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

A

addAttribute(String, String) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DADNASequence

addDatabase(Database) - Method in class uk.ac.roslin.ensembl.dao.database.DBCollectionSpecies

addDatabase(Database) - Method in class uk.ac.roslin.ensembl.dao.database.DBSpecies

addDatabase(Database) - Method in interface uk.ac.roslin.ensembl.model.core.Species

addDatabases(TreeSet<? extends CollectionDatabase>) - Method in class uk.ac.roslin.ensembl.dao.database.DBCollection

addDatabases(TreeSet<? extends Database>) - Method in class uk.ac.roslin.ensembl.dao.database.DBCollectionSpecies

addDatabases(TreeSet<? extends Database>) - Method in class uk.ac.roslin.ensembl.dao.database.DBSpecies

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

addException(AssemblyExceptionType, Mapping) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAChromosome

public method called by the DA infrastructure when adding an AssemblyException mapping of the indicated type.

addExon(Exon) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DATranscript

Method used by the ExonDAO to add an Exon to the 'exonHash', hashed on the 'Rank' integer held by the Exon.

addFeatureCS(String, Integer, Integer, Species) - Method in class uk.ac.roslin.ensembl.dao.database.DBCollectionCoreDatabase

addFeatureCS(String, Integer, Integer) - Method in class uk.ac.roslin.ensembl.dao.database.DBSingleSpeciesCoreDatabase

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

addGeneByIDOnParent(Integer, DNASequence) - Method in interface uk.ac.roslin.ensembl.dao.coreaccess.GeneDAO

addGeneByIDOnParent(Integer, DNASequence) - Method in class uk.ac.roslin.ensembl.dao.database.coreaccess.DBGeneDAO

addGeneByStableIDOnParent(String, DNASequence) - Method in interface uk.ac.roslin.ensembl.dao.coreaccess.GeneDAO

addGeneByStableIDOnParent(String, DNASequence) - Method in class uk.ac.roslin.ensembl.dao.database.coreaccess.DBGeneDAO

The gene returned has mapping to a sequence region - and the id for the coordinate system that this region belongs to

addHomology(EnsemblComparaDivision, DAHomologyPairRelationship) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAGene

addMappedObjectType(ObjectType) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAFeature

addMappedObjectType(ObjectType) - Method in class uk.ac.roslin.ensembl.datasourceaware.variation.DAVariation

addMappedObjectType(ObjectType) - Method in interface uk.ac.roslin.ensembl.model.core.Feature

addMapping(Mapping) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DADNASequence

addMapping(Mapping) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAFeature

addMapping(Mapping) - Method in class uk.ac.roslin.ensembl.datasourceaware.variation.DAVariation

addMapping(Mapping) - Method in interface uk.ac.roslin.ensembl.model.MappableObject

addReverseMapping(VariationMapping) - Static method in class uk.ac.roslin.ensembl.datasourceaware.variation.VariationMapping

addReverseMapping(Mapping) - Static method in class uk.ac.roslin.ensembl.model.Mapping

addSessionAlias(String, String) - Method in class uk.ac.roslin.ensembl.dao.database.DBRegistry

Method for an adhoc alias to be added by the user in this session.

addSessionAlias(Species, String) - Method in class uk.ac.roslin.ensembl.dao.database.DBRegistry

addSessionAlias(String, String) - Method in interface uk.ac.roslin.ensembl.model.database.Registry

addSessionAlias(Species, String) - Method in interface uk.ac.roslin.ensembl.model.database.Registry

addSpecies(Collection<? extends CollectionSpecies>) - Method in class uk.ac.roslin.ensembl.dao.database.DBCollection

addSpecies(CollectionSpecies) - Method in class uk.ac.roslin.ensembl.dao.database.DBCollection

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

addTranscript(Transcript) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAGene

addTranslation(DATranslation) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DATranscript

Package method to add a Translation to the 'translationHash', hashed on the internal database ID of the Translation, and to set the canonicalTranlation/ID where applicable.

addTranslations(Collection<DATranslation>) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DATranscript

Method used by the TranslationDAO to add Translations to the 'translationHash', hashed on the internal database ID of the Translation.

addTypedXRefs(ExternalDBType, Collection<? extends XRef>) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAGene

addTypedXRefs(ExternalDBType, Collection<? extends XRef>) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DATranscript

addTypedXRefs(ExternalDBType, Collection<? extends XRef>) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DATranslation

addVariationXRef(XRef) - Method in class uk.ac.roslin.ensembl.dao.database.factory.DBDAOSingleSpeciesVariationFactory

addVariationXRef(XRef) - Method in interface uk.ac.roslin.ensembl.dao.factory.DAOVariationFactory

aliases - Variable in class uk.ac.roslin.ensembl.dao.database.DBSpecies

allChromosomesRetrieved - Variable in class uk.ac.roslin.ensembl.dao.database.DBSpecies

allDatabases - Variable in class uk.ac.roslin.ensembl.dao.database.DBRegistry

allFragmentsRetrieved - Variable in class uk.ac.roslin.ensembl.dao.database.DBSpecies

alreadyInitialized - Variable in class uk.ac.roslin.ensembl.dao.database.DBRegistry

alreadyParsed - Variable in class uk.ac.roslin.ensembl.dao.database.DBRegistry

ALT_ALLELE - Static variable in class uk.ac.roslin.ensembl.model.compara.HomologyType

Ensembl pipeline annotates alt_allele

ALTERNATIVE_YEAST_NUCLEAR - Static variable in class uk.ac.roslin.ensembl.config.CodonTable

analysis - Static variable in class uk.ac.roslin.ensembl.config.EnsemblCoreObjectType

Analysis - Class in uk.ac.roslin.ensembl.demo

Analysis() - Constructor for class uk.ac.roslin.ensembl.demo.Analysis

Analysis - Interface in uk.ac.roslin.ensembl.model.core

AnalysisDAO - Interface in uk.ac.roslin.ensembl.dao

Both the Core and Funcgen DB Types have Analyses

AnalysisMapper - Interface in uk.ac.roslin.ensembl.mapper

Analyzed - 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

ancestralAllele - Variable in class uk.ac.roslin.ensembl.datasourceaware.variation.DAVariation

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

ArchivesConnection - Class in uk.ac.roslin.ensembl.demo

ArchivesConnection() - Constructor for class uk.ac.roslin.ensembl.demo.ArchivesConnection

ASCIDIAN_MITOCHONDRIAL - Static variable in class uk.ac.roslin.ensembl.config.CodonTable

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

assemblyAccession - Variable in class uk.ac.roslin.ensembl.dao.database.DBSingleSpeciesCoreDatabase

assemblyAccessionsByVersion - Variable in class uk.ac.roslin.ensembl.dao.database.DBSpecies

assemblyAccessionStemForAliasHash - Variable in class uk.ac.roslin.ensembl.dao.database.DBRegistry

AssemblyDAO - Interface in uk.ac.roslin.ensembl.dao.coreaccess

AssemblyExceptions - Class in uk.ac.roslin.ensembl.demo

AssemblyExceptions() - Constructor for class uk.ac.roslin.ensembl.demo.AssemblyExceptions

AssemblyExceptionType - Class in uk.ac.roslin.ensembl.config

AssemblyExceptionTypeHandler - Class in uk.ac.roslin.ensembl.mapper.handler

AssemblyExceptionTypeHandler() - Constructor for class uk.ac.roslin.ensembl.mapper.handler.AssemblyExceptionTypeHandler

assemblyName - Variable in class uk.ac.roslin.ensembl.dao.database.DBSingleSpeciesCoreDatabase

assemblyNamesByVersion - Variable in class uk.ac.roslin.ensembl.dao.database.DBSpecies

assemblyStart - Variable in class uk.ac.roslin.ensembl.datasourceaware.core.DAAssembly

assemblyStop - Variable in class uk.ac.roslin.ensembl.datasourceaware.core.DAAssembly

B

BACTERIA - Static variable in class uk.ac.roslin.ensembl.config.EnsemblComparaDivision

BacteriaConnection - Class in uk.ac.roslin.ensembl.demo

BacteriaConnection() - Constructor for class uk.ac.roslin.ensembl.demo.BacteriaConnection

BACTERIAL - Static variable in class uk.ac.roslin.ensembl.config.CodonTable

BacterialCollectionException - Exception in uk.ac.roslin.ensembl.exception

BacterialCollectionException() - Constructor for exception uk.ac.roslin.ensembl.exception.BacterialCollectionException

BacterialCollectionException(String) - Constructor for exception uk.ac.roslin.ensembl.exception.BacterialCollectionException

BacterialCollectionException(String, Exception) - Constructor for exception uk.ac.roslin.ensembl.exception.BacterialCollectionException

BacterialCollectionException(Exception) - Constructor for exception uk.ac.roslin.ensembl.exception.BacterialCollectionException

BacterialGeneHomologues - Class in uk.ac.roslin.ensembl.demo

BacterialGeneHomologues() - Constructor for class uk.ac.roslin.ensembl.demo.BacterialGeneHomologues

BacterialSyntenies - Class in uk.ac.roslin.ensembl.demo

BacterialSyntenies() - Constructor for class uk.ac.roslin.ensembl.demo.BacterialSyntenies

BinaryRelationship<CLAZZ extends IdentifiableObject> - Interface in uk.ac.roslin.ensembl.model.relationship

BioinformaticsPublicationExamples - Class in uk.ac.roslin.ensembl.demo

BioinformaticsPublicationExamples() - Constructor for class uk.ac.roslin.ensembl.demo.BioinformaticsPublicationExamples

BLEPHARISMA_MACRONUCLEAR - Static variable in class uk.ac.roslin.ensembl.config.CodonTable

BooleanTypeHandler - Class in uk.ac.roslin.ensembl.mapper.handler

BooleanTypeHandler() - Constructor for class uk.ac.roslin.ensembl.mapper.handler.BooleanTypeHandler

C

CCDS - Static variable in class uk.ac.roslin.ensembl.config.ExternalDBType

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

checkInitialized() - Method in class uk.ac.roslin.ensembl.datasourceaware.variation.DAVariation

This is a hack to classigy the loaded mapping by type, because MyBatis apparently sets 'mappings' by reflection, not with the setter, so objectTypeMappings is not initialized by the MyBatis call.

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

Chromosome - Class in uk.ac.roslin.ensembl.test

Chromosome() - Constructor for class uk.ac.roslin.ensembl.test.Chromosome

ChromosomeCaching - Class in uk.ac.roslin.ensembl.demo

ChromosomeCaching() - Constructor for class uk.ac.roslin.ensembl.demo.ChromosomeCaching

ChromosomeDAO - Interface in uk.ac.roslin.ensembl.dao.coreaccess

ChromosomeMapper - Interface in uk.ac.roslin.ensembl.mapper.core

chromosomes - Variable in class uk.ac.roslin.ensembl.dao.database.DBSpecies

chunk - Static variable in class uk.ac.roslin.ensembl.config.EnsemblCoordSystemType

CILIATE_NUCLEAR - Static variable in class uk.ac.roslin.ensembl.config.CodonTable

clearAllMappings() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DADNASequence

clearAllMappings() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAFeature

clearAllMappings() - Method in class uk.ac.roslin.ensembl.datasourceaware.variation.DAVariation

clearAllMappings() - Method in interface uk.ac.roslin.ensembl.model.MappableObject

clone - Static variable in class uk.ac.roslin.ensembl.config.EnsemblCoordSystemType

CodonTable - Class in uk.ac.roslin.ensembl.config

CodonTable() - Constructor for class uk.ac.roslin.ensembl.config.CodonTable

codonTableID - Variable in class uk.ac.roslin.ensembl.datasourceaware.core.DADNASequence

collection - Variable in class uk.ac.roslin.ensembl.dao.database.DBCollectionDatabase

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

collectionDatabases - Variable in class uk.ac.roslin.ensembl.dao.database.DBRegistry

collectionName - Variable in class uk.ac.roslin.ensembl.dao.database.DBCollectionDatabase

collectionNameDBVersionHash - Variable in class uk.ac.roslin.ensembl.dao.database.DBRegistry

CollectionOfSpecies - Interface in uk.ac.roslin.ensembl.model.core

collections - Variable in class uk.ac.roslin.ensembl.dao.database.DBRegistry

CollectionSpecies - Interface in uk.ac.roslin.ensembl.model.core

collectionspeciesHashByGCAccession - Variable in class uk.ac.roslin.ensembl.dao.database.DBRegistry

collFactory - Variable in class uk.ac.roslin.ensembl.dao.database.coreaccess.DBCoreObjectDAO

CommandLineConfiguration - Class in uk.ac.roslin.ensembl.demo

CommandLineConfiguration() - Constructor for class uk.ac.roslin.ensembl.demo.CommandLineConfiguration

commonName - Variable in class uk.ac.roslin.ensembl.dao.database.DBSpecies

compara - Static variable in class uk.ac.roslin.ensembl.config.EnsemblDBType

A concrete instantiation of an DatabaseType object representing the ensembl compara database sType

Compara - Class in uk.ac.roslin.ensembl.test

Compara() - Constructor for class uk.ac.roslin.ensembl.test.Compara

comparaDBByDivision - Variable in class uk.ac.roslin.ensembl.dao.database.DBRegistry

comparaFactories - Variable in class uk.ac.roslin.ensembl.datasourceaware.core.DACoreObject

comparaFactories - Variable in class uk.ac.roslin.ensembl.datasourceaware.core.DADNASequence

comparaName - Variable in class uk.ac.roslin.ensembl.dao.database.DBSingleSpeciesCoreDatabase

comparaNameByVersion - Variable in class uk.ac.roslin.ensembl.dao.database.DBSpecies

compare(DAObject, DAObject) - Method in class uk.ac.roslin.ensembl.datasourceaware.DAObject.DAComparator

compareTo(EnsemblComparaDivision) - Method in class uk.ac.roslin.ensembl.config.EnsemblComparaDivision

compareTo(EnsemblDBType) - Method in class uk.ac.roslin.ensembl.config.EnsemblDBType

compareTo(Object) - Method in class uk.ac.roslin.ensembl.dao.database.DBCollectionSpecies

compareTo(Database) - Method in class uk.ac.roslin.ensembl.dao.database.DBDatabase

compareTo(Coordinate) - Method in class uk.ac.roslin.ensembl.model.Coordinate

Implements compareTo(another Coordinate) method for the Comparable interface.

ComparisonDatabase - Interface in uk.ac.roslin.ensembl.model.database

comparisonDatabases - Variable in class uk.ac.roslin.ensembl.dao.database.DBRegistry

ComponentAssembledSequencesOfChromosomes - Class in uk.ac.roslin.ensembl.demo

ComponentAssembledSequencesOfChromosomes() - Constructor for class uk.ac.roslin.ensembl.demo.ComponentAssembledSequencesOfChromosomes

componentMappings - Variable in class uk.ac.roslin.ensembl.datasourceaware.core.DAAssembly

compoundSet - Variable in class uk.ac.roslin.ensembl.datasourceaware.core.DAEnsemblDNASequenceReader

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

configProperties - Variable in class uk.ac.roslin.ensembl.dao.database.DBRegistry

configuration - Variable in class uk.ac.roslin.ensembl.dao.database.DBBaseDAO

configuration - Variable in class uk.ac.roslin.ensembl.dao.database.factory.DBDAOFactory

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

ConsequencesHandler - Class in uk.ac.roslin.ensembl.mapper.handler

ConsequencesHandler() - Constructor for class uk.ac.roslin.ensembl.mapper.handler.ConsequencesHandler

containsCoordinateWithoutGaps(Coordinate) - Method in class uk.ac.roslin.ensembl.model.CoordinateSet

Returns whether a test Coordinate is contained in this CoordinateSet range WITHOUT any gaps.

containsPoint(Integer) - Method in class uk.ac.roslin.ensembl.model.Coordinate

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

convertChromosomePositionToFeature(Integer) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAFeature

Converts an Integer position on the TopLevel-annotated Target (typically the Chromosome) to the position on this feature.

convertChromosomeToPrimaryTranscriptPosition(Integer) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DATranscript

Returns the mapped relative primaryTranscript position for a given Chromosome (or other Toplevel genomic) position.

convertChromosomeToProcessedTranscriptPosition(Integer) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DATranscript

Converts an Integer position on the TopLevel-annotated Target (typically the Chromosome) to the position on the processed (spliced) Transcript.

convertPrimaryToProcessedTranscriptPosition(Integer) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DATranscript

Returns the mapped position on the Processed transcript equivalent to the given position on the Primary (unprocessed) transcript

convertPrimaryTranscriptPositionToChromosome(Integer) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DATranscript

Returns the mapped Chromosomal position for a given primaryTranscript position.

convertProcessedToPrimaryTranscriptPosition(Integer) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DATranscript

Returns the mapped position on the Primary transcript equivalent to the given position on the processed transcript

convertProcessedTranscriptPositionToChromosome(Integer) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DATranscript

Converts an Integer position on the processed (spliced) transcript to the position on the TopLevel-annotated Target (typically the Chromosome).

convertToTargetCoordinate(Integer, Integer) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAFeature

Converts a given range (relative to the annotation start site) to the Coordinates on the annotated target TopLevel (genomic) sequence.

convertToTargetPosition(Integer) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAFeature

Converts an Integer relative to the annotation start site to the position on the annotated TopLevel target (genomic) sequence.

Coordinate - Class in uk.ac.roslin.ensembl.model

In general a Coordinate must have a non-null non-zero value for both start and end.

Coordinate() - Constructor for class uk.ac.roslin.ensembl.model.Coordinate

Parameterless constructor.

Coordinate(Integer, Integer) - Constructor for class uk.ac.roslin.ensembl.model.Coordinate

Utility constructor that takes start and stop integer positions with no defined Strand.

Coordinate(Integer, Integer, Integer) - Constructor for class uk.ac.roslin.ensembl.model.Coordinate

Utility constructor that takes start and stop integer positions and an Integer defining the Strand to be used (FORWARD_STRAND for '+1' and REVERSE_STRAND for '-1' - otherwise NULL).

Coordinate(Integer, Integer, Coordinate.Strand) - Constructor for class uk.ac.roslin.ensembl.model.Coordinate

Full constructor that takes start and stop integer positions and a specified Strand (FORWARD_STRAND, REVERSE_STRAND, otherwise NULL).

Coordinate.Strand - Enum in uk.ac.roslin.ensembl.model

Public enumeration of the two alternate Strands, FORWARD and REVERSE.

CoordinateSet - Class in uk.ac.roslin.ensembl.model

Extension of a TreeSet for holding COordinates ordered using their Comparator which orders Coordinate objects by the plus strand start, or the plus strand end if the starts are identical.

CoordinateSet() - Constructor for class uk.ac.roslin.ensembl.model.CoordinateSet

Public Constructor for a new Empty instance.

CoordinateSystem - Interface in uk.ac.roslin.ensembl.model.core

CoordinateSystemDAO - Interface in uk.ac.roslin.ensembl.dao.coreaccess

CoordinateSystemDefaultVersionTypeHandler - Class in uk.ac.roslin.ensembl.mapper.handler

CoordinateSystemDefaultVersionTypeHandler() - Constructor for class uk.ac.roslin.ensembl.mapper.handler.CoordinateSystemDefaultVersionTypeHandler

coordinateSystemID - Variable in class uk.ac.roslin.ensembl.mapper.query.FeatureQuery

CoordinateSystemSeqLevelTypeHandler - Class in uk.ac.roslin.ensembl.mapper.handler

CoordinateSystemSeqLevelTypeHandler() - Constructor for class uk.ac.roslin.ensembl.mapper.handler.CoordinateSystemSeqLevelTypeHandler

CoordinateSystemTypeHandler - Class in uk.ac.roslin.ensembl.mapper.handler

CoordinateSystemTypeHandler() - Constructor for class uk.ac.roslin.ensembl.mapper.handler.CoordinateSystemTypeHandler

coordSystem - Variable in class uk.ac.roslin.ensembl.datasourceaware.core.DADNASequence

coordSystemID - Variable in class uk.ac.roslin.ensembl.datasourceaware.core.DAEnsemblDNASequenceReader

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

coreexpressionatlas - Static variable in class uk.ac.roslin.ensembl.config.EnsemblDBType

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

countCompounds(NucleotideCompound...) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAEnsemblDNASequenceReader

createEmptyRegistry() - Static method in class uk.ac.roslin.ensembl.dao.database.DBRegistry

createRegistryForConfiguration(RegistryConfiguration) - Static method in class uk.ac.roslin.ensembl.dao.database.DBRegistry

createRegistryForDataSource(DBConnection.DataSource) - Static method in class uk.ac.roslin.ensembl.dao.database.DBRegistry

createRegistryForDataSourceAtReleaseVersion(DBConnection.DataSource, Integer) - Static method in class uk.ac.roslin.ensembl.dao.database.DBRegistry

createRegistryForDataSourceCurrentRelease(DBConnection.DataSource) - Static method in class uk.ac.roslin.ensembl.dao.database.DBRegistry

createUninitializedRegistryForConfiguration(RegistryConfiguration) - Static method in class uk.ac.roslin.ensembl.dao.database.DBRegistry

createUninitializedRegistryForDataSource(DBConnection.DataSource) - Static method in class uk.ac.roslin.ensembl.dao.database.DBRegistry

creationDate - Variable in class uk.ac.roslin.ensembl.datasourceaware.core.DACoreObject

csID - Variable in class uk.ac.roslin.ensembl.datasourceaware.core.DADNASequence

current - Variable in class uk.ac.roslin.ensembl.datasourceaware.core.DAFeature

D

DAAnalysis - Class in uk.ac.roslin.ensembl.datasourceaware

DAAnalysis() - Constructor for class uk.ac.roslin.ensembl.datasourceaware.DAAnalysis

DAAnalyzedFeature - Class in uk.ac.roslin.ensembl.datasourceaware.core

DAAnalyzedFeature() - Constructor for class uk.ac.roslin.ensembl.datasourceaware.core.DAAnalyzedFeature

DAAnalyzedFeature(DAOCoreFactory) - Constructor for class uk.ac.roslin.ensembl.datasourceaware.core.DAAnalyzedFeature

DAAssembledDNASequence - Class in uk.ac.roslin.ensembl.datasourceaware.core

DAAssembledDNASequence() - Constructor for class uk.ac.roslin.ensembl.datasourceaware.core.DAAssembledDNASequence

DAAssembledDNASequence(DAOCoreFactory) - Constructor for class uk.ac.roslin.ensembl.datasourceaware.core.DAAssembledDNASequence

DAAssembly - Class in uk.ac.roslin.ensembl.datasourceaware.core

DAAssembly() - Constructor for class uk.ac.roslin.ensembl.datasourceaware.core.DAAssembly

DAChromosome - Class in uk.ac.roslin.ensembl.datasourceaware.core

A DAChromosome is a particular type of DAAssembledDNASequence for representing whole chromosomes.

DAChromosome() - Constructor for class uk.ac.roslin.ensembl.datasourceaware.core.DAChromosome

DAChromosome(DAOCoreFactory) - Constructor for class uk.ac.roslin.ensembl.datasourceaware.core.DAChromosome

daComparator - Static variable in class uk.ac.roslin.ensembl.datasourceaware.DAObject

DACoordinateSystem - Class in uk.ac.roslin.ensembl.datasourceaware.core

DACoordinateSystem() - Constructor for class uk.ac.roslin.ensembl.datasourceaware.core.DACoordinateSystem

DACoreObject - Class in uk.ac.roslin.ensembl.datasourceaware.core

DACoreObject() - Constructor for class uk.ac.roslin.ensembl.datasourceaware.core.DACoreObject

DACoreObject(DAOCoreFactory) - Constructor for class uk.ac.roslin.ensembl.datasourceaware.core.DACoreObject

DADNASequence - Class in uk.ac.roslin.ensembl.datasourceaware.core

DADNASequence() - Constructor for class uk.ac.roslin.ensembl.datasourceaware.core.DADNASequence

DADNASequence(DAEnsemblDNASequenceReader) - Constructor for class uk.ac.roslin.ensembl.datasourceaware.core.DADNASequence

DADNASequence(String) - Constructor for class uk.ac.roslin.ensembl.datasourceaware.core.DADNASequence

DADNASequence(DAOCoreFactory) - Constructor for class uk.ac.roslin.ensembl.datasourceaware.core.DADNASequence

DAEnsemblDNASequenceReader - Class in uk.ac.roslin.ensembl.datasourceaware.core

DAEnsemblDNASequenceReader() - Constructor for class uk.ac.roslin.ensembl.datasourceaware.core.DAEnsemblDNASequenceReader

DAEnsemblDNASequenceReader(Integer, Integer, Integer, String, DAOCoreFactory) - Constructor for class uk.ac.roslin.ensembl.datasourceaware.core.DAEnsemblDNASequenceReader

DAEnsemblDNASequenceReader.EmptyIterator<NucleotideCompound> - Class in uk.ac.roslin.ensembl.datasourceaware.core

DAEnsemblDNASequenceReader.EmptyIterator() - Constructor for class uk.ac.roslin.ensembl.datasourceaware.core.DAEnsemblDNASequenceReader.EmptyIterator

DAExon - Class in uk.ac.roslin.ensembl.datasourceaware.core

DAExon() - Constructor for class uk.ac.roslin.ensembl.datasourceaware.core.DAExon

DAExon(DAOCoreFactory) - Constructor for class uk.ac.roslin.ensembl.datasourceaware.core.DAExon

DAFeature - Class in uk.ac.roslin.ensembl.datasourceaware.core

DAFeature() - Constructor for class uk.ac.roslin.ensembl.datasourceaware.core.DAFeature

DAFeature(DAOCoreFactory) - Constructor for class uk.ac.roslin.ensembl.datasourceaware.core.DAFeature

DAFeature.Status - Enum in uk.ac.roslin.ensembl.datasourceaware.core

DAGene - Class in uk.ac.roslin.ensembl.datasourceaware.core

DAGene() - Constructor for class uk.ac.roslin.ensembl.datasourceaware.core.DAGene

DAGene(DAOCoreFactory) - Constructor for class uk.ac.roslin.ensembl.datasourceaware.core.DAGene

DAHomologyPairRelationship - Class in uk.ac.roslin.ensembl.datasourceaware.compara

DAHomologyPairRelationship() - Constructor for class uk.ac.roslin.ensembl.datasourceaware.compara.DAHomologyPairRelationship

DAHomologyRelationship - Class in uk.ac.roslin.ensembl.datasourceaware.compara

DAHomologyRelationship() - Constructor for class uk.ac.roslin.ensembl.datasourceaware.compara.DAHomologyRelationship

DAObject - Class in uk.ac.roslin.ensembl.datasourceaware

DAObject() - Constructor for class uk.ac.roslin.ensembl.datasourceaware.DAObject

DAObject(DAOFactory) - Constructor for class uk.ac.roslin.ensembl.datasourceaware.DAObject

DAObject.DAComparator - Class in uk.ac.roslin.ensembl.datasourceaware

DAObject.DAComparator() - Constructor for class uk.ac.roslin.ensembl.datasourceaware.DAObject.DAComparator

DAOCollectionCoreFactory - Interface in uk.ac.roslin.ensembl.dao.factory

DAOCollectionFactory - Interface in uk.ac.roslin.ensembl.dao.factory

DAOCollectionFuncgenFactory - Interface in uk.ac.roslin.ensembl.dao.factory

DAOCollectionVariationFactory - Interface in uk.ac.roslin.ensembl.dao.factory

DAOComparaFactory - Interface in uk.ac.roslin.ensembl.dao.factory

DAOCoreFactory - Interface in uk.ac.roslin.ensembl.dao.factory

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

daoFactory - Variable in class uk.ac.roslin.ensembl.dao.database.DBBaseDAO

DAOFactory - Interface in uk.ac.roslin.ensembl.dao.factory

daoFactory - Variable in class uk.ac.roslin.ensembl.datasourceaware.core.DADNASequence

daoFactory - Variable in class uk.ac.roslin.ensembl.datasourceaware.DAObject

DAOFactoryWithAnalyses - Interface in uk.ac.roslin.ensembl.dao.factory

DAOFuncgenFactory - Interface in uk.ac.roslin.ensembl.dao.factory

DAOSingleSpeciesCoreFactory - Interface in uk.ac.roslin.ensembl.dao.factory

DAOSingleSpeciesFactory - Interface in uk.ac.roslin.ensembl.dao.factory

DAOSpeciesFactory - Interface in uk.ac.roslin.ensembl.dao.factory

DAOVariationFactory - Interface in uk.ac.roslin.ensembl.dao.factory

DAProteinFeature - Class in uk.ac.roslin.ensembl.datasourceaware.core

DAProteinFeature() - Constructor for class uk.ac.roslin.ensembl.datasourceaware.core.DAProteinFeature

DAProteinFeature(DAOCoreFactory) - Constructor for class uk.ac.roslin.ensembl.datasourceaware.core.DAProteinFeature

dASequence - Variable in class uk.ac.roslin.ensembl.datasourceaware.core.DAEnsemblDNASequenceReader

database - Variable in class uk.ac.roslin.ensembl.dao.database.factory.DBDAOFactory

Database - Interface in uk.ac.roslin.ensembl.model.database

DatabaseDAO - Interface in uk.ac.roslin.ensembl.dao

DatabaseMapper - Interface in uk.ac.roslin.ensembl.mapper

databaseName - Variable in class uk.ac.roslin.ensembl.dao.database.factory.DBDAOFactory

databaseStyleSpeciesName - Variable in class uk.ac.roslin.ensembl.dao.database.DBSpecies

databaseType - Variable in class uk.ac.roslin.ensembl.dao.database.factory.DBDAOFactory

DatabaseType - Interface in uk.ac.roslin.ensembl.model.database

Interface for representing static DatabaseTypes

DatabaseWithExternalDBs - Interface in uk.ac.roslin.ensembl.model.database

DATranscript - Class in uk.ac.roslin.ensembl.datasourceaware.core

DATranscript() - Constructor for class uk.ac.roslin.ensembl.datasourceaware.core.DATranscript

DATranscript(DAOCoreFactory) - Constructor for class uk.ac.roslin.ensembl.datasourceaware.core.DATranscript

DATranslation - Class in uk.ac.roslin.ensembl.datasourceaware.core

DATranslation() - Constructor for class uk.ac.roslin.ensembl.datasourceaware.core.DATranslation

DAVariation - Class in uk.ac.roslin.ensembl.datasourceaware.variation

DAVariation() - Constructor for class uk.ac.roslin.ensembl.datasourceaware.variation.DAVariation

DAVariation(DAOVariationFactory) - Constructor for class uk.ac.roslin.ensembl.datasourceaware.variation.DAVariation

DAVariationXRef - Class in uk.ac.roslin.ensembl.datasourceaware.variation

DAVariationXRef() - Constructor for class uk.ac.roslin.ensembl.datasourceaware.variation.DAVariationXRef

DAXRef - Class in uk.ac.roslin.ensembl.datasourceaware

DAXRef() - Constructor for class uk.ac.roslin.ensembl.datasourceaware.DAXRef

DBAnalysisDAO - Class in uk.ac.roslin.ensembl.dao.database

DBAnalysisDAO() - Constructor for class uk.ac.roslin.ensembl.dao.database.DBAnalysisDAO

DBAnalysisDAO(DAOFactory) - Constructor for class uk.ac.roslin.ensembl.dao.database.DBAnalysisDAO

DBAssemblyDAO - Class in uk.ac.roslin.ensembl.dao.database.coreaccess

DBAssemblyDAO() - Constructor for class uk.ac.roslin.ensembl.dao.database.coreaccess.DBAssemblyDAO

DBAssemblyDAO(DAOSingleSpeciesCoreFactory) - Constructor for class uk.ac.roslin.ensembl.dao.database.coreaccess.DBAssemblyDAO

DBAssemblyDAO(DAOCollectionCoreFactory) - Constructor for class uk.ac.roslin.ensembl.dao.database.coreaccess.DBAssemblyDAO

DBAssemblyDAO.PARMappingHandler - Class in uk.ac.roslin.ensembl.dao.database.coreaccess

DBAssemblyDAO.PARMappingHandler(List<HashMap>, DAChromosome, DAChromosome) - Constructor for class uk.ac.roslin.ensembl.dao.database.coreaccess.DBAssemblyDAO.PARMappingHandler

DBBaseDAO - Class in uk.ac.roslin.ensembl.dao.database

DBBaseDAO() - Constructor for class uk.ac.roslin.ensembl.dao.database.DBBaseDAO

DBBaseDAO(DAOFactory) - Constructor for class uk.ac.roslin.ensembl.dao.database.DBBaseDAO

Constructor for (subclasses of) this class.

DBBaseDAO(Properties) - Constructor for class uk.ac.roslin.ensembl.dao.database.DBBaseDAO

Constructor for (subclasses of) this class.

DBChromosomeDAO - Class in uk.ac.roslin.ensembl.dao.database.coreaccess

DBChromosomeDAO() - Constructor for class uk.ac.roslin.ensembl.dao.database.coreaccess.DBChromosomeDAO

DBChromosomeDAO(DAOSingleSpeciesCoreFactory) - Constructor for class uk.ac.roslin.ensembl.dao.database.coreaccess.DBChromosomeDAO

DBChromosomeDAO(DAOCollectionCoreFactory) - Constructor for class uk.ac.roslin.ensembl.dao.database.coreaccess.DBChromosomeDAO

DBChromosomeDAO.AssemblyExceptionRowHandler - Class in uk.ac.roslin.ensembl.dao.database.coreaccess

DBChromosomeDAO.AssemblyExceptionRowHandler(TreeMap<String, DAChromosome>, List<HashMap>) - Constructor for class uk.ac.roslin.ensembl.dao.database.coreaccess.DBChromosomeDAO.AssemblyExceptionRowHandler

DBCollection - Class in uk.ac.roslin.ensembl.dao.database

DBCollection() - Constructor for class uk.ac.roslin.ensembl.dao.database.DBCollection

DBCollection(DBCollectionCoreDatabase) - Constructor for class uk.ac.roslin.ensembl.dao.database.DBCollection

DBCollectionCoreDatabase - Class in uk.ac.roslin.ensembl.dao.database

DBCollectionCoreDatabase(String, EnsemblDBType, Registry) - Constructor for class uk.ac.roslin.ensembl.dao.database.DBCollectionCoreDatabase

DBCollectionDatabase - Class in uk.ac.roslin.ensembl.dao.database

DBCollectionDatabase(String, EnsemblDBType, Registry) - Constructor for class uk.ac.roslin.ensembl.dao.database.DBCollectionDatabase

DBCollectionSpecies - Class in uk.ac.roslin.ensembl.dao.database

DBCollectionSpecies() - Constructor for class uk.ac.roslin.ensembl.dao.database.DBCollectionSpecies

DBCollectionSpecies(DBCollectionCoreDatabase) - Constructor for class uk.ac.roslin.ensembl.dao.database.DBCollectionSpecies

DBComparisonDatabase - Class in uk.ac.roslin.ensembl.dao.database

DBComparisonDatabase(String, EnsemblDBType, DBRegistry) - Constructor for class uk.ac.roslin.ensembl.dao.database.DBComparisonDatabase

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 - Variable in class uk.ac.roslin.ensembl.dao.database.DBRegistry

DBConnection.DataSource - Enum in uk.ac.roslin.ensembl.config

DBCoordinateSystemDAO - Class in uk.ac.roslin.ensembl.dao.database.coreaccess

DBCoordinateSystemDAO() - Constructor for class uk.ac.roslin.ensembl.dao.database.coreaccess.DBCoordinateSystemDAO

DBCoordinateSystemDAO(DAOSingleSpeciesCoreFactory) - Constructor for class uk.ac.roslin.ensembl.dao.database.coreaccess.DBCoordinateSystemDAO

DBCoordinateSystemDAO(DAOCollectionCoreFactory) - Constructor for class uk.ac.roslin.ensembl.dao.database.coreaccess.DBCoordinateSystemDAO

DBCoreObjectDAO - Class in uk.ac.roslin.ensembl.dao.database.coreaccess

DBCoreObjectDAO() - Constructor for class uk.ac.roslin.ensembl.dao.database.coreaccess.DBCoreObjectDAO

DBCoreObjectDAO(DAOSingleSpeciesCoreFactory) - Constructor for class uk.ac.roslin.ensembl.dao.database.coreaccess.DBCoreObjectDAO

DBCoreObjectDAO(DAOCollectionCoreFactory) - Constructor for class uk.ac.roslin.ensembl.dao.database.coreaccess.DBCoreObjectDAO

DBDAOCollectionCoreFactory - Class in uk.ac.roslin.ensembl.dao.database.factory

DBDAOCollectionCoreFactory() - Constructor for class uk.ac.roslin.ensembl.dao.database.factory.DBDAOCollectionCoreFactory

DBDAOCollectionCoreFactory(CollectionDatabase, CollectionSpecies) - Constructor for class uk.ac.roslin.ensembl.dao.database.factory.DBDAOCollectionCoreFactory

DBDAOCollectionFactory - Class in uk.ac.roslin.ensembl.dao.database.factory

DBDAOCollectionFactory() - Constructor for class uk.ac.roslin.ensembl.dao.database.factory.DBDAOCollectionFactory

DBDAOCollectionFactory(CollectionDatabase, CollectionSpecies) - Constructor for class uk.ac.roslin.ensembl.dao.database.factory.DBDAOCollectionFactory

DBDAOCollectionFuncgenFactory - Class in uk.ac.roslin.ensembl.dao.database.factory

DBDAOCollectionFuncgenFactory() - Constructor for class uk.ac.roslin.ensembl.dao.database.factory.DBDAOCollectionFuncgenFactory

DBDAOCollectionFuncgenFactory(CollectionDatabase, CollectionSpecies) - Constructor for class uk.ac.roslin.ensembl.dao.database.factory.DBDAOCollectionFuncgenFactory

DBDAOCollectionVariationFactory - Class in uk.ac.roslin.ensembl.dao.database.factory

DBDAOCollectionVariationFactory() - Constructor for class uk.ac.roslin.ensembl.dao.database.factory.DBDAOCollectionVariationFactory

DBDAOCollectionVariationFactory(CollectionDatabase, CollectionSpecies) - Constructor for class uk.ac.roslin.ensembl.dao.database.factory.DBDAOCollectionVariationFactory

DBDAOComparaFactory - Class in uk.ac.roslin.ensembl.dao.database.factory

DBDAOComparaFactory() - Constructor for class uk.ac.roslin.ensembl.dao.database.factory.DBDAOComparaFactory

DBDAOComparaFactory(ComparisonDatabase) - Constructor for class uk.ac.roslin.ensembl.dao.database.factory.DBDAOComparaFactory

DBDAOFactory - Class in uk.ac.roslin.ensembl.dao.database.factory

DBDAOFactory() - Constructor for class uk.ac.roslin.ensembl.dao.database.factory.DBDAOFactory

DBDAOFactory(Database) - Constructor for class uk.ac.roslin.ensembl.dao.database.factory.DBDAOFactory

DBDAOSingleSpeciesCoreFactory - Class in uk.ac.roslin.ensembl.dao.database.factory

DBDAOSingleSpeciesCoreFactory() - Constructor for class uk.ac.roslin.ensembl.dao.database.factory.DBDAOSingleSpeciesCoreFactory

DBDAOSingleSpeciesCoreFactory(SingleSpeciesDatabase) - Constructor for class uk.ac.roslin.ensembl.dao.database.factory.DBDAOSingleSpeciesCoreFactory

DBDAOSingleSpeciesFactory - Class in uk.ac.roslin.ensembl.dao.database.factory

DBDAOSingleSpeciesFactory() - Constructor for class uk.ac.roslin.ensembl.dao.database.factory.DBDAOSingleSpeciesFactory

DBDAOSingleSpeciesFactory(SingleSpeciesDatabase) - Constructor for class uk.ac.roslin.ensembl.dao.database.factory.DBDAOSingleSpeciesFactory

DBDAOSingleSpeciesFuncgenFactory - Class in uk.ac.roslin.ensembl.dao.database.factory

DBDAOSingleSpeciesFuncgenFactory() - Constructor for class uk.ac.roslin.ensembl.dao.database.factory.DBDAOSingleSpeciesFuncgenFactory

DBDAOSingleSpeciesFuncgenFactory(SingleSpeciesDatabase) - Constructor for class uk.ac.roslin.ensembl.dao.database.factory.DBDAOSingleSpeciesFuncgenFactory

DBDAOSingleSpeciesVariationFactory - Class in uk.ac.roslin.ensembl.dao.database.factory

DBDAOSingleSpeciesVariationFactory() - Constructor for class uk.ac.roslin.ensembl.dao.database.factory.DBDAOSingleSpeciesVariationFactory

DBDAOSingleSpeciesVariationFactory(SingleSpeciesDatabase) - Constructor for class uk.ac.roslin.ensembl.dao.database.factory.DBDAOSingleSpeciesVariationFactory

DBDAOSpeciesFactory - Class in uk.ac.roslin.ensembl.dao.database.factory

DBDAOSpeciesFactory() - Constructor for class uk.ac.roslin.ensembl.dao.database.factory.DBDAOSpeciesFactory

DBDAOSpeciesFactory(SingleSpeciesDatabase) - Constructor for class uk.ac.roslin.ensembl.dao.database.factory.DBDAOSpeciesFactory

DBDAOSpeciesFactory(CollectionDatabase, CollectionSpecies) - Constructor for class uk.ac.roslin.ensembl.dao.database.factory.DBDAOSpeciesFactory

DBDatabase - Class in uk.ac.roslin.ensembl.dao.database

DBDatabase() - Constructor for class uk.ac.roslin.ensembl.dao.database.DBDatabase

DBDatabase(String, EnsemblDBType, Registry) - Constructor for class uk.ac.roslin.ensembl.dao.database.DBDatabase

DBDNASequenceDAO - Class in uk.ac.roslin.ensembl.dao.database.coreaccess

DBDNASequenceDAO() - Constructor for class uk.ac.roslin.ensembl.dao.database.coreaccess.DBDNASequenceDAO

DBDNASequenceDAO(DAOSingleSpeciesCoreFactory) - Constructor for class uk.ac.roslin.ensembl.dao.database.coreaccess.DBDNASequenceDAO

DBDNASequenceDAO(DAOCollectionCoreFactory) - Constructor for class uk.ac.roslin.ensembl.dao.database.coreaccess.DBDNASequenceDAO

DBDNASequenceDAO.SequenceRowHandler - Class in uk.ac.roslin.ensembl.dao.database.coreaccess

DBDNASequenceDAO.SequenceRowHandler(List<HashMap>) - Constructor for class uk.ac.roslin.ensembl.dao.database.coreaccess.DBDNASequenceDAO.SequenceRowHandler

DBExonDAO - Class in uk.ac.roslin.ensembl.dao.database.coreaccess

DBExonDAO() - Constructor for class uk.ac.roslin.ensembl.dao.database.coreaccess.DBExonDAO

DBExonDAO(DAOSingleSpeciesCoreFactory) - Constructor for class uk.ac.roslin.ensembl.dao.database.coreaccess.DBExonDAO

DBExonDAO(DAOCollectionCoreFactory) - Constructor for class uk.ac.roslin.ensembl.dao.database.coreaccess.DBExonDAO

DBExonDAO.ExonRowHandler - Class in uk.ac.roslin.ensembl.dao.database.coreaccess

DBExonDAO.ExonRowHandler(List<HashMap>, DATranscript) - Constructor for class uk.ac.roslin.ensembl.dao.database.coreaccess.DBExonDAO.ExonRowHandler

DBExonDAO.ExonRowHandler(List<HashMap>) - Constructor for class uk.ac.roslin.ensembl.dao.database.coreaccess.DBExonDAO.ExonRowHandler

DBGeneDAO - Class in uk.ac.roslin.ensembl.dao.database.coreaccess

DBGeneDAO() - Constructor for class uk.ac.roslin.ensembl.dao.database.coreaccess.DBGeneDAO

DBGeneDAO(DAOSingleSpeciesCoreFactory) - Constructor for class uk.ac.roslin.ensembl.dao.database.coreaccess.DBGeneDAO

DBGeneDAO(DAOCollectionCoreFactory) - Constructor for class uk.ac.roslin.ensembl.dao.database.coreaccess.DBGeneDAO

DBGeneDAO.GeneMappingRowHandler - Class in uk.ac.roslin.ensembl.dao.database.coreaccess

DBGeneDAO.GeneMappingRowHandler(List<HashMap>) - Constructor for class uk.ac.roslin.ensembl.dao.database.coreaccess.DBGeneDAO.GeneMappingRowHandler

DBGeneDAO.GeneMappingRowHandler(List<HashMap>, DADNASequence) - Constructor for class uk.ac.roslin.ensembl.dao.database.coreaccess.DBGeneDAO.GeneMappingRowHandler

DBGeneDAO.MappingRowHandler - Class in uk.ac.roslin.ensembl.dao.database.coreaccess

DBGeneDAO.MappingRowHandler(List<HashMap>) - Constructor for class uk.ac.roslin.ensembl.dao.database.coreaccess.DBGeneDAO.MappingRowHandler

DBGeneDAO.MappingRowHandler(List<HashMap>, DADNASequence) - Constructor for class uk.ac.roslin.ensembl.dao.database.coreaccess.DBGeneDAO.MappingRowHandler

DBHomologyDAO - Class in uk.ac.roslin.ensembl.dao.database.compara

DBHomologyDAO(DAOComparaFactory) - Constructor for class uk.ac.roslin.ensembl.dao.database.compara.DBHomologyDAO

DBProteinFeatureDAO - Class in uk.ac.roslin.ensembl.dao.database.coreaccess

DBProteinFeatureDAO() - Constructor for class uk.ac.roslin.ensembl.dao.database.coreaccess.DBProteinFeatureDAO

DBProteinFeatureDAO(DAOSingleSpeciesCoreFactory) - Constructor for class uk.ac.roslin.ensembl.dao.database.coreaccess.DBProteinFeatureDAO

DBProteinFeatureDAO(DAOCollectionCoreFactory) - Constructor for class uk.ac.roslin.ensembl.dao.database.coreaccess.DBProteinFeatureDAO

DBRegistry - Class in uk.ac.roslin.ensembl.dao.database

DBResultHandler - Interface in uk.ac.roslin.ensembl.mapper.handler

DBSeqLength - Variable in class uk.ac.roslin.ensembl.datasourceaware.core.DADNASequence

DBSingleSpeciesCoreDatabase - Class in uk.ac.roslin.ensembl.dao.database

DBSingleSpeciesCoreDatabase(String, EnsemblDBType, Registry) - Constructor for class uk.ac.roslin.ensembl.dao.database.DBSingleSpeciesCoreDatabase

DBSingleSpeciesDatabase - Class in uk.ac.roslin.ensembl.dao.database

DBSingleSpeciesDatabase(String, EnsemblDBType, Registry) - Constructor for class uk.ac.roslin.ensembl.dao.database.DBSingleSpeciesDatabase

DBSingleSpeciesVariationDatabase - Class in uk.ac.roslin.ensembl.dao.database

DBSingleSpeciesVariationDatabase(String, EnsemblDBType, Registry) - Constructor for class uk.ac.roslin.ensembl.dao.database.DBSingleSpeciesVariationDatabase

DBSpecies - Class in uk.ac.roslin.ensembl.dao.database

DBSpecies() - Constructor for class uk.ac.roslin.ensembl.dao.database.DBSpecies

DBSpecies(DBSingleSpeciesCoreDatabase) - Constructor for class uk.ac.roslin.ensembl.dao.database.DBSpecies

dbSpeciesName - Variable in class uk.ac.roslin.ensembl.dao.database.DBSingleSpeciesDatabase

dbSpeciesName - Variable in class uk.ac.roslin.ensembl.datasourceaware.core.DADNASequence

dbStyleNameByVersion - Variable in class uk.ac.roslin.ensembl.dao.database.DBSpecies

DBTranscriptDAO - Class in uk.ac.roslin.ensembl.dao.database.coreaccess

DBTranscriptDAO() - Constructor for class uk.ac.roslin.ensembl.dao.database.coreaccess.DBTranscriptDAO

DBTranscriptDAO(DAOSingleSpeciesCoreFactory) - Constructor for class uk.ac.roslin.ensembl.dao.database.coreaccess.DBTranscriptDAO

DBTranscriptDAO(DAOCollectionCoreFactory) - Constructor for class uk.ac.roslin.ensembl.dao.database.coreaccess.DBTranscriptDAO

DBTranscriptDAO.TranscriptRowHandler - Class in uk.ac.roslin.ensembl.dao.database.coreaccess

DBTranscriptDAO.TranscriptRowHandler(List<HashMap>, DAGene) - Constructor for class uk.ac.roslin.ensembl.dao.database.coreaccess.DBTranscriptDAO.TranscriptRowHandler

DBTranscriptDAO.TranscriptRowHandler(List<HashMap>) - Constructor for class uk.ac.roslin.ensembl.dao.database.coreaccess.DBTranscriptDAO.TranscriptRowHandler

DBTranslationDAO - Class in uk.ac.roslin.ensembl.dao.database.coreaccess

DBTranslationDAO() - Constructor for class uk.ac.roslin.ensembl.dao.database.coreaccess.DBTranslationDAO

DBTranslationDAO(DAOSingleSpeciesCoreFactory) - Constructor for class uk.ac.roslin.ensembl.dao.database.coreaccess.DBTranslationDAO

DBTranslationDAO(DAOCollectionCoreFactory) - Constructor for class uk.ac.roslin.ensembl.dao.database.coreaccess.DBTranslationDAO

dBType - Variable in class uk.ac.roslin.ensembl.dao.database.factory.DBDAOFactory

DBVariationDAO - Class in uk.ac.roslin.ensembl.dao.database.variation

DBVariationDAO() - Constructor for class uk.ac.roslin.ensembl.dao.database.variation.DBVariationDAO

DBVariationDAO(DAOVariationFactory) - Constructor for class uk.ac.roslin.ensembl.dao.database.variation.DBVariationDAO

dbVersion - Variable in class uk.ac.roslin.ensembl.dao.database.factory.DBDAOFactory

dbVersion - Variable in class uk.ac.roslin.ensembl.datasourceaware.core.DADNASequence

dbVersion - Variable in class uk.ac.roslin.ensembl.datasourceaware.DAObject

dbVersions - Variable in class uk.ac.roslin.ensembl.dao.database.DBSpecies

DBXRefDAO - Class in uk.ac.roslin.ensembl.dao.database

DBXRefDAO() - Constructor for class uk.ac.roslin.ensembl.dao.database.DBXRefDAO

DBXRefDAO(DAOFactory) - Constructor for class uk.ac.roslin.ensembl.dao.database.DBXRefDAO

defaultVersion - Static variable in class uk.ac.roslin.ensembl.config.EnsemblCoordSystemType

defaultVersion - Variable in class uk.ac.roslin.ensembl.datasourceaware.core.DACoordinateSystem

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

description - Variable in class uk.ac.roslin.ensembl.datasourceaware.core.DAFeature

DisplayID - Static variable in class uk.ac.roslin.ensembl.config.ExternalDBType

displayName - Variable in class uk.ac.roslin.ensembl.datasourceaware.core.DAFeature

DisplayTerm - Variable in class uk.ac.roslin.ensembl.model.variation.VariationType

displayXRef - Variable in class uk.ac.roslin.ensembl.datasourceaware.core.DAFeature

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

DNASequenceDAO - Interface in uk.ac.roslin.ensembl.dao.coreaccess

DNASequences - Class in uk.ac.roslin.ensembl.demo

DNASequences() - Constructor for class uk.ac.roslin.ensembl.demo.DNASequences

E

ECHINODERM_MITOCHONDRIAL - Static variable in class uk.ac.roslin.ensembl.config.CodonTable

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.

EnsemblConnection - Class in uk.ac.roslin.ensembl.demo

EnsemblConnection() - Constructor for class uk.ac.roslin.ensembl.demo.EnsemblConnection

EnsemblCoordSystemType - Class in uk.ac.roslin.ensembl.config

EnsemblCoreObjectType - Class in uk.ac.roslin.ensembl.config

EnsemblCoreObjectType(String) - 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

EnsemblGeneHomologues - Class in uk.ac.roslin.ensembl.demo

EnsemblGeneHomologues() - Constructor for class uk.ac.roslin.ensembl.demo.EnsemblGeneHomologues

ensemblNameForAliasHash - Variable in class uk.ac.roslin.ensembl.dao.database.DBRegistry

EnsemblRuntimeException - Exception in uk.ac.roslin.ensembl.exception

EnsemblRuntimeException() - Constructor for exception uk.ac.roslin.ensembl.exception.EnsemblRuntimeException

EnsemblRuntimeException(String) - Constructor for exception uk.ac.roslin.ensembl.exception.EnsemblRuntimeException

EnsemblRuntimeException(String, Exception) - Constructor for exception uk.ac.roslin.ensembl.exception.EnsemblRuntimeException

EnsemblRuntimeException(Exception) - Constructor for exception uk.ac.roslin.ensembl.exception.EnsemblRuntimeException

ensemblSchema - Variable in class uk.ac.roslin.ensembl.dao.database.factory.DBDAOFactory

ensemblStablePrefix - Variable in class uk.ac.roslin.ensembl.dao.database.DBSpecies

EnsemblSyntenies - Class in uk.ac.roslin.ensembl.demo

EnsemblSyntenies() - Constructor for class uk.ac.roslin.ensembl.demo.EnsemblSyntenies

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.dao.database.DBCollectionSpecies

equals(Object) - Method in class uk.ac.roslin.ensembl.model.ExternalDB

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

EUPLOTID_NUCLEAR - Static variable in class uk.ac.roslin.ensembl.config.CodonTable

Evidence - Class in uk.ac.roslin.ensembl.model

Evidence() - Constructor for class uk.ac.roslin.ensembl.model.Evidence

ExaminingObjectHashCodes - Class in uk.ac.roslin.ensembl.demo

ExaminingObjectHashCodes() - Constructor for class uk.ac.roslin.ensembl.demo.ExaminingObjectHashCodes

ExistsTypeHandler - Class in uk.ac.roslin.ensembl.mapper.handler

ExistsTypeHandler() - Constructor for class uk.ac.roslin.ensembl.mapper.handler.ExistsTypeHandler

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

ExonDAO - Interface in uk.ac.roslin.ensembl.dao.coreaccess

ExonMapper - Interface in uk.ac.roslin.ensembl.mapper.core

ExonsTranscriptionAndTranslation - Class in uk.ac.roslin.ensembl.demo

ExonsTranscriptionAndTranslation() - Constructor for class uk.ac.roslin.ensembl.demo.ExonsTranscriptionAndTranslation

externalDB - Static variable in class uk.ac.roslin.ensembl.config.EnsemblCoreObjectType

ExternalDB - Class in uk.ac.roslin.ensembl.model

ExternalDB() - Constructor for class uk.ac.roslin.ensembl.model.ExternalDB

ExternalDBType - Class in uk.ac.roslin.ensembl.config

ExternalDBTypeHandler - Class in uk.ac.roslin.ensembl.mapper.handler

ExternalDBTypeHandler() - Constructor for class uk.ac.roslin.ensembl.mapper.handler.ExternalDBTypeHandler

F

factory - Variable in class uk.ac.roslin.ensembl.datasourceaware.core.DAEnsemblDNASequenceReader

Feature - Interface in uk.ac.roslin.ensembl.model.core

featureID - Variable in class uk.ac.roslin.ensembl.mapper.query.FeatureQuery

featureName - Variable in class uk.ac.roslin.ensembl.mapper.query.FeatureQuery

FeatureQuery - Class in uk.ac.roslin.ensembl.mapper.query

FeatureQuery() - Constructor for class uk.ac.roslin.ensembl.mapper.query.FeatureQuery

featureStableID - Variable in class uk.ac.roslin.ensembl.mapper.query.FeatureQuery

FeatureType - Class in uk.ac.roslin.ensembl.config

findMybatisSchemaForSchemaVersion(DatabaseType, String) - Method in class uk.ac.roslin.ensembl.dao.database.DBRegistry

findMybatisSchemaForSchemaVersion(DatabaseType, String) - Method in interface uk.ac.roslin.ensembl.model.database.Registry

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

FLATWORM_MITOCHONDRIAL - Static variable in class uk.ac.roslin.ensembl.config.CodonTable

flipped - Variable in class uk.ac.roslin.ensembl.datasourceaware.variation.DAVariation

fragments - Variable in class uk.ac.roslin.ensembl.dao.database.DBSpecies

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

GapSequence - Class in uk.ac.roslin.ensembl.datasourceaware.core

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

Gene - Interface in uk.ac.roslin.ensembl.model.core

GENE_SPLIT - Static variable in class uk.ac.roslin.ensembl.model.compara.HomologyType

Ensembl pipeline annotates gene_split

GeneDAO - Interface in uk.ac.roslin.ensembl.dao.coreaccess

geneID - Variable in class uk.ac.roslin.ensembl.mapper.query.FeatureQuery

GeneMapper - Interface in uk.ac.roslin.ensembl.mapper.core

Genes - Class in uk.ac.roslin.ensembl.demo

Genes() - Constructor for class uk.ac.roslin.ensembl.demo.Genes

genescaffold - Static variable in class uk.ac.roslin.ensembl.config.EnsemblCoordSystemType

GenomesConnection - Class in uk.ac.roslin.ensembl.demo

GenomesConnection() - Constructor for class uk.ac.roslin.ensembl.demo.GenomesConnection

genus_species - Variable in class uk.ac.roslin.ensembl.dao.database.factory.DBDAOSingleSpeciesFactory

getAAPositionFromChromosome(Integer) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DATranslation

Returns the amino acid position on this translation for a given Chromosomal Position

getAAPositionFromPrimaryTranscript(Integer) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DATranslation

Returns the amino acid position on this translation for a given Primary Transcript Position

getAAPositionFromProcessedTranscript(Integer) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DATranslation

Returns the amino acid position on this translation for a given Processed Transcript Position

getAccession() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAEnsemblDNASequenceReader

getAliases() - Method in class uk.ac.roslin.ensembl.dao.database.DBSpecies

getAliases() - Method in interface uk.ac.roslin.ensembl.model.core.Species

getAllCoreDatabaseNames(int) - Method in interface uk.ac.roslin.ensembl.mapper.DatabaseMapper

getAllCoreDatabasesForVersion(int) - Method in interface uk.ac.roslin.ensembl.dao.DatabaseDAO

getAllDatabaseNames() - Method in interface uk.ac.roslin.ensembl.mapper.DatabaseMapper

getAllDatabaseTypes() - Static method in class uk.ac.roslin.ensembl.config.EnsemblDBType

getAlleleString() - Method in class uk.ac.roslin.ensembl.datasourceaware.variation.VariationMapping

getAllHits() - Method in exception uk.ac.roslin.ensembl.exception.NonUniqueException

getAllSynonyms(XRefed) - Method in class uk.ac.roslin.ensembl.dao.database.DBXRefDAO

getAllSynonyms(XRefed) - Method in interface uk.ac.roslin.ensembl.dao.XRefDAO

getAllSynonyms() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAGene

getAllSynonyms() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DATranscript

getAllSynonyms() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DATranslation

getAllSynonyms() - Method in class uk.ac.roslin.ensembl.datasourceaware.variation.DAVariation

getAllSynonyms(FeatureQuery) - Method in interface uk.ac.roslin.ensembl.mapper.XRefMapper

getAllSynonyms() - Method in interface uk.ac.roslin.ensembl.model.variation.Variation

getAllSynonyms() - Method in interface uk.ac.roslin.ensembl.model.XRefed

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

getAllXRefs(IdentifiableObject) - Method in class uk.ac.roslin.ensembl.dao.database.DBXRefDAO

getAllXRefs(IdentifiableObject) - Method in interface uk.ac.roslin.ensembl.dao.XRefDAO

getAllXRefs() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAGene

getAllXRefs() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DATranscript

getAllXRefs() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DATranslation

getAllXRefs() - Method in interface uk.ac.roslin.ensembl.model.XRefed

getAnalyses() - Method in interface uk.ac.roslin.ensembl.dao.AnalysisDAO

getAnalyses() - Method in class uk.ac.roslin.ensembl.dao.database.DBAnalysisDAO

getAnalyses() - Method in class uk.ac.roslin.ensembl.dao.database.DBCollectionCoreDatabase

Analyses are cached at the Database level

getAnalyses() - Method in class uk.ac.roslin.ensembl.dao.database.DBSingleSpeciesCoreDatabase

Analyses are cached at the Database level

getAnalyses() - Method in interface uk.ac.roslin.ensembl.mapper.AnalysisMapper

getAnalyses() - Method in interface uk.ac.roslin.ensembl.model.database.CoreDatabase

getAnalysis(Integer) - Method in class uk.ac.roslin.ensembl.dao.database.factory.DBDAOCollectionCoreFactory

getAnalysis(Integer) - Method in class uk.ac.roslin.ensembl.dao.database.factory.DBDAOCollectionFuncgenFactory

getAnalysis(Integer) - Method in class uk.ac.roslin.ensembl.dao.database.factory.DBDAOSingleSpeciesCoreFactory

getAnalysis(Integer) - Method in class uk.ac.roslin.ensembl.dao.database.factory.DBDAOSingleSpeciesFuncgenFactory

getAnalysis(Integer) - Method in interface uk.ac.roslin.ensembl.dao.factory.DAOFactoryWithAnalyses

getAnalysis() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAAnalyzedFeature

getAnalysis() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAProteinFeature

getAnalysis() - Method in interface uk.ac.roslin.ensembl.model.core.Analyzed

getAnalysisDAO() - Method in class uk.ac.roslin.ensembl.dao.database.factory.DBDAOCollectionCoreFactory

getAnalysisDAO() - Method in class uk.ac.roslin.ensembl.dao.database.factory.DBDAOCollectionFuncgenFactory

getAnalysisDAO() - Method in class uk.ac.roslin.ensembl.dao.database.factory.DBDAOSingleSpeciesCoreFactory

getAnalysisDAO() - Method in class uk.ac.roslin.ensembl.dao.database.factory.DBDAOSingleSpeciesFuncgenFactory

getAnalysisDAO() - Method in interface uk.ac.roslin.ensembl.dao.factory.DAOFactoryWithAnalyses

getAnalysisID() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAAnalyzedFeature

getAnalysisID() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAProteinFeature

getAnalysisID() - Method in interface uk.ac.roslin.ensembl.model.core.Analyzed

getAncestralAllele() - Method in class uk.ac.roslin.ensembl.datasourceaware.variation.DAVariation

getAncestralAllele() - Method in interface uk.ac.roslin.ensembl.model.variation.Variation

getAnnotationLevelMappings() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAFeature

getAsList() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAEnsemblDNASequenceReader

getAssayType() - Method in class uk.ac.roslin.ensembl.datasourceaware.variation.DAVariationXRef

getAssembly(DAAssembledDNASequence) - Static method in class uk.ac.roslin.ensembl.datasourceaware.core.DAAssembly

getAssembly(DAAssembledDNASequence, Integer, Integer) - Static method in class uk.ac.roslin.ensembl.datasourceaware.core.DAAssembly

getAssembly() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DACoreObject

getAssembly() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DADNASequence

getAssembly() - Method in interface uk.ac.roslin.ensembl.model.core.CoreObject

getAssemblyAccession(CollectionSpecies) - Method in class uk.ac.roslin.ensembl.dao.database.DBCollectionCoreDatabase

Returns the AssemblyAccession value for this species.

getAssemblyAccession(String) - Method in class uk.ac.roslin.ensembl.dao.database.DBCollectionSpecies

getAssemblyAccession() - Method in class uk.ac.roslin.ensembl.dao.database.DBSingleSpeciesCoreDatabase

getAssemblyAccession(String) - Method in class uk.ac.roslin.ensembl.dao.database.DBSpecies

getAssemblyAccession(String) - Method in interface uk.ac.roslin.ensembl.model.core.Species

getAssemblyAccession(CollectionSpecies) - Method in interface uk.ac.roslin.ensembl.model.database.CollectionCoreDatabase

getAssemblyAccession() - Method in interface uk.ac.roslin.ensembl.model.database.SingleSpeciesCoreDatabase

getAssemblyAccessionStem() - Method in class uk.ac.roslin.ensembl.dao.database.DBSpecies

getAssemblyAccessionStem(String) - Method in class uk.ac.roslin.ensembl.dao.database.DBSpecies

getAssemblyAccessionStem() - Method in interface uk.ac.roslin.ensembl.model.core.Species

getAssemblyAccessionStem(String) - Method in interface uk.ac.roslin.ensembl.model.core.Species

getAssemblyDAO() - Method in class uk.ac.roslin.ensembl.dao.database.factory.DBDAOCollectionCoreFactory

getAssemblyDAO() - Method in class uk.ac.roslin.ensembl.dao.database.factory.DBDAOSingleSpeciesCoreFactory

getAssemblyDAO() - Method in interface uk.ac.roslin.ensembl.dao.factory.DAOCoreFactory

getAssemblyExceptions(AssemblyExceptionType) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAChromosome

Returns a MappingSet of AssemblyExceptions of the indicated AssemblyExceptionType.

getAssemblyExceptions(HashMap) - Method in interface uk.ac.roslin.ensembl.mapper.core.ChromosomeMapper

getAssemblyName(CollectionSpecies) - Method in class uk.ac.roslin.ensembl.dao.database.DBCollectionCoreDatabase

Returns the AssemblyName value for this species.

getAssemblyName(String) - Method in class uk.ac.roslin.ensembl.dao.database.DBCollectionSpecies

getAssemblyName() - Method in class uk.ac.roslin.ensembl.dao.database.DBSingleSpeciesCoreDatabase

getAssemblyName(String) - Method in class uk.ac.roslin.ensembl.dao.database.DBSpecies

getAssemblyName(String) - Method in interface uk.ac.roslin.ensembl.model.core.Species

getAssemblyName(CollectionSpecies) - Method in interface uk.ac.roslin.ensembl.model.database.CollectionCoreDatabase

getAssemblyName() - Method in interface uk.ac.roslin.ensembl.model.database.SingleSpeciesCoreDatabase

getAssemblyStart() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAAssembly

getAssemblyStart() - Method in interface uk.ac.roslin.ensembl.model.core.Assembly

getAssemblyStop() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAAssembly

getAssemblyStop() - Method in interface uk.ac.roslin.ensembl.model.core.Assembly

getAttribute(String) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DADNASequence

getAttributes() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DADNASequence

getBacterialSpeciesForAliasBeginning(String) - Method in class uk.ac.roslin.ensembl.dao.database.DBRegistry

getBacterialSpeciesForAliasBeginning(String) - Method in interface uk.ac.roslin.ensembl.model.database.Registry

getBacterialSpeciesForAliasContaining(String) - Method in class uk.ac.roslin.ensembl.dao.database.DBRegistry

getBacterialSpeciesForAliasContaining(String) - Method in interface uk.ac.roslin.ensembl.model.database.Registry

getBaseMybatis() - Method in class uk.ac.roslin.ensembl.config.SchemaVersion

getBasePositionFromChromosome(Integer) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DATranslation

Returns the nucleotide position on this translation sequence for a given Chromosomal Position

getBasePositionFromPrimaryTranscript(Integer) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DATranslation

Returns the nucleotide position on this translation sequence for a given primary Transcript position

getBasePositionFromProcessedTranscript(Integer) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DATranslation

Returns the nucleotide position on this translation sequence for a given processed (spliced) transcript position.

getBinaryRelationship() - Method in class uk.ac.roslin.ensembl.datasourceaware.compara.InverseHomologyPairRelationshipView

getBinaryRelationship() - Method in interface uk.ac.roslin.ensembl.model.relationship.InverseBinaryRelationshipView

Returns the underlying binary relationship that this is a view on

getBioEnd() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DADNASequence

getBiotype() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAGene

getBiotype() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DATranscript

getBiotype() - Method in interface uk.ac.roslin.ensembl.model.core.Gene

getbReg() - Static method in class uk.ac.roslin.ensembl.test.RegistryProvider

getBriefRegistryReport() - Method in class uk.ac.roslin.ensembl.dao.database.DBRegistry

Reports the connection and available database versions etc. for an initialized Registry.

getBriefRegistryReport() - Method in interface uk.ac.roslin.ensembl.model.database.Registry

getBuild() - Method in class uk.ac.roslin.ensembl.dao.database.DBDatabase

getBuild() - Method in interface uk.ac.roslin.ensembl.model.database.Database

getBuildCoordSystem(Species, String) - Method in class uk.ac.roslin.ensembl.dao.database.DBCollectionCoreDatabase

getBuildCoordSystem(String) - Method in class uk.ac.roslin.ensembl.dao.database.DBSingleSpeciesCoreDatabase

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 class uk.ac.roslin.ensembl.dao.database.DBCollectionCoreDatabase

getBuildLevel(String) - Method in class uk.ac.roslin.ensembl.dao.database.DBSingleSpeciesCoreDatabase

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

getBuildLevelMappings() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAFeature

getBuildLevels(CollectionSpecies) - Method in class uk.ac.roslin.ensembl.dao.database.DBCollectionCoreDatabase

getBuildLevels() - Method in class uk.ac.roslin.ensembl.dao.database.DBSingleSpeciesCoreDatabase

getCachedChromosome(DAChromosome) - Method in class uk.ac.roslin.ensembl.dao.database.DBSpecies

getCachedFragment(DAAssembledDNASequence) - Method in class uk.ac.roslin.ensembl.dao.database.DBSpecies

getCanonicalTranscript() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAGene

getCanonicalTranscript() - Method in interface uk.ac.roslin.ensembl.model.core.Gene

getCanonicalTranscriptID() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAGene

getCanonicalTranslation() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAGene

getCanonicalTranslation() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DATranscript

Returns the canonical Translation for this Transcript (if there is one).

getCanonicalTranslation() - Method in interface uk.ac.roslin.ensembl.model.core.Gene

getCanonicalTranslation() - Method in interface uk.ac.roslin.ensembl.model.core.Transcript

getCanonicalTranslationID() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DATranscript

Returns the internal database ID for the Translation object marked as 'Canonical'.

getCcdsID() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DATranscript

Returns any curated CCDS for this transcript.

getCcdsID() - Method in interface uk.ac.roslin.ensembl.model.core.Transcript

Returns any curated CCDS for this transcript.

getCcdsTranscripts(String) - Method in interface uk.ac.roslin.ensembl.mapper.core.TranscriptMapper

getCCDSXRefs() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DATranscript

getCCDSXRefs() - Method in interface uk.ac.roslin.ensembl.model.core.Transcript

getChromosomeByName(String) - Method in interface uk.ac.roslin.ensembl.dao.coreaccess.ChromosomeDAO

getChromosomeByName(String) - Method in class uk.ac.roslin.ensembl.dao.database.coreaccess.DBChromosomeDAO

getChromosomeByName(Species, String) - Method in class uk.ac.roslin.ensembl.dao.database.DBCollectionCoreDatabase

getChromosomeByName(String, String) - Method in class uk.ac.roslin.ensembl.dao.database.DBCollectionSpecies

getChromosomeByName(String) - Method in class uk.ac.roslin.ensembl.dao.database.DBSingleSpeciesCoreDatabase

getChromosomeByName(String) - Method in class uk.ac.roslin.ensembl.dao.database.DBSpecies

getChromosomeByName(String, String) - Method in class uk.ac.roslin.ensembl.dao.database.DBSpecies

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

getChromosomeByName_CoordSysID(HashMap) - Method in interface uk.ac.roslin.ensembl.mapper.core.ChromosomeMapper

getChromosomeDAO() - Method in class uk.ac.roslin.ensembl.dao.database.factory.DBDAOCollectionCoreFactory

getChromosomeDAO() - Method in class uk.ac.roslin.ensembl.dao.database.factory.DBDAOSingleSpeciesCoreFactory

getChromosomeDAO() - Method in interface uk.ac.roslin.ensembl.dao.factory.DAOCoreFactory

getChromosomeLevelCoordSystem() - Method in class uk.ac.roslin.ensembl.dao.database.DBSingleSpeciesCoreDatabase

getChromosomeLevelCoordSystem() - Method in interface uk.ac.roslin.ensembl.model.database.SingleSpeciesCoreDatabase

getChromosomeLevelCS(Species) - Method in class uk.ac.roslin.ensembl.dao.database.DBCollectionCoreDatabase

getChromosomeLevelCS(Species) - Method in interface uk.ac.roslin.ensembl.model.database.CollectionCoreDatabase

getChromosomeMapping(Chromosome) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAFeature

Utility method to pull back a single mapping of this Feature on a Given chromosome.

getChromosomeMapping() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAFeature

Utility method to pull back a unique chromosomal mapping of this Feature.

getChromosomeMapping(Chromosome) - Method in class uk.ac.roslin.ensembl.datasourceaware.variation.DAVariation

Utility method to pull back a single mapping of this Feature on a Given chromosome.

getChromosomeMapping() - Method in class uk.ac.roslin.ensembl.datasourceaware.variation.DAVariation

Utility method to pull back a unique chromosomal mapping of this Feature.

getChromosomeMapping(Chromosome) - Method in interface uk.ac.roslin.ensembl.model.core.Feature

getChromosomeMapping() - Method in interface uk.ac.roslin.ensembl.model.core.Feature

getChromosomeMappings() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAFeature

Method to return all chromosomal mappings for this feature.

getChromosomeMappings() - Method in class uk.ac.roslin.ensembl.datasourceaware.variation.DAVariation

Method to return all chromosomal mappings for this feature.

getChromosomeMappings() - Method in interface uk.ac.roslin.ensembl.model.core.Feature

getChromosomeName() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAChromosome

getChromosomeName() - Method in interface uk.ac.roslin.ensembl.model.core.Chromosome

getChromosomePositionFromAA(Integer) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DATranslation

Returns the mapped chromosomal coordinates of an amino acid position.

getChromosomePositionFromBASE(Integer) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DATranslation

Returns the mapped chromosomal position of a translation (nucleotide) position.

getChromosomes() - Method in interface uk.ac.roslin.ensembl.dao.coreaccess.ChromosomeDAO

getChromosomes() - Method in class uk.ac.roslin.ensembl.dao.database.coreaccess.DBChromosomeDAO

getChromosomes(Species) - Method in class uk.ac.roslin.ensembl.dao.database.DBCollectionCoreDatabase

getChromosomes(String) - Method in class uk.ac.roslin.ensembl.dao.database.DBCollectionSpecies

getChromosomes() - Method in class uk.ac.roslin.ensembl.dao.database.DBSingleSpeciesCoreDatabase

Note that Chromosomes are not cached by the Database object - but by the Species Object

getChromosomes() - Method in class uk.ac.roslin.ensembl.dao.database.DBSpecies

getChromosomes(String) - Method in class uk.ac.roslin.ensembl.dao.database.DBSpecies

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

getChromosomesByCoordSysID(HashMap) - Method in interface uk.ac.roslin.ensembl.mapper.core.ChromosomeMapper

getCigarLine() - Method in class uk.ac.roslin.ensembl.model.compara.HomologyAlignmentProperties

getCode() - Method in class uk.ac.roslin.ensembl.model.GoEvidence

getCodonTableID() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DADNASequence

getCodonTableID() - Method in interface uk.ac.roslin.ensembl.model.core.DNASequence

getCollection() - Method in class uk.ac.roslin.ensembl.dao.database.DBCollectionDatabase

getCollection(String, String) - Method in class uk.ac.roslin.ensembl.dao.database.DBRegistry

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 class uk.ac.roslin.ensembl.dao.database.DBCollection

getCollectionName() - Method in class uk.ac.roslin.ensembl.dao.database.DBCollectionDatabase

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 class uk.ac.roslin.ensembl.dao.database.DBRegistry

getCollectionRegistriesByName(String) - Method in interface uk.ac.roslin.ensembl.model.database.Registry

getCollections() - Method in class uk.ac.roslin.ensembl.dao.database.DBRegistry

getCollections() - Method in interface uk.ac.roslin.ensembl.model.database.Registry

getCollectionsByDBVersion(String) - Method in class uk.ac.roslin.ensembl.dao.database.DBRegistry

getCollectionsByDBVersion(String) - Method in interface uk.ac.roslin.ensembl.model.database.Registry

getCollectionSpecies() - Method in class uk.ac.roslin.ensembl.dao.database.DBRegistry

Returns the combined list of DBCollectionSpecies that are indexed by dbstylename (old_style_ and those indexed by GCAssemblyAccession (new style, post v16)

getCollectionSpecies() - Method in interface uk.ac.roslin.ensembl.model.database.Registry

getCollectionSpeciesProperties(CollectionCoreDatabase) - Method in interface uk.ac.roslin.ensembl.dao.DatabaseDAO

getCommonName() - Method in class uk.ac.roslin.ensembl.dao.database.DBSpecies

getCommonName() - Method in interface uk.ac.roslin.ensembl.model.core.Species

getComparaDatabase(EnsemblComparaDivision, String) - Method in class uk.ac.roslin.ensembl.dao.database.DBRegistry

getComparaDatabase(EnsemblComparaDivision, String) - Method in interface uk.ac.roslin.ensembl.model.database.Registry

getComparaDB() - Method in interface uk.ac.roslin.ensembl.dao.coreaccess.GeneDAO

getComparaDB() - Method in class uk.ac.roslin.ensembl.dao.database.coreaccess.DBGeneDAO

getComparaDB() - Method in class uk.ac.roslin.ensembl.mapper.query.FeatureQuery

getComparaDivision() - Method in class uk.ac.roslin.ensembl.dao.database.DBSpecies

getComparaDivision() - Method in class uk.ac.roslin.ensembl.dao.database.factory.DBDAOComparaFactory

getComparaDivision() - Method in interface uk.ac.roslin.ensembl.dao.factory.DAOComparaFactory

getComparaDivision() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DACoreObject

getComparaDivision() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DADNASequence

Note the special case for Bacteria in collections in DB >16

getComparaDivision() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAGene

Note the special case for Bacteria in collections in DB >16

getComparaDivision() - Method in interface uk.ac.roslin.ensembl.model.core.Species

getComparaFactory() - Method in class uk.ac.roslin.ensembl.dao.database.DBComparisonDatabase

getComparaFactory(EnsemblComparaDivision) - Method in class uk.ac.roslin.ensembl.dao.database.factory.DBDAOCollectionCoreFactory

getComparaFactory(EnsemblComparaDivision) - Method in class uk.ac.roslin.ensembl.dao.database.factory.DBDAOSingleSpeciesCoreFactory

getComparaFactory(EnsemblComparaDivision) - Method in interface uk.ac.roslin.ensembl.dao.factory.DAOCoreFactory

getComparaFactory(EnsemblComparaDivision) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DACoreObject

getComparaFactory() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DACoreObject

getComparaFactory(EnsemblComparaDivision) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DADNASequence

getComparaFactory() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DADNASequence

getComparaName(String) - Method in class uk.ac.roslin.ensembl.dao.database.DBCollectionSpecies

getComparaName() - Method in class uk.ac.roslin.ensembl.dao.database.DBSingleSpeciesCoreDatabase

getComparaName(String) - Method in class uk.ac.roslin.ensembl.dao.database.DBSpecies

getComparaName(String) - Method in interface uk.ac.roslin.ensembl.model.core.Species

getComparaName() - Method in interface uk.ac.roslin.ensembl.model.database.SingleSpeciesCoreDatabase

getComparisonDivision() - Method in class uk.ac.roslin.ensembl.dao.database.DBComparisonDatabase

getComparisonDivision() - Method in interface uk.ac.roslin.ensembl.model.database.ComparisonDatabase

getCompleteAssembly() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAAssembledDNASequence

getCompleteAssembly() - Method in interface uk.ac.roslin.ensembl.model.core.AssembledDNASequence

getComponentMappingsByStartStop(DNASequence, Integer, Integer) - Method in interface uk.ac.roslin.ensembl.dao.coreaccess.AssemblyDAO

getComponentMappingsByStartStop(DNASequence, Integer, Integer) - Method in class uk.ac.roslin.ensembl.dao.database.coreaccess.DBAssemblyDAO

getComponentSequences(HashMap) - Method in interface uk.ac.roslin.ensembl.mapper.core.SequenceMapper

getCompoundAt(int) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAEnsemblDNASequenceReader

getCompoundSet() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAEnsemblDNASequenceReader

getConfigProperties() - Method in class uk.ac.roslin.ensembl.dao.database.DBRegistry

getConfigProperties() - Method in interface uk.ac.roslin.ensembl.model.database.Registry

getConfiguration() - Method in class uk.ac.roslin.ensembl.dao.database.factory.DBDAOFactory

getConfiguration() - Method in interface uk.ac.roslin.ensembl.dao.factory.DAOFactory

getConfigurationProperties() - Method in class uk.ac.roslin.ensembl.config.DBConnection

getConfigurationProperties() - Method in class uk.ac.roslin.ensembl.config.SchemaVersion

getConfiguredDatasource() - Method in class uk.ac.roslin.ensembl.config.DBConnection

getConsequences() - Method in class uk.ac.roslin.ensembl.datasourceaware.variation.VariationMapping

getCoordinateSystemDAO() - Method in class uk.ac.roslin.ensembl.dao.database.factory.DBDAOCollectionCoreFactory

getCoordinateSystemDAO() - Method in class uk.ac.roslin.ensembl.dao.database.factory.DBDAOSingleSpeciesCoreFactory

getCoordinateSystemDAO() - Method in interface uk.ac.roslin.ensembl.dao.factory.DAOCoreFactory

getCoordinateSystemID() - Method in class uk.ac.roslin.ensembl.mapper.query.FeatureQuery

getCoordinateSystems() - Method in interface uk.ac.roslin.ensembl.dao.coreaccess.CoordinateSystemDAO

getCoordinateSystems() - Method in class uk.ac.roslin.ensembl.dao.database.coreaccess.DBCoordinateSystemDAO

getCoordinateSystems() - Method in class uk.ac.roslin.ensembl.dao.database.DBSingleSpeciesCoreDatabase

getCoords() - Method in class uk.ac.roslin.ensembl.model.compara.HomologyAlignmentProperties

getCoordSystem() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DADNASequence

getCoordSystem() - Method in interface uk.ac.roslin.ensembl.model.core.DNASequence

getCoordSystemID() - Method in interface uk.ac.roslin.ensembl.biojava3.EnsemblDNASequenceReader

getCoordSystemID() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAEnsemblDNASequenceReader

getCoordSystems(HashMap) - Method in interface uk.ac.roslin.ensembl.mapper.core.SpeciesMapper

getCoreDatabase() - Method in class uk.ac.roslin.ensembl.dao.database.DBCollection

getCoreDatabase() - Method in interface uk.ac.roslin.ensembl.model.core.CollectionOfSpecies

getCoreDB() - Method in class uk.ac.roslin.ensembl.dao.database.DBSingleSpeciesVariationDatabase

getCoreFactory(Species) - Method in class uk.ac.roslin.ensembl.dao.database.DBCollectionCoreDatabase

getCoreFactory() - Method in class uk.ac.roslin.ensembl.dao.database.DBSingleSpeciesCoreDatabase

getCoreFactory(Species) - Method in interface uk.ac.roslin.ensembl.model.database.CollectionCoreDatabase

getCoreFactory() - Method in interface uk.ac.roslin.ensembl.model.database.SingleSpeciesCoreDatabase

getCreationDate() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DACoreObject

getCreationDate() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAFeature

getCreationDate() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DATranslation

getCreationDate() - Method in class uk.ac.roslin.ensembl.datasourceaware.DAAnalysis

getCreationDate() - Method in interface uk.ac.roslin.ensembl.model.StableID

getCSByID(Species, Integer) - Method in class uk.ac.roslin.ensembl.dao.database.DBCollectionCoreDatabase

getCSByID(Integer) - Method in class uk.ac.roslin.ensembl.dao.database.DBSingleSpeciesCoreDatabase

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 class uk.ac.roslin.ensembl.dao.database.DBCollectionCoreDatabase

getCSForFeature(ObjectType) - Method in class uk.ac.roslin.ensembl.dao.database.DBSingleSpeciesCoreDatabase

getCSForFeature(ObjectType) - Method in class uk.ac.roslin.ensembl.dao.database.DBSingleSpeciesVariationDatabase

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

getCsID() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DADNASequence

getCSpeciesByGCAccessionStem(String) - Method in class uk.ac.roslin.ensembl.dao.database.DBRegistry

getCurrentEnsemblVersion() - Method in class uk.ac.roslin.ensembl.config.SchemaVersion

getCurrentGenomesVersion() - Method in class uk.ac.roslin.ensembl.config.SchemaVersion

getDAOFactory() - Method in class uk.ac.roslin.ensembl.dao.database.coreaccess.DBCoreObjectDAO

getDaoFactory() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DACoreObject

getDaoFactory() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DADNASequence

getDaoFactory() - Method in class uk.ac.roslin.ensembl.datasourceaware.DAObject

getDaoFactory() - Method in class uk.ac.roslin.ensembl.datasourceaware.DAXRef

getDaoFactory() - Method in class uk.ac.roslin.ensembl.datasourceaware.variation.DAVariation

getDatabase(String) - Method in class uk.ac.roslin.ensembl.dao.database.DBRegistry

getDatabase(String, String) - Method in class uk.ac.roslin.ensembl.dao.database.DBRegistry

getDatabase(String, DatabaseType, String) - Method in class uk.ac.roslin.ensembl.dao.database.DBRegistry

getDatabase() - Method in class uk.ac.roslin.ensembl.dao.database.factory.DBDAOCollectionCoreFactory

getDatabase() - Method in class uk.ac.roslin.ensembl.dao.database.factory.DBDAOCollectionFactory

getDatabase() - Method in class uk.ac.roslin.ensembl.dao.database.factory.DBDAOComparaFactory

getDatabase() - Method in class uk.ac.roslin.ensembl.dao.database.factory.DBDAOFactory

getDatabase() - Method in class uk.ac.roslin.ensembl.dao.database.factory.DBDAOSingleSpeciesCoreFactory

getDatabase() - Method in class uk.ac.roslin.ensembl.dao.database.factory.DBDAOSingleSpeciesFactory

getDatabase() - Method in class uk.ac.roslin.ensembl.dao.database.factory.DBDAOSingleSpeciesVariationFactory

getDatabase() - Method in interface uk.ac.roslin.ensembl.dao.factory.DAOCollectionCoreFactory

getDatabase() - Method in interface uk.ac.roslin.ensembl.dao.factory.DAOCoreFactory

getDatabase() - Method in interface uk.ac.roslin.ensembl.dao.factory.DAOFactory

getDatabase() - Method in interface uk.ac.roslin.ensembl.dao.factory.DAOSingleSpeciesCoreFactory

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 class uk.ac.roslin.ensembl.dao.database.DBCollectionSpecies

getDatabaseByTypeAndVersion(DatabaseType, String) - Method in class uk.ac.roslin.ensembl.dao.database.DBSpecies

getDatabaseByTypeAndVersion(DatabaseType, String) - Method in interface uk.ac.roslin.ensembl.model.core.Species

getDatabaseForFullName(String) - Method in class uk.ac.roslin.ensembl.dao.database.DBRegistry

getDatabaseForFullName(String) - Method in interface uk.ac.roslin.ensembl.model.database.Registry

getDatabaseName() - Method in class uk.ac.roslin.ensembl.dao.database.factory.DBDAOFactory

getDatabaseName() - Method in interface uk.ac.roslin.ensembl.dao.factory.DAOFactory

getDatabases() - Method in class uk.ac.roslin.ensembl.dao.database.DBCollection

getDatabases() - Method in class uk.ac.roslin.ensembl.dao.database.DBCollectionSpecies

getDatabases() - Method in class uk.ac.roslin.ensembl.dao.database.DBSpecies

getDatabases() - Method in interface uk.ac.roslin.ensembl.dao.DatabaseDAO

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 class uk.ac.roslin.ensembl.dao.database.DBCollection

getDatabasesByType(DatabaseType) - Method in class uk.ac.roslin.ensembl.dao.database.DBCollectionSpecies

getDatabasesByType(DatabaseType) - Method in class uk.ac.roslin.ensembl.dao.database.DBRegistry

getDatabasesByType(DatabaseType) - Method in class uk.ac.roslin.ensembl.dao.database.DBSpecies

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 class uk.ac.roslin.ensembl.dao.database.DBCollectionSpecies

getDatabasesByVersion(String) - Method in class uk.ac.roslin.ensembl.dao.database.DBSpecies

getDatabasesByVersion(String) - Method in interface uk.ac.roslin.ensembl.model.core.Species

getDatabaseStyleName() - Method in class uk.ac.roslin.ensembl.dao.database.DBSpecies

getDatabaseStyleName() - Method in interface uk.ac.roslin.ensembl.model.core.Species

getDatabaseStyleSpeciesName(Integer) - Method in class uk.ac.roslin.ensembl.dao.database.DBSpecies

getDataSource(String) - Static method in class uk.ac.roslin.ensembl.config.DBConnection

getDatasourceStyle() - Method in class uk.ac.roslin.ensembl.config.DBConnection

getDatasourceType() - Method in class uk.ac.roslin.ensembl.dao.database.DBRegistry

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 class uk.ac.roslin.ensembl.datasourceaware.DAXRef

getDB() - Method in interface uk.ac.roslin.ensembl.model.XRef

getdBClassifier() - Method in class uk.ac.roslin.ensembl.dao.database.DBDatabase

getdBClassifier() - Method in interface uk.ac.roslin.ensembl.model.database.Database

getDBDescription() - Method in class uk.ac.roslin.ensembl.model.ExternalDB

getDBDisplayName() - Method in class uk.ac.roslin.ensembl.datasourceaware.DAXRef

getDBDisplayName() - Method in class uk.ac.roslin.ensembl.datasourceaware.variation.DAVariationXRef

getDBDisplayName() - Method in class uk.ac.roslin.ensembl.model.ExternalDB

getDBDisplayName() - Method in interface uk.ac.roslin.ensembl.model.XRef

getDBName(String) - Static method in class uk.ac.roslin.ensembl.config.EnsemblComparaDivision

getdBName() - Method in class uk.ac.roslin.ensembl.dao.database.DBDatabase

getdBName() - Method in class uk.ac.roslin.ensembl.dao.database.DBSingleSpeciesDatabase

Returns the real DBName as read from the getDatabases query.

getDBName() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DADNASequence

getDBName() - Method in class uk.ac.roslin.ensembl.datasourceaware.variation.DAVariationXRef

getdBName() - Method in interface uk.ac.roslin.ensembl.model.database.Database

getDBName() - Method in class uk.ac.roslin.ensembl.model.ExternalDB

getDBRelease() - Method in class uk.ac.roslin.ensembl.model.ExternalDB

getDBSeqLength() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DADNASequence

getDBSeqLength() - Method in interface uk.ac.roslin.ensembl.model.core.DNASequence

getDBSpeciesID(String) - Method in class uk.ac.roslin.ensembl.dao.database.DBCollectionSpecies

getDBSpeciesID() - Method in class uk.ac.roslin.ensembl.dao.database.DBCollectionSpecies

Deprecated.

getDBSpeciesID(String) - Method in class uk.ac.roslin.ensembl.dao.database.DBSpecies

getDBSpeciesID() - Method in class uk.ac.roslin.ensembl.dao.database.DBSpecies

getDBSpeciesID(String) - Method in interface uk.ac.roslin.ensembl.model.core.Species

getDbSpeciesName() - Method in class uk.ac.roslin.ensembl.dao.database.DBSingleSpeciesDatabase

getDbSpeciesName() - Method in interface uk.ac.roslin.ensembl.model.database.SingleSpeciesDatabase

getDBStatus() - Method in class uk.ac.roslin.ensembl.model.ExternalDB

getDBType() - Method in class uk.ac.roslin.ensembl.dao.database.factory.DBDAOFactory

getDBType() - Method in interface uk.ac.roslin.ensembl.dao.factory.DAOFactory

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 class uk.ac.roslin.ensembl.dao.database.DBCollection

getDBVersion() - Method in class uk.ac.roslin.ensembl.dao.database.DBDatabase

getDBVersion() - Method in class uk.ac.roslin.ensembl.dao.database.factory.DBDAOFactory

getDBVersion() - Method in interface uk.ac.roslin.ensembl.dao.factory.DAOFactory

getDBVersion() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DADNASequence

getDBVersion() - Method in class uk.ac.roslin.ensembl.datasourceaware.DAObject

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 class uk.ac.roslin.ensembl.dao.database.DBSpecies

getDBVersions() - Method in interface uk.ac.roslin.ensembl.model.core.Species

getDefaultTranscriptionEngine() - Method in class uk.ac.roslin.ensembl.dao.database.DBRegistry

note by default translation by this default engine is configured to convert non-Methionine initiations to Methionine

getDefaultTranscriptionEngine() - Method in interface uk.ac.roslin.ensembl.model.database.Registry

getDescription() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAFeature

getDescription() - Method in class uk.ac.roslin.ensembl.datasourceaware.DAAnalysis

getDescription() - Method in class uk.ac.roslin.ensembl.datasourceaware.DAXRef

getDescription() - Method in interface uk.ac.roslin.ensembl.model.core.Analysis

getDescription() - Method in interface uk.ac.roslin.ensembl.model.core.Gene

getDescription() - Method in interface uk.ac.roslin.ensembl.model.XRef

getDisplayID() - Method in class uk.ac.roslin.ensembl.datasourceaware.DAXRef

getDisplayID() - Method in interface uk.ac.roslin.ensembl.model.XRef

getDisplayLabel() - Method in class uk.ac.roslin.ensembl.datasourceaware.DAAnalysis

getDisplayLabel() - Method in interface uk.ac.roslin.ensembl.model.core.Analysis

getDisplayName() - Method in class uk.ac.roslin.ensembl.dao.database.DBSpecies

getDisplayName() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAExon

getDisplayName() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAFeature

getDisplayName() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAGene

getDisplayName() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DATranscript

getDisplayName() - Method in interface uk.ac.roslin.ensembl.model.core.Species

getDisplayTerm() - Method in class uk.ac.roslin.ensembl.model.variation.VariationType

getDisplayXRef() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAGene

getDisplayXRef() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DATranscript

Triggers lazyload if Transcript is not initialized.

getDisplayXRef() - Method in interface uk.ac.roslin.ensembl.model.core.WithDisplayXRef

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

Returns the very last position of the last Coordinate in this CoordinateSet.

getEndPhase() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAExon

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 class uk.ac.roslin.ensembl.dao.database.DBRegistry

Looks up the ensembl_genus_species_name for the given alias from the ensemblNameForAliasHash hash of aliases in this Registry.

getEnsemblNameForAlias(String) - Method in interface uk.ac.roslin.ensembl.model.database.Registry

getEnsemblNamesForAliasBeginning(String) - Method in class uk.ac.roslin.ensembl.dao.database.DBRegistry

getEnsemblNamesForAliasBeginning(String) - Method in interface uk.ac.roslin.ensembl.model.database.Registry

getEnsemblNamesForAliasContaining(String) - Method in class uk.ac.roslin.ensembl.dao.database.DBRegistry

getEnsemblNamesForAliasContaining(String) - Method in interface uk.ac.roslin.ensembl.model.database.Registry

getEnsemblSchemaVersion() - Method in class uk.ac.roslin.ensembl.dao.database.factory.DBDAOFactory

getEnsemblSchemaVersion() - Method in interface uk.ac.roslin.ensembl.dao.factory.DAOFactory

getEnsemblStablePrefix() - Method in class uk.ac.roslin.ensembl.dao.database.DBSpecies

getEnsemblStablePrefix() - Method in interface uk.ac.roslin.ensembl.model.core.Species

geteReg() - Static method in class uk.ac.roslin.ensembl.test.RegistryProvider

getEValue() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAProteinFeature

getEValue() - Method in interface uk.ac.roslin.ensembl.model.core.ProteinFeature

getEvidence() - Method in class uk.ac.roslin.ensembl.datasourceaware.DAXRef

getEvidence() - Method in interface uk.ac.roslin.ensembl.model.XRef

getExon(FeatureQuery) - Method in interface uk.ac.roslin.ensembl.mapper.core.ExonMapper

getExonByID(Integer) - Method in interface uk.ac.roslin.ensembl.dao.coreaccess.ExonDAO

getExonByID(Integer) - Method in class uk.ac.roslin.ensembl.dao.database.coreaccess.DBExonDAO

getExonByStableID(String) - Method in interface uk.ac.roslin.ensembl.dao.coreaccess.ExonDAO

getExonByStableID(String) - Method in class uk.ac.roslin.ensembl.dao.database.coreaccess.DBExonDAO

getExonDAO() - Method in class uk.ac.roslin.ensembl.dao.database.factory.DBDAOCollectionCoreFactory

getExonDAO() - Method in class uk.ac.roslin.ensembl.dao.database.factory.DBDAOSingleSpeciesCoreFactory

getExonDAO() - Method in interface uk.ac.roslin.ensembl.dao.factory.DAOCoreFactory

getExons() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DATranscript

Returns a Collection of Exons for this Transcript.

getExons() - Method in interface uk.ac.roslin.ensembl.model.core.Transcript

getExonsForTranscript(Transcript) - Method in interface uk.ac.roslin.ensembl.dao.coreaccess.ExonDAO

getExonsForTranscript(Transcript) - Method in class uk.ac.roslin.ensembl.dao.database.coreaccess.DBExonDAO

getExtent() - Method in class uk.ac.roslin.ensembl.model.MappingSet

Returns a Coordinate representing the extent or range of this MappingSet.

getExternalDatabaseName() - Method in class uk.ac.roslin.ensembl.datasourceaware.DAAnalysis

Get the value of externalDatabaseName

getExternalDatabaseName() - Method in interface uk.ac.roslin.ensembl.model.core.Analysis

getExternalDatabaseVersion() - Method in class uk.ac.roslin.ensembl.datasourceaware.DAAnalysis

Get the value of externalDatabaseVersion

getExternalDatabaseVersion() - Method in interface uk.ac.roslin.ensembl.model.core.Analysis

getExternalDB(Integer) - Method in class uk.ac.roslin.ensembl.dao.database.DBCollectionCoreDatabase

getExternalDB(Integer) - Method in class uk.ac.roslin.ensembl.dao.database.DBSingleSpeciesCoreDatabase

getExternalDB(Integer) - Method in interface uk.ac.roslin.ensembl.model.database.DatabaseWithExternalDBs

getExternalDBs() - Method in interface uk.ac.roslin.ensembl.mapper.XRefMapper

getFactory() - Method in class uk.ac.roslin.ensembl.dao.database.DBBaseDAO

getFactory() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAEnsemblDNASequenceReader

getFakeid() - Method in class uk.ac.roslin.ensembl.mapper.handler.HashMapHolder

Get the value of fakeid

getFeatureID() - Method in class uk.ac.roslin.ensembl.mapper.query.FeatureQuery

Get the value of featureID

getFeatureName() - Method in class uk.ac.roslin.ensembl.mapper.query.FeatureQuery

getFeaturesForCS(Species, CoordinateSystem) - Method in class uk.ac.roslin.ensembl.dao.database.DBCollectionCoreDatabase

getFeaturesForCS(CoordinateSystem) - Method in class uk.ac.roslin.ensembl.dao.database.DBSingleSpeciesCoreDatabase

getFeaturesForCS(CoordinateSystem) - Method in class uk.ac.roslin.ensembl.dao.database.DBSingleSpeciesVariationDatabase

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

getFeatureStableID() - Method in class uk.ac.roslin.ensembl.mapper.query.FeatureQuery

Get the value of featureStableID

getFeatureType(String) - Static method in class uk.ac.roslin.ensembl.config.FeatureType

getFeatureType() - Method in class uk.ac.roslin.ensembl.mapper.query.FeatureQuery

Get the value of featureType

getFirstExon() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DATranslation

Returns the first Exon of this Translation.

getFirstExonID() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DATranslation

Returns the internal database ID of the first Exon for this translation.

getFirstExonStart() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DATranslation

Returns the (relative) position of the translational start in the first exon of this Translation.

getFlankingTargetSequenceAsString(Integer, Integer) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAFeature

Retrieves the String representation of the target (genomic) sequence that this feature is annotated upon, for the given range.

getFragmentByName(String) - Method in interface uk.ac.roslin.ensembl.dao.coreaccess.ChromosomeDAO

getFragmentByName(String) - Method in class uk.ac.roslin.ensembl.dao.database.coreaccess.DBChromosomeDAO

getFragmentByName(Species, String) - Method in class uk.ac.roslin.ensembl.dao.database.DBCollectionCoreDatabase

getFragmentByName(String, String) - Method in class uk.ac.roslin.ensembl.dao.database.DBCollectionSpecies

getFragmentByName(String) - Method in class uk.ac.roslin.ensembl.dao.database.DBSingleSpeciesCoreDatabase

a Fragment is TopLevelAssembledDNASequence ( where there are no chromosomes )

getFragmentByName(String) - Method in class uk.ac.roslin.ensembl.dao.database.DBSpecies

getFragmentByName(String, String) - Method in class uk.ac.roslin.ensembl.dao.database.DBSpecies

getFragmentByName(String) - Method in interface uk.ac.roslin.ensembl.model.core.Species

getFragmentByName(String, String) - Method in interface uk.ac.roslin.ensembl.model.core.Species

getFragmentByName(Species, String) - Method in interface uk.ac.roslin.ensembl.model.database.CollectionCoreDatabase

getFragmentByName(String) - Method in interface uk.ac.roslin.ensembl.model.database.SingleSpeciesCoreDatabase

getFragments() - Method in interface uk.ac.roslin.ensembl.dao.coreaccess.ChromosomeDAO

getFragments() - Method in class uk.ac.roslin.ensembl.dao.database.coreaccess.DBChromosomeDAO

getFragments(Species) - Method in class uk.ac.roslin.ensembl.dao.database.DBCollectionCoreDatabase

getFragments(String) - Method in class uk.ac.roslin.ensembl.dao.database.DBCollectionSpecies

getFragments() - Method in class uk.ac.roslin.ensembl.dao.database.DBSingleSpeciesCoreDatabase

Fragments are TopLevelAssembledDNASequences

getFragments() - Method in class uk.ac.roslin.ensembl.dao.database.DBSpecies

getFragments(String) - Method in class uk.ac.roslin.ensembl.dao.database.DBSpecies

getFragments() - Method in interface uk.ac.roslin.ensembl.model.core.Species

getFragments(String) - Method in interface uk.ac.roslin.ensembl.model.core.Species

getFragments(Species) - Method in interface uk.ac.roslin.ensembl.model.database.CollectionCoreDatabase

getFragments() - Method in interface uk.ac.roslin.ensembl.model.database.SingleSpeciesCoreDatabase

getFullSequence(EnsemblDNASequenceReader) - Method in interface uk.ac.roslin.ensembl.dao.coreaccess.DNASequenceDAO

getFullSequence(EnsemblDNASequenceReader) - Method in class uk.ac.roslin.ensembl.dao.database.coreaccess.DBDNASequenceDAO

getGaps() - Method in class uk.ac.roslin.ensembl.model.CoordinateSet

Returns a CoordinateSet containing Coordinates for all of the gaps in this CoordinateSet.

getGapString(Integer) - Static method in class uk.ac.roslin.ensembl.datasourceaware.core.GapSequence

getGapString(Integer, char) - Static method in class uk.ac.roslin.ensembl.datasourceaware.core.GapSequence

getGCAccessionedCollectionSpecies() - Method in class uk.ac.roslin.ensembl.dao.database.DBRegistry

Utility method to return only those DBCOllectionSpecies that possess and are indexed by a GCAssemblyAccession(Stem or Chain)

getGCAssemblyAccessionForAlias(String) - Method in class uk.ac.roslin.ensembl.dao.database.DBRegistry

Looks up the GC_assembly_accession_stem for the given alias of a collectionspecies.

getGCAssemblyAccessionsForAliasBeginning(String) - Method in class uk.ac.roslin.ensembl.dao.database.DBRegistry

getGCAssemblyAccessionsForAliasBeginning(String) - Method in interface uk.ac.roslin.ensembl.model.database.Registry

getGCAssemblyAccessionsForAliasContaining(String) - Method in class uk.ac.roslin.ensembl.dao.database.DBRegistry

getGCAssemblyAccessionsForAliasContaining(String) - Method in interface uk.ac.roslin.ensembl.model.database.Registry

getGene() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DATranscript

Gets the Gene associated with this transcript, using the stableID for the gene set on Transcript initialization.

getGene() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DATranslation

Gets the Gene associated with this Translation via the associated Transcript.

getGene(FeatureQuery) - Method in interface uk.ac.roslin.ensembl.mapper.core.GeneMapper

getGene() - Method in interface uk.ac.roslin.ensembl.model.core.Transcript

getGeneByID(Integer) - Method in interface uk.ac.roslin.ensembl.dao.coreaccess.GeneDAO

getGeneByID(Integer) - Method in class uk.ac.roslin.ensembl.dao.database.coreaccess.DBGeneDAO

getGeneByStableID(String) - Method in interface uk.ac.roslin.ensembl.dao.coreaccess.GeneDAO

getGeneByStableID(String) - Method in class uk.ac.roslin.ensembl.dao.database.coreaccess.DBGeneDAO

getGeneByStableID(String, String) - Method in class uk.ac.roslin.ensembl.dao.database.DBCollectionSpecies

getGeneByStableID(String) - Method in class uk.ac.roslin.ensembl.dao.database.DBSpecies

getGeneByStableID(String, String) - Method in class uk.ac.roslin.ensembl.dao.database.DBSpecies

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

getGeneDAO() - Method in class uk.ac.roslin.ensembl.dao.database.factory.DBDAOCollectionCoreFactory

getGeneDAO() - Method in class uk.ac.roslin.ensembl.dao.database.factory.DBDAOSingleSpeciesCoreFactory

getGeneDAO() - Method in interface uk.ac.roslin.ensembl.dao.factory.DAOCoreFactory

getGeneID() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DATranscript

getGeneID() - Method in class uk.ac.roslin.ensembl.mapper.query.FeatureQuery

Get the value of geneID

getGeneID() - Method in class uk.ac.roslin.ensembl.model.compara.HomologyAlignmentProperties

getGeneMappingsOnRegion(DNASequence, Coordinate) - Method in interface uk.ac.roslin.ensembl.dao.coreaccess.GeneDAO

getGeneMappingsOnRegion(DNASequence, Coordinate) - Method in class uk.ac.roslin.ensembl.dao.database.coreaccess.DBGeneDAO

getGenesByExactName(String) - Method in interface uk.ac.roslin.ensembl.dao.coreaccess.GeneDAO

getGenesByExactName(String) - Method in class uk.ac.roslin.ensembl.dao.database.coreaccess.DBGeneDAO

getGenesByName(FeatureQuery) - Method in interface uk.ac.roslin.ensembl.mapper.core.GeneMapper

getGenesByNameBeginning(String) - Method in interface uk.ac.roslin.ensembl.dao.coreaccess.GeneDAO

getGenesByNameBeginning(String) - Method in class uk.ac.roslin.ensembl.dao.database.coreaccess.DBGeneDAO

getGenesForExactName(String, String) - Method in class uk.ac.roslin.ensembl.dao.database.DBCollectionSpecies

getGenesForExactName(String) - Method in class uk.ac.roslin.ensembl.dao.database.DBSpecies

getGenesForExactName(String, String) - Method in class uk.ac.roslin.ensembl.dao.database.DBSpecies

getGenesForExactName(String) - Method in interface uk.ac.roslin.ensembl.model.core.Species

getGenesForExactName(String, String) - Method in interface uk.ac.roslin.ensembl.model.core.Species

getGenesForNameBeginning(String) - Method in class uk.ac.roslin.ensembl.dao.database.DBSpecies

getGenesForNameBeginning(String, String) - Method in class uk.ac.roslin.ensembl.dao.database.DBSpecies

getGenesForNameBeginning(String) - Method in interface uk.ac.roslin.ensembl.model.core.Species

getGenesForNameBeginning(String, String) - Method in interface uk.ac.roslin.ensembl.model.core.Species

getGenesForVegaID(String) - Method in interface uk.ac.roslin.ensembl.dao.coreaccess.GeneDAO

getGenesForVegaID(String) - Method in class uk.ac.roslin.ensembl.dao.database.coreaccess.DBGeneDAO

Returns a list of Ensembl Genes matching the query VegaID string.

getGenesForVegaID(String, String) - Method in class uk.ac.roslin.ensembl.dao.database.DBCollectionSpecies

Method returns a List of Genes that have been mapped to the given Vega Identifier.

getGenesForVegaID(String) - Method in class uk.ac.roslin.ensembl.dao.database.DBSpecies

Method returns a List of Genes that have been mapped to the given Vega Identifier.

getGenesForVegaID(String, String) - Method in class uk.ac.roslin.ensembl.dao.database.DBSpecies

Method returns a List of Genes that have been mapped to the given Vega Identifier.

getGenesForVegaID(String) - Method in interface uk.ac.roslin.ensembl.model.core.Species

getGenesForVegaID(String, String) - Method in interface uk.ac.roslin.ensembl.model.core.Species

getGenesOnRegion(Coordinate) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DADNASequence

Returns a List of Genes on the specified Coordinate region.

getGenesOnRegion(Integer, Integer, Coordinate.Strand) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DADNASequence

Returns a List of Genes on the specified Region.

getGenesOnRegion(Integer, Integer) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DADNASequence

Returns a List of Genes on the specified Region.

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

getGenus_Species() - Method in class uk.ac.roslin.ensembl.dao.database.factory.DBDAOSingleSpeciesFactory

getGenus_Species() - Method in interface uk.ac.roslin.ensembl.dao.factory.DAOSingleSpeciesFactory

getGffFeature() - Method in class uk.ac.roslin.ensembl.datasourceaware.DAAnalysis

getGffFeature() - Method in interface uk.ac.roslin.ensembl.model.core.Analysis

getGffSource() - Method in class uk.ac.roslin.ensembl.datasourceaware.DAAnalysis

getGffSource() - Method in interface uk.ac.roslin.ensembl.model.core.Analysis

getGoEvidence(String) - Static method in class uk.ac.roslin.ensembl.config.GoEvidenceCodes

getgReg() - Static method in class uk.ac.roslin.ensembl.test.RegistryProvider

getHashID() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DADNASequence

getHashID() - Method in class uk.ac.roslin.ensembl.datasourceaware.DAObject

getHashID() - Method in interface uk.ac.roslin.ensembl.model.IdentifiableObject

getHighestDBRelease() - Method in class uk.ac.roslin.ensembl.dao.database.DBSpecies

getHighestDBRelease() - Method in interface uk.ac.roslin.ensembl.model.core.Species

getHighestEnsemblSchemaVersion() - Method in class uk.ac.roslin.ensembl.dao.database.DBRegistry

getHighestEnsemblSchemaVersion() - Method in interface uk.ac.roslin.ensembl.model.database.Registry

getHighestReleaseVersion() - Method in class uk.ac.roslin.ensembl.dao.database.DBRegistry

getHighestReleaseVersion() - Method in interface uk.ac.roslin.ensembl.model.database.Registry

getHomoeologueCount() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAGene

getHomologies() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAGene

Returns all Homologies (as a List of HomologyPairRelationships) in the default ComparaDivision for this Gene.

getHomologies(EnsemblComparaDivision) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAGene

Returns all Homologies (as a List of HomologyPairRelationships) in the specified ComparaDivision for this Gene.

getHomologies(Species) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAGene

Returns Homologies (as a List of HomologyPairRelationships) in the default ComparaDivision for this Gene for the specified Species.

getHomologies(EnsemblComparaDivision, Species) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAGene

Returns Homologies (as a List of HomologyPairRelationships) in the specified ComparaDivision for the specified Species.

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

getHomologiesForGene(Gene) - Method in interface uk.ac.roslin.ensembl.dao.compara.HomologyDAO

Specification of Data Access method to retrieve all of the homologies (i.e. to all species) for a given gene with a stableID.

getHomologiesForGene(Gene) - Method in class uk.ac.roslin.ensembl.dao.database.compara.DBHomologyDAO

Data Access method to retrieve all of the homologies (i.e. to all species) for a given gene with a stableID.

getHomologiesForGene(Gene) - Method in interface uk.ac.roslin.ensembl.mapper.compara.HomologyPairMapper

getHomologiesForGenesBySpecies(List<? extends Gene>, Species, String) - Method in interface uk.ac.roslin.ensembl.dao.compara.HomologyDAO

Specification of Data Access method to retrieve all of the homologies in the specified target species for a List of genes with stableIDs.

getHomologiesForGenesBySpecies(List<? extends Gene>, Species, String) - Method in class uk.ac.roslin.ensembl.dao.database.compara.DBHomologyDAO

Data Access method to retrieve all of the homologies in the specified target species for a List of genes with stableIDs.

getHomologiesForGenesBySpecies(HashMap) - Method in interface uk.ac.roslin.ensembl.mapper.compara.HomologyPairMapper

getHomologiesWithoutLazyLoad() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAGene

Utility method to get all of the current DAHomologyPairRelationships for this Gene

getHomologiesWithoutLazyLoad() - Method in interface uk.ac.roslin.ensembl.model.core.Gene

getHomologyDAO() - Method in class uk.ac.roslin.ensembl.dao.database.factory.DBDAOComparaFactory

getHomologyDAO() - Method in interface uk.ac.roslin.ensembl.dao.factory.DAOComparaFactory

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 class uk.ac.roslin.ensembl.datasourceaware.core.DACoordinateSystem

Get the value of id

getId() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DADNASequence

getId() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAFeature

getId() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DATranslation

getId() - Method in class uk.ac.roslin.ensembl.datasourceaware.DAObject

getId() - Method in class uk.ac.roslin.ensembl.datasourceaware.variation.VariationMapping

getId() - Method in interface uk.ac.roslin.ensembl.model.core.CoordinateSystem

getId() - Method in class uk.ac.roslin.ensembl.model.ExternalDB

getId() - Method in interface uk.ac.roslin.ensembl.model.IdentifiableObject

getIndexOf(NucleotideCompound) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAEnsemblDNASequenceReader

getInfo() - Method in class uk.ac.roslin.ensembl.datasourceaware.DAXRef

getInfo() - Method in interface uk.ac.roslin.ensembl.model.XRef

getInfoType() - Method in class uk.ac.roslin.ensembl.datasourceaware.DAXRef

getInfoType() - Method in interface uk.ac.roslin.ensembl.model.XRef

getIntDBVersion() - Method in class uk.ac.roslin.ensembl.dao.database.DBDatabase

getIntDBVersion() - Method in interface uk.ac.roslin.ensembl.model.database.Database

getIntSchemaVersion() - Method in class uk.ac.roslin.ensembl.dao.database.DBDatabase

getIntSchemaVersion() - Method in interface uk.ac.roslin.ensembl.model.database.Database

getInverse() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAEnsemblDNASequenceReader

getKnownGenomesReleases() - Method in class uk.ac.roslin.ensembl.config.SchemaVersion

getKnownSchemaVersions() - Method in class uk.ac.roslin.ensembl.dao.database.DBRegistry

getLastCommonAncestor() - Method in class uk.ac.roslin.ensembl.datasourceaware.compara.DAHomologyRelationship

getLastCommonAncestor() - Method in class uk.ac.roslin.ensembl.datasourceaware.compara.InverseHomologyPairRelationshipView

getLastCommonAncestor() - Method in interface uk.ac.roslin.ensembl.model.compara.HomologyRelationship

getLastExon() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DATranslation

Returns the last Exon of this Translation.

getLastExonEnd() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DATranslation

Returns the (relative) position of the translational end in the last exon of this Translation.

getLastExonID() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DATranslation

Returns the internal database ID of the last Exon for this translation.

getLastIndexOf(NucleotideCompound) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAEnsemblDNASequenceReader

getLength() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DADNASequence

getLength() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAEnsemblDNASequenceReader

getLength() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAFeature

Returns the length of this feature, as calculated from its mapped coordinates on the top level annotated sequence (typically the chromosome).

getLength() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DATranslation

Returns the length of the translated nucleotide sequence, i.e. from first nucleotide of the start codon to end of the stop codon.

getLength() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.GapSequence

getLength() - Method in class uk.ac.roslin.ensembl.model.Coordinate

Returns the length of this Coordinate - taking into consideration whether the range spans the 'absent' Zero.

getLength() - Method in class uk.ac.roslin.ensembl.model.CoordinateSet

Returns the length of the extent/range of this CoordinateSet (accounting for any span of the absent ZERO).

getLengthInteger() - Method in interface uk.ac.roslin.ensembl.biojava3.EnsemblDNASequenceReader

getLengthInteger() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAEnsemblDNASequenceReader

getListResult() - Method in class uk.ac.roslin.ensembl.dao.database.coreaccess.DBAssemblyDAO.PARMappingHandler

getListResult() - Method in class uk.ac.roslin.ensembl.dao.database.coreaccess.DBChromosomeDAO.AssemblyExceptionRowHandler

getListResult() - Method in class uk.ac.roslin.ensembl.dao.database.coreaccess.DBDNASequenceDAO.SequenceRowHandler

getListResult() - Method in class uk.ac.roslin.ensembl.dao.database.coreaccess.DBExonDAO.ExonRowHandler

getListResult() - Method in class uk.ac.roslin.ensembl.dao.database.coreaccess.DBGeneDAO.GeneMappingRowHandler

getListResult() - Method in class uk.ac.roslin.ensembl.dao.database.coreaccess.DBGeneDAO.MappingRowHandler

getListResult() - Method in class uk.ac.roslin.ensembl.dao.database.coreaccess.DBTranscriptDAO.TranscriptRowHandler

getListResult() - Method in interface uk.ac.roslin.ensembl.mapper.handler.DBResultHandler

getLoadedMappings() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DADNASequence

getLoadedMappings(ObjectType) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DADNASequence

getLoadedMappings() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAFeature

getLoadedMappings(ObjectType) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAFeature

getLoadedMappings(ObjectType) - Method in class uk.ac.roslin.ensembl.datasourceaware.variation.DAVariation

getLoadedMappings() - Method in class uk.ac.roslin.ensembl.datasourceaware.variation.DAVariation

getLoadedMappings(ObjectType) - Method in interface uk.ac.roslin.ensembl.model.MappableObject

getLoadedMappings() - Method in interface uk.ac.roslin.ensembl.model.MappableObject

getLogicalName() - Method in class uk.ac.roslin.ensembl.datasourceaware.DAAnalysis

Get the value of logicalName

getLogicalName() - Method in interface uk.ac.roslin.ensembl.model.core.Analysis

getMap() - Method in class uk.ac.roslin.ensembl.mapper.handler.HashMapHolder

getMappedRegions() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DADNASequence

getMappedRegions() - Method in interface uk.ac.roslin.ensembl.model.core.DNASequence

getMappings() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAAssembly

Returns the MappingSet 'componentMappings' of all of the mappings of all of the DNASequences that make up this assembly.

getMappings() - Method in class uk.ac.roslin.ensembl.datasourceaware.variation.DAVariation

getMappings() - Method in interface uk.ac.roslin.ensembl.model.core.Assembly

getMappingsOnParentSequence(FeatureQuery) - Method in interface uk.ac.roslin.ensembl.mapper.variation.VariationMapper

getMaximumFeatureLength() - Method in class uk.ac.roslin.ensembl.mapper.query.FeatureQuery

getMaxLengthForFeature(Species, ObjectType, CoordinateSystem) - Method in class uk.ac.roslin.ensembl.dao.database.DBCollectionCoreDatabase

getMaxLengthForFeature(ObjectType, CoordinateSystem) - Method in class uk.ac.roslin.ensembl.dao.database.DBSingleSpeciesCoreDatabase

getMaxLengthForFeature(ObjectType, CoordinateSystem) - Method in class uk.ac.roslin.ensembl.dao.database.DBSingleSpeciesVariationDatabase

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 class uk.ac.roslin.ensembl.datasourceaware.compara.DAHomologyPairRelationship

getMembers() - Method in class uk.ac.roslin.ensembl.datasourceaware.compara.DAHomologyRelationship

getMembers() - Method in class uk.ac.roslin.ensembl.datasourceaware.compara.InverseHomologyPairRelationshipView

getMembers() - Method in interface uk.ac.roslin.ensembl.model.relationship.GroupRelationship

getModificationDate() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DACoreObject

getModificationDate() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAFeature

getModificationDate() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DATranslation

getModificationDate() - Method in interface uk.ac.roslin.ensembl.model.StableID

getModuleName() - Method in class uk.ac.roslin.ensembl.datasourceaware.DAAnalysis

getModuleName() - Method in interface uk.ac.roslin.ensembl.model.core.Analysis

getModuleVersion() - Method in class uk.ac.roslin.ensembl.datasourceaware.DAAnalysis

getModuleVersion() - Method in interface uk.ac.roslin.ensembl.model.core.Analysis

getMostRecentCollection(String) - Method in class uk.ac.roslin.ensembl.dao.database.DBRegistry

getMostRecentCollection(String) - Method in interface uk.ac.roslin.ensembl.model.database.Registry

getMostRecentCoreDatabase() - Method in class uk.ac.roslin.ensembl.dao.database.DBCollectionSpecies

getMostRecentCoreDatabase() - Method in class uk.ac.roslin.ensembl.dao.database.DBSpecies

getMostRecentCoreDatabase() - Method in interface uk.ac.roslin.ensembl.model.core.Species

getMostRecentDBVersion(String) - Method in class uk.ac.roslin.ensembl.dao.database.DBRegistry

getMostRecentEnsemblVersion() - Method in class uk.ac.roslin.ensembl.dao.database.DBRegistry

getMostRecentEnsemblVersion() - Method in interface uk.ac.roslin.ensembl.model.database.Registry

getMostRecentSpeciesByAlias(String) - Method in class uk.ac.roslin.ensembl.dao.database.DBRegistry

Returns the most recent Species matching the alias.

getMostRecentSpeciesByAlias(String) - Method in interface uk.ac.roslin.ensembl.model.database.Registry

getMybatisSchemaFilePath() - Method in class uk.ac.roslin.ensembl.dao.database.factory.DBDAOFactory

getMybatisSchemaFilePath() - Method in interface uk.ac.roslin.ensembl.dao.factory.DAOFactory

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 class uk.ac.roslin.ensembl.datasourceaware.core.DADNASequence

getName() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAEnsemblDNASequenceReader

getName() - Method in class uk.ac.roslin.ensembl.datasourceaware.variation.DAVariation

getName() - Method in interface uk.ac.roslin.ensembl.model.core.DNASequence

getName() - Method in interface uk.ac.roslin.ensembl.model.variation.Variation

getNamedCollectionSpecies() - Method in class uk.ac.roslin.ensembl.dao.database.DBRegistry

Utility method to return only those DBCOllectionSpecies that do not possess and are therefore not indexed by a GCAssemblyAccession but bey dbstylename

getNewSqlSession() - Method in class uk.ac.roslin.ensembl.dao.database.DBDatabase

getNewSqlSession() - Method in class uk.ac.roslin.ensembl.dao.database.factory.DBDAOCollectionCoreFactory

getNewSqlSession() - Method in class uk.ac.roslin.ensembl.dao.database.factory.DBDAOFactory

getNewSqlSession() - Method in class uk.ac.roslin.ensembl.dao.database.factory.DBDAOSingleSpeciesCoreFactory

getNewSqlSession() - Method in class uk.ac.roslin.ensembl.dao.database.factory.DBDAOSingleSpeciesVariationFactory

getNewSqlSession() - Method in interface uk.ac.roslin.ensembl.dao.factory.DAOFactory

getNewSqlSession() - Method in interface uk.ac.roslin.ensembl.model.database.Database

getObjectResult() - Method in class uk.ac.roslin.ensembl.dao.database.coreaccess.DBAssemblyDAO.PARMappingHandler

getObjectResult() - Method in class uk.ac.roslin.ensembl.dao.database.coreaccess.DBChromosomeDAO.AssemblyExceptionRowHandler

getObjectResult() - Method in class uk.ac.roslin.ensembl.dao.database.coreaccess.DBDNASequenceDAO.SequenceRowHandler

getObjectResult() - Method in class uk.ac.roslin.ensembl.dao.database.coreaccess.DBExonDAO.ExonRowHandler

getObjectResult() - Method in class uk.ac.roslin.ensembl.dao.database.coreaccess.DBGeneDAO.GeneMappingRowHandler

getObjectResult() - Method in class uk.ac.roslin.ensembl.dao.database.coreaccess.DBGeneDAO.MappingRowHandler

getObjectResult() - Method in class uk.ac.roslin.ensembl.dao.database.coreaccess.DBTranscriptDAO.TranscriptRowHandler

getObjectResult() - Method in interface uk.ac.roslin.ensembl.mapper.handler.DBResultHandler

getObjectTypeMappings() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DADNASequence

getObjectTypeMappings() - Method in interface uk.ac.roslin.ensembl.model.core.DNASequence

getOccurrences() - Method in class uk.ac.roslin.ensembl.datasourceaware.variation.DAVariation

getOccurrences() - Method in interface uk.ac.roslin.ensembl.model.variation.Variation

getOldStyleBacterialSpeciesForAliasBeginning(String) - Method in class uk.ac.roslin.ensembl.dao.database.DBRegistry

getOldStyleBacterialSpeciesForAliasBeginning(String) - Method in interface uk.ac.roslin.ensembl.model.database.Registry

getOldStyleBacterialSpeciesForAliasContaining(String) - Method in class uk.ac.roslin.ensembl.dao.database.DBRegistry

getOldStyleBacterialSpeciesForAliasContaining(String) - Method in interface uk.ac.roslin.ensembl.model.database.Registry

getOriginalDBName() - Method in class uk.ac.roslin.ensembl.dao.database.DBSingleSpeciesDatabase

Returns the original DBName as read from the getDatabases query.

getOriginalDBSpeciesName() - Method in class uk.ac.roslin.ensembl.dao.database.DBSingleSpeciesDatabase

Returns the original DBSpeciesName as parsed from the originalDName.

getOrthologueCount() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAGene

getOverlap(Coordinate) - Method in class uk.ac.roslin.ensembl.model.Coordinate

Returns the overlap extent (as a Coordinate) between this Coordinate and a test Coordinate.

getPaddedFlankingTargetSequenceAsString(Integer, Integer) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAFeature

Retrieves the String representation of the target (genomic) sequence that this feature is annotated upon, for the given range.

getPaddedReverseComplementSequenceAsString(Integer, Integer) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAAssembledDNASequence

getPaddedReverseComplementSequenceAsString(Integer, Integer) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAAssembly

Returns a String representation of the reverse complement of theassembly sequence for the given range.

getPaddedReverseComplementSequenceAsString(Integer, Integer) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DADNASequence

Method to get a string representation of the reverse complement of the sequence for the given range.

getPaddedReverseComplementSequenceAsString(Integer, Integer) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.GapSequence

getPaddedReverseComplementSequenceAsString(Integer, Integer) - Method in interface uk.ac.roslin.ensembl.model.core.DNASequence

getPaddedRNASequenceAsString(Integer, Integer) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.GapSequence

getPaddedSequenceAsString(Integer, Integer) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAAssembledDNASequence

getPaddedSequenceAsString(Integer, Integer) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAAssembly

Returns a String representation of the assembly sequence for the given range.

getPaddedSequenceAsString(Integer, Integer) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DADNASequence

Method to get a string representation of the sequence for the given range.

getPaddedSequenceAsString(Integer, Integer) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.GapSequence

getPaddedSequenceAsString(Integer, Integer) - Method in interface uk.ac.roslin.ensembl.model.core.DNASequence

getPanComparaSpecies(String) - Method in class uk.ac.roslin.ensembl.dao.database.DBRegistry

getPanComparaSpecies(String) - Method in interface uk.ac.roslin.ensembl.mapper.DatabaseMapper

getParalogueCount() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAGene

getParChromosome() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAChromosome

Returns the sex-linked 'PAR' chromosome associated with this Chromosome.

getParChromosome() - Method in interface uk.ac.roslin.ensembl.model.core.Chromosome

getParent() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAAssembly

Returns the DAAssembledDNASequence that this assembly holds (its 'Parent').

getParent() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAEnsemblDNASequenceReader

getParent() - Method in interface uk.ac.roslin.ensembl.model.core.Assembly

getParentSequenceID() - Method in class uk.ac.roslin.ensembl.mapper.query.FeatureQuery

Get the value of parentSequenceID

getParentStart() - Method in class uk.ac.roslin.ensembl.mapper.query.FeatureQuery

getParentStop() - Method in class uk.ac.roslin.ensembl.mapper.query.FeatureQuery

getPARMappingsByStartStop(Chromosome, Integer, Integer) - Method in interface uk.ac.roslin.ensembl.dao.coreaccess.AssemblyDAO

getPARMappingsByStartStop(Chromosome, Integer, Integer) - Method in class uk.ac.roslin.ensembl.dao.database.coreaccess.DBAssemblyDAO

getPARSequences(HashMap) - Method in interface uk.ac.roslin.ensembl.mapper.core.SequenceMapper

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.datasourceaware.core.DAProteinFeature

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 class uk.ac.roslin.ensembl.datasourceaware.core.DAExon

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

getPrimaryAccession() - Method in class uk.ac.roslin.ensembl.datasourceaware.DAXRef

getPrimaryAccession() - Method in interface uk.ac.roslin.ensembl.model.XRef

getPrimaryTranscript() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DATranscript

Returns a DADNASequence object representing the unprocessed primary Transcript.

getPrimaryTranscriptLength() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DATranscript

Returns the length of the unprocessed (primary) version of this Transcript.

getPrimaryTranscriptPositionFromAA(Integer) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DATranslation

Returns the mapped coordinates of an amino acid position on the unprocessed primary transcript that provides this translation.

getPrimaryTranscriptPositionFromBASE(Integer) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DATranslation

Returns the mapped position of a translation (nucleotide) position on the unprocessed primary transcript that provides this translation.

getPrimaryTranscriptRNASequence() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DATranscript

Preferred method to explicitly get the RNASequence object representing the PrimaryTranscript.

getPrimaryTranscriptRNASequenceAsString() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DATranscript

Preferred method to explicitly get a String representing the RNA sequence of the PrimaryTranscript.

getPrimaryTranscriptRNASequenceAsString(Integer, Integer) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DATranscript

Preferred method to explicitly get a String representing the RNA sequence of the PrimaryTranscript, for the given range.

getProcessedTranscript() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DATranscript

Returns a DADNASequence object representing the processed (spliced exons) version of this Transcript.

getProcessedTranscriptLength() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DATranscript

Returns the length of the processed (spliced exons) version of this Transcript.

getProcessedTranscriptPositionFromAA(Integer) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DATranslation

Returns the mapped coordinates of an amino acid position on the (spliced) processed transcript that provides this translation.

getProcessedTranscriptPositionFromBASE(Integer) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DATranslation

Returns the mapped position of a translation (nucleotide) position on the (spliced) processed transcript that provides this translation.

getProcessedTranscriptRNASequence() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DATranscript

Returns an RNASequence object representing the Processed (RNA spliced) Transcript.

getProcessedTranscriptRNASequenceAsString() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DATranscript

Returns a String representing the RNA sequence of the Processed (RNA spliced) Transcript.

getProcessedTranscriptRNASequenceAsString(Integer, Integer) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DATranscript

Returns a String representing the RNA sequence of the Processed (RNA spliced) Transcript, for the given range.

getProgramName() - Method in class uk.ac.roslin.ensembl.datasourceaware.DAAnalysis

getProgramName() - Method in interface uk.ac.roslin.ensembl.model.core.Analysis

getProgramParameters() - Method in class uk.ac.roslin.ensembl.datasourceaware.DAAnalysis

getProgramParameters() - Method in interface uk.ac.roslin.ensembl.model.core.Analysis

getProgramVersion() - Method in class uk.ac.roslin.ensembl.datasourceaware.DAAnalysis

getProgramVersion() - Method in interface uk.ac.roslin.ensembl.model.core.Analysis

getProteinFeatureDAO() - Method in class uk.ac.roslin.ensembl.dao.database.factory.DBDAOCollectionCoreFactory

getProteinFeatureDAO() - Method in class uk.ac.roslin.ensembl.dao.database.factory.DBDAOSingleSpeciesCoreFactory

getProteinFeatureDAO() - Method in interface uk.ac.roslin.ensembl.dao.factory.DAOCoreFactory

getProteinFeatures() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DATranslation

getProteinFeatures() - Method in interface uk.ac.roslin.ensembl.model.core.Translation

getProteinFeaturesByTranslationID(int) - Method in interface uk.ac.roslin.ensembl.dao.coreaccess.ProteinFeatureDAO

getProteinFeaturesByTranslationID(int) - Method in class uk.ac.roslin.ensembl.dao.database.coreaccess.DBProteinFeatureDAO

getProteinFeaturesByTranslationID(int) - Method in interface uk.ac.roslin.ensembl.mapper.core.ProteinFeatureMapper

getProteinSequence(Integer) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DATranslation

Returns a (BioJava) ProteinSequence for this Translation using the specified Codon Table ID to retrieve the appropriate (BioJava) TranscriptionEngine.

getProteinSequence(TranscriptionEngine) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DATranslation

Returns a (BioJava) ProteinSequence for this Translation using the specified (BioJava) TranscriptionEngine.

getProteinSequence() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DATranslation

Returns a (BioJava) ProteinSequence for this Translation.

getProteinSequence() - Method in interface uk.ac.roslin.ensembl.model.core.Translation

getProteinSequenceAsString() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DATranslation

Convenience method to get the Amino Acid sequence of the protein product of this translation.

getProteinSequenceAsString(Integer) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DATranslation

Convenience method to get the Amino Acid sequence of the protein product of this translation.

getProteinSequenceAsString(TranscriptionEngine) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DATranslation

Convenience method to get the Amino Acid sequence of the protein product of this translation.

getProteinSequenceAsString(Integer, Integer) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DATranslation

Convenience method to get the Amino Acid sequence of the given range of the protein product of this translation.

getProteinSequenceAsString(Integer, Integer, Integer) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DATranslation

Convenience method to get the Amino Acid sequence of the given range of the protein product of this translation.

getProteinSequenceAsString(TranscriptionEngine, Integer, Integer) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DATranslation

Convenience method to get the Amino Acid sequence of the given range of the protein product of this translation.

getPseudoAutosomalRegion() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAChromosome

getPseudoAutosomalRegion() - Method in interface uk.ac.roslin.ensembl.model.core.Chromosome

getQueryIntegerList() - Method in class uk.ac.roslin.ensembl.mapper.query.FeatureQuery

getQueryStringList() - Method in class uk.ac.roslin.ensembl.mapper.query.FeatureQuery

getRange() - Method in class uk.ac.roslin.ensembl.model.CoordinateSet

Returns a Coordinate representing the extent or range of this CoordinateSet

getRank() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DACoordinateSystem

Get the value of rank

getRank() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAExon

getRank() - Method in interface uk.ac.roslin.ensembl.model.core.CoordinateSystem

getRegionsOfConservedSynteny(DNASequence, Coordinate, Species) - Method in interface uk.ac.roslin.ensembl.dao.compara.HomologyDAO

Specification of Data Access method to retrieve all of the regions on DNASequences for the specified target species, holding genes with homologies to genes found in the given region of the source query sequence.

getRegionsOfConservedSynteny(DNASequence, Coordinate, Species, String) - Method in interface uk.ac.roslin.ensembl.dao.compara.HomologyDAO

Specification of Data Access method to retrieve any potential region of conserved synteny on a given Chromosome/fragment for the specified target species, holding genes with homologies to genes found in the given region of the source query sequence.

getRegionsOfConservedSynteny(DNASequence, Coordinate, Species) - Method in class uk.ac.roslin.ensembl.dao.database.compara.DBHomologyDAO

Data Access method to retrieve all of the regions on DNASequences for the specified target species, holding genes with homologies to genes found in the given region of the source query sequence.

getRegionsOfConservedSynteny(DNASequence, Coordinate, Species, String) - Method in class uk.ac.roslin.ensembl.dao.database.compara.DBHomologyDAO

Data Access method to retrieve any potential region of conserved synteny on a given Chromosome/fragment for the specified target species, holding genes with homologies to genes found in the given region of the source query sequence.

getRegionsOfConservedSynteny(Coordinate, Species) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DADNASequence

Specifies method to retrieve all potential regions of conserved synteny (i.e. multiple chromosome regions) in the specified target Species

getRegionsOfConservedSynteny(Coordinate, Species, String) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DADNASequence

Method to retrieve a single potential region of conserved synteny for the named chromosome in the specified target Species.

getRegionsOfConservedSynteny(Coordinate, Species) - Method in interface uk.ac.roslin.ensembl.model.core.DNASequence

Specifies method to retrieve all potential regions of conserved synteny (i.e. multiple chromosome regions) in the specified target Species

getRegionsOfConservedSynteny(Coordinate, Species, String) - Method in interface uk.ac.roslin.ensembl.model.core.DNASequence

Specifies method to retrieve a single potential region of conserved synteny for the named chromosome in the specified target Species.

getRegisteredSchemas() - Method in class uk.ac.roslin.ensembl.config.SchemaVersion

getRegistry() - Method in class uk.ac.roslin.ensembl.dao.database.DBDatabase

getRegistry() - Method in class uk.ac.roslin.ensembl.dao.database.factory.DBDAOFactory

getRegistry() - Method in interface uk.ac.roslin.ensembl.dao.factory.DAOFactory

getRegistry() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DADNASequence

getRegistry() - Method in class uk.ac.roslin.ensembl.datasourceaware.DAObject

getRegistry() - Method in interface uk.ac.roslin.ensembl.model.database.Database

getRegistryReport() - Method in class uk.ac.roslin.ensembl.dao.database.DBRegistry

Reports the connection, available database versions, species and actual database names for an initialized Registry.

getRegistryReport() - Method in interface uk.ac.roslin.ensembl.model.database.Registry

getRelationshipType() - Method in class uk.ac.roslin.ensembl.datasourceaware.compara.DAHomologyRelationship

getRelationshipType() - Method in class uk.ac.roslin.ensembl.datasourceaware.compara.InverseHomologyPairRelationshipView

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

getRenamedDBName() - Method in class uk.ac.roslin.ensembl.dao.database.DBSingleSpeciesDatabase

Returns the renamed DBName if it was changed on instantiation due to a rewrite rule in the database configuration file.

getRenamedDBs() - Method in class uk.ac.roslin.ensembl.config.DBConnection

getRenamedDBs() - Method in class uk.ac.roslin.ensembl.dao.database.DBRegistry

getRenamedDBs() - Method in interface uk.ac.roslin.ensembl.model.database.Registry

getResult(ResultSet, String) - Method in class uk.ac.roslin.ensembl.mapper.handler.AssemblyExceptionTypeHandler

getResult(CallableStatement, int) - Method in class uk.ac.roslin.ensembl.mapper.handler.AssemblyExceptionTypeHandler

getResult(ResultSet, String) - Method in class uk.ac.roslin.ensembl.mapper.handler.BooleanTypeHandler

getResult(CallableStatement, int) - Method in class uk.ac.roslin.ensembl.mapper.handler.BooleanTypeHandler

getResult(ResultSet, String) - Method in class uk.ac.roslin.ensembl.mapper.handler.ConsequencesHandler

getResult(CallableStatement, int) - Method in class uk.ac.roslin.ensembl.mapper.handler.ConsequencesHandler

getResult(ResultSet, String) - Method in class uk.ac.roslin.ensembl.mapper.handler.CoordinateSystemDefaultVersionTypeHandler

getResult(CallableStatement, int) - Method in class uk.ac.roslin.ensembl.mapper.handler.CoordinateSystemDefaultVersionTypeHandler

getResult(ResultSet, String) - Method in class uk.ac.roslin.ensembl.mapper.handler.CoordinateSystemSeqLevelTypeHandler

getResult(CallableStatement, int) - Method in class uk.ac.roslin.ensembl.mapper.handler.CoordinateSystemSeqLevelTypeHandler

getResult(ResultSet, String) - Method in class uk.ac.roslin.ensembl.mapper.handler.CoordinateSystemTypeHandler

getResult(CallableStatement, int) - Method in class uk.ac.roslin.ensembl.mapper.handler.CoordinateSystemTypeHandler

getResult(ResultSet, String) - Method in class uk.ac.roslin.ensembl.mapper.handler.ExistsTypeHandler

getResult(CallableStatement, int) - Method in class uk.ac.roslin.ensembl.mapper.handler.ExistsTypeHandler

getResult(ResultSet, String) - Method in class uk.ac.roslin.ensembl.mapper.handler.ExternalDBTypeHandler

getResult(CallableStatement, int) - Method in class uk.ac.roslin.ensembl.mapper.handler.ExternalDBTypeHandler

getResult(ResultSet, String) - Method in class uk.ac.roslin.ensembl.mapper.handler.GoEvidenceCodeTypeHandler

getResult(CallableStatement, int) - Method in class uk.ac.roslin.ensembl.mapper.handler.GoEvidenceCodeTypeHandler

getResult(ResultSet, String) - Method in class uk.ac.roslin.ensembl.mapper.handler.HomologyTypeHandler

getResult(CallableStatement, int) - Method in class uk.ac.roslin.ensembl.mapper.handler.HomologyTypeHandler

getResult(ResultSet, String) - Method in class uk.ac.roslin.ensembl.mapper.handler.VariationTypeHandler

getResult(CallableStatement, int) - Method in class uk.ac.roslin.ensembl.mapper.handler.VariationTypeHandler

getResult(ResultSet, String) - Method in class uk.ac.roslin.ensembl.mapper.handler.VariationXRefHandler

getResult(CallableStatement, int) - Method in class uk.ac.roslin.ensembl.mapper.handler.VariationXRefHandler

getReverseComplementSequenceAsString(Integer, Integer) - Method in interface uk.ac.roslin.ensembl.biojava3.EnsemblDNASequenceReader

getReverseComplementSequenceAsString(Integer, Integer) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAAssembledDNASequence

getReverseComplementSequenceAsString() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAAssembledDNASequence

Default case is to assume strand is positive because only CDSSequence can be either positive or negative Strand.

getReverseComplementSequenceAsString(Integer, Integer) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAAssembly

Returns a String representation of the reverse complement of the assembly sequence for the given range.

getReverseComplementSequenceAsString(Integer, Integer) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DADNASequence

Method to get a string representation of the reverse complement of the sequence for the given range.

getReverseComplementSequenceAsString() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DADNASequence

Method to get a string representation of the reverse complement of the sequence.

getReverseComplementSequenceAsString(Integer, Integer) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAEnsemblDNASequenceReader

getReverseComplementSequenceAsString() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.GapSequence

getReverseComplementSequenceAsString(Integer, Integer) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.GapSequence

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.datasourceaware.variation.VariationMapping

getReverseMapping() - Method in class uk.ac.roslin.ensembl.model.Mapping

getRNASequence() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAFeature

Returns an RNASequence object trancribed from the DNASequence representing the extent of this annotation.

getRNASequence() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DATranscript

Deprecated.

getRNASequence() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DATranslation

Returns a (BioJava) RNASequence for this Translation using the default (BioJava) TranscriptionEngine or one assigned to this Gene/Organism.

getRNASequence(TranscriptionEngine) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DATranslation

Returns a (BioJava) RNASequence for this Translation using the specified (BioJava) TranscriptionEngine or one assigned to this Gene/Organism.

getRNASequenceAsString() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAFeature

Returns a string representation of the RNASequence object trancribed from the DNASequence representing the extent of this annotation.

getRNASequenceAsString(Integer, Integer) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAFeature

Returns a string representation for the given range of the RNASequence object trancribed from the DNASequence representing the extent of this annotation.

getRNASequenceAsString() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DATranscript

Deprecated.

getRNASequenceAsString(Integer, Integer) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DATranscript

Deprecated.

getRNASequenceAsString() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DATranslation

getRNASequenceAsString(TranscriptionEngine) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DATranslation

getRNASequenceAsString(Integer, Integer) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DATranslation

getRNASequenceAsString(TranscriptionEngine, Integer, Integer) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DATranslation

getRNASequenceAsString() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.GapSequence

getRNASequenceAsString(Integer, Integer) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.GapSequence

getSchema() - Method in class uk.ac.roslin.ensembl.config.RegistryConfiguration

Returns the SchemaVersionobject set on this RegistryConfiguration object.

getSchemaVersion() - Method in class uk.ac.roslin.ensembl.dao.database.DBCollection

getSchemaVersion() - Method in class uk.ac.roslin.ensembl.dao.database.DBDatabase

getSchemaVersion() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DADNASequence

getSchemaVersion() - Method in class uk.ac.roslin.ensembl.datasourceaware.DAObject

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 class uk.ac.roslin.ensembl.dao.database.DBSpecies

getSchemaVersions() - Method in interface uk.ac.roslin.ensembl.model.core.Species

getScore() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAProteinFeature

getScore() - Method in interface uk.ac.roslin.ensembl.model.core.ProteinFeature

getSeqRegionID() - Method in interface uk.ac.roslin.ensembl.biojava3.EnsemblDNASequenceReader

getSeqRegionID() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAEnsemblDNASequenceReader

getSequence() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAFeature

Returns the sequence covered by this feature (i.e. a new DADNASequence object representing this region of the genome, it might be a GAPSequence if no sequence info is available).

getSequence(HashMap) - Method in interface uk.ac.roslin.ensembl.mapper.core.SequenceMapper

getSequenceAsString(Integer, Integer) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAAssembledDNASequence

Method to get a string representation for the given range of the assembled sequence.

getSequenceAsString(Integer, Integer, Strand) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAAssembledDNASequence

Deprecated.

getSequenceAsString() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAAssembledDNASequence

Default case is to assume strand is positive because only CDSSequence can be either positive or negative Strand.

getSequenceAsString(Integer, Integer) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAAssembly

Returns a String representation of the assembly sequence for the given range.

getSequenceAsString(Integer, Integer) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DADNASequence

Method to get a string representation of the sequence for the given range.

getSequenceAsString(Integer, Integer, Strand) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DADNASequence

Deprecated.

getSequenceAsString() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAEnsemblDNASequenceReader

getSequenceAsString(Integer, Integer, Strand) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAEnsemblDNASequenceReader

getSequenceAsString() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAFeature

Returns the string representation of the (genomic) sequence that this feature is annotated upon (at 'top level').

getSequenceAsString(Integer, Integer) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAFeature

Returns the string representation of the (genomic) sequence that this feature is annotated upon (at 'top level'), for the specified range.

getSequenceAsString() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.GapSequence

getSequenceAsString(Integer, Integer) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.GapSequence

getSequenceAsString(Integer, Integer, Strand) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.GapSequence

Deprecated.

getSequenceAsString(Integer, Integer) - Method in interface uk.ac.roslin.ensembl.model.core.DNASequence

getSequenceByID(Integer) - Method in interface uk.ac.roslin.ensembl.dao.coreaccess.DNASequenceDAO

getSequenceByID(Integer) - Method in class uk.ac.roslin.ensembl.dao.database.coreaccess.DBDNASequenceDAO

getSequenceByID(HashMap) - Method in interface uk.ac.roslin.ensembl.mapper.core.SequenceMapper

getSequenceByStartStop(EnsemblDNASequenceReader, Integer, Integer) - Method in interface uk.ac.roslin.ensembl.dao.coreaccess.DNASequenceDAO

getSequenceByStartStop(EnsemblDNASequenceReader, Integer, Integer) - Method in class uk.ac.roslin.ensembl.dao.database.coreaccess.DBDNASequenceDAO

getSequenceDAO() - Method in class uk.ac.roslin.ensembl.dao.database.factory.DBDAOCollectionCoreFactory

getSequenceDAO() - Method in class uk.ac.roslin.ensembl.dao.database.factory.DBDAOSingleSpeciesCoreFactory

getSequenceDAO() - Method in interface uk.ac.roslin.ensembl.dao.factory.DAOCoreFactory

getSequenceLevelCoordSystem() - Method in class uk.ac.roslin.ensembl.dao.database.DBSingleSpeciesCoreDatabase

getSequenceLevelCoordSystem() - Method in interface uk.ac.roslin.ensembl.model.database.SingleSpeciesCoreDatabase

getSequenceLevelCS(Species) - Method in class uk.ac.roslin.ensembl.dao.database.DBCollectionCoreDatabase

getSequenceLevelCS(Species) - Method in interface uk.ac.roslin.ensembl.model.database.CollectionCoreDatabase

getSequenceName() - Method in class uk.ac.roslin.ensembl.model.compara.HomologyAlignmentProperties

getSequenceStart(HashMap) - Method in interface uk.ac.roslin.ensembl.mapper.core.SequenceMapper

getSequenceStartStop(HashMap) - Method in interface uk.ac.roslin.ensembl.mapper.core.SequenceMapper

getSessionFactory() - Method in class uk.ac.roslin.ensembl.dao.database.DBDatabase

getSetID() - Method in class uk.ac.roslin.ensembl.model.variation.VariationType

getSetOfEverySpeciesByAlias(String) - Method in class uk.ac.roslin.ensembl.dao.database.DBRegistry

Returns a HashSet of all DBSpecies and old and newstyle CollectionSpecies matching the given alias.

getSetOfEverySpeciesByAlias(String) - Method in interface uk.ac.roslin.ensembl.model.database.Registry

getSetOfSpeciesByAlias(String) - Method in class uk.ac.roslin.ensembl.dao.database.DBRegistry

Returns a HashSet matching the given alias.

getSetOfSpeciesByAlias(String) - Method in interface uk.ac.roslin.ensembl.model.database.Registry

getSexLinkedChromosome(Chromosome) - Method in interface uk.ac.roslin.ensembl.dao.coreaccess.ChromosomeDAO

getSexLinkedChromosome(Chromosome) - Method in class uk.ac.roslin.ensembl.dao.database.coreaccess.DBChromosomeDAO

getSexLinkedChromosomeName(HashMap) - Method in interface uk.ac.roslin.ensembl.mapper.core.ChromosomeMapper

getShortName() - Method in class uk.ac.roslin.ensembl.dao.database.DBSpecies

getShortName() - Method in interface uk.ac.roslin.ensembl.model.core.Species

getSingleSpeciesDatabaseTypes() - Static method in class uk.ac.roslin.ensembl.config.EnsemblDBType

getSOAccession() - Method in class uk.ac.roslin.ensembl.model.variation.VariationType

getSOTerm() - Method in class uk.ac.roslin.ensembl.model.variation.VariationType

getSource() - Method in class uk.ac.roslin.ensembl.datasourceaware.compara.DAHomologyPairRelationship

getSource() - Method in class uk.ac.roslin.ensembl.datasourceaware.compara.InverseHomologyPairRelationshipView

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

getSourceCoordinates() - Method in class uk.ac.roslin.ensembl.model.MappingSet

Returns a CoordinateSet containing all of the Source Coordinates of Mappings in this MappingSet.

getSourceEnd() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAProteinFeature

getSourceEnd() - Method in interface uk.ac.roslin.ensembl.model.core.ProteinFeature

getSourceHashID() - Method in class uk.ac.roslin.ensembl.model.Mapping

getSourceProperties() - Method in class uk.ac.roslin.ensembl.datasourceaware.compara.DAHomologyPairRelationship

getSourceProperties() - Method in class uk.ac.roslin.ensembl.datasourceaware.compara.InverseHomologyPairRelationshipView

getSourceProperties() - Method in interface uk.ac.roslin.ensembl.model.compara.HomologyPairRelationship

getSourceStart() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAProteinFeature

getSourceStart() - Method in interface uk.ac.roslin.ensembl.model.core.ProteinFeature

getSourceType() - Method in class uk.ac.roslin.ensembl.model.Mapping

getSpecies() - Method in class uk.ac.roslin.ensembl.dao.database.coreaccess.DBCoreObjectDAO

getSpecies() - Method in class uk.ac.roslin.ensembl.dao.database.DBCollection

getSpecies() - Method in class uk.ac.roslin.ensembl.dao.database.DBRegistry

Fetches the list of all DBSpecies objects for this Registry.

getSpecies() - Method in class uk.ac.roslin.ensembl.dao.database.DBSingleSpeciesDatabase

getSpecies() - Method in class uk.ac.roslin.ensembl.dao.database.factory.DBDAOCollectionFactory

getSpecies() - Method in class uk.ac.roslin.ensembl.dao.database.factory.DBDAOSpeciesFactory

getSpecies() - Method in interface uk.ac.roslin.ensembl.dao.factory.DAOCollectionFactory

getSpecies() - Method in interface uk.ac.roslin.ensembl.dao.factory.DAOSpeciesFactory

getSpecies() - Method in class uk.ac.roslin.ensembl.datasourceaware.compara.DAHomologyPairRelationship

getSpecies() - Method in class uk.ac.roslin.ensembl.datasourceaware.compara.DAHomologyRelationship

getSpecies() - Method in class uk.ac.roslin.ensembl.datasourceaware.compara.InverseHomologyPairRelationshipView

getSpecies() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DACoreObject

getSpecies() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DADNASequence

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 class uk.ac.roslin.ensembl.dao.database.DBSpecies

getSpeciesBinomial() - Method in interface uk.ac.roslin.ensembl.model.core.Species

getSpeciesByAlias(String) - Method in class uk.ac.roslin.ensembl.dao.database.DBRegistry

Wraps getSetOfSpeciesByAlias(String alias_or_name) to return a single species if the returned Collection has only one member.

getSpeciesByAlias(String, String) - Method in class uk.ac.roslin.ensembl.dao.database.DBRegistry

Wraps getSetOfEverySpeciesByAlias(String alias_or_name) to return a single species if the returned Collection has only one member with the desired alias and version.

getSpeciesByAlias(String) - Method in interface uk.ac.roslin.ensembl.model.database.Registry

getSpeciesByAlias(String, String) - Method in interface uk.ac.roslin.ensembl.model.database.Registry

getSpeciesByEnsemblName(String) - Method in class uk.ac.roslin.ensembl.dao.database.DBRegistry

getSpeciesByEnsemblName(String) - Method in interface uk.ac.roslin.ensembl.model.database.Registry

getSpeciesComparisonDatabaseTypes() - Static method in class uk.ac.roslin.ensembl.config.EnsemblDBType

getSpeciesForAliasBeginning(String) - Method in class uk.ac.roslin.ensembl.dao.database.DBRegistry

getSpeciesForAliasBeginning(String) - Method in interface uk.ac.roslin.ensembl.model.database.Registry

getSpeciesForAliasContaining(String) - Method in class uk.ac.roslin.ensembl.dao.database.DBRegistry

getSpeciesForAliasContaining(String) - Method in interface uk.ac.roslin.ensembl.model.database.Registry

getSpeciesFromCollection(String) - Method in interface uk.ac.roslin.ensembl.mapper.DatabaseMapper

getSpeciesID() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DACoordinateSystem

Get the value of speciesID

getSpeciesID() - Method in class uk.ac.roslin.ensembl.mapper.query.FeatureQuery

getSpeciesID() - Method in interface uk.ac.roslin.ensembl.model.core.CoordinateSystem

getSpeciesName() - Method in class uk.ac.roslin.ensembl.model.compara.HomologyAlignmentProperties

getSpeciesProperties(SingleSpeciesCoreDatabase) - Method in interface uk.ac.roslin.ensembl.dao.DatabaseDAO

getSpeciesProperties(String) - Method in interface uk.ac.roslin.ensembl.mapper.DatabaseMapper

getStableID() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DACoreObject

getStableID() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAGene

getStableID() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DATranslation

getStableID() - Method in interface uk.ac.roslin.ensembl.model.StableID

getStart() - Method in class uk.ac.roslin.ensembl.model.Coordinate

getStart() - Method in class uk.ac.roslin.ensembl.model.CoordinateSet

Returns the very first position of the first Coordinate in this CoordinateSet.

getStatus() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAFeature

getStitchedMappings() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAAssembly

Returns the MappingSet 'stitchedComponentMappings' of all of the mappings of all of the DNASequences that make up this assembly, that have been 'edited', i.e. stitched together into a single continuous gap free assembly.

getStitchedMappings(Integer, Integer) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAAssembly

For a given range, returns a subset of the MappingSet 'stitchedComponentMappings' of all of the mappings of all of the DNASequences that make up this assembly, that have been 'edited', i.e. stitched together into a single continuous gap free assembly.

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

getSubSequence(Integer, Integer) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAEnsemblDNASequenceReader

getSynonym() - Method in class uk.ac.roslin.ensembl.datasourceaware.variation.DAVariation

getSynonym() - Method in interface uk.ac.roslin.ensembl.model.variation.Variation

getSynonyms(XRef) - Method in class uk.ac.roslin.ensembl.dao.database.DBXRefDAO

getSynonyms(XRef) - Method in interface uk.ac.roslin.ensembl.dao.XRefDAO

getSynonyms(XRef) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAGene

getSynonyms(XRef) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DATranscript

getSynonyms(XRef) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DATranslation

getSynonyms() - Method in class uk.ac.roslin.ensembl.datasourceaware.DAXRef

getSynonyms(XRef) - Method in interface uk.ac.roslin.ensembl.mapper.XRefMapper

getSynonyms() - Method in interface uk.ac.roslin.ensembl.model.XRef

getSynonyms(XRef) - Method in interface uk.ac.roslin.ensembl.model.XRefed

getTarget() - Method in class uk.ac.roslin.ensembl.datasourceaware.compara.DAHomologyPairRelationship

getTarget() - Method in class uk.ac.roslin.ensembl.datasourceaware.compara.InverseHomologyPairRelationshipView

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

getTargetCoordinates() - Method in class uk.ac.roslin.ensembl.model.MappingSet

Returns a CoordinateSet containing all of the Target Coordinates of Mappings in this MappingSet.

getTargetEnd() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAProteinFeature

getTargetEnd() - Method in interface uk.ac.roslin.ensembl.model.core.ProteinFeature

getTargetHashID() - Method in class uk.ac.roslin.ensembl.model.Mapping

getTargetName() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAProteinFeature

getTargetName() - Method in interface uk.ac.roslin.ensembl.model.core.ProteinFeature

getTargetProperties() - Method in class uk.ac.roslin.ensembl.datasourceaware.compara.DAHomologyPairRelationship

getTargetProperties() - Method in class uk.ac.roslin.ensembl.datasourceaware.compara.InverseHomologyPairRelationshipView

getTargetProperties() - Method in interface uk.ac.roslin.ensembl.model.compara.HomologyPairRelationship

getTargetSequence() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAFeature

Returns the (genomic) sequence that this feature is annotated upon (at 'top level').

getTargetStart() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAProteinFeature

getTargetStart() - Method in interface uk.ac.roslin.ensembl.model.core.ProteinFeature

getTargetType() - Method in class uk.ac.roslin.ensembl.model.Mapping

getTaxonomyID() - Method in class uk.ac.roslin.ensembl.dao.database.DBSpecies

getTaxonomyID() - Method in interface uk.ac.roslin.ensembl.model.core.Species

getTissueSource() - Method in class uk.ac.roslin.ensembl.datasourceaware.variation.DAVariationXRef

getTopLevelCoordSystem() - Method in class uk.ac.roslin.ensembl.dao.database.DBSingleSpeciesCoreDatabase

getTopLevelCoordSystem() - Method in interface uk.ac.roslin.ensembl.model.database.SingleSpeciesCoreDatabase

getTopLevelCS(Species) - Method in class uk.ac.roslin.ensembl.dao.database.DBCollectionCoreDatabase

getTopLevelCS(Species) - Method in interface uk.ac.roslin.ensembl.model.database.CollectionCoreDatabase

getTopLevelFragmentByName_CoordSysID(HashMap) - Method in interface uk.ac.roslin.ensembl.mapper.core.ChromosomeMapper

getTopLevelFragmentsByCoordSysID(HashMap) - Method in interface uk.ac.roslin.ensembl.mapper.core.ChromosomeMapper

getTopLevelMappings() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAFeature

getTopLevelTargetCoordinates() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAFeature

getTopLevelTargetSequence() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAFeature

getTranscript() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAExon

getTranscript() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DATranslation

getTranscript(FeatureQuery) - Method in interface uk.ac.roslin.ensembl.mapper.core.TranscriptMapper

getTranscript() - Method in interface uk.ac.roslin.ensembl.model.core.Translation

getTranscriptByID(Integer) - Method in interface uk.ac.roslin.ensembl.dao.coreaccess.TranscriptDAO

getTranscriptByID(Integer) - Method in class uk.ac.roslin.ensembl.dao.database.coreaccess.DBTranscriptDAO

getTranscriptByStableID(String) - Method in interface uk.ac.roslin.ensembl.dao.coreaccess.TranscriptDAO

getTranscriptByStableID(String) - Method in class uk.ac.roslin.ensembl.dao.database.coreaccess.DBTranscriptDAO

getTranscriptByStableID(String, String) - Method in class uk.ac.roslin.ensembl.dao.database.DBCollectionSpecies

getTranscriptByStableID(String) - Method in class uk.ac.roslin.ensembl.dao.database.DBSpecies

getTranscriptByStableID(String, String) - Method in class uk.ac.roslin.ensembl.dao.database.DBSpecies

getTranscriptByStableID(String) - Method in interface uk.ac.roslin.ensembl.model.core.Species

getTranscriptByStableID(String, String) - Method in interface uk.ac.roslin.ensembl.model.core.Species

getTranscriptDAO() - Method in class uk.ac.roslin.ensembl.dao.database.factory.DBDAOCollectionCoreFactory

getTranscriptDAO() - Method in class uk.ac.roslin.ensembl.dao.database.factory.DBDAOSingleSpeciesCoreFactory

getTranscriptDAO() - Method in interface uk.ac.roslin.ensembl.dao.factory.DAOCoreFactory

getTranscriptID() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAExon

getTranscriptID() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DATranslation

getTranscriptID() - Method in class uk.ac.roslin.ensembl.mapper.query.FeatureQuery

Get the value of transcriptID

getTranscriptionEngine(Integer) - Method in class uk.ac.roslin.ensembl.dao.database.DBRegistry

getTranscriptionEngine(Integer) - Method in interface uk.ac.roslin.ensembl.model.database.Registry

getTranscripts() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAGene

getTranscripts() - Method in interface uk.ac.roslin.ensembl.model.core.Gene

getTranscriptsForCcdsID(String) - Method in interface uk.ac.roslin.ensembl.dao.coreaccess.TranscriptDAO

Returns a list of Ensembl Transcripts matching the query CCDS ID string.

getTranscriptsForCcdsID(String) - Method in class uk.ac.roslin.ensembl.dao.database.coreaccess.DBTranscriptDAO

Returns a list of Ensembl Transcripts matching the query CCDS ID string.

getTranscriptsForCcdsID(String, String) - Method in class uk.ac.roslin.ensembl.dao.database.DBCollectionSpecies

Method returns a List of Transcripts that have been mapped to the given CCDS Identifier (This may be the CCDS accession or the CCDS accession.schemaVersion).

getTranscriptsForCcdsID(String) - Method in class uk.ac.roslin.ensembl.dao.database.DBSpecies

getTranscriptsForCcdsID(String, String) - Method in class uk.ac.roslin.ensembl.dao.database.DBSpecies

Method returns a List of Transcripts that have been mapped to the given CCDS Identifier (This may be the CCDS accession or the CCDS accession.version).

getTranscriptsForCcdsID(String) - Method in interface uk.ac.roslin.ensembl.model.core.Species

getTranscriptsForCcdsID(String, String) - Method in interface uk.ac.roslin.ensembl.model.core.Species

getTranscriptsForGene(Gene) - Method in interface uk.ac.roslin.ensembl.dao.coreaccess.TranscriptDAO

getTranscriptsForGene(Gene) - Method in class uk.ac.roslin.ensembl.dao.database.coreaccess.DBTranscriptDAO

getTranscriptsForVegaID(String) - Method in interface uk.ac.roslin.ensembl.dao.coreaccess.TranscriptDAO

Returns a list of Ensembl Transcripts matching the query VegaID string.

getTranscriptsForVegaID(String) - Method in class uk.ac.roslin.ensembl.dao.database.coreaccess.DBTranscriptDAO

Returns a list of Ensembl Transcripts matching the query VegaID string.

getTranscriptsForVegaID(String, String) - Method in class uk.ac.roslin.ensembl.dao.database.DBCollectionSpecies

Method returns a List of Transcripts that have been mapped to the given Vega Identifier.

getTranscriptsForVegaID(String) - Method in class uk.ac.roslin.ensembl.dao.database.DBSpecies

Method returns a List of Transcripts that have been mapped to the given Vega Identifier.

getTranscriptsForVegaID(String, String) - Method in class uk.ac.roslin.ensembl.dao.database.DBSpecies

Method returns a List of Transcripts that have been mapped to the given Vega Identifier.

getTranscriptsForVegaID(String) - Method in interface uk.ac.roslin.ensembl.model.core.Species

getTranscriptsForVegaID(String, String) - Method in interface uk.ac.roslin.ensembl.model.core.Species

getTranslatedSequence() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DATranslation

Returns a DNASequence object representing the translation.

getTranslatedSequenceAsString() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DATranslation

Returns a String representation of this Translation ( i.e. the DNA Sequence...).

getTranslatedSequenceAsString(Integer, Integer) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DATranslation

Returns a String representation of this Translation for the given range (i.e. the DNA Sequence...).

getTranslation(FeatureQuery) - Method in interface uk.ac.roslin.ensembl.mapper.core.TranslationMapper

getTranslationByID(Integer) - Method in interface uk.ac.roslin.ensembl.dao.coreaccess.TranslationDAO

getTranslationByID(Integer) - Method in class uk.ac.roslin.ensembl.dao.database.coreaccess.DBTranslationDAO

getTranslationByStableID(String) - Method in interface uk.ac.roslin.ensembl.dao.coreaccess.TranslationDAO

getTranslationByStableID(String) - Method in class uk.ac.roslin.ensembl.dao.database.coreaccess.DBTranslationDAO

getTranslationByStableID(String, String) - Method in class uk.ac.roslin.ensembl.dao.database.DBCollectionSpecies

getTranslationByStableID(String) - Method in class uk.ac.roslin.ensembl.dao.database.DBSpecies

getTranslationByStableID(String, String) - Method in class uk.ac.roslin.ensembl.dao.database.DBSpecies

getTranslationByStableID(String) - Method in interface uk.ac.roslin.ensembl.model.core.Species

getTranslationByStableID(String, String) - Method in interface uk.ac.roslin.ensembl.model.core.Species

getTranslationDAO() - Method in class uk.ac.roslin.ensembl.dao.database.factory.DBDAOCollectionCoreFactory

getTranslationDAO() - Method in class uk.ac.roslin.ensembl.dao.database.factory.DBDAOSingleSpeciesCoreFactory

getTranslationDAO() - Method in interface uk.ac.roslin.ensembl.dao.factory.DAOCoreFactory

getTranslationID() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAProteinFeature

getTranslationID() - Method in interface uk.ac.roslin.ensembl.model.core.ProteinFeature

getTranslationMappings() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DATranslation

Returns the Set of Mappings between coordinates on this Translation and the Primary transcript.

getTranslations() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DATranscript

Returns all of the Translation objects associated with this Transcript (typically there will only be one, the canonical translation, there may also be no translation for a transcript).

getTranslations() - Method in interface uk.ac.roslin.ensembl.model.core.Transcript

getTranslationsForTranscript(Transcript) - Method in interface uk.ac.roslin.ensembl.dao.coreaccess.TranslationDAO

getTranslationsForTranscript(Transcript) - Method in class uk.ac.roslin.ensembl.dao.database.coreaccess.DBTranslationDAO

getTranslationsForTranscript(Transcript) - Method in interface uk.ac.roslin.ensembl.mapper.core.TranslationMapper

getTranslationsForVegaID(String) - Method in interface uk.ac.roslin.ensembl.dao.coreaccess.TranslationDAO

getTranslationsForVegaID(String) - Method in class uk.ac.roslin.ensembl.dao.database.coreaccess.DBTranslationDAO

Returns a list of Ensembl Translations matching the query VegaID string.

getTranslationsForVegaID(String, String) - Method in class uk.ac.roslin.ensembl.dao.database.DBCollectionSpecies

Method returns a List of Translations that have been mapped to the given Vega Identifier.

getTranslationsForVegaID(String) - Method in class uk.ac.roslin.ensembl.dao.database.DBSpecies

Method returns a List of Translations that have been mapped to the given Vega Identifier.

getTranslationsForVegaID(String, String) - Method in class uk.ac.roslin.ensembl.dao.database.DBSpecies

Method returns a List of Translations that have been mapped to the given Vega Identifier.

getTranslationsForVegaID(String) - Method in interface uk.ac.roslin.ensembl.model.core.Species

getTranslationsForVegaID(String, String) - Method in interface uk.ac.roslin.ensembl.model.core.Species

getType(String) - Static method in class uk.ac.roslin.ensembl.config.AssemblyExceptionType

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 class uk.ac.roslin.ensembl.dao.database.DBDatabase

getType() - Method in class uk.ac.roslin.ensembl.datasourceaware.compara.DAHomologyRelationship

getType() - Method in class uk.ac.roslin.ensembl.datasourceaware.compara.InverseHomologyPairRelationshipView

getType() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAChromosome

getType() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DACoordinateSystem

Get the value of type

getType() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DADNASequence

getType() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAExon

getType() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAGene

getType() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAProteinFeature

getType() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DATranscript

getType() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DATranslation

getType() - Method in class uk.ac.roslin.ensembl.datasourceaware.DAAnalysis

getType() - Method in class uk.ac.roslin.ensembl.datasourceaware.DAXRef

getType() - Method in class uk.ac.roslin.ensembl.datasourceaware.variation.DAVariation

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 class uk.ac.roslin.ensembl.model.ExternalDB

getType() - Method in interface uk.ac.roslin.ensembl.model.IdentifiableObject

getUncoveredRegions(Coordinate) - Method in class uk.ac.roslin.ensembl.model.CoordinateSet

Returns the CoordinateSet (ordered set of Coordinates) that define regions of the test Coordinate not represented (covered) in this CoordinateSet.

getUniquelyMappedVariation(String) - Method in class uk.ac.roslin.ensembl.dao.database.variation.DBVariationDAO

getUniquelyMappedVariation(String) - Method in interface uk.ac.roslin.ensembl.dao.variation.VariationDAO

getUniquelyMappedVariations(List<String>) - Method in class uk.ac.roslin.ensembl.dao.database.variation.DBVariationDAO

getUniquelyMappedVariations(List<String>) - Method in interface uk.ac.roslin.ensembl.dao.variation.VariationDAO

getUniquelyMappedVariations(FeatureQuery) - Method in interface uk.ac.roslin.ensembl.mapper.variation.VariationMapper

getUrl() - Method in class uk.ac.roslin.ensembl.datasourceaware.variation.DAVariationXRef

getUrlName() - Method in class uk.ac.roslin.ensembl.dao.database.DBSpecies

getValidatedSequence(DNASequence) - Method in interface uk.ac.roslin.ensembl.dao.coreaccess.DNASequenceDAO

getValidatedSequence(DNASequence) - Method in class uk.ac.roslin.ensembl.dao.database.coreaccess.DBDNASequenceDAO

getValidatedSequences(List<? extends DNASequence>) - Method in interface uk.ac.roslin.ensembl.dao.coreaccess.DNASequenceDAO

getValidatedSequences(List<? extends DNASequence>) - Method in class uk.ac.roslin.ensembl.dao.database.coreaccess.DBDNASequenceDAO

getValue() - Method in class uk.ac.roslin.ensembl.model.GoEvidence

getVariationDAO() - Method in class uk.ac.roslin.ensembl.dao.database.factory.DBDAOSingleSpeciesVariationFactory

getVariationDAO() - Method in interface uk.ac.roslin.ensembl.dao.factory.DAOVariationFactory

getVariationFactory() - Method in class uk.ac.roslin.ensembl.dao.database.DBSingleSpeciesVariationDatabase

getVariationFactory() - Method in class uk.ac.roslin.ensembl.dao.database.factory.DBDAOCollectionCoreFactory

getVariationFactory() - Method in class uk.ac.roslin.ensembl.dao.database.factory.DBDAOSingleSpeciesCoreFactory

getVariationFactory() - Method in interface uk.ac.roslin.ensembl.dao.factory.DAOCoreFactory

getVariationFactory() - Method in interface uk.ac.roslin.ensembl.model.database.SingleSpeciesVariationDatabase

getVariationMappingsOnRegion(DNASequence, Coordinate) - Method in class uk.ac.roslin.ensembl.dao.database.variation.DBVariationDAO

getVariationMappingsOnRegion(DNASequence, Coordinate) - Method in interface uk.ac.roslin.ensembl.dao.variation.VariationDAO

getVariationMappingsOnRegion(Coordinate) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DADNASequence

Returns List of Mappings of Variations on specified Coordinate Region.

getVariationMappingsOnRegion(Integer, Integer) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DADNASequence

Returns List of Mappings of Variations on specified Coordinate Region.

getVariationMappingsOnRegion(Coordinate) - Method in interface uk.ac.roslin.ensembl.model.core.DNASequence

getVariationMappingsOnRegion(Integer, Integer) - Method in interface uk.ac.roslin.ensembl.model.core.DNASequence

getVariationsOnParentSequence(FeatureQuery) - Method in interface uk.ac.roslin.ensembl.mapper.variation.VariationMapper

getVariationsOnRegion(DNASequence, Coordinate) - Method in class uk.ac.roslin.ensembl.dao.database.variation.DBVariationDAO

getVariationsOnRegion(DNASequence, Coordinate) - Method in interface uk.ac.roslin.ensembl.dao.variation.VariationDAO

getVariationsOnRegion(Coordinate) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DADNASequence

Returns list of Variations on specified Coordinate Region.

getVariationsOnRegion(Integer, Integer) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DADNASequence

Returns list of Variations on specified Region.

getVariationsOnRegion(Coordinate) - Method in interface uk.ac.roslin.ensembl.model.core.DNASequence

getVariationsOnRegion(Integer, Integer) - Method in interface uk.ac.roslin.ensembl.model.core.DNASequence

getVariationXRef(Integer) - Method in class uk.ac.roslin.ensembl.dao.database.factory.DBDAOSingleSpeciesVariationFactory

getVariationXRef(Integer) - Method in interface uk.ac.roslin.ensembl.dao.factory.DAOVariationFactory

getVarTypeBySetID(Integer) - Method in class uk.ac.roslin.ensembl.dao.database.factory.DBDAOSingleSpeciesVariationFactory

getVarTypeBySetID(Integer) - Method in interface uk.ac.roslin.ensembl.dao.factory.DAOVariationFactory

getVarTypeBySOTerm(String) - Method in class uk.ac.roslin.ensembl.dao.database.factory.DBDAOSingleSpeciesVariationFactory

getVarTypeBySOTerm(String) - Method in interface uk.ac.roslin.ensembl.dao.factory.DAOVariationFactory

getVegaGenes(String) - Method in interface uk.ac.roslin.ensembl.mapper.core.GeneMapper

getVegaID() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAGene

Returns any curated VegaID for the Gene, forcing lazy load if not set, and defaulting to an empty string if absent (e.g. for all the invertebrate species in EnsemblGenomes).

getVegaID() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DATranscript

Returns any curated VegaID for the Transcript, forcing lazy load if not set, and defaulting to an empty string if absent (e.g. for all the invertebrate species in EnsemblGenomes).

getVegaID() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DATranslation

Returns any curated VegaID for the Translation, forcing lazy load if not set, and defaulting to an empty string if absent (e.g. for all the invertebrate species in EnsemblGenomes).

getVegaID() - Method in interface uk.ac.roslin.ensembl.model.core.VegaFeature

getVegaTranscripts(String) - Method in interface uk.ac.roslin.ensembl.mapper.core.TranscriptMapper

getVegaTranslations(String) - Method in interface uk.ac.roslin.ensembl.mapper.core.TranslationMapper

getVegaXRefs() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAGene

getVegaXRefs() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DATranscript

getVegaXRefs() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DATranslation

getVegaXRefs() - Method in interface uk.ac.roslin.ensembl.model.core.VegaFeature

getVersion() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DACoordinateSystem

Get the value of version

getVersion() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DACoreObject

getVersion() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAFeature

getVersion() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DATranslation

getVersion() - Method in class uk.ac.roslin.ensembl.datasourceaware.DAXRef

getVersion() - Method in interface uk.ac.roslin.ensembl.model.core.CoordinateSystem

getVersion() - Method in interface uk.ac.roslin.ensembl.model.StableID

getVersion() - Method in interface uk.ac.roslin.ensembl.model.XRef

getVersionReport() - Method in class uk.ac.roslin.ensembl.dao.database.DBRegistry

Reports the available database versions for this Registry.

getVersionReport() - Method in interface uk.ac.roslin.ensembl.model.database.Registry

Reports the available database versions for this Registry.

getXdbType() - Method in class uk.ac.roslin.ensembl.mapper.query.FeatureQuery

Get the value of xdbType

getXRef() - Method in class uk.ac.roslin.ensembl.datasourceaware.variation.DAVariation

getXRef() - Method in interface uk.ac.roslin.ensembl.model.variation.Variation

getXRefDAO() - Method in class uk.ac.roslin.ensembl.dao.database.factory.DBDAOCollectionCoreFactory

getXRefDAO() - Method in class uk.ac.roslin.ensembl.dao.database.factory.DBDAOSingleSpeciesCoreFactory

getXRefDAO() - Method in interface uk.ac.roslin.ensembl.dao.factory.DAOCoreFactory

getXRefs(ExternalDBType) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAGene

Returns preloaded XRefs of given type: Note - does not lazy load these

getXRefs(ExternalDBType) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DATranscript

Beware: this method does not trigger lazyloading of typed XRefs.

getXRefs(ExternalDBType) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DATranslation

Returns preloaded XRefs of given type: Note - does not lazy load these.

getXRefs(FeatureQuery) - Method in interface uk.ac.roslin.ensembl.mapper.XRefMapper

go - Static variable in class uk.ac.roslin.ensembl.config.EnsemblDBType

A concrete instantiation of an DatabaseType object representing the ensembl go database sType

GoEvidence - Class in uk.ac.roslin.ensembl.model

GoEvidence(String, String) - Constructor for class uk.ac.roslin.ensembl.model.GoEvidence

GoEvidenceCodes - Class in uk.ac.roslin.ensembl.config

GoEvidenceCodes() - Constructor for class uk.ac.roslin.ensembl.config.GoEvidenceCodes

GoEvidenceCodeTypeHandler - Class in uk.ac.roslin.ensembl.mapper.handler

GoEvidenceCodeTypeHandler() - Constructor for class uk.ac.roslin.ensembl.mapper.handler.GoEvidenceCodeTypeHandler

GroupRelationship<CLAZZ extends IdentifiableObject> - Interface in uk.ac.roslin.ensembl.model.relationship

H

handleResult() - Method in class uk.ac.roslin.ensembl.dao.database.coreaccess.DBAssemblyDAO.PARMappingHandler

handleResult() - Method in class uk.ac.roslin.ensembl.dao.database.coreaccess.DBChromosomeDAO.AssemblyExceptionRowHandler

handleResult() - Method in class uk.ac.roslin.ensembl.dao.database.coreaccess.DBDNASequenceDAO.SequenceRowHandler

handleResult() - Method in class uk.ac.roslin.ensembl.dao.database.coreaccess.DBExonDAO.ExonRowHandler

handleResult() - Method in class uk.ac.roslin.ensembl.dao.database.coreaccess.DBGeneDAO.GeneMappingRowHandler

handleResult() - Method in class uk.ac.roslin.ensembl.dao.database.coreaccess.DBGeneDAO.MappingRowHandler

handleResult() - Method in class uk.ac.roslin.ensembl.dao.database.coreaccess.DBTranscriptDAO.TranscriptRowHandler

HAP - Static variable in class uk.ac.roslin.ensembl.config.AssemblyExceptionType

hasExceptions() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAChromosome

Returns whether this chromosome has any AssemblyExceptions.

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.dao.database.DBCollectionSpecies

hashCode() - Method in class uk.ac.roslin.ensembl.model.ExternalDB

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.

HashMapHolder - Class in uk.ac.roslin.ensembl.mapper.handler

HashMapHolder() - Constructor for class uk.ac.roslin.ensembl.mapper.handler.HashMapHolder

hasNext() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAEnsemblDNASequenceReader.EmptyIterator

hasPAR - Variable in class uk.ac.roslin.ensembl.datasourceaware.core.DAAssembly

hasVariationFactory() - Method in class uk.ac.roslin.ensembl.dao.database.factory.DBDAOCollectionCoreFactory

hasVariationFactory() - Method in class uk.ac.roslin.ensembl.dao.database.factory.DBDAOSingleSpeciesCoreFactory

hasVariationFactory() - Method in interface uk.ac.roslin.ensembl.dao.factory.DAOCoreFactory

highestDBRelease - Variable in class uk.ac.roslin.ensembl.dao.database.DBSpecies

HOMOEOLOG_MANY2MANY - Static variable in class uk.ac.roslin.ensembl.model.compara.HomologyType

orthology relationships between the component genomes - eg in hexaploid wheat Ensembl pipeline annotates as homoeolog_many2many see http://Nov2010.archive.ensembl.org/info/docs/compara/homology_method.html

HOMOEOLOG_ONE2MANY - Static variable in class uk.ac.roslin.ensembl.model.compara.HomologyType

orthology relationships between the component genomes - eg in hexaploid wheat Ensembl pipeline annotates as homoeolog_one2many see http://Nov2010.archive.ensembl.org/info/docs/compara/homology_method.html

HOMOEOLOG_ONE2ONE - Static variable in class uk.ac.roslin.ensembl.model.compara.HomologyType

orthology relationships between the component genomes - eg in hexaploid wheat Ensembl pipeline annotates as homoeolog_one2one see http://Nov2010.archive.ensembl.org/info/docs/compara/homology_method.html

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

HomologyCounts - Class in uk.ac.roslin.ensembl.demo

HomologyCounts() - Constructor for class uk.ac.roslin.ensembl.demo.HomologyCounts

HomologyDAO - Interface in uk.ac.roslin.ensembl.dao.compara

HomologyPairMapper - Interface in uk.ac.roslin.ensembl.mapper.compara

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

HomologyTypeHandler - Class in uk.ac.roslin.ensembl.mapper.handler

HomologyTypeHandler() - Constructor for class uk.ac.roslin.ensembl.mapper.handler.HomologyTypeHandler

I

ibatisSchemaFilePath - Variable in class uk.ac.roslin.ensembl.dao.database.factory.DBDAOFactory

id - Variable in class uk.ac.roslin.ensembl.datasourceaware.core.DACoordinateSystem

id - Variable in class uk.ac.roslin.ensembl.datasourceaware.core.DADNASequence

id - Variable in class uk.ac.roslin.ensembl.datasourceaware.DAObject

IdentifiableObject - Interface in uk.ac.roslin.ensembl.model

INCOMPLETE_SEARCH - Static variable in class uk.ac.roslin.ensembl.config.EnsemblComparaDivision

InitialisationMapper - Interface in uk.ac.roslin.ensembl.mapper.variation

initialize(Integer) - Method in class uk.ac.roslin.ensembl.dao.database.DBRegistry

private initialisation method for the registry which connects to ensembl via a DBDatasourceDAO and retrieves details on all the current tables and creates database objects of the appropriate type for each.

initialized - Variable in class uk.ac.roslin.ensembl.datasourceaware.core.DAFeature

initialized - Variable in class uk.ac.roslin.ensembl.datasourceaware.DAXRef

initializeExternalDBs() - Method in class uk.ac.roslin.ensembl.dao.database.DBCollectionCoreDatabase

initializeExternalDBs() - Method in class uk.ac.roslin.ensembl.dao.database.DBSingleSpeciesCoreDatabase

initializeExternalDBs() - Method in interface uk.ac.roslin.ensembl.model.database.DatabaseWithExternalDBs

inititializeTopLevel() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAFeature

This method is used to initialize the 'topLevelCS', the 'topLevelTargetCoordinates' and the 'topLevelTargetSequence' fields.

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

InverseHomologyPairRelationshipView - Class in uk.ac.roslin.ensembl.datasourceaware.compara

InverseHomologyPairRelationshipView(DAHomologyPairRelationship) - Constructor for class uk.ac.roslin.ensembl.datasourceaware.compara.InverseHomologyPairRelationshipView

INVERTEBRATE_MITOCHONDRIAL - Static variable in class uk.ac.roslin.ensembl.config.CodonTable

isCanonical() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DATranscript

Returns true if this Transcript has been annotated by Ensembl as 'Canonical', according to the following rules: A 'Canonical' Transcript is the longest CCDS model in a gene.

isCanonical() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DATranslation

Returns whether this Translation is marked as the Canonical Translation for its transcript.

isConnectionOK() - Method in class uk.ac.roslin.ensembl.config.DBConnection

isConstitutive() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAExon

isConstitutive() - Method in interface uk.ac.roslin.ensembl.model.core.Exon

isCurrent() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAFeature

isCurrent() - Method in class uk.ac.roslin.ensembl.datasourceaware.variation.DAVariation

isCurrent() - Method in interface uk.ac.roslin.ensembl.model.core.Feature

isDBNameValid(String) - Method in class uk.ac.roslin.ensembl.config.DBConnection

isDBRenamed() - Method in class uk.ac.roslin.ensembl.dao.database.DBSingleSpeciesDatabase

Has the database been renamed due to a rule in the database configuration file.

isDefaultVersion() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DACoordinateSystem

isDefaultVersion() - Method in interface uk.ac.roslin.ensembl.model.core.CoordinateSystem

isFlipped() - Method in class uk.ac.roslin.ensembl.datasourceaware.variation.DAVariation

isFlipped() - Method in interface uk.ac.roslin.ensembl.model.variation.Variation

isInitialized() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAFeature

isInitialized() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DATranslation

isInitialized() - Method in class uk.ac.roslin.ensembl.datasourceaware.DAXRef

isInPanCompara(String) - Method in class uk.ac.roslin.ensembl.dao.database.DBSpecies

isInPanCompara(String) - Method in interface uk.ac.roslin.ensembl.model.core.Species

isLazyloadAllowed() - Method in class uk.ac.roslin.ensembl.datasourceaware.DAObject

isObjectTypeMapped(ObjectType) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAFeature

isObjectTypeMapped(ObjectType) - Method in class uk.ac.roslin.ensembl.datasourceaware.variation.DAVariation

isObjectTypeMapped(ObjectType) - Method in interface uk.ac.roslin.ensembl.model.core.Feature

isPAR() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAChromosome

isPAR() - Method in interface uk.ac.roslin.ensembl.model.core.Chromosome

isSequenceLevel() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DACoordinateSystem

isSequenceLevel() - Method in interface uk.ac.roslin.ensembl.model.core.CoordinateSystem

isSingleSpecies() - Method in class uk.ac.roslin.ensembl.dao.database.coreaccess.DBCoreObjectDAO

isSomatic() - Method in class uk.ac.roslin.ensembl.datasourceaware.variation.DAVariation

isSomatic() - Method in interface uk.ac.roslin.ensembl.model.variation.Variation

isSpeciesInPanHomology(Species, String) - Method in class uk.ac.roslin.ensembl.dao.database.DBRegistry

isSpeciesInPanHomology(Species, String) - Method in interface uk.ac.roslin.ensembl.model.database.Registry

isTopLevel() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DACoordinateSystem

returns true if this CCS is the default version CS with lowest rank number i.e.

isTopLevel() - Method in interface uk.ac.roslin.ensembl.model.core.CoordinateSystem

isTranslated() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DATranscript

Returns whether this Transcript has (at least one, canonical) Translation.

isTranslated() - Method in interface uk.ac.roslin.ensembl.model.core.Transcript

iterator() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAEnsemblDNASequenceReader

K

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

knownSchemaVersions - Variable in class uk.ac.roslin.ensembl.dao.database.DBRegistry

L

label - Variable in class uk.ac.roslin.ensembl.config.EnsemblType

label - Variable in class uk.ac.roslin.ensembl.model.Evidence

lazyLoaded - Variable in class uk.ac.roslin.ensembl.datasourceaware.core.DADNASequence

lazyLoadMetadata() - Method in class uk.ac.roslin.ensembl.dao.database.DBSingleSpeciesCoreDatabase

length - Variable in class uk.ac.roslin.ensembl.datasourceaware.core.DAEnsemblDNASequenceReader

length - Variable in class uk.ac.roslin.ensembl.datasourceaware.core.DAFeature

liesWithinCoordinate(Coordinate) - Method in class uk.ac.roslin.ensembl.model.Coordinate

Tests whether this Coordinate lies TOTALLY within the range of another test Coordinate.

LoadLocalConfigurationProperties - Class in uk.ac.roslin.ensembl.demo

LoadLocalConfigurationProperties() - Constructor for class uk.ac.roslin.ensembl.demo.LoadLocalConfigurationProperties

LoadLocalDatasourceProperties - Class in uk.ac.roslin.ensembl.demo

LoadLocalDatasourceProperties() - Constructor for class uk.ac.roslin.ensembl.demo.LoadLocalDatasourceProperties

LogicFromArkMAP - Class in uk.ac.roslin.ensembl.demo

LogicFromArkMAP() - Constructor for class uk.ac.roslin.ensembl.demo.LogicFromArkMAP

LogicFromSavantPlugin - Class in uk.ac.roslin.ensembl.demo

LogicFromSavantPlugin() - Constructor for class uk.ac.roslin.ensembl.demo.LogicFromSavantPlugin

lrg - Static variable in class uk.ac.roslin.ensembl.config.EnsemblCoordSystemType

M

main(String[]) - Static method in class uk.ac.roslin.ensembl.demo.Analysis

main(String[]) - Static method in class uk.ac.roslin.ensembl.demo.ArchivesConnection

main(String[]) - Static method in class uk.ac.roslin.ensembl.demo.AssemblyExceptions

main(String[]) - Static method in class uk.ac.roslin.ensembl.demo.BacteriaConnection

main(String[]) - Static method in class uk.ac.roslin.ensembl.demo.BacterialGeneHomologues

main(String[]) - Static method in class uk.ac.roslin.ensembl.demo.BacterialSyntenies

main(String[]) - Static method in class uk.ac.roslin.ensembl.demo.BioinformaticsPublicationExamples

main(String[]) - Static method in class uk.ac.roslin.ensembl.demo.ChromosomeCaching

main(String[]) - Static method in class uk.ac.roslin.ensembl.demo.CommandLineConfiguration

main(String[]) - Static method in class uk.ac.roslin.ensembl.demo.ComponentAssembledSequencesOfChromosomes

main(String[]) - Static method in class uk.ac.roslin.ensembl.demo.DNASequences

main(String[]) - Static method in class uk.ac.roslin.ensembl.demo.EnsemblConnection

main(String[]) - Static method in class uk.ac.roslin.ensembl.demo.EnsemblGeneHomologues

main(String[]) - Static method in class uk.ac.roslin.ensembl.demo.EnsemblSyntenies

main(String[]) - Static method in class uk.ac.roslin.ensembl.demo.ExaminingObjectHashCodes

main(String[]) - Static method in class uk.ac.roslin.ensembl.demo.ExonsTranscriptionAndTranslation

main(String[]) - Static method in class uk.ac.roslin.ensembl.demo.Genes

main(String[]) - Static method in class uk.ac.roslin.ensembl.demo.GenomesConnection

main(String[]) - Static method in class uk.ac.roslin.ensembl.demo.HomologyCounts

main(String[]) - Static method in class uk.ac.roslin.ensembl.demo.LoadLocalConfigurationProperties

main(String[]) - Static method in class uk.ac.roslin.ensembl.demo.LoadLocalDatasourceProperties

main(String[]) - Static method in class uk.ac.roslin.ensembl.demo.LogicFromArkMAP

main(String[]) - Static method in class uk.ac.roslin.ensembl.demo.LogicFromSavantPlugin

main(String[]) - Static method in class uk.ac.roslin.ensembl.demo.PlantGeneHomologues

main(String[]) - Static method in class uk.ac.roslin.ensembl.demo.PlantsSyntenies

main(String[]) - Static method in class uk.ac.roslin.ensembl.demo.RegistryFactory

main(String[]) - Static method in class uk.ac.roslin.ensembl.demo.RevalidateAndLazyLoadSequences

main(String[]) - Static method in class uk.ac.roslin.ensembl.demo.scratch

main(String[]) - Static method in class uk.ac.roslin.ensembl.demo.SpeciesAliases

main(String[]) - Static method in class uk.ac.roslin.ensembl.demo.SpeciesVersions

main(String[]) - Static method in class uk.ac.roslin.ensembl.demo.SpeciesWithNoChromosomes

main(String[]) - Static method in class uk.ac.roslin.ensembl.demo.Synonyms

main(String[]) - Static method in class uk.ac.roslin.ensembl.demo.TranscriptionAndTranslation

main(String[]) - Static method in class uk.ac.roslin.ensembl.demo.TranscriptionAndTranslationReverse

main(String[]) - Static method in class uk.ac.roslin.ensembl.demo.UserChristelle

main(String[]) - Static method in class uk.ac.roslin.ensembl.demo.UserJeanPhilippe

main(String[]) - Static method in class uk.ac.roslin.ensembl.demo.UserSetzermann

main(String[]) - Static method in class uk.ac.roslin.ensembl.demo.Variations

main(String[]) - Static method in class uk.ac.roslin.ensembl.demo.VariationScript

main(String[]) - Static method in class uk.ac.roslin.ensembl.demo.VegaAndCCDSIDs

main(String[]) - Static method in class uk.ac.roslin.ensembl.demo.XRefs

main(String[]) - Static method in class uk.ac.roslin.ensembl.test.Chromosome

main(String[]) - Static method in class uk.ac.roslin.ensembl.test.Compara

main(String[]) - Static method in class uk.ac.roslin.ensembl.test.Registry

main(String[]) - Static method in class uk.ac.roslin.ensembl.test.Variation

makeDatabase(String) - Method in class uk.ac.roslin.ensembl.dao.database.DBRegistry

makeDatabase(String) - Method in interface uk.ac.roslin.ensembl.model.database.Registry

makeFactory(CollectionDatabase, CollectionSpecies) - Static method in class uk.ac.roslin.ensembl.dao.database.factory.DBDAOCollectionFactory

makeFactory(SingleSpeciesDatabase) - Static method in class uk.ac.roslin.ensembl.dao.database.factory.DBDAOSingleSpeciesFactory

makeGap(Integer) - Static method in class uk.ac.roslin.ensembl.datasourceaware.core.GapSequence

MappableObject - Interface in uk.ac.roslin.ensembl.model

mappedObjectTypes - Variable in class uk.ac.roslin.ensembl.datasourceaware.core.DAFeature

mappedObjectTypes - Variable in class uk.ac.roslin.ensembl.datasourceaware.variation.DAVariation

mappedRegions - Variable in class uk.ac.roslin.ensembl.datasourceaware.core.DADNASequence

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

mappings - Variable in class uk.ac.roslin.ensembl.datasourceaware.core.DADNASequence

mappings - Variable in class uk.ac.roslin.ensembl.datasourceaware.core.DAFeature

mappings - Variable in class uk.ac.roslin.ensembl.datasourceaware.variation.DAVariation

MappingSet - Class in uk.ac.roslin.ensembl.model

Used to be abstract with signature public abstract class MappingSet<CLAZZ extends Mapping> extends TreeSet<CLAZZ> implements Serializable {

MappingSet() - Constructor for class uk.ac.roslin.ensembl.model.MappingSet

Parameterless constructor creates a MappingSet, that is sorted using the Mapping.mappingOnSourceComparator.

MappingSet(Comparator) - Constructor for class uk.ac.roslin.ensembl.model.MappingSet

Alternative constructor allowing specification of an alternative comparator for sorting (e.g.

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

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

maximumFeatureLength - Variable in class uk.ac.roslin.ensembl.mapper.query.FeatureQuery

METAZOA - Static variable in class uk.ac.roslin.ensembl.config.EnsemblComparaDivision

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

modificationDate - Variable in class uk.ac.roslin.ensembl.datasourceaware.core.DACoreObject

MOLD_MITOCHONDRIAL - Static variable in class uk.ac.roslin.ensembl.config.CodonTable

mostRecentEnsemblSchemaVersion - Variable in class uk.ac.roslin.ensembl.dao.database.DBSpecies

MULTI - Static variable in class uk.ac.roslin.ensembl.config.EnsemblComparaDivision

mybatisSchemaFilePath - Variable in class uk.ac.roslin.ensembl.dao.database.factory.DBDAOFactory

N

name - Variable in class uk.ac.roslin.ensembl.datasourceaware.core.DADNASequence

name - Variable in class uk.ac.roslin.ensembl.datasourceaware.core.DAEnsemblDNASequenceReader

name - Variable in class uk.ac.roslin.ensembl.datasourceaware.variation.DAVariation

newline - Variable in class uk.ac.roslin.ensembl.config.DBConnection

newline - Variable in class uk.ac.roslin.ensembl.dao.database.DBRegistry

next() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAEnsemblDNASequenceReader.EmptyIterator

NONE - Static variable in class uk.ac.roslin.ensembl.model.core.Exon.Phase

NonUniqueException - Exception in uk.ac.roslin.ensembl.exception

NonUniqueException() - Constructor for exception uk.ac.roslin.ensembl.exception.NonUniqueException

Creates a new instance of NonUniqueException without detail message.

NonUniqueException(String) - Constructor for exception uk.ac.roslin.ensembl.exception.NonUniqueException

Constructs an instance of NonUniqueException with the specified detail message.

NonUniqueException(String, Exception) - Constructor for exception uk.ac.roslin.ensembl.exception.NonUniqueException

NonUniqueException(Exception) - Constructor for exception uk.ac.roslin.ensembl.exception.NonUniqueException

NonUniqueException(String, Collection) - Constructor for exception uk.ac.roslin.ensembl.exception.NonUniqueException

O

ObjectType - Interface in uk.ac.roslin.ensembl.model

objectTypeMappings - Variable in class uk.ac.roslin.ensembl.datasourceaware.core.DADNASequence

objectTypeMappings - Variable in class uk.ac.roslin.ensembl.datasourceaware.core.DAFeature

objectTypeMappings - Variable in class uk.ac.roslin.ensembl.datasourceaware.variation.DAVariation

occurrences - Variable in class uk.ac.roslin.ensembl.datasourceaware.variation.DAVariation

oldstyle_collectionspeciesHashByDBName - Variable in class uk.ac.roslin.ensembl.dao.database.DBRegistry

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

originalDBName - Variable in class uk.ac.roslin.ensembl.dao.database.DBSingleSpeciesDatabase

originalDBSpeciesName - Variable in class uk.ac.roslin.ensembl.dao.database.DBSingleSpeciesDatabase

originalHashCode() - Method in class uk.ac.roslin.ensembl.model.ExternalDB

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

Returns whether this Coordinate overlaps with the extent of a test Coordinate.

P

PAN_HOMOLOGY - Static variable in class uk.ac.roslin.ensembl.config.EnsemblComparaDivision

PAR - Static variable in class uk.ac.roslin.ensembl.config.AssemblyExceptionType

parent - Variable in class uk.ac.roslin.ensembl.datasourceaware.core.DAEnsemblDNASequenceReader

parentSequenceID - Variable in class uk.ac.roslin.ensembl.mapper.query.FeatureQuery

parentStart - Variable in class uk.ac.roslin.ensembl.mapper.query.FeatureQuery

parentStop - Variable in class uk.ac.roslin.ensembl.mapper.query.FeatureQuery

pARMappings - Variable in class uk.ac.roslin.ensembl.datasourceaware.core.DAAssembly

PATCH_FIX - Static variable in class uk.ac.roslin.ensembl.config.AssemblyExceptionType

PATCH_NOVEL - Static variable in class uk.ac.roslin.ensembl.config.AssemblyExceptionType

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

PlantGeneHomologues - Class in uk.ac.roslin.ensembl.demo

PlantGeneHomologues() - Constructor for class uk.ac.roslin.ensembl.demo.PlantGeneHomologues

PLANTS - Static variable in class uk.ac.roslin.ensembl.config.EnsemblComparaDivision

PlantsSyntenies - Class in uk.ac.roslin.ensembl.demo

PlantsSyntenies() - Constructor for class uk.ac.roslin.ensembl.demo.PlantsSyntenies

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

PROJECTION_ALTERED - Static variable in class uk.ac.roslin.ensembl.model.compara.HomologyType

relationship between genes on a human chromosome assembly and an assembly patch

PROJECTION_UNCHANGED - Static variable in class uk.ac.roslin.ensembl.model.compara.HomologyType

relationship between genes on a human chromosome assembly and an assembly patch

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 - Static variable in class uk.ac.roslin.ensembl.config.EnsemblCoreObjectType

ProteinFeature - Interface in uk.ac.roslin.ensembl.model.core

ProteinFeatureDAO - Interface in uk.ac.roslin.ensembl.dao.coreaccess

ProteinFeatureMapper - Interface in uk.ac.roslin.ensembl.mapper.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

queryIntegerList - Variable in class uk.ac.roslin.ensembl.mapper.query.FeatureQuery

queryStringList - Variable in class uk.ac.roslin.ensembl.mapper.query.FeatureQuery

R

RangeException - Exception in uk.ac.roslin.ensembl.exception

Range Exception has been changed to a Runtime Exception so that we don't have to check for it.

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

rank - Variable in class uk.ac.roslin.ensembl.datasourceaware.core.DACoordinateSystem

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

reader - Variable in class uk.ac.roslin.ensembl.dao.database.DBRegistry

regConfig - Variable in class uk.ac.roslin.ensembl.dao.database.DBRegistry

registry - Variable in class uk.ac.roslin.ensembl.dao.database.DBSpecies

registry - Variable in class uk.ac.roslin.ensembl.dao.database.factory.DBDAOFactory

registry - Variable in class uk.ac.roslin.ensembl.datasourceaware.core.DADNASequence

registry - Variable in class uk.ac.roslin.ensembl.datasourceaware.DAObject

Registry - Interface in uk.ac.roslin.ensembl.model.database

Registry - Class in uk.ac.roslin.ensembl.test

Registry() - Constructor for class uk.ac.roslin.ensembl.test.Registry

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.

RegistryFactory - Class in uk.ac.roslin.ensembl.demo

RegistryFactory() - Constructor for class uk.ac.roslin.ensembl.demo.RegistryFactory

RegistryProvider - Class in uk.ac.roslin.ensembl.test

RegistryProvider() - Constructor for class uk.ac.roslin.ensembl.test.RegistryProvider

ReInitializationDAO - Interface in uk.ac.roslin.ensembl.dao.coreaccess

reInitialize(IdentifiableObject) - Method in interface uk.ac.roslin.ensembl.dao.coreaccess.ReInitializationDAO

reInitialize(IdentifiableObject) - Method in class uk.ac.roslin.ensembl.dao.database.coreaccess.DBExonDAO

Uses the stableid of an object to fill in missing data

reInitialize(IdentifiableObject) - Method in class uk.ac.roslin.ensembl.dao.database.coreaccess.DBGeneDAO

Uses the stableid of an object to fill in missing data that would have been present if the the gene had intially been made by a call to getGeneByStableID or getGeneByID.

reInitialize(IdentifiableObject) - Method in class uk.ac.roslin.ensembl.dao.database.coreaccess.DBTranscriptDAO

Uses the stableid of an object to fill in missing data

reInitialize(IdentifiableObject) - Method in class uk.ac.roslin.ensembl.dao.database.coreaccess.DBTranslationDAO

reInitialize(IdentifiableObject) - Method in class uk.ac.roslin.ensembl.dao.database.DBXRefDAO

Uses the xref_id of an xref to fill in missing data that would have been present if the the xref had initially been made by a call to getXRefs on the identifiable object.

reInitialize() - Method in class uk.ac.roslin.ensembl.datasourceaware.variation.DAVariationXRef

reInitialize(FeatureQuery) - Method in interface uk.ac.roslin.ensembl.mapper.XRefMapper

RelationshipType - Class in uk.ac.roslin.ensembl.model.relationship

RelationshipType(String) - Constructor for class uk.ac.roslin.ensembl.model.relationship.RelationshipType

remove() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAEnsemblDNASequenceReader.EmptyIterator

renamedDBs - Variable in class uk.ac.roslin.ensembl.config.DBConnection

renamedDBs - Variable in class uk.ac.roslin.ensembl.dao.database.DBRegistry

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

report() - Method in class uk.ac.roslin.ensembl.config.DBConnection

resortSpecies() - Method in class uk.ac.roslin.ensembl.dao.database.DBCollection

Finalization method to be called after all species have been added to all collections.

RevalidateAndLazyLoadSequences - Class in uk.ac.roslin.ensembl.demo

RevalidateAndLazyLoadSequences() - Constructor for class uk.ac.roslin.ensembl.demo.RevalidateAndLazyLoadSequences

reverseMapping - Variable in class uk.ac.roslin.ensembl.model.Mapping

rnaseq - Static variable in class uk.ac.roslin.ensembl.config.EnsemblDBType

S

scaffold - Static variable in class uk.ac.roslin.ensembl.config.EnsemblCoordSystemType

SCENEDESMUS_MITOCHONDRIAL - Static variable in class uk.ac.roslin.ensembl.config.CodonTable

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

schemaVersion - Variable in class uk.ac.roslin.ensembl.dao.database.DBRegistry

schemaVersion - Variable in class uk.ac.roslin.ensembl.dao.database.factory.DBDAOFactory

schemaVersion - Variable in class uk.ac.roslin.ensembl.datasourceaware.core.DADNASequence

schemaVersion - Variable in class uk.ac.roslin.ensembl.datasourceaware.DAObject

schemaVersions - Variable in class uk.ac.roslin.ensembl.dao.database.DBSpecies

scratch - Class in uk.ac.roslin.ensembl.demo

scratch() - Constructor for class uk.ac.roslin.ensembl.demo.scratch

seqRegionID - Variable in class uk.ac.roslin.ensembl.datasourceaware.core.DADNASequence

seqRegionID - Variable in class uk.ac.roslin.ensembl.datasourceaware.core.DAEnsemblDNASequenceReader

sequence - Variable in class uk.ac.roslin.ensembl.datasourceaware.core.DAEnsemblDNASequenceReader

sequenceLevel - Static variable in class uk.ac.roslin.ensembl.config.EnsemblCoordSystemType

sequenceLevel - Variable in class uk.ac.roslin.ensembl.datasourceaware.core.DACoordinateSystem

SequenceMapper - Interface in uk.ac.roslin.ensembl.mapper.core

set(String, String) - Method in class uk.ac.roslin.ensembl.model.variation.VariationType

setAlleleString(String) - Method in class uk.ac.roslin.ensembl.datasourceaware.variation.VariationMapping

setAnalysisID(Integer) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAAnalyzedFeature

setAnalysisID(Integer) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAProteinFeature

setAnalysisID(Integer) - Method in interface uk.ac.roslin.ensembl.model.core.Analyzed

setAncestralAllele(String) - Method in class uk.ac.roslin.ensembl.datasourceaware.variation.DAVariation

setAssayType(String) - Method in class uk.ac.roslin.ensembl.datasourceaware.variation.DAVariationXRef

setAssemblyAccession(String) - Method in class uk.ac.roslin.ensembl.dao.database.DBSingleSpeciesCoreDatabase

setAssemblyAccession(String, String) - Method in class uk.ac.roslin.ensembl.dao.database.DBSpecies

setAssemblyAccession(String) - Method in interface uk.ac.roslin.ensembl.model.database.SingleSpeciesCoreDatabase

setAssemblyExceptions(TreeMap<String, ? extends Chromosome>) - Method in interface uk.ac.roslin.ensembl.dao.coreaccess.ChromosomeDAO

setAssemblyExceptions(TreeMap<String, ? extends Chromosome>) - Method in class uk.ac.roslin.ensembl.dao.database.coreaccess.DBChromosomeDAO

setAssemblyExceptions(String) - Method in class uk.ac.roslin.ensembl.dao.database.DBCollectionSpecies

setAssemblyExceptions(String) - Method in class uk.ac.roslin.ensembl.dao.database.DBSpecies

setAssemblyExceptions(String) - Method in interface uk.ac.roslin.ensembl.model.core.Species

setAssemblyName(String) - Method in class uk.ac.roslin.ensembl.dao.database.DBSingleSpeciesCoreDatabase

setAssemblyName(String, String) - Method in class uk.ac.roslin.ensembl.dao.database.DBSpecies

setAssemblyName(String) - Method in interface uk.ac.roslin.ensembl.model.database.SingleSpeciesCoreDatabase

setAssemblyStart(Integer) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAAssembly

setAssemblyStart(Integer) - Method in interface uk.ac.roslin.ensembl.model.core.Assembly

setAssemblyStop(Integer) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAAssembly

setAssemblyStop(Integer) - Method in interface uk.ac.roslin.ensembl.model.core.Assembly

setAttributes(HashMap<String, String>) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DADNASequence

setBiotype(String) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAGene

setBiotype(String) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DATranscript

setBuild(String) - Method in class uk.ac.roslin.ensembl.dao.database.DBDatabase

setBuildLevel(String, String) - Method in class uk.ac.roslin.ensembl.dao.database.DBSingleSpeciesCoreDatabase

setBuildLevel(String, String) - Method in interface uk.ac.roslin.ensembl.model.database.SingleSpeciesCoreDatabase

setBuildLevels(Species, HashMap<String, String>) - Method in class uk.ac.roslin.ensembl.dao.database.DBCollectionCoreDatabase

setBuildLevels(Species, HashMap<String, String>) - Method in interface uk.ac.roslin.ensembl.model.database.CollectionCoreDatabase

setCanonical(boolean) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DATranscript

setCanonical(boolean) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DATranslation

setCanonicalTranscript(DATranscript) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAGene

setCanonicalTranscriptID(Integer) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAGene

setCanonicalTranslationID(Integer) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DATranscript

setChromosomeName(String) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAChromosome

setChromosomeName(String) - Method in interface uk.ac.roslin.ensembl.model.core.Chromosome

setCigarLine(String) - Method in class uk.ac.roslin.ensembl.model.compara.HomologyAlignmentProperties

setCodonTableID(Integer) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DADNASequence

setCollection(CollectionOfSpecies) - Method in class uk.ac.roslin.ensembl.dao.database.DBCollectionDatabase

setCollection(CollectionOfSpecies) - Method in interface uk.ac.roslin.ensembl.model.database.CollectionDatabase

setCollectionName(String) - Method in class uk.ac.roslin.ensembl.dao.database.DBCollectionDatabase

setCollectionName(String) - Method in interface uk.ac.roslin.ensembl.model.database.CollectionDatabase

setCommonName(String) - Method in class uk.ac.roslin.ensembl.dao.database.DBSpecies

setComparaDB(String) - Method in class uk.ac.roslin.ensembl.mapper.query.FeatureQuery

setComparaDivision(String) - Method in class uk.ac.roslin.ensembl.dao.database.DBSpecies

setComparaDivision(EnsemblComparaDivision) - Method in class uk.ac.roslin.ensembl.dao.database.DBSpecies

setComparaName(String) - Method in class uk.ac.roslin.ensembl.dao.database.DBSingleSpeciesCoreDatabase

setComparaName(String, String) - Method in class uk.ac.roslin.ensembl.dao.database.DBSpecies

setComparaName(String) - Method in interface uk.ac.roslin.ensembl.model.database.SingleSpeciesCoreDatabase

setCompoundSet(CompoundSet) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAEnsemblDNASequenceReader

setConfiguration(Properties) - Method in class uk.ac.roslin.ensembl.dao.database.DBBaseDAO

setConfiguration(RegistryConfiguration) - Method in class uk.ac.roslin.ensembl.dao.database.DBRegistry

setConfiguration(DBConnection.DataSource) - Method in class uk.ac.roslin.ensembl.dao.database.DBRegistry

setConsequences(List<VariationType>) - Method in class uk.ac.roslin.ensembl.datasourceaware.variation.VariationMapping

setConstitutive(Boolean) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAExon

setContents(String) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAEnsemblDNASequenceReader

setCoordinateSystemID(Integer) - Method in class uk.ac.roslin.ensembl.mapper.query.FeatureQuery

setCoords(Coordinate) - Method in class uk.ac.roslin.ensembl.model.compara.HomologyAlignmentProperties

setCoordSystem(CoordinateSystem) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DADNASequence

setCoordSystem(CoordinateSystem) - Method in interface uk.ac.roslin.ensembl.model.core.DNASequence

setCoordSystemID(Integer) - Method in interface uk.ac.roslin.ensembl.biojava3.EnsemblDNASequenceReader

setCoordSystemID(Integer) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAEnsemblDNASequenceReader

setCoreDB(SingleSpeciesCoreDatabase) - Method in class uk.ac.roslin.ensembl.dao.database.DBSingleSpeciesVariationDatabase

setCreationDate(Date) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DACoreObject

setCreationDate(Date) - Method in class uk.ac.roslin.ensembl.datasourceaware.DAAnalysis

setCreationDate(Date) - Method in interface uk.ac.roslin.ensembl.model.StableID

setCsID(Integer) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DADNASequence

setCurrent(Boolean) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAFeature

setDaoFactory(DAOFactory) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DADNASequence

setDaoFactory(DAOFactory) - Method in class uk.ac.roslin.ensembl.datasourceaware.DAObject

setDatabase(Database) - Method in class uk.ac.roslin.ensembl.dao.database.factory.DBDAOFactory

setDatabase(CoreDatabase) - Method in class uk.ac.roslin.ensembl.mapper.handler.ExternalDBTypeHandler

setDatabaseName(String) - Method in class uk.ac.roslin.ensembl.dao.database.factory.DBDAOFactory

setDatabaseName(String) - Method in interface uk.ac.roslin.ensembl.dao.factory.DAOFactory

setDatabaseStyleSpeciesName(String) - Method in class uk.ac.roslin.ensembl.dao.database.DBSpecies

setDatabaseStyleSpeciesName(Integer, String) - Method in class uk.ac.roslin.ensembl.dao.database.DBSpecies

setDB(ExternalDB) - Method in class uk.ac.roslin.ensembl.datasourceaware.DAXRef

setDBByFile(File) - Method in class uk.ac.roslin.ensembl.config.RegistryConfiguration

Sets DBConnection on this RegistryConfiguration object from a given File of Properties.

setDBDescription(String) - Method in class uk.ac.roslin.ensembl.model.ExternalDB

setDBDisplayName(String) - Method in class uk.ac.roslin.ensembl.model.ExternalDB

setdBName(String) - Method in class uk.ac.roslin.ensembl.dao.database.DBDatabase

setDBName(String) - Method in class uk.ac.roslin.ensembl.datasourceaware.variation.DAVariationXRef

setDBName(String) - Method in class uk.ac.roslin.ensembl.model.ExternalDB

setDBProperties(Properties) - Method in class uk.ac.roslin.ensembl.config.RegistryConfiguration

Sets DBConnection on this RegistryConfiguration object from a given set of Properties.

setDBRelease(String) - Method in class uk.ac.roslin.ensembl.model.ExternalDB

setDBSeqLength(Integer) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DADNASequence

setDBSeqLength(Integer) - Method in interface uk.ac.roslin.ensembl.model.core.DNASequence

setDbSpeciesName(String) - Method in class uk.ac.roslin.ensembl.dao.database.DBSingleSpeciesDatabase

setDbSpeciesName(String) - Method in interface uk.ac.roslin.ensembl.model.database.SingleSpeciesDatabase

setDBStatus(String) - Method in class uk.ac.roslin.ensembl.model.ExternalDB

setDBType(DatabaseType) - Method in class uk.ac.roslin.ensembl.dao.database.factory.DBDAOFactory

setDBType(DatabaseType) - Method in interface uk.ac.roslin.ensembl.dao.factory.DAOFactory

setDBVersion(String) - Method in class uk.ac.roslin.ensembl.dao.database.DBDatabase

setDBVersion(String) - Method in class uk.ac.roslin.ensembl.dao.database.factory.DBDAOFactory

setDBVersion(String) - Method in interface uk.ac.roslin.ensembl.dao.factory.DAOFactory

setDBVersion(String) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DACoreObject

setDefaultVersion(Boolean) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DACoordinateSystem

setDefaultVersion(Boolean) - Method in interface uk.ac.roslin.ensembl.model.core.CoordinateSystem

setDescription(String) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAFeature

setDescription(String) - Method in class uk.ac.roslin.ensembl.datasourceaware.DAAnalysis

setDescription(String) - Method in class uk.ac.roslin.ensembl.datasourceaware.DAXRef

setDescription(String) - Method in interface uk.ac.roslin.ensembl.model.core.Analysis

setDisplayID(String) - Method in class uk.ac.roslin.ensembl.datasourceaware.DAXRef

setDisplayLabel(String) - Method in class uk.ac.roslin.ensembl.datasourceaware.DAAnalysis

setDisplayLabel(String) - Method in interface uk.ac.roslin.ensembl.model.core.Analysis

setDisplayName(String) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAFeature

setDisplayTerm(String) - Method in class uk.ac.roslin.ensembl.model.variation.VariationType

setDisplayXRef(DAXRef) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAGene

setDisplayXRef(DAXRef) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DATranscript

setEnd(Integer) - Method in class uk.ac.roslin.ensembl.model.Coordinate

public setter for the End of the Coordinate, will swap start and end if new end is less than start.

setEndPhase(int) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAExon

setEnsemblSchemaVersion(String) - Method in class uk.ac.roslin.ensembl.dao.database.factory.DBDAOFactory

setEnsemblSchemaVersion(String) - Method in interface uk.ac.roslin.ensembl.dao.factory.DAOFactory

setEnsemblStablePrefix(String) - Method in class uk.ac.roslin.ensembl.dao.database.DBSpecies

setEValue(Double) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAProteinFeature

setEValue(Double) - Method in interface uk.ac.roslin.ensembl.model.core.ProteinFeature

setEvidence(Evidence) - Method in class uk.ac.roslin.ensembl.datasourceaware.DAXRef

setExceptions(boolean) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAChromosome

flag method to create the 'exceptions' HashMap for this chromosome if necessary.

setExternalDatabaseName(String) - Method in class uk.ac.roslin.ensembl.datasourceaware.DAAnalysis

Set the value of externalDatabaseName

setExternalDatabaseName(String) - Method in interface uk.ac.roslin.ensembl.model.core.Analysis

setExternalDatabaseVersion(String) - Method in class uk.ac.roslin.ensembl.datasourceaware.DAAnalysis

Set the value of externalDatabaseVersion

setExternalDatabaseVersion(String) - Method in interface uk.ac.roslin.ensembl.model.core.Analysis

setFactory(DAOSingleSpeciesCoreFactory) - Method in class uk.ac.roslin.ensembl.dao.database.coreaccess.DBCoreObjectDAO

setFactory(DAOCollectionCoreFactory) - Method in class uk.ac.roslin.ensembl.dao.database.coreaccess.DBCoreObjectDAO

setFactory(DAOFactory) - Method in class uk.ac.roslin.ensembl.dao.database.DBBaseDAO

setFactory(DAOCoreFactory) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAEnsemblDNASequenceReader

setFactory(DAOVariationFactory) - Method in class uk.ac.roslin.ensembl.mapper.handler.ConsequencesHandler

setFactory(DAOVariationFactory) - Method in class uk.ac.roslin.ensembl.mapper.handler.VariationTypeHandler

setFactory(DAOVariationFactory) - Method in class uk.ac.roslin.ensembl.mapper.handler.VariationXRefHandler

setFakeid(String) - Method in class uk.ac.roslin.ensembl.mapper.handler.HashMapHolder

Set the value of fakeid

setFeatureCS() - Method in interface uk.ac.roslin.ensembl.dao.coreaccess.CoordinateSystemDAO

setFeatureCS() - Method in class uk.ac.roslin.ensembl.dao.database.coreaccess.DBCoordinateSystemDAO

setFeatureCS(HashMap) - Method in interface uk.ac.roslin.ensembl.mapper.core.SpeciesMapper

setFeatureCS() - Method in interface uk.ac.roslin.ensembl.mapper.variation.VariationMapper

setFeatureID(Integer) - Method in class uk.ac.roslin.ensembl.mapper.query.FeatureQuery

Set the value of featureID

setFeatureName(String) - Method in class uk.ac.roslin.ensembl.mapper.query.FeatureQuery

setFeatureStableID(String) - Method in class uk.ac.roslin.ensembl.mapper.query.FeatureQuery

Set the value of featureStableID

setFeatureType(String) - Method in class uk.ac.roslin.ensembl.mapper.query.FeatureQuery

Set the value of featureType

setFirstExonID(Integer) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DATranslation

setFirstExonStart(Integer) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DATranslation

setFlipped(Boolean) - Method in class uk.ac.roslin.ensembl.datasourceaware.variation.DAVariation

setGene(DAGene) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DATranscript

setGeneID(Integer) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DATranscript

setGeneID(Integer) - Method in class uk.ac.roslin.ensembl.mapper.query.FeatureQuery

Set the value of geneID

setGeneID(String) - Method in class uk.ac.roslin.ensembl.model.compara.HomologyAlignmentProperties

setGenus_Species(String) - Method in class uk.ac.roslin.ensembl.dao.database.factory.DBDAOSingleSpeciesFactory

setGenus_Species(String) - Method in interface uk.ac.roslin.ensembl.dao.factory.DAOSingleSpeciesFactory

setGffFeature(String) - Method in class uk.ac.roslin.ensembl.datasourceaware.DAAnalysis

setGffFeature(String) - Method in interface uk.ac.roslin.ensembl.model.core.Analysis

setGffSource(String) - Method in class uk.ac.roslin.ensembl.datasourceaware.DAAnalysis

setGffSource(String) - Method in interface uk.ac.roslin.ensembl.model.core.Analysis

setHomoeologueCount(Integer) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAGene

setId(Integer) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DACoordinateSystem

Set the value of id

setId(Integer) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DADNASequence

setId(Integer) - Method in class uk.ac.roslin.ensembl.datasourceaware.DAObject

setId(Integer) - Method in class uk.ac.roslin.ensembl.datasourceaware.variation.VariationMapping

setId(Integer) - Method in interface uk.ac.roslin.ensembl.model.core.CoordinateSystem

setId(Integer) - Method in class uk.ac.roslin.ensembl.model.ExternalDB

setId(Integer) - Method in interface uk.ac.roslin.ensembl.model.IdentifiableObject

setID - Variable in class uk.ac.roslin.ensembl.model.variation.VariationType

setIDForVersion(Integer, String) - Method in class uk.ac.roslin.ensembl.dao.database.DBCollectionSpecies

setInfo(String) - Method in class uk.ac.roslin.ensembl.datasourceaware.DAXRef

setInfoType(String) - Method in class uk.ac.roslin.ensembl.datasourceaware.DAXRef

setInitialized(boolean) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAFeature

setInitialized(boolean) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DATranslation

setInitialized(boolean) - Method in class uk.ac.roslin.ensembl.datasourceaware.DAXRef

setIntDBVersion(int) - Method in class uk.ac.roslin.ensembl.dao.database.DBDatabase

setIntSchemaVersion(int) - Method in class uk.ac.roslin.ensembl.dao.database.DBDatabase

setLastCommonAncestor(String) - Method in class uk.ac.roslin.ensembl.datasourceaware.compara.DAHomologyRelationship

setLastExonEnd(Integer) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DATranslation

setLastExonID(Integer) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DATranslation

setLazyloadAllowed(boolean) - Method in class uk.ac.roslin.ensembl.datasourceaware.DAObject

setLazyLoaded(boolean) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DADNASequence

setLength(Integer) - Method in interface uk.ac.roslin.ensembl.biojava3.EnsemblDNASequenceReader

setLength(Integer) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAEnsemblDNASequenceReader

setLength(Integer) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAFeature

setLogicalName(String) - Method in class uk.ac.roslin.ensembl.datasourceaware.DAAnalysis

Set the value of logicalName

setLogicalName(String) - Method in interface uk.ac.roslin.ensembl.model.core.Analysis

setMap(HashMap) - Method in class uk.ac.roslin.ensembl.mapper.handler.HashMapHolder

setMappings(MappingSet) - Method in class uk.ac.roslin.ensembl.datasourceaware.variation.DAVariation

setMaximumFeatureLength(Integer) - Method in class uk.ac.roslin.ensembl.mapper.query.FeatureQuery

setModificationDate(Date) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DACoreObject

setModificationDate(Date) - Method in interface uk.ac.roslin.ensembl.model.StableID

setModuleName(String) - Method in class uk.ac.roslin.ensembl.datasourceaware.DAAnalysis

setModuleName(String) - Method in interface uk.ac.roslin.ensembl.model.core.Analysis

setModuleVersion(String) - Method in class uk.ac.roslin.ensembl.datasourceaware.DAAnalysis

setModuleVersion(String) - Method in interface uk.ac.roslin.ensembl.model.core.Analysis

setMostRecentCoreDatabase(DBCollectionCoreDatabase) - Method in class uk.ac.roslin.ensembl.dao.database.DBCollectionSpecies

setMybatisSchemaFilePath(String) - Method in class uk.ac.roslin.ensembl.dao.database.factory.DBDAOFactory

setMybatisSchemaFilePath(String) - Method in interface uk.ac.roslin.ensembl.dao.factory.DAOFactory

setName(String) - Method in interface uk.ac.roslin.ensembl.biojava3.EnsemblDNASequenceReader

setName(String) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DADNASequence

setName(String) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAEnsemblDNASequenceReader

setName(String) - Method in class uk.ac.roslin.ensembl.datasourceaware.variation.DAVariation

setName(String) - Method in interface uk.ac.roslin.ensembl.model.core.DNASequence

setName(String) - Method in interface uk.ac.roslin.ensembl.model.variation.Variation

setOccurrences(int) - Method in class uk.ac.roslin.ensembl.datasourceaware.variation.DAVariation

setOrthologueCount(Integer) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAGene

setPAR(boolean) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAChromosome

setParalogueCount(Integer) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAGene

setParameter(PreparedStatement, int, Object, JdbcType) - Method in class uk.ac.roslin.ensembl.mapper.handler.AssemblyExceptionTypeHandler

setParameter(PreparedStatement, int, Object, JdbcType) - Method in class uk.ac.roslin.ensembl.mapper.handler.BooleanTypeHandler

setParameter(PreparedStatement, int, Object, JdbcType) - Method in class uk.ac.roslin.ensembl.mapper.handler.ConsequencesHandler

setParameter(PreparedStatement, int, Object, JdbcType) - Method in class uk.ac.roslin.ensembl.mapper.handler.CoordinateSystemDefaultVersionTypeHandler

setParameter(PreparedStatement, int, Object, JdbcType) - Method in class uk.ac.roslin.ensembl.mapper.handler.CoordinateSystemSeqLevelTypeHandler

setParameter(PreparedStatement, int, Object, JdbcType) - Method in class uk.ac.roslin.ensembl.mapper.handler.CoordinateSystemTypeHandler

setParameter(PreparedStatement, int, Object, JdbcType) - Method in class uk.ac.roslin.ensembl.mapper.handler.ExistsTypeHandler

setParameter(PreparedStatement, int, Object, JdbcType) - Method in class uk.ac.roslin.ensembl.mapper.handler.ExternalDBTypeHandler

setParameter(PreparedStatement, int, Object, JdbcType) - Method in class uk.ac.roslin.ensembl.mapper.handler.GoEvidenceCodeTypeHandler

setParameter(PreparedStatement, int, Object, JdbcType) - Method in class uk.ac.roslin.ensembl.mapper.handler.HomologyTypeHandler

setParameter(PreparedStatement, int, Object, JdbcType) - Method in class uk.ac.roslin.ensembl.mapper.handler.VariationTypeHandler

setParameter(PreparedStatement, int, Object, JdbcType) - Method in class uk.ac.roslin.ensembl.mapper.handler.VariationXRefHandler

setParent(AssembledDNASequence) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAAssembly

Sets the DAAssembledDNASequence that this assembly holds (its 'Parent').

setParent(DADNASequence) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAEnsemblDNASequenceReader

setParent(AssembledDNASequence) - Method in interface uk.ac.roslin.ensembl.model.core.Assembly

setParentSequenceID(Integer) - Method in class uk.ac.roslin.ensembl.mapper.query.FeatureQuery

Set the value of parentSequenceID

setParentStart(Integer) - Method in class uk.ac.roslin.ensembl.mapper.query.FeatureQuery

setParentStop(Integer) - Method in class uk.ac.roslin.ensembl.mapper.query.FeatureQuery

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(Double) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAProteinFeature

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

setPhase(int) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAExon

setPrimaryAccession(String) - Method in class uk.ac.roslin.ensembl.datasourceaware.DAXRef

setPrimaryCoreDatabase(DBCollectionCoreDatabase) - Method in class uk.ac.roslin.ensembl.dao.database.DBCollection

setProgramName(String) - Method in class uk.ac.roslin.ensembl.datasourceaware.DAAnalysis

setProgramName(String) - Method in interface uk.ac.roslin.ensembl.model.core.Analysis

setProgramParameters(String) - Method in class uk.ac.roslin.ensembl.datasourceaware.DAAnalysis

setProgramParameters(String) - Method in interface uk.ac.roslin.ensembl.model.core.Analysis

setProgramVersion(String) - Method in class uk.ac.roslin.ensembl.datasourceaware.DAAnalysis

setProgramVersion(String) - Method in interface uk.ac.roslin.ensembl.model.core.Analysis

setProperty(String, HashMap) - Method in class uk.ac.roslin.ensembl.dao.database.DBCollection

setProperty(HashMap) - Method in class uk.ac.roslin.ensembl.dao.database.DBCollectionSpecies

setProperty(HashMap) - Method in class uk.ac.roslin.ensembl.dao.database.DBSpecies

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

setQueryIntegerList(List<Integer>) - Method in class uk.ac.roslin.ensembl.mapper.query.FeatureQuery

setQueryStringList(List<String>) - Method in class uk.ac.roslin.ensembl.mapper.query.FeatureQuery

setRank(Integer) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DACoordinateSystem

Set the value of rank

setRank(Integer) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAExon

setRank(Integer) - Method in interface uk.ac.roslin.ensembl.model.core.CoordinateSystem

setRegistry(Registry) - Method in class uk.ac.roslin.ensembl.dao.database.DBDatabase

setRegistry(Registry) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DADNASequence

setRegistry(Registry) - Method in class uk.ac.roslin.ensembl.datasourceaware.DAObject

setRelationshipType(RelationshipType) - Method in class uk.ac.roslin.ensembl.datasourceaware.compara.DAHomologyRelationship

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.

setSchemaVersion(String) - Method in class uk.ac.roslin.ensembl.dao.database.DBDatabase

setScore(Double) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAProteinFeature

setScore(Double) - Method in interface uk.ac.roslin.ensembl.model.core.ProteinFeature

setSearchedHomologies(EnsemblComparaDivision) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAGene

setSeqRegionID(Integer) - Method in interface uk.ac.roslin.ensembl.biojava3.EnsemblDNASequenceReader

setSeqRegionID(Integer) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAEnsemblDNASequenceReader

setSequenceLevel(Boolean) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DACoordinateSystem

setSequenceLevel(Boolean) - Method in interface uk.ac.roslin.ensembl.model.core.CoordinateSystem

setSequenceName(String) - Method in class uk.ac.roslin.ensembl.model.compara.HomologyAlignmentProperties

setSequenceStorage(DAEnsemblDNASequenceReader) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DADNASequence

setSetID(Integer) - Method in class uk.ac.roslin.ensembl.model.variation.VariationType

setShortName(String) - Method in class uk.ac.roslin.ensembl.dao.database.DBSpecies

setSOAccession(String) - Method in class uk.ac.roslin.ensembl.model.variation.VariationType

setSomatic(Boolean) - Method in class uk.ac.roslin.ensembl.datasourceaware.variation.DAVariation

setSOTerm(String) - Method in class uk.ac.roslin.ensembl.model.variation.VariationType

setSOTerms() - Method in interface uk.ac.roslin.ensembl.mapper.variation.InitialisationMapper

setSource(DAGene) - Method in class uk.ac.roslin.ensembl.datasourceaware.compara.DAHomologyPairRelationship

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

Sets the source coordinate by creating a new Coordinate object form the given parameters.

setSourceCoordinates(Integer, Integer, Integer) - Method in class uk.ac.roslin.ensembl.model.Mapping

Sets the source coordinate by creating a new Coordinate object form the given parameters.

setSourceEnd(int) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAProteinFeature

setSourceEnd(int) - Method in interface uk.ac.roslin.ensembl.model.core.ProteinFeature

setSourceProperties(HomologyAlignmentProperties) - Method in class uk.ac.roslin.ensembl.datasourceaware.compara.DAHomologyPairRelationship

setSourceStart(int) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAProteinFeature

setSourceStart(int) - Method in interface uk.ac.roslin.ensembl.model.core.ProteinFeature

setSpecies(Species) - Method in class uk.ac.roslin.ensembl.dao.database.DBSingleSpeciesDatabase

setSpecies(Species) - Method in class uk.ac.roslin.ensembl.dao.database.factory.DBDAOSpeciesFactory

setSpecies(Species) - Method in interface uk.ac.roslin.ensembl.dao.factory.DAOSpeciesFactory

setSpecies(Species) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DACoreObject

setSpecies(Species) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DADNASequence

setSpecies(Species) - Method in interface uk.ac.roslin.ensembl.model.core.CoreObject

setSpecies(Species) - Method in interface uk.ac.roslin.ensembl.model.database.SingleSpeciesDatabase

setSpeciesBinomial(String) - Method in class uk.ac.roslin.ensembl.dao.database.DBSpecies

setSpeciesID(Integer) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DACoordinateSystem

Set the value of speciesID

setSpeciesID(Integer) - Method in class uk.ac.roslin.ensembl.mapper.query.FeatureQuery

setSpeciesID(Integer) - Method in interface uk.ac.roslin.ensembl.model.core.CoordinateSystem

setSpeciesMetadata(CoreDatabase) - Method in class uk.ac.roslin.ensembl.dao.database.DBRegistry

should only be called for non current singlespecies core databases

setSpeciesMetadata(CoreDatabase) - Method in interface uk.ac.roslin.ensembl.model.database.Registry

setSpeciesName(String) - Method in class uk.ac.roslin.ensembl.model.compara.HomologyAlignmentProperties

setStableID(String) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DACoreObject

setStableID(String) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAGene

setStableID(String) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DATranslation

setStableID(String) - Method in interface uk.ac.roslin.ensembl.model.StableID

setStart(Integer) - Method in class uk.ac.roslin.ensembl.model.Coordinate

public setter for the start of the Coordinate, will swap start and end if new start is more than the end.

setStatus(String) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAFeature

setStrand(Coordinate.Strand) - Method in class uk.ac.roslin.ensembl.model.Coordinate

setStrandInt(Integer) - Method in class uk.ac.roslin.ensembl.model.Coordinate

Utility method to set the Strand using an Integer (FORWARD_STRAND for '+1' and REVERSE_STRAND for '-1' - otherwise NULL).

setSynonym(String) - Method in class uk.ac.roslin.ensembl.datasourceaware.variation.DAVariation

setSynonym(String) - Method in interface uk.ac.roslin.ensembl.model.variation.Variation

setTarget(DAGene) - Method in class uk.ac.roslin.ensembl.datasourceaware.compara.DAHomologyPairRelationship

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

Sets the target coordinate by creating a new Coordinate object form the given parameters.

setTargetCoordinates(Integer, Integer, Integer) - Method in class uk.ac.roslin.ensembl.model.Mapping

Sets the target coordinate by creating a new Coordinate object form the given parameters.

setTargetEnd(int) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAProteinFeature

setTargetEnd(int) - Method in interface uk.ac.roslin.ensembl.model.core.ProteinFeature

setTargetName(String) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAProteinFeature

setTargetName(String) - Method in interface uk.ac.roslin.ensembl.model.core.ProteinFeature

setTargetProperties(HomologyAlignmentProperties) - Method in class uk.ac.roslin.ensembl.datasourceaware.compara.DAHomologyPairRelationship

setTargetStart(int) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAProteinFeature

setTargetStart(int) - Method in interface uk.ac.roslin.ensembl.model.core.ProteinFeature

setTaxonomyID(String) - Method in class uk.ac.roslin.ensembl.dao.database.DBSpecies

setTissueSource(String) - Method in class uk.ac.roslin.ensembl.datasourceaware.variation.DAVariationXRef

setTopLevel(boolean) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DACoordinateSystem

setTranscript(Transcript) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAExon

setTranscript(Transcript) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DATranslation

setTranscript(Transcript) - Method in interface uk.ac.roslin.ensembl.model.core.Translation

setTranscriptID(Integer) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAExon

setTranscriptID(Integer) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DATranslation

setTranscriptID(Integer) - Method in class uk.ac.roslin.ensembl.mapper.query.FeatureQuery

Set the value of transcriptID

setTranslationID(int) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAProteinFeature

setTranslationID(int) - Method in interface uk.ac.roslin.ensembl.model.core.ProteinFeature

setType(EnsemblDBType) - Method in class uk.ac.roslin.ensembl.dao.database.DBDatabase

setType(HomologyType) - Method in class uk.ac.roslin.ensembl.datasourceaware.compara.DAHomologyRelationship

setType(CoordSystemType) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DACoordinateSystem

Set the value of type

setType(CoordSystemType) - Method in interface uk.ac.roslin.ensembl.model.core.CoordinateSystem

setUrl(String) - Method in class uk.ac.roslin.ensembl.datasourceaware.variation.DAVariationXRef

setUrlName(String) - Method in class uk.ac.roslin.ensembl.dao.database.DBSpecies

setValues(Integer, Integer) - Method in class uk.ac.roslin.ensembl.model.Coordinate

public setter for the start and end of the Coordinate, will swap start and end if end is less than start.

setVarType(VariationType) - Method in class uk.ac.roslin.ensembl.datasourceaware.variation.DAVariation

setVegaProteinID(String) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DATranslation

setVersion(String) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DACoordinateSystem

Set the value of version

setVersion(Integer) - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DACoreObject

setVersion(String) - Method in class uk.ac.roslin.ensembl.datasourceaware.DAXRef

setVersion(String) - Method in interface uk.ac.roslin.ensembl.model.core.CoordinateSystem

setVersion(Integer) - Method in interface uk.ac.roslin.ensembl.model.StableID

setXdbType(String) - Method in class uk.ac.roslin.ensembl.mapper.query.FeatureQuery

Set the value of xdbType

setXRef(DAVariationXRef) - Method in class uk.ac.roslin.ensembl.datasourceaware.variation.DAVariation

setXRefs() - Method in interface uk.ac.roslin.ensembl.mapper.variation.InitialisationMapper

shortName - Variable in class uk.ac.roslin.ensembl.dao.database.DBSpecies

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

singleSpecies - Variable in class uk.ac.roslin.ensembl.dao.database.coreaccess.DBCoreObjectDAO

SingleSpeciesCoreDatabase - Interface in uk.ac.roslin.ensembl.model.database

SingleSpeciesDatabase - Interface in uk.ac.roslin.ensembl.model.database

singleSpeciesDatabases - Variable in class uk.ac.roslin.ensembl.dao.database.DBRegistry

SingleSpeciesVariationDatabase - Interface in uk.ac.roslin.ensembl.model.database

SOAccession - Variable in class uk.ac.roslin.ensembl.model.variation.VariationType

somatic - Variable in class uk.ac.roslin.ensembl.datasourceaware.variation.DAVariation

SOTerm - Variable in class uk.ac.roslin.ensembl.model.variation.VariationType

source - Variable in class uk.ac.roslin.ensembl.model.Mapping

source_coords - Variable in class uk.ac.roslin.ensembl.dao.database.coreaccess.DBChromosomeDAO.AssemblyExceptionRowHandler

sourceChrID - Variable in class uk.ac.roslin.ensembl.dao.database.coreaccess.DBChromosomeDAO.AssemblyExceptionRowHandler

sourceChrName - Variable in class uk.ac.roslin.ensembl.dao.database.coreaccess.DBChromosomeDAO.AssemblyExceptionRowHandler

sourceCoordinates - Variable in class uk.ac.roslin.ensembl.model.Mapping

sourceCoordSystem - Variable in class uk.ac.roslin.ensembl.model.Mapping

species - Variable in class uk.ac.roslin.ensembl.dao.database.coreaccess.DBCoreObjectDAO

species - Variable in class uk.ac.roslin.ensembl.dao.database.DBSingleSpeciesDatabase

species - Variable in class uk.ac.roslin.ensembl.dao.database.factory.DBDAOSpeciesFactory

species - Variable in class uk.ac.roslin.ensembl.datasourceaware.core.DACoreObject

species - Variable in class uk.ac.roslin.ensembl.datasourceaware.core.DADNASequence

Species - Interface in uk.ac.roslin.ensembl.model.core

SpeciesAliases - Class in uk.ac.roslin.ensembl.demo

SpeciesAliases() - Constructor for class uk.ac.roslin.ensembl.demo.SpeciesAliases

speciesBinomial - Variable in class uk.ac.roslin.ensembl.dao.database.DBSpecies

speciesHash - Variable in class uk.ac.roslin.ensembl.dao.database.DBRegistry

speciesID - Variable in class uk.ac.roslin.ensembl.datasourceaware.core.DACoordinateSystem

speciesID - Variable in class uk.ac.roslin.ensembl.mapper.query.FeatureQuery

SpeciesMapper - Interface in uk.ac.roslin.ensembl.mapper.core

SpeciesVersions - Class in uk.ac.roslin.ensembl.demo

SpeciesVersions() - Constructor for class uk.ac.roslin.ensembl.demo.SpeciesVersions

SpeciesWithNoChromosomes - Class in uk.ac.roslin.ensembl.demo

SpeciesWithNoChromosomes() - Constructor for class uk.ac.roslin.ensembl.demo.SpeciesWithNoChromosomes

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

sqlMapper - Variable in class uk.ac.roslin.ensembl.dao.database.DBRegistry

sqlSessionFactory - Variable in class uk.ac.roslin.ensembl.dao.database.factory.DBDAOFactory

ssFactory - Variable in class uk.ac.roslin.ensembl.dao.database.coreaccess.DBCoreObjectDAO

stableID - Variable in class uk.ac.roslin.ensembl.datasourceaware.core.DACoreObject

StableID - Interface in uk.ac.roslin.ensembl.model

status - Variable in class uk.ac.roslin.ensembl.datasourceaware.core.DAFeature

stitchComponents() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAAssembly

Protected method to join together (stitch) all of the component sub-sequences of the assembly, together with GapSequences to form a single continuous ungapped assembly, held in the MappingSet 'stitchedComponentMappings';

stitchedComponentMappings - Variable in class uk.ac.roslin.ensembl.datasourceaware.core.DAAssembly

strand(Integer) - Static method in enum uk.ac.roslin.ensembl.model.Coordinate.Strand

Static Strand provider returns FORWARD_STRAND for '+1' and REVERSE_STRAND for '-1' - otherwise NULL

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

supercontig - Static variable in class uk.ac.roslin.ensembl.config.EnsemblCoordSystemType

superscaffold - Static variable in class uk.ac.roslin.ensembl.config.EnsemblCoordSystemType

synonym - Variable in class uk.ac.roslin.ensembl.datasourceaware.variation.DAVariation

synonyms - Variable in class uk.ac.roslin.ensembl.datasourceaware.variation.DAVariation

Synonyms - Class in uk.ac.roslin.ensembl.demo

Synonyms() - Constructor for class uk.ac.roslin.ensembl.demo.Synonyms

T

target - Variable in class uk.ac.roslin.ensembl.dao.database.coreaccess.DBChromosomeDAO.AssemblyExceptionRowHandler

target - Variable in class uk.ac.roslin.ensembl.model.Mapping

target_coords - Variable in class uk.ac.roslin.ensembl.dao.database.coreaccess.DBChromosomeDAO.AssemblyExceptionRowHandler

targetCoordinates - Variable in class uk.ac.roslin.ensembl.model.Mapping

targetCoordSystem - Variable in class uk.ac.roslin.ensembl.model.Mapping

targetCSID - Variable in class uk.ac.roslin.ensembl.dao.database.coreaccess.DBChromosomeDAO.AssemblyExceptionRowHandler

taxonomyID - Variable in class uk.ac.roslin.ensembl.dao.database.DBSpecies

testAssembly() - Method in class uk.ac.roslin.ensembl.test.Chromosome

testBacteria() - Method in class uk.ac.roslin.ensembl.demo.RegistryFactory

testBacteriaGeneCompara() - Method in class uk.ac.roslin.ensembl.test.Compara

testBacterialRegistry() - Method in class uk.ac.roslin.ensembl.test.Registry

testBacteriaSyntenyCompara() - Method in class uk.ac.roslin.ensembl.test.Compara

testChromosomeCache() - Method in class uk.ac.roslin.ensembl.test.Chromosome

testChromosomeValidation() - Method in class uk.ac.roslin.ensembl.test.Chromosome

testChromosomeVariations() - Method in class uk.ac.roslin.ensembl.test.Variation

testConnection() - Method in class uk.ac.roslin.ensembl.config.DBConnection

testEnsembl() - Method in class uk.ac.roslin.ensembl.demo.RegistryFactory

testEnsemblGeneCompara() - Method in class uk.ac.roslin.ensembl.test.Compara

testEnsemblRegistry() - Method in class uk.ac.roslin.ensembl.test.Registry

testEnsemblSyntenyCompara() - Method in class uk.ac.roslin.ensembl.test.Compara

testGenes() - Method in class uk.ac.roslin.ensembl.test.Chromosome

testGenomes() - Method in class uk.ac.roslin.ensembl.demo.RegistryFactory

testGenomesGeneCompara() - Method in class uk.ac.roslin.ensembl.test.Compara

testGenomesRegistry() - Method in class uk.ac.roslin.ensembl.test.Registry

testGenomesSyntenyCompara() - Method in class uk.ac.roslin.ensembl.test.Compara

testPAR() - Method in class uk.ac.roslin.ensembl.test.Chromosome

testProperties() - Method in class uk.ac.roslin.ensembl.test.Chromosome

testSchemaVersion() - Method in class uk.ac.roslin.ensembl.demo.RegistryFactory

testSequence() - Method in class uk.ac.roslin.ensembl.test.Chromosome

thisDBUrl - Variable in class uk.ac.roslin.ensembl.dao.database.factory.DBDAOFactory

thisSequence - Variable in class uk.ac.roslin.ensembl.datasourceaware.core.DAFeature

tooNewDB - Variable in class uk.ac.roslin.ensembl.dao.database.DBRegistry

topLevel - Variable in class uk.ac.roslin.ensembl.datasourceaware.core.DACoordinateSystem

toShortString() - Method in class uk.ac.roslin.ensembl.model.Coordinate

Returns String representation in format '1 - 2345' etc.

toString() - Method in class uk.ac.roslin.ensembl.config.AssemblyExceptionType

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.dao.database.DBCollection

toString() - Method in class uk.ac.roslin.ensembl.dao.database.DBDatabase

toString() - Method in class uk.ac.roslin.ensembl.dao.database.DBSpecies

toString() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DAChromosome

toString() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.DADNASequence

toString() - Method in class uk.ac.roslin.ensembl.datasourceaware.core.GapSequence

toString() - Method in class uk.ac.roslin.ensembl.model.Coordinate

Returns String representation in of format '1 - 5987 REVERSE_STRAND', '1 - 5987 FORWARD_STRAND', '1 - 5987 UNSPECIFIED_STRAND' etc.

toString() - Method in class uk.ac.roslin.ensembl.model.Evidence

toString() - Method in class uk.ac.roslin.ensembl.model.variation.VariationType

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

Transcript - Interface in uk.ac.roslin.ensembl.model.core

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

TranscriptDAO - Interface in uk.ac.roslin.ensembl.dao.coreaccess

transcriptID - Variable in class uk.ac.roslin.ensembl.mapper.query.FeatureQuery

TranscriptionAndTranslation - Class in uk.ac.roslin.ensembl.demo

TranscriptionAndTranslation() - Constructor for class uk.ac.roslin.ensembl.demo.TranscriptionAndTranslation

TranscriptionAndTranslationReverse - Class in uk.ac.roslin.ensembl.demo

TranscriptionAndTranslationReverse() - Constructor for class uk.ac.roslin.ensembl.demo.TranscriptionAndTranslationReverse

TranscriptMapper - Interface in uk.ac.roslin.ensembl.mapper.core

translation - Static variable in class uk.ac.roslin.ensembl.config.EnsemblCoreObjectType

Translation - Interface in uk.ac.roslin.ensembl.model.core

TranslationDAO - Interface in uk.ac.roslin.ensembl.dao.coreaccess

TranslationMapper - Interface in uk.ac.roslin.ensembl.mapper.core

TREMATODE_MITOCHONDRIAL - Static variable in class uk.ac.roslin.ensembl.config.CodonTable

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

TWOCHLOROPHYCEAN_MITOCHONDRIAL - Static variable in class uk.ac.roslin.ensembl.config.CodonTable

type - Variable in class uk.ac.roslin.ensembl.dao.database.coreaccess.DBChromosomeDAO.AssemblyExceptionRowHandler

type - Variable in class uk.ac.roslin.ensembl.datasourceaware.core.DACoordinateSystem

typedXRefs - Variable in class uk.ac.roslin.ensembl.datasourceaware.core.DAGene

typedXRefs - Variable in class uk.ac.roslin.ensembl.datasourceaware.core.DATranscript

typedXRefs - Variable in class uk.ac.roslin.ensembl.datasourceaware.core.DATranslation

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.dao - package uk.ac.roslin.ensembl.dao

uk.ac.roslin.ensembl.dao.compara - package uk.ac.roslin.ensembl.dao.compara

uk.ac.roslin.ensembl.dao.coreaccess - package uk.ac.roslin.ensembl.dao.coreaccess

uk.ac.roslin.ensembl.dao.database - package uk.ac.roslin.ensembl.dao.database

uk.ac.roslin.ensembl.dao.database.compara - package uk.ac.roslin.ensembl.dao.database.compara

uk.ac.roslin.ensembl.dao.database.coreaccess - package uk.ac.roslin.ensembl.dao.database.coreaccess

uk.ac.roslin.ensembl.dao.database.factory - package uk.ac.roslin.ensembl.dao.database.factory

uk.ac.roslin.ensembl.dao.database.variation - package uk.ac.roslin.ensembl.dao.database.variation

uk.ac.roslin.ensembl.dao.factory - package uk.ac.roslin.ensembl.dao.factory

uk.ac.roslin.ensembl.dao.variation - package uk.ac.roslin.ensembl.dao.variation

uk.ac.roslin.ensembl.datasourceaware - package uk.ac.roslin.ensembl.datasourceaware

uk.ac.roslin.ensembl.datasourceaware.compara - package uk.ac.roslin.ensembl.datasourceaware.compara

uk.ac.roslin.ensembl.datasourceaware.core - package uk.ac.roslin.ensembl.datasourceaware.core

uk.ac.roslin.ensembl.datasourceaware.variation - package uk.ac.roslin.ensembl.datasourceaware.variation

uk.ac.roslin.ensembl.demo - package uk.ac.roslin.ensembl.demo

uk.ac.roslin.ensembl.exception - package uk.ac.roslin.ensembl.exception

uk.ac.roslin.ensembl.mapper - package uk.ac.roslin.ensembl.mapper

uk.ac.roslin.ensembl.mapper.compara - package uk.ac.roslin.ensembl.mapper.compara

uk.ac.roslin.ensembl.mapper.core - package uk.ac.roslin.ensembl.mapper.core

uk.ac.roslin.ensembl.mapper.handler - package uk.ac.roslin.ensembl.mapper.handler

uk.ac.roslin.ensembl.mapper.query - package uk.ac.roslin.ensembl.mapper.query

uk.ac.roslin.ensembl.mapper.variation - package uk.ac.roslin.ensembl.mapper.variation

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

uk.ac.roslin.ensembl.model.variation - package uk.ac.roslin.ensembl.model.variation

uk.ac.roslin.ensembl.test - package uk.ac.roslin.ensembl.test

ultracontig - Static variable in class uk.ac.roslin.ensembl.config.EnsemblCoordSystemType

UNIVERSAL - Static variable in class uk.ac.roslin.ensembl.config.CodonTable

UNKNOWN - Static variable in class uk.ac.roslin.ensembl.config.AssemblyExceptionType

unknown - Static variable in class uk.ac.roslin.ensembl.config.EnsemblCoordSystemType

UNKNOWN - Static variable in class uk.ac.roslin.ensembl.model.relationship.RelationshipType

UNKNOWN_HOMOLOGY_TYPE - Static variable in class uk.ac.roslin.ensembl.model.compara.HomologyType

a catch all

unknownDB - Variable in class uk.ac.roslin.ensembl.dao.database.DBRegistry

urlName - Variable in class uk.ac.roslin.ensembl.dao.database.DBSpecies

UserChristelle - Class in uk.ac.roslin.ensembl.demo

UserChristelle() - Constructor for class uk.ac.roslin.ensembl.demo.UserChristelle

UserJeanPhilippe - Class in uk.ac.roslin.ensembl.demo

UserJeanPhilippe() - Constructor for class uk.ac.roslin.ensembl.demo.UserJeanPhilippe

UserSetzermann - Class in uk.ac.roslin.ensembl.demo

UserSetzermann() - Constructor for class uk.ac.roslin.ensembl.demo.UserSetzermann

V

validateExternalDB(ExternalDB) - Method in class uk.ac.roslin.ensembl.dao.database.DBCollectionCoreDatabase

Validates a givenExternalDB object, to return a pre-existing version id present.

validateExternalDB(ExternalDB) - Method in class uk.ac.roslin.ensembl.dao.database.DBSingleSpeciesCoreDatabase

Validates a givenExternalDB object, to return a pre-existing version id present.

validateExternalDB(ExternalDB) - Method in interface uk.ac.roslin.ensembl.model.database.DatabaseWithExternalDBs

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.datasourceaware.core.DAFeature.Status

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 class uk.ac.roslin.ensembl.config.AssemblyExceptionType

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.datasourceaware.core.DAFeature.Status

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

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

Variation - Interface in uk.ac.roslin.ensembl.model.variation

Variation - Class in uk.ac.roslin.ensembl.test

Variation() - Constructor for class uk.ac.roslin.ensembl.test.Variation

VariationDAO - Interface in uk.ac.roslin.ensembl.dao.variation

VariationDatabase - Interface in uk.ac.roslin.ensembl.model.database

VariationMapper - Interface in uk.ac.roslin.ensembl.mapper.variation

VariationMapping - Class in uk.ac.roslin.ensembl.datasourceaware.variation

VariationMapping() - Constructor for class uk.ac.roslin.ensembl.datasourceaware.variation.VariationMapping

Variations - Class in uk.ac.roslin.ensembl.demo

Variations() - Constructor for class uk.ac.roslin.ensembl.demo.Variations

VariationScript - Class in uk.ac.roslin.ensembl.demo

VariationScript() - Constructor for class uk.ac.roslin.ensembl.demo.VariationScript

VariationType - Class in uk.ac.roslin.ensembl.model.variation

VariationType() - Constructor for class uk.ac.roslin.ensembl.model.variation.VariationType

VariationTypeHandler - Class in uk.ac.roslin.ensembl.mapper.handler

VariationTypeHandler() - Constructor for class uk.ac.roslin.ensembl.mapper.handler.VariationTypeHandler

VariationXRefHandler - Class in uk.ac.roslin.ensembl.mapper.handler

VariationXRefHandler() - Constructor for class uk.ac.roslin.ensembl.mapper.handler.VariationXRefHandler

varType - Variable in class uk.ac.roslin.ensembl.datasourceaware.variation.DAVariation

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

VegaAndCCDSIDs - Class in uk.ac.roslin.ensembl.demo

VegaAndCCDSIDs() - Constructor for class uk.ac.roslin.ensembl.demo.VegaAndCCDSIDs

VegaFeature - Interface in uk.ac.roslin.ensembl.model.core

VegaGene - Static variable in class uk.ac.roslin.ensembl.config.ExternalDBType

VegaProtein - Static variable in class uk.ac.roslin.ensembl.config.ExternalDBType

VegaTranscript - Static variable in class uk.ac.roslin.ensembl.config.ExternalDBType

version - Variable in class uk.ac.roslin.ensembl.datasourceaware.core.DACoordinateSystem

version - Variable in class uk.ac.roslin.ensembl.datasourceaware.core.DACoreObject

version - Variable in class uk.ac.roslin.ensembl.datasourceaware.DAXRef

versionIDmap - Variable in class uk.ac.roslin.ensembl.dao.database.DBCollectionSpecies

VERTEBRATE_MITOCHONDRIAL - Static variable in class uk.ac.roslin.ensembl.config.CodonTable

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

WithDisplayXRef - Interface in uk.ac.roslin.ensembl.model.core

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 - Variable in class uk.ac.roslin.ensembl.datasourceaware.variation.DAVariation

XRef - Interface in uk.ac.roslin.ensembl.model

XRefDAO - Interface in uk.ac.roslin.ensembl.dao

XRefed - Interface in uk.ac.roslin.ensembl.model

XRefMapper - Interface in uk.ac.roslin.ensembl.mapper

xrefs - Variable in class uk.ac.roslin.ensembl.datasourceaware.core.DAGene

xrefs - Variable in class uk.ac.roslin.ensembl.datasourceaware.core.DATranscript

xrefs - Variable in class uk.ac.roslin.ensembl.datasourceaware.core.DATranslation

XRefs - Class in uk.ac.roslin.ensembl.demo

XRefs() - Constructor for class uk.ac.roslin.ensembl.demo.XRefs

Y

YEAST_MITOCHONDRIAL - Static variable in class uk.ac.roslin.ensembl.config.CodonTable

Z

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

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