType() - Constructor for class uk.ac.roslin.ensembl.config.EnsemblType
 
equals(Object) - Method in class uk.ac.roslin.ensembl.config.EnsemblDBType
Overrides the Object method to test for equality
equals(Object) - Method in class uk.ac.roslin.ensembl.model.Mapping
 
equals(Object) - Method in class uk.ac.roslin.ensembl.model.relationship.RelationshipType
Overrides the Object method to test for equality
exon - Static variable in class uk.ac.roslin.ensembl.config.FeatureType
 
Exon - Interface in uk.ac.roslin.ensembl.model.core
 
Exon.Phase - Class in uk.ac.roslin.ensembl.model.core
 
Exon.Phase() - Constructor for class uk.ac.roslin.ensembl.model.core.Exon.Phase
 
externalDB - Static variable in class uk.ac.roslin.ensembl.config.EnsemblCoreObjectType
 
ExternalDB - Interface in uk.ac.roslin.ensembl.model
 

F

Feature - Interface in uk.ac.roslin.ensembl.model.core
 
FeatureType - Class in uk.ac.roslin.ensembl.config
 
findMybatisSchemaForSchemaVersion(DatabaseType, String) - Method in interface uk.ac.roslin.ensembl.model.database.Registry
 
funcgen - Static variable in class uk.ac.roslin.ensembl.config.EnsemblDBType
A concrete instantiation of an DatabaseType object representing the ensembl species funcgen database sType
FUNGI - Static variable in class uk.ac.roslin.ensembl.config.EnsemblComparaDivision
 

G

gene - Static variable in class uk.ac.roslin.ensembl.config.FeatureType
 
Gene - Interface in uk.ac.roslin.ensembl.model.core
 
getAliases() - Method in interface uk.ac.roslin.ensembl.model.core.Species
 
getAllDatabaseTypes() - Static method in class uk.ac.roslin.ensembl.config.EnsemblDBType
 
getAllTypes() - Static method in class uk.ac.roslin.ensembl.config.EnsemblComparaDivision
 
getAllTypes() - Static method in class uk.ac.roslin.ensembl.config.FeatureType
 
getAllTypes() - Static method in class uk.ac.roslin.ensembl.model.compara.HomologyType
 
getAllTypes() - Static method in class uk.ac.roslin.ensembl.model.relationship.RelationshipType
 
getAnalysis() - Method in interface uk.ac.roslin.ensembl.model.core.Gene
 
getAnalysisID() - Method in interface uk.ac.roslin.ensembl.model.core.ProteinFeature
 
getAssemblies(CollectionDatabase) - Method in interface uk.ac.roslin.ensembl.model.database.Registry
 
getAssembly() - Method in interface uk.ac.roslin.ensembl.model.core.CoreObject
 
getAssembly() - Method in interface uk.ac.roslin.ensembl.model.core.Species
 
getAssembly(String) - Method in interface uk.ac.roslin.ensembl.model.core.Species
 
getAssembly(CollectionSpecies) - Method in interface uk.ac.roslin.ensembl.model.database.CollectionDatabase
 
getAssembly(SingleSpeciesDatabase) - Method in interface uk.ac.roslin.ensembl.model.database.Registry
 
getAssembly() - Method in interface uk.ac.roslin.ensembl.model.database.SingleSpeciesDatabase
 
getAssemblyStart() - Method in interface uk.ac.roslin.ensembl.model.core.Assembly
 
getAssemblyStop() - Method in interface uk.ac.roslin.ensembl.model.core.Assembly
 
getBaseMybatis() - Method in class uk.ac.roslin.ensembl.config.SchemaVersion
 
getBinaryRelationship() - Method in interface uk.ac.roslin.ensembl.model.relationship.InverseBinaryRelationshipView
Returns the underlying binary relationship that this is a view on
getBiotype() - Method in interface uk.ac.roslin.ensembl.model.core.Gene
 
getBuild() - Method in interface uk.ac.roslin.ensembl.model.database.Database
 
getBuildCoordSystem(Species, String) - Method in interface uk.ac.roslin.ensembl.model.database.CollectionCoreDatabase
 
getBuildCoordSystem(String) - Method in interface uk.ac.roslin.ensembl.model.database.SingleSpeciesCoreDatabase
 
getBuildLevel(Species, String) - Method in interface uk.ac.roslin.ensembl.model.database.CollectionCoreDatabase
 
getBuildLevel(String) - Method in interface uk.ac.roslin.ensembl.model.database.SingleSpeciesCoreDatabase
 
getCanonicalTranscript() - Method in interface uk.ac.roslin.ensembl.model.core.Gene
 
getCanonicalTranslation() - Method in interface uk.ac.roslin.ensembl.model.core.Gene
 
getChromosomeByName(String) - Method in interface uk.ac.roslin.ensembl.model.core.Species
 
getChromosomeByName(String, String) - Method in interface uk.ac.roslin.ensembl.model.core.Species
 
getChromosomeByName(Species, String) - Method in interface uk.ac.roslin.ensembl.model.database.CollectionCoreDatabase
 
getChromosomeByName(String) - Method in interface uk.ac.roslin.ensembl.model.database.SingleSpeciesCoreDatabase
 
getChromosomeLevelCoordSystem() - Method in interface uk.ac.roslin.ensembl.model.database.SingleSpeciesCoreDatabase
 
getChromosomeLevelCS(Species) - Method in interface uk.ac.roslin.ensembl.model.database.CollectionCoreDatabase
 
getChromosomeMapping(Chromosome) - Method in interface uk.ac.roslin.ensembl.model.core.Feature
 
getChromosomeName() - Method in interface uk.ac.roslin.ensembl.model.core.Chromosome
 
getChromosomes() - Method in interface uk.ac.roslin.ensembl.model.core.Species
 
getChromosomes(String) - Method in interface uk.ac.roslin.ensembl.model.core.Species
 
getChromosomes(Species) - Method in interface uk.ac.roslin.ensembl.model.database.CollectionCoreDatabase
 
getChromosomes() - Method in interface uk.ac.roslin.ensembl.model.database.SingleSpeciesCoreDatabase
 
getCigarEnd() - Method in class uk.ac.roslin.ensembl.model.compara.HomologyAlignmentProperties
 
getCigarLine() - Method in class uk.ac.roslin.ensembl.model.compara.HomologyAlignmentProperties
 
getCigarStart() - Method in class uk.ac.roslin.ensembl.model.compara.HomologyAlignmentProperties
 
getCollection() - Method in interface uk.ac.roslin.ensembl.model.database.CollectionDatabase
 
getCollection(String, String) - Method in interface uk.ac.roslin.ensembl.model.database.Registry
 
getCollectionDatabaseTypes() - Static method in class uk.ac.roslin.ensembl.config.EnsemblDBType
 
getCollectionName() - Method in interface uk.ac.roslin.ensembl.model.core.CollectionOfSpecies
 
getCollectionName() - Method in interface uk.ac.roslin.ensembl.model.database.CollectionDatabase
 
getCollectionRegistriesByName(String) - Method in interface uk.ac.roslin.ensembl.model.database.Registry
 
getCollections() - Method in interface uk.ac.roslin.ensembl.model.database.Registry
 
getCollectionsByDBVersion(String) - Method in interface uk.ac.roslin.ensembl.model.database.Registry
 
getCollectionSpecies() - Method in interface uk.ac.roslin.ensembl.model.database.Registry
 
getCommonName() - Method in interface uk.ac.roslin.ensembl.model.core.Species
 
getComparaDatabase(EnsemblComparaDivision, String) - Method in interface uk.ac.roslin.ensembl.model.database.Registry
 
getComparaDivision() - Method in interface uk.ac.roslin.ensembl.model.core.Species
 
getComparaName() - Method in interface uk.ac.roslin.ensembl.model.core.Species
 
getComparisonDivision() - Method in interface uk.ac.roslin.ensembl.model.database.ComparisonDatabase
 
getCompleteAssembly() - Method in interface uk.ac.roslin.ensembl.model.core.AssembledDNASequence
 
getConfigProperties() - Method in interface uk.ac.roslin.ensembl.model.database.Registry
 
getConfigurationProperties() - Method in class uk.ac.roslin.ensembl.config.DBConnection
 
getConfigurationProperties() - Method in class uk.ac.roslin.ensembl.config.SchemaVersion
 
getCoords() - Method in class uk.ac.roslin.ensembl.model.compara.HomologyAlignmentProperties
 
getCoordSystem() - Method in interface uk.ac.roslin.ensembl.model.core.DNASequence
 
getCoordSystemID() - Method in interface uk.ac.roslin.ensembl.biojava3.EnsemblDNASequenceReader
 
getCoreDatabase() - Method in interface uk.ac.roslin.ensembl.model.core.CollectionOfSpecies
 
getCoreFactory(Species) - Method in interface uk.ac.roslin.ensembl.model.database.CollectionCoreDatabase
 
getCoreFactory() - Method in interface uk.ac.roslin.ensembl.model.database.SingleSpeciesCoreDatabase
 
getCSByID(Species, Integer) - Method in interface uk.ac.roslin.ensembl.model.database.CollectionCoreDatabase
 
getCSByID(Integer) - Method in interface uk.ac.roslin.ensembl.model.database.SingleSpeciesCoreDatabase
 
getCSForFeature(Species, ObjectType) - Method in interface uk.ac.roslin.ensembl.model.database.CollectionCoreDatabase
 
getCSForFeature(ObjectType) - Method in interface uk.ac.roslin.ensembl.model.database.SingleSpeciesCoreDatabase
 
getCurrentCoreDatabase() - Method in interface uk.ac.roslin.ensembl.model.core.Species
 
getCurrentEnsemblVersion() - Method in class uk.ac.roslin.ensembl.config.SchemaVersion
 
getCurrentGenomesVersion() - Method in class uk.ac.roslin.ensembl.config.SchemaVersion
 
getDatabase(String) - Method in interface uk.ac.roslin.ensembl.model.database.Registry
 
getDatabase(String, String) - Method in interface uk.ac.roslin.ensembl.model.database.Registry
 
getDatabase(String, DatabaseType, String) - Method in interface uk.ac.roslin.ensembl.model.database.Registry
 
getDatabaseByTypeAndVersion(DatabaseType, String) - Method in interface uk.ac.roslin.ensembl.model.core.Species
 
getDatabaseForFullName(String) - Method in interface uk.ac.roslin.ensembl.model.database.Registry
 
getDatabases() - Method in interface uk.ac.roslin.ensembl.model.core.CollectionOfSpecies
 
getDatabases() - Method in interface uk.ac.roslin.ensembl.model.core.Species
 
getDatabasesByType(DatabaseType) - Method in interface uk.ac.roslin.ensembl.model.core.CollectionOfSpecies
 
getDatabasesByType(DatabaseType) - Method in interface uk.ac.roslin.ensembl.model.core.Species
 
getDatabasesByType(DatabaseType) - Method in interface uk.ac.roslin.ensembl.model.database.Registry
 
getDatabasesByVersion(String) - Method in interface uk.ac.roslin.ensembl.model.core.Species
 
getDatabaseStyleName() - Method in interface uk.ac.roslin.ensembl.model.core.Species
 
getDatasourceStyle() - Method in class uk.ac.roslin.ensembl.config.DBConnection
 
getDatasourceType() - Method in interface uk.ac.roslin.ensembl.model.database.Registry
 
getDb() - Method in class uk.ac.roslin.ensembl.config.RegistryConfiguration
Returns the DBCOnnection object set on this RegistryConfigurationobject, or throws an ConfigurationException if there is no DBConnection set.
getDB() - Method in interface uk.ac.roslin.ensembl.model.XRef
 
getDBDisplayName() - Method in interface uk.ac.roslin.ensembl.model.ExternalDB
 
getDBName(String) - Static method in class uk.ac.roslin.ensembl.config.EnsemblComparaDivision
 
getdBName() - Method in interface uk.ac.roslin.ensembl.model.database.Database
 
getDBName() - Method in interface uk.ac.roslin.ensembl.model.ExternalDB
 
getDBRelease() - Method in interface uk.ac.roslin.ensembl.model.ExternalDB
 
getDBSeqLength() - Method in interface uk.ac.roslin.ensembl.model.core.DNASequence
 
getDBSpeciesID(String) - Method in interface uk.ac.roslin.ensembl.model.core.Species
 
getDbSpeciesName() - Method in interface uk.ac.roslin.ensembl.model.database.SingleSpeciesDatabase
 
getDBStatus() - Method in interface uk.ac.roslin.ensembl.model.ExternalDB
 
getDBType() - Method in interface uk.ac.roslin.ensembl.model.ExternalDB
 
getDBTypeForName(String) - Static method in class uk.ac.roslin.ensembl.config.EnsemblDBType
Public Method to return the static EnsemblDBType for a typeName.
getDBVersion() - Method in interface uk.ac.roslin.ensembl.model.core.CollectionOfSpecies
 
getDBVersion() - Method in interface uk.ac.roslin.ensembl.model.database.Database
 
getDBVersion() - Method in interface uk.ac.roslin.ensembl.model.IdentifiableObject
 
getDBVersions() - Method in interface uk.ac.roslin.ensembl.model.core.Species
 
getDescription() - Method in interface uk.ac.roslin.ensembl.model.core.Gene
 
getDescription() - Method in interface uk.ac.roslin.ensembl.model.XRef
 
getDisplayID() - Method in interface uk.ac.roslin.ensembl.model.XRef
 
getDNACompoundSet() - Static method in class uk.ac.roslin.ensembl.biojava3.EnsemblDNACompoundSet
 
getEnd() - Method in class uk.ac.roslin.ensembl.model.Coordinate
 
getEnd() - Method in class uk.ac.roslin.ensembl.model.CoordinateSet
 
getEnsemblComparaDivision(String) - Static method in class uk.ac.roslin.ensembl.config.EnsemblComparaDivision
 
getEnsemblComparaDivisionByMetaValue(String) - Static method in class uk.ac.roslin.ensembl.config.EnsemblComparaDivision
 
getEnsemblNameForAlias(String) - Method in interface uk.ac.roslin.ensembl.model.database.Registry
 
getEnsemblStablePrefix() - Method in interface uk.ac.roslin.ensembl.model.core.Species
 
getEValue() - Method in interface uk.ac.roslin.ensembl.model.core.ProteinFeature
 
getExons() - Method in interface uk.ac.roslin.ensembl.model.core.Transcript
 
getExtent() - Method in class uk.ac.roslin.ensembl.model.MappingSet
 
getFeaturesForCS(Species, CoordinateSystem) - Method in interface uk.ac.roslin.ensembl.model.database.CollectionCoreDatabase
 
getFeaturesForCS(CoordinateSystem) - Method in interface uk.ac.roslin.ensembl.model.database.SingleSpeciesCoreDatabase
 
getFeatureType(String) - Static method in class uk.ac.roslin.ensembl.config.FeatureType
 
getGaps() - Method in class uk.ac.roslin.ensembl.model.CoordinateSet
 
getGene() - Method in interface uk.ac.roslin.ensembl.model.core.Transcript
 
getGeneByID(Integer) - Method in interface uk.ac.roslin.ensembl.model.core.Species
 
getGeneByID(Integer, String) - Method in interface uk.ac.roslin.ensembl.model.core.Species
 
getGeneByStableID(String) - Method in interface uk.ac.roslin.ensembl.model.core.Species
 
getGeneByStableID(String, String) - Method in interface uk.ac.roslin.ensembl.model.core.Species
 
getGeneID() - Method in class uk.ac.roslin.ensembl.model.compara.HomologyAlignmentProperties
 
getGenesOnRegion(Coordinate) - Method in interface uk.ac.roslin.ensembl.model.core.DNASequence
 
getGenesOnRegion(Integer, Integer) - Method in interface uk.ac.roslin.ensembl.model.core.DNASequence
 
getGenesOnRegion(Integer, Integer, Coordinate.Strand) - Method in interface uk.ac.roslin.ensembl.model.core.DNASequence
 
getHashID() - Method in interface uk.ac.roslin.ensembl.model.IdentifiableObject
 
getHighestDBVersion() - Method in interface uk.ac.roslin.ensembl.model.database.Registry
 
getHighestEnsemblSchemaVersion() - Method in interface uk.ac.roslin.ensembl.model.database.Registry
 
getHomologies() - Method in interface uk.ac.roslin.ensembl.model.core.Gene
 
getHomologies(Species) - Method in interface uk.ac.roslin.ensembl.model.core.Gene
 
getHomologies(EnsemblComparaDivision) - Method in interface uk.ac.roslin.ensembl.model.core.Gene
 
getHomologies(EnsemblComparaDivision, Species) - Method in interface uk.ac.roslin.ensembl.model.core.Gene
 
getHomologiesWithoutLazyLoad() - Method in interface uk.ac.roslin.ensembl.model.core.Gene
 
getHomologyTypeByName(String) - Static method in class uk.ac.roslin.ensembl.model.compara.HomologyType
Checks to see if the supplied type is the name of a valid HomologyType and returns the corresponding HomologyType object if it is.
getId() - Method in interface uk.ac.roslin.ensembl.model.core.CoordinateSystem
 
getId() - Method in interface uk.ac.roslin.ensembl.model.IdentifiableObject
 
getInfo() - Method in interface uk.ac.roslin.ensembl.model.XRef
 
getInfoType() - Method in interface uk.ac.roslin.ensembl.model.XRef
 
getIntDBVersion() - Method in interface uk.ac.roslin.ensembl.model.database.Database
 
getIntSchemaVersion() - Method in interface uk.ac.roslin.ensembl.model.database.Database
 
getLastCommonAncestor() - Method in interface uk.ac.roslin.ensembl.model.compara.HomologyRelationship
 
getLengthInteger() - Method in interface uk.ac.roslin.ensembl.biojava3.EnsemblDNASequenceReader
 
getMappedRegions() - Method in interface uk.ac.roslin.ensembl.model.core.DNASequence
 
getMappings() - Method in interface uk.ac.roslin.ensembl.model.core.Assembly
 
getMappings(ObjectType) - Method in interface uk.ac.roslin.ensembl.model.MappableObject
 
getMappings() - Method in interface uk.ac.roslin.ensembl.model.MappableObject
 
getMaxLengthForFeature(Species, ObjectType, CoordinateSystem) - Method in interface uk.ac.roslin.ensembl.model.database.CollectionCoreDatabase
 
getMaxLengthForFeature(ObjectType, CoordinateSystem) - Method in interface uk.ac.roslin.ensembl.model.database.SingleSpeciesCoreDatabase
 
getMembers() - Method in interface uk.ac.roslin.ensembl.model.relationship.GroupRelationship
 
getMostRecentDBVersion() - Method in interface uk.ac.roslin.ensembl.model.database.Registry
 
getMostRecentEnsemblVersion() - Method in interface uk.ac.roslin.ensembl.model.database.Registry
 
getMybatisSchemaPath(String, String) - Method in class uk.ac.roslin.ensembl.config.SchemaVersion
 
getName() - Method in interface uk.ac.roslin.ensembl.biojava3.EnsemblDNASequenceReader
 
getName() - Method in interface uk.ac.roslin.ensembl.model.core.DNASequence
 
getNewSqlSession() - Method in interface uk.ac.roslin.ensembl.model.database.Database
 
getObjectTypeMappings() - Method in interface uk.ac.roslin.ensembl.model.core.DNASequence
 
getOverlap(Coordinate) - Method in class uk.ac.roslin.ensembl.model.Coordinate
 
getParent() - Method in interface uk.ac.roslin.ensembl.model.core.Assembly
 
getPeptideID() - Method in class uk.ac.roslin.ensembl.model.compara.HomologyAlignmentProperties
 
getPercentCovered() - Method in class uk.ac.roslin.ensembl.model.compara.HomologyAlignmentProperties
 
getPercentIdentity() - Method in class uk.ac.roslin.ensembl.model.compara.HomologyAlignmentProperties
 
getPercentIdentity() - Method in interface uk.ac.roslin.ensembl.model.core.ProteinFeature
 
getPercentSimilar() - Method in class uk.ac.roslin.ensembl.model.compara.HomologyAlignmentProperties
 
getPhase() - Method in interface uk.ac.roslin.ensembl.model.core.Exon
 
getPhase(int) - Static method in class uk.ac.roslin.ensembl.model.core.Exon.Phase
 
getProteinFeatures() - Method in interface uk.ac.roslin.ensembl.model.core.Translation
 
getRange() - Method in class uk.ac.roslin.ensembl.model.CoordinateSet
 
getRank() - Method in interface uk.ac.roslin.ensembl.model.core.CoordinateSystem
 
getRegionsOfConservedSynteny(Coordinate, Species) - Method in interface uk.ac.roslin.ensembl.model.core.Chromosome
 
getRegisteredSchemas() - Method in class uk.ac.roslin.ensembl.config.SchemaVersion
 
getRegistry() - Method in interface uk.ac.roslin.ensembl.model.database.Database
 
getRelationshipType() - Method in interface uk.ac.roslin.ensembl.model.compara.HomologyRelationship
 
getRelationshipType(String) - Static method in class uk.ac.roslin.ensembl.model.compara.HomologyType
 
getRelationshipType() - Method in interface uk.ac.roslin.ensembl.model.relationship.GroupRelationship
Gets the RelationshipType of this Relationship
getRelationshipType(String) - Static method in class uk.ac.roslin.ensembl.model.relationship.RelationshipType
 
getReverseComplementSequenceAsString(Integer, Integer) - Method in interface uk.ac.roslin.ensembl.biojava3.EnsemblDNASequenceReader
 
getReverseComplementSequenceAsString(Integer, Integer) - Method in interface uk.ac.roslin.ensembl.model.core.DNASequence
 
getReverseComplementSequenceAsString() - Method in interface uk.ac.roslin.ensembl.model.core.DNASequence
 
getReverseMapping() - Method in class uk.ac.roslin.ensembl.model.Mapping
 
getSchema() - Method in class uk.ac.roslin.ensembl.config.RegistryConfiguration
Returns the SchemaVersionobject set on this RegistryConfiguration object.
getSchemaVersion() - Method in interface uk.ac.roslin.ensembl.model.core.CollectionOfSpecies
 
getSchemaVersion() - Method in interface uk.ac.roslin.ensembl.model.database.Database
 
getSchemaVersion() - Method in interface uk.ac.roslin.ensembl.model.IdentifiableObject
 
getSchemaVersions() - Method in interface uk.ac.roslin.ensembl.model.core.Species
 
getScore() - Method in interface uk.ac.roslin.ensembl.model.core.ProteinFeature
 
getSeqRegionID() - Method in interface uk.ac.roslin.ensembl.biojava3.EnsemblDNASequenceReader
 
getSequenceAsString(Integer, Integer) - Method in interface uk.ac.roslin.ensembl.model.core.DNASequence
 
getSequenceLevelCoordSystem() - Method in interface uk.ac.roslin.ensembl.model.database.SingleSpeciesCoreDatabase
 
getSequenceLevelCS(Species) - Method in interface uk.ac.roslin.ensembl.model.database.CollectionCoreDatabase
 
getSequenceName() - Method in class uk.ac.roslin.ensembl.model.compara.HomologyAlignmentProperties
 
getShortName() - Method in interface uk.ac.roslin.ensembl.model.core.Species
 
getSingleSpeciesDatabaseTypes() - Static method in class uk.ac.roslin.ensembl.config.EnsemblDBType
 
getSource() - Method in class uk.ac.roslin.ensembl.model.Mapping
 
getSource() - Method in interface uk.ac.roslin.ensembl.model.relationship.BinaryRelationship
Returns the source Attributable in the relationship
getSource() - Method in interface uk.ac.roslin.ensembl.model.relationship.InverseBinaryRelationshipView
Returns the source Attributable in the relationship
getSourceCoordinates() - Method in class uk.ac.roslin.ensembl.model.Mapping
 
getSourceEnd() - Method in interface uk.ac.roslin.ensembl.model.core.ProteinFeature
 
getSourceHashID() - Method in class uk.ac.roslin.ensembl.model.Mapping
 
getSourceProperties() - Method in interface uk.ac.roslin.ensembl.model.compara.HomologyPairRelationship
 
getSourceStart() - Method in interface uk.ac.roslin.ensembl.model.core.ProteinFeature
 
getSourceType() - Method in class uk.ac.roslin.ensembl.model.Mapping
 
getSpecies() - Method in interface uk.ac.roslin.ensembl.model.compara.HomologyRelationship
 
getSpecies() - Method in interface uk.ac.roslin.ensembl.model.core.CollectionOfSpecies
 
getSpecies() - Method in interface uk.ac.roslin.ensembl.model.core.CoreObject
 
getSpecies() - Method in interface uk.ac.roslin.ensembl.model.database.Registry
 
getSpecies() - Method in interface uk.ac.roslin.ensembl.model.database.SingleSpeciesDatabase
 
getSpeciesBinomial() - Method in interface uk.ac.roslin.ensembl.model.core.Species
 
getSpeciesByAlias(String) - Method in interface uk.ac.roslin.ensembl.model.database.Registry
 
getSpeciesByEnsemblName(String) - Method in interface uk.ac.roslin.ensembl.model.database.Registry
 
getSpeciesComparisonDatabaseTypes() - Static method in class uk.ac.roslin.ensembl.config.EnsemblDBType
 
getSpeciesID() - Method in interface uk.ac.roslin.ensembl.model.core.CoordinateSystem
 
getSpeciesName() - Method in class uk.ac.roslin.ensembl.model.compara.HomologyAlignmentProperties
 
getStart() - Method in class uk.ac.roslin.ensembl.model.Coordinate
 
getStart() - Method in class uk.ac.roslin.ensembl.model.CoordinateSet
 
getStitchedMappings() - Method in interface uk.ac.roslin.ensembl.model.core.Assembly
 
getStrand() - Method in class uk.ac.roslin.ensembl.model.Coordinate
 
getStrandInt() - Method in class uk.ac.roslin.ensembl.model.Coordinate
 
getTarget() - Method in class uk.ac.roslin.ensembl.model.Mapping
 
getTarget() - Method in interface uk.ac.roslin.ensembl.model.relationship.BinaryRelationship
Returns the target IdentifiableObject in the relationship
getTarget() - Method in interface uk.ac.roslin.ensembl.model.relationship.InverseBinaryRelationshipView
Returns the target IdentifiableObject in the relationship
getTargetCoordinates() - Method in class uk.ac.roslin.ensembl.model.Mapping
 
getTargetEnd() - Method in interface uk.ac.roslin.ensembl.model.core.ProteinFeature
 
getTargetHashID() - Method in class uk.ac.roslin.ensembl.model.Mapping
 
getTargetName() - Method in interface uk.ac.roslin.ensembl.model.core.ProteinFeature
 
getTargetProperties() - Method in interface uk.ac.roslin.ensembl.model.compara.HomologyPairRelationship
 
getTargetStart() - Method in interface uk.ac.roslin.ensembl.model.core.ProteinFeature
 
getTargetType() - Method in class uk.ac.roslin.ensembl.model.Mapping
 
getTaxonomyID() - Method in interface uk.ac.roslin.ensembl.model.core.Species
 
getTopLevelCoordSystem() - Method in interface uk.ac.roslin.ensembl.model.database.SingleSpeciesCoreDatabase
 
getTopLevelCS(Species) - Method in interface uk.ac.roslin.ensembl.model.database.CollectionCoreDatabase
 
getTranscript() - Method in interface uk.ac.roslin.ensembl.model.core.Translation
 
getTranscripts() - Method in interface uk.ac.roslin.ensembl.model.core.Gene
 
getTranslation() - Method in interface uk.ac.roslin.ensembl.model.core.Transcript
 
getTranslationID() - Method in interface uk.ac.roslin.ensembl.model.core.ProteinFeature
 
getType(String) - Static method in class uk.ac.roslin.ensembl.config.EnsemblCoordSystemType
 
getType() - Method in class uk.ac.roslin.ensembl.config.RegistryConfiguration
Returns the current DataSource type of this RegistryConfiguration object.
getType() - Method in interface uk.ac.roslin.ensembl.model.core.CoordinateSystem
 
getType() - Method in interface uk.ac.roslin.ensembl.model.database.Database
 
getType() - Method in interface uk.ac.roslin.ensembl.model.IdentifiableObject
 
getUncoveredRegions(Coordinate) - Method in class uk.ac.roslin.ensembl.model.CoordinateSet
 
getVersion() - Method in interface uk.ac.roslin.ensembl.model.core.CoordinateSystem
 
getVersion() - Method in interface uk.ac.roslin.ensembl.model.XRef
 
go - Static variable in class uk.ac.roslin.ensembl.config.EnsemblDBType
A concrete instantiation of an DatabaseType object representing the ensembl go database sType
GroupRelationship<CLAZZ extends IdentifiableObject> - Interface in uk.ac.roslin.ensembl.model.relationship
 

H

hashCode() - Method in class uk.ac.roslin.ensembl.config.EnsemblDBType
Overrides Object method to generate a hashCode
hashCode() - Method in class uk.ac.roslin.ensembl.model.Mapping
 
hashCode() - Method in class uk.ac.roslin.ensembl.model.relationship.RelationshipType
hashCode() is overriden because we have overridden equals.
HomologyAlignmentProperties - Class in uk.ac.roslin.ensembl.model.compara
Utility class used to hold properties of an aligned homology object (gene) in a HomologyPairRelationship.
HomologyAlignmentProperties() - Constructor for class uk.ac.roslin.ensembl.model.compara.HomologyAlignmentProperties
 
HomologyPairRelationship<CLAZZ extends Gene> - Interface in uk.ac.roslin.ensembl.model.compara
extends HomologyRelationship for those Relationships that are binary
HomologyRelationship<CLAZZ extends Gene> - Interface in uk.ac.roslin.ensembl.model.compara
Ensembl schema and PerlAPI claims that homology relationships are not necessarily only binary, i.e. the could have more than two members.
HomologyType - Class in uk.ac.roslin.ensembl.model.compara
 

I

IdentifiableObject - Interface in uk.ac.roslin.ensembl.model
 
intron - Static variable in class uk.ac.roslin.ensembl.config.FeatureType
 
InverseBinaryRelationshipView<CLAZZ extends BinaryRelationship<? extends IdentifiableObject>> - Interface in uk.ac.roslin.ensembl.model.relationship
 
isConnectionOK() - Method in class uk.ac.roslin.ensembl.config.DBConnection
 
isConstitutive() - Method in interface uk.ac.roslin.ensembl.model.core.Exon
 
isCurrent() - Method in interface uk.ac.roslin.ensembl.model.core.Feature
 
isDBNameValid(String) - Method in class uk.ac.roslin.ensembl.config.DBConnection
 
isDefaultVersion() - Method in interface uk.ac.roslin.ensembl.model.core.CoordinateSystem
 
isObjectTypeMapped(ObjectType) - Method in interface uk.ac.roslin.ensembl.model.core.Feature
 
isSequenceLevel() - Method in interface uk.ac.roslin.ensembl.model.core.CoordinateSystem
 
isTopLevel() - Method in interface uk.ac.roslin.ensembl.model.core.CoordinateSystem
 

K

karyotype_band - Static variable in class uk.ac.roslin.ensembl.config.FeatureType
 

L

label - Variable in class uk.ac.roslin.ensembl.config.EnsemblType
 
liesWithinCoordinate(Coordinate) - Method in class uk.ac.roslin.ensembl.model.Coordinate
 
lrg - Static variable in class uk.ac.roslin.ensembl.config.EnsemblCoordSystemType
 

M

makeDatabase(String) - Method in interface uk.ac.roslin.ensembl.model.database.Registry
 
MappableObject - Interface in uk.ac.roslin.ensembl.model
 
Mapping - Class in uk.ac.roslin.ensembl.model
Used to be abstract
Mapping() - Constructor for class uk.ac.roslin.ensembl.model.Mapping
 
mappingOnSourceComparator - Static variable in class uk.ac.roslin.ensembl.model.Mapping
 
mappingOnTargetComparator - Static variable in class uk.ac.roslin.ensembl.model.Mapping
 
MappingSet - Class in uk.ac.roslin.ensembl.model
Used to be abstract with signature public abstract class MappingSet extends TreeSet implements Serializable {
MappingSet() - Constructor for class uk.ac.roslin.ensembl.model.MappingSet
 
MappingSet(Comparator) - Constructor for class uk.ac.roslin.ensembl.model.MappingSet
 
marker_feature - Static variable in class uk.ac.roslin.ensembl.config.FeatureType
 
METAZOA - Static variable in class uk.ac.roslin.ensembl.config.EnsemblComparaDivision
 
misc_feature - Static variable in class uk.ac.roslin.ensembl.config.FeatureType
 
MULTI - Static variable in class uk.ac.roslin.ensembl.config.EnsemblComparaDivision
 

N

newline - Variable in class uk.ac.roslin.ensembl.config.DBConnection
 
NONE - Static variable in class uk.ac.roslin.ensembl.model.core.Exon.Phase
 

O

ObjectType - Interface in uk.ac.roslin.ensembl.model
 
ONE - Static variable in class uk.ac.roslin.ensembl.model.core.Exon.Phase
 
ontology - Static variable in class uk.ac.roslin.ensembl.config.EnsemblDBType
A concrete instantiation of an DatabaseType object representing the ensembl ontology database sType
ORTHOLOG_MANY2MANY - Static variable in class uk.ac.roslin.ensembl.model.compara.HomologyType
two homologous objects derived by speciation Ensembl pipeline annotates as ortholog_many2many see http://Nov2010.archive.ensembl.org/info/docs/compara/homology_method.html
ORTHOLOG_ONE2MANY - Static variable in class uk.ac.roslin.ensembl.model.compara.HomologyType
two homologous objects derived by speciation Ensembl pipeline annotates as ortholog_one2many see http://Nov2010.archive.ensembl.org/info/docs/compara/homology_method.html
ORTHOLOG_ONE2ONE - Static variable in class uk.ac.roslin.ensembl.model.compara.HomologyType
two homologous objects derived by speciation Ensembl pipeline annotates as ortholog_one2one see http://Nov2010.archive.ensembl.org/info/docs/compara/homology_method.html
OTHER_PARALOG - Static variable in class uk.ac.roslin.ensembl.model.compara.HomologyType
two homologous objects derived by duplication Ensembl pipeline annotates as other_paralog see http://Nov2010.archive.ensembl.org/info/docs/compara/homology_method.html
otherfeatures - Static variable in class uk.ac.roslin.ensembl.config.EnsemblDBType
A concrete instantiation of an DatabaseType object representing the ensembl species otherfeatures database sType
overlaps(Coordinate) - Method in class uk.ac.roslin.ensembl.model.Coordinate
 

P

PAN_HOMOLOGY - Static variable in class uk.ac.roslin.ensembl.config.EnsemblComparaDivision
 
peptide_dna_align_feature - Static variable in class uk.ac.roslin.ensembl.config.FeatureType
 
PLANTS - Static variable in class uk.ac.roslin.ensembl.config.EnsemblComparaDivision
 
plasmid - Static variable in class uk.ac.roslin.ensembl.config.EnsemblCoordSystemType
 
plastid - Static variable in class uk.ac.roslin.ensembl.config.EnsemblCoordSystemType
 
POSSIBLE_ORTHOLOG - Static variable in class uk.ac.roslin.ensembl.model.compara.HomologyType
two homologous objects derived by speciation Ensembl pipeline annotates as possible_ortholog see http://Nov2010.archive.ensembl.org/info/docs/compara/homology_method.html
prediction_exon - Static variable in class uk.ac.roslin.ensembl.config.FeatureType
 
prediction_transcript - Static variable in class uk.ac.roslin.ensembl.config.FeatureType
 
printRegistryReport() - Method in interface uk.ac.roslin.ensembl.model.database.Registry
 
protein_align_feature - Static variable in class uk.ac.roslin.ensembl.config.FeatureType
 
protein_feature - Static variable in class uk.ac.roslin.ensembl.config.FeatureType
 
ProteinFeature - Interface in uk.ac.roslin.ensembl.model.core
 
PROTISTS - Static variable in class uk.ac.roslin.ensembl.config.EnsemblComparaDivision
 
PUTATIVE_GENE_SPLIT - Static variable in class uk.ac.roslin.ensembl.model.compara.HomologyType
two homologous objects derived by duplication Ensembl pipeline annotates as putative_gene_split see http://Nov2010.archive.ensembl.org/info/docs/compara/homology_method.html

Q

qtl_feature - Static variable in class uk.ac.roslin.ensembl.config.FeatureType
 

R

RangeException - Exception in uk.ac.roslin.ensembl.exception
 
RangeException() - Constructor for exception uk.ac.roslin.ensembl.exception.RangeException
 
RangeException(String) - Constructor for exception uk.ac.roslin.ensembl.exception.RangeException
 
RangeException(String, Exception) - Constructor for exception uk.ac.roslin.ensembl.exception.RangeException
 
RangeException(Exception) - Constructor for exception uk.ac.roslin.ensembl.exception.RangeException
 
Registry - Interface in uk.ac.roslin.ensembl.model.database
 
RegistryConfiguration - Class in uk.ac.roslin.ensembl.config
 
RegistryConfiguration() - Constructor for class uk.ac.roslin.ensembl.config.RegistryConfiguration
Constructor for a non-configured RegistryConfiguration object.
RegistryConfiguration(DBConnection.DataSource) - Constructor for class uk.ac.roslin.ensembl.config.RegistryConfiguration
Constructs a RegistryConfiguration object after calling setType, which will set the DBConnection if DataSource is of a known valid type.
RelationshipType - Class in uk.ac.roslin.ensembl.model.relationship
 
RelationshipType(String) - Constructor for class uk.ac.roslin.ensembl.model.relationship.RelationshipType
 
repeat_feature - Static variable in class uk.ac.roslin.ensembl.config.FeatureType
 
report() - Method in class uk.ac.roslin.ensembl.config.DBConnection
 
reverseMapping - Variable in class uk.ac.roslin.ensembl.model.Mapping
 

S

scaffold - Static variable in class uk.ac.roslin.ensembl.config.EnsemblCoordSystemType
 
SchemaVersion - Class in uk.ac.roslin.ensembl.config
 
SchemaVersion() - Constructor for class uk.ac.roslin.ensembl.config.SchemaVersion
 
SchemaVersion(Properties) - Constructor for class uk.ac.roslin.ensembl.config.SchemaVersion
 
sequenceLevel - Static variable in class uk.ac.roslin.ensembl.config.EnsemblCoordSystemType
 
setAnalysisID(int) - Method in interface uk.ac.roslin.ensembl.model.core.ProteinFeature
 
setAssemblyStart(Integer) - Method in interface uk.ac.roslin.ensembl.model.core.Assembly
 
setAssemblyStop(Integer) - Method in interface uk.ac.roslin.ensembl.model.core.Assembly
 
setBuildLevel(String, String) - Method in interface uk.ac.roslin.ensembl.model.database.SingleSpeciesCoreDatabase
 
setBuildLevels(Species, HashMap<String, String>) - Method in interface uk.ac.roslin.ensembl.model.database.CollectionCoreDatabase
 
setChromosomeName(String) - Method in interface uk.ac.roslin.ensembl.model.core.Chromosome
 
setCigarEnd(Integer) - Method in class uk.ac.roslin.ensembl.model.compara.HomologyAlignmentProperties
 
setCigarLine(String) - Method in class uk.ac.roslin.ensembl.model.compara.HomologyAlignmentProperties
 
setCigarStart(Integer) - Method in class uk.ac.roslin.ensembl.model.compara.HomologyAlignmentProperties
 
setCollection(CollectionOfSpecies) - Method in interface uk.ac.roslin.ensembl.model.database.CollectionDatabase
 
setCollectionName(String) - Method in interface uk.ac.roslin.ensembl.model.database.CollectionDatabase
 
setCoords(Coordinate) - Method in class uk.ac.roslin.ensembl.model.compara.HomologyAlignmentProperties
 
setCoordSystem(CoordinateSystem) - Method in interface uk.ac.roslin.ensembl.model.core.DNASequence
 
setCoordSystemID(Integer) - Method in interface uk.ac.roslin.ensembl.biojava3.EnsemblDNASequenceReader
 
setCoreDBBuildLevels(SingleSpeciesCoreDatabase) - Method in interface uk.ac.roslin.ensembl.model.database.Registry
 
setDBByFile(File) - Method in class uk.ac.roslin.ensembl.config.RegistryConfiguration
Sets DBConnection on this RegistryConfiguration object from a given File of Properties.
setDBProperties(Properties) - Method in class uk.ac.roslin.ensembl.config.RegistryConfiguration
Sets DBConnection on this RegistryConfiguration object from a given set of Properties.
setDBSeqLength(Integer) - Method in interface uk.ac.roslin.ensembl.model.core.DNASequence
 
setDbSpeciesName(String) - Method in interface uk.ac.roslin.ensembl.model.database.SingleSpeciesDatabase
 
setDefaultVersion(Boolean) - Method in interface uk.ac.roslin.ensembl.model.core.CoordinateSystem
 
setEnd(Integer) - Method in class uk.ac.roslin.ensembl.model.Coordinate
 
setEValue(Double) - Method in interface uk.ac.roslin.ensembl.model.core.ProteinFeature
 
setGeneID(String) - Method in class uk.ac.roslin.ensembl.model.compara.HomologyAlignmentProperties
 
setId(Integer) - Method in interface uk.ac.roslin.ensembl.model.core.CoordinateSystem
 
setId(Integer) - Method in interface uk.ac.roslin.ensembl.model.IdentifiableObject
 
setLength(Integer) - Method in interface uk.ac.roslin.ensembl.biojava3.EnsemblDNASequenceReader
 
setName(String) - Method in interface uk.ac.roslin.ensembl.biojava3.EnsemblDNASequenceReader
 
setName(String) - Method in interface uk.ac.roslin.ensembl.model.core.DNASequence
 
setParent(AssembledDNASequence) - Method in interface uk.ac.roslin.ensembl.model.core.Assembly
 
setPeptideID(String) - Method in class uk.ac.roslin.ensembl.model.compara.HomologyAlignmentProperties
 
setPercentCovered(Integer) - Method in class uk.ac.roslin.ensembl.model.compara.HomologyAlignmentProperties
 
setPercentIdentity(Integer) - Method in class uk.ac.roslin.ensembl.model.compara.HomologyAlignmentProperties
 
setPercentIdentity(Double) - Method in interface uk.ac.roslin.ensembl.model.core.ProteinFeature
 
setPercentSimilar(Integer) - Method in class uk.ac.roslin.ensembl.model.compara.HomologyAlignmentProperties
 
setProperty(String, HashMap) - Method in interface uk.ac.roslin.ensembl.model.core.CollectionOfSpecies
 
setProperty(HashMap) - Method in interface uk.ac.roslin.ensembl.model.core.Species
 
setRank(Integer) - Method in interface uk.ac.roslin.ensembl.model.core.CoordinateSystem
 
setRelationshipType(RelationshipType) - Method in interface uk.ac.roslin.ensembl.model.relationship.GroupRelationship
Sets the RelationshipType of this Relationship
setReverseMapping(Mapping) - Method in class uk.ac.roslin.ensembl.model.Mapping
 
setSchemaByFile(File) - Method in class uk.ac.roslin.ensembl.config.RegistryConfiguration
Sets the SchemaVersion object on this RegistryConfiguration object using a File with Properties values.
setSchemaProperties(Properties) - Method in class uk.ac.roslin.ensembl.config.RegistryConfiguration
Sets the SchemaVersion object on this RegistryConfiguration object using the given Properties.
setScore(Double) - Method in interface uk.ac.roslin.ensembl.model.core.ProteinFeature
 
setSeqRegionID(Integer) - Method in interface uk.ac.roslin.ensembl.biojava3.EnsemblDNASequenceReader
 
setSequenceLevel(Boolean) - Method in interface uk.ac.roslin.ensembl.model.core.CoordinateSystem
 
setSequenceName(String) - Method in class uk.ac.roslin.ensembl.model.compara.HomologyAlignmentProperties
 
setSource(MappableObject) - Method in class uk.ac.roslin.ensembl.model.Mapping
 
setSource(CLAZZ) - Method in interface uk.ac.roslin.ensembl.model.relationship.BinaryRelationship
sets the IdentifiableObject source in the relationship
setSourceCoordinates(Coordinate) - Method in class uk.ac.roslin.ensembl.model.Mapping
 
setSourceCoordinates(Integer, Integer, Coordinate.Strand) - Method in class uk.ac.roslin.ensembl.model.Mapping
 
setSourceCoordinates(Integer, Integer, Integer) - Method in class uk.ac.roslin.ensembl.model.Mapping
 
setSourceEnd(int) - Method in interface uk.ac.roslin.ensembl.model.core.ProteinFeature
 
setSourceStart(int) - Method in interface uk.ac.roslin.ensembl.model.core.ProteinFeature
 
setSpecies(Species) - Method in interface uk.ac.roslin.ensembl.model.core.CoreObject
 
setSpecies(Species) - Method in interface uk.ac.roslin.ensembl.model.database.SingleSpeciesDatabase
 
setSpeciesID(Integer) - Method in interface uk.ac.roslin.ensembl.model.core.CoordinateSystem
 
setSpeciesName(String) - Method in class uk.ac.roslin.ensembl.model.compara.HomologyAlignmentProperties
 
setStart(Integer) - Method in class uk.ac.roslin.ensembl.model.Coordinate
 
setStrand(Coordinate.Strand) - Method in class uk.ac.roslin.ensembl.model.Coordinate
 
setStrandInt(Integer) - Method in class uk.ac.roslin.ensembl.model.Coordinate
 
setTarget(MappableObject) - Method in class uk.ac.roslin.ensembl.model.Mapping
 
setTarget(CLAZZ) - Method in interface uk.ac.roslin.ensembl.model.relationship.BinaryRelationship
Sets the IdentifiableObject target in the relationship
setTargetCoordinates(Coordinate) - Method in class uk.ac.roslin.ensembl.model.Mapping
 
setTargetCoordinates(Integer, Integer, Coordinate.Strand) - Method in class uk.ac.roslin.ensembl.model.Mapping
 
setTargetCoordinates(Integer, Integer, Integer) - Method in class uk.ac.roslin.ensembl.model.Mapping
 
setTargetEnd(int) - Method in interface uk.ac.roslin.ensembl.model.core.ProteinFeature
 
setTargetName(String) - Method in interface uk.ac.roslin.ensembl.model.core.ProteinFeature
 
setTargetStart(int) - Method in interface uk.ac.roslin.ensembl.model.core.ProteinFeature
 
setTranslationID(int) - Method in interface uk.ac.roslin.ensembl.model.core.ProteinFeature
 
setType(CoordSystemType) - Method in interface uk.ac.roslin.ensembl.model.core.CoordinateSystem
 
setVersion(String) - Method in interface uk.ac.roslin.ensembl.model.core.CoordinateSystem
 
simple_feature - Static variable in class uk.ac.roslin.ensembl.config.FeatureType
 
SingleSpeciesCoreDatabase - Interface in uk.ac.roslin.ensembl.model.database
 
SingleSpeciesDatabase - Interface in uk.ac.roslin.ensembl.model.database
 
source - Variable in class uk.ac.roslin.ensembl.model.Mapping
 
sourceCoordinates - Variable in class uk.ac.roslin.ensembl.model.Mapping
 
sourceCoordSystem - Variable in class uk.ac.roslin.ensembl.model.Mapping
 
Species - Interface in uk.ac.roslin.ensembl.model.core
 
splicing_event - Static variable in class uk.ac.roslin.ensembl.config.FeatureType
 
strand(int) - Static method in enum uk.ac.roslin.ensembl.model.Coordinate.Strand
 
strand(Integer) - Static method in enum uk.ac.roslin.ensembl.model.Coordinate.Strand
 
supercontig - Static variable in class uk.ac.roslin.ensembl.config.EnsemblCoordSystemType
 

T

target - Variable in class uk.ac.roslin.ensembl.model.Mapping
 
targetCoordinates - Variable in class uk.ac.roslin.ensembl.model.Mapping
 
targetCoordSystem - Variable in class uk.ac.roslin.ensembl.model.Mapping
 
testConnection() - Method in class uk.ac.roslin.ensembl.config.DBConnection
 
toString() - Method in enum uk.ac.roslin.ensembl.config.DBConnection.DataSource
 
toString() - Method in class uk.ac.roslin.ensembl.config.EnsemblCoordSystemType
 
toString() - Method in class uk.ac.roslin.ensembl.config.EnsemblDBType
We often use the constants in a String context, so this routine allows us to do that easily
toString() - Method in class uk.ac.roslin.ensembl.config.EnsemblType
We often use the constants in a String context, so this routine allows us to do that easily
toString() - Method in class uk.ac.roslin.ensembl.model.Coordinate
 
transcript - Static variable in class uk.ac.roslin.ensembl.config.FeatureType
 
Transcript - Interface in uk.ac.roslin.ensembl.model.core
 
translation - Static variable in class uk.ac.roslin.ensembl.config.EnsemblCoreObjectType
 
Translation - Interface in uk.ac.roslin.ensembl.model.core
 
TWO - Static variable in class uk.ac.roslin.ensembl.model.core.Exon.Phase
 

U

uk.ac.roslin.ensembl.biojava3 - package uk.ac.roslin.ensembl.biojava3
 
uk.ac.roslin.ensembl.config - package uk.ac.roslin.ensembl.config
 
uk.ac.roslin.ensembl.exception - package uk.ac.roslin.ensembl.exception
 
uk.ac.roslin.ensembl.model - package uk.ac.roslin.ensembl.model
 
uk.ac.roslin.ensembl.model.compara - package uk.ac.roslin.ensembl.model.compara
 
uk.ac.roslin.ensembl.model.core - package uk.ac.roslin.ensembl.model.core
 
uk.ac.roslin.ensembl.model.database - package uk.ac.roslin.ensembl.model.database
 
uk.ac.roslin.ensembl.model.relationship - package uk.ac.roslin.ensembl.model.relationship
 
unknown - Static variable in class uk.ac.roslin.ensembl.config.EnsemblCoordSystemType
 
UNKNOWN - Static variable in class uk.ac.roslin.ensembl.model.relationship.RelationshipType
 

V

valueOf(String) - Static method in enum uk.ac.roslin.ensembl.config.DBConnection.DataSource
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum uk.ac.roslin.ensembl.model.Coordinate.Strand
Returns the enum constant of this type with the specified name.
values() - Static method in enum uk.ac.roslin.ensembl.config.DBConnection.DataSource
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum uk.ac.roslin.ensembl.model.Coordinate.Strand
Returns an array containing the constants of this enum type, in the order they are declared.
variation - Static variable in class uk.ac.roslin.ensembl.config.EnsemblDBType
A concrete instantiation of an DatabaseType object representing the ensembl species variation database sType
vega - Static variable in class uk.ac.roslin.ensembl.config.EnsemblDBType
A concrete instantiation of an DatabaseType object representing the ensembl species vega database sType

W

website - Static variable in class uk.ac.roslin.ensembl.config.EnsemblDBType
A concrete instantiation of an DatabaseType object representing the ensembl website database sType
WITHIN_SPECIES_PARALOG - Static variable in class uk.ac.roslin.ensembl.model.compara.HomologyType
two homologous objects derived by duplication Ensembl pipeline annotates as within_species_paralog see http://Nov2010.archive.ensembl.org/info/docs/compara/homology_method.html

X

xref - Static variable in class uk.ac.roslin.ensembl.config.EnsemblCoreObjectType
 
XRef - Interface in uk.ac.roslin.ensembl.model
 

Z

ZERO - Static variable in class uk.ac.roslin.ensembl.model.core.Exon.Phase
 

A B C D E F G H I K L M N O P Q R S T U V W X Z
Ensembl Model
v1.09

Ensembl Model v1.09
© Roslin Institute 2010. GNU General Public License, version3