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

## A

ASCENDING_ORDER - Static variable in class org.ensembl.datamodel.AssemblyLocation
  Deprecated. Returns a comparator that orders `AssemblyLocation` by the following fields in this order: chromosome, start, end and strand.
ASCENDING_ORDER - Static variable in class org.ensembl.datamodel.CloneFragmentLocation
  Returns a comparator that orders `CloneFragmentLocation` by the following fields in this order: cloneFragmentInternalID, start, end and strand.
Accessioned - interface org.ensembl.datamodel.Accessioned.
  Object is capable of having an accession (stable id) which is stable across Ensembl data releases and has a version, creation and last modified date.
Adaptor - interface org.ensembl.driver.Adaptor.
  Provides access to some datatype in some datasource.
AdaptorException - exception org.ensembl.driver.AdaptorException.
  Thrown when a problem occurs running code in ensj.
AdaptorException() - Constructor for class org.ensembl.driver.AdaptorException
AdaptorException(String) - Constructor for class org.ensembl.driver.AdaptorException
AdaptorException(String, Exception) - Constructor for class org.ensembl.driver.AdaptorException
AdaptorException(Exception) - Constructor for class org.ensembl.driver.AdaptorException
Allele - interface org.ensembl.variation.datamodel.Allele.
  A single allele of a nucleotide variation.
AlleleConsequence - class org.ensembl.variation.datamodel.AlleleConsequence.
  Represents part or all of the effect of a single allele on a transcript.
AlleleConsequence(Location, String, String) - Constructor for class org.ensembl.variation.datamodel.AlleleConsequence
AlleleConsequenceAdaptor - interface org.ensembl.variation.datamodel.AlleleConsequenceAdaptor.
  Adaptor for retrievning and computing AlleleConsequences.
AlleleFeature - interface org.ensembl.variation.datamodel.AlleleFeature.
  An allele located on a genome.
AlleleFeatureAdaptor - interface org.ensembl.variation.driver.AlleleFeatureAdaptor.
  Used to retrieve AlleleFeatures.
AlleleGroup - interface org.ensembl.variation.datamodel.AlleleGroup.
  Ensembl representation of a grouping of alleles (aka haplotype).
AlleleGroupAdaptor - interface org.ensembl.variation.driver.AlleleGroupAdaptor.
  Retrieves Allele groups from an ensembl database.
Analysis - interface org.ensembl.datamodel.Analysis.
  Represents a process used to create features such as genes.
AnalysisAdaptor - interface org.ensembl.driver.AnalysisAdaptor.
  Provides access to Analyses in the datasource.
ArchiveStableID - interface org.ensembl.datamodel.ArchiveStableID.
  Represents a single immutable archive stable ID.
ArrayIterator - class org.ensembl.util.ArrayIterator.
ArrayIterator(Object[]) - Constructor for class org.ensembl.util.ArrayIterator
AscendingInternalIDComparator - class org.ensembl.util.AscendingInternalIDComparator.
AscendingInternalIDComparator() - Constructor for class org.ensembl.util.AscendingInternalIDComparator
AssemblyElement - interface org.ensembl.datamodel.AssemblyElement.
AssemblyException - class org.ensembl.datamodel.AssemblyException.
  Defines how some semi-virtual sequence regions (PAR/Haplotypes) are partially constructed from other sequence regions.
AssemblyException(long, Location, Location, String) - Constructor for class org.ensembl.datamodel.AssemblyException
AssemblyExceptionAdaptor - interface org.ensembl.driver.AssemblyExceptionAdaptor.
  Adaptor for retrieving and handling AssemblyExceptions which are used to represent PARs and haplotypes.
AssemblyLocation - class org.ensembl.datamodel.AssemblyLocation.
  Deprecated. Create instances of Location directly. The specific location types such as AssemblyLocation have been superseded by the more generic Location class.
AssemblyLocation(CoordinateSystem, String, int, int, int) - Constructor for class org.ensembl.datamodel.AssemblyLocation
  Deprecated.
AssemblyLocation(String, int, int, int) - Constructor for class org.ensembl.datamodel.AssemblyLocation
  Deprecated. Sets map to AssemblyLocation.DEFAULT_CS.
AssemblyLocation(boolean, int) - Constructor for class org.ensembl.datamodel.AssemblyLocation
  Deprecated. Constructs a location with map=AssemblyLocation.DEFAULT_MAP, start=1, end=length+1, strand=unset and whether it is a gap.
AssemblyLocation(CoordinateSystem, boolean, int) - Constructor for class org.ensembl.datamodel.AssemblyLocation
  Deprecated. Constructs a location with specified map, start=1, end=length+1, strand=unset and whether it is a gap.
AssemblyLocation() - Constructor for class org.ensembl.datamodel.AssemblyLocation
  Deprecated. Sets map to AssemblyLocation.DEFAULT_MAP.
AssemblyMapper - interface org.ensembl.datamodel.AssemblyMapper.
AssemblyMapperAdaptor - interface org.ensembl.driver.AssemblyMapperAdaptor.
Attribute - interface org.ensembl.datamodel.Attribute.
  A generic attribute that can be associatted with a features such as MiscFeature.
AttributeException - exception org.ensembl.datamodel.AttributeException.
AttributeException() - Constructor for class org.ensembl.datamodel.AttributeException
AttributeException(String) - Constructor for class org.ensembl.datamodel.AttributeException
activeSize() - Method in class org.ensembl.util.ConnectionPoolDataSource
add(Attribute) - Method in interface org.ensembl.datamodel.MiscFeature
  Adds attribute.
add(MiscSet) - Method in interface org.ensembl.datamodel.MiscFeature
  Adds MiscSet.
add(String, DriverGroup) - Method in class org.ensembl.registry.Registry
  Adds the named group to the registry.
add(RegistryLoader) - Method in class org.ensembl.registry.Registry
  Add the DriverGroups from the loader.
add(Persistent) - Method in class org.ensembl.util.IDSet
add(int, Object) - Method in class org.ensembl.util.LocatableList
add(Object) - Method in class org.ensembl.util.LocatableList
  Adds a locatable instance to the list.
add(long) - Method in class org.ensembl.util.LongList
add(long[]) - Method in class org.ensembl.util.LongList
add(long) - Method in class org.ensembl.util.LongSet
add(Long) - Method in class org.ensembl.util.LongSet
add(Object) - Method in class org.ensembl.util.LongSet
  This method throws an exception as it should not be used.
add(Persistent) - Method in class org.ensembl.util.PersistentSet
add(Object) - Method in class org.ensembl.util.PersistentSet
addAdaptor(Adaptor) - Method in interface org.ensembl.driver.EnsemblDriver
  Attempts to connects to the database if not already connected.
addAll(Collection) - Method in class org.ensembl.util.LocatableList
  Adds all the Locatables from the collection into this list.
addAll(int, Collection) - Method in class org.ensembl.util.LocatableList
  Adds all the Locatables from the collection into this list.
addAll(long[]) - Method in class org.ensembl.util.LongSet
addAll(Collection) - Method in class org.ensembl.util.PersistentSet
addAllele(Allele) - Method in interface org.ensembl.variation.datamodel.Variation
addArrayWithProbeName(OligoArray, String) - Method in interface org.ensembl.datamodel.OligoProbe
  Adds the array-probename pair to the probe.
addAttribute(Attribute) - Method in interface org.ensembl.datamodel.SequenceRegion
addAttribute(Attribute) - Method in interface org.ensembl.datamodel.Transcript
  Add attribute.
addAttribute(Attribute) - Method in interface org.ensembl.datamodel.Translation
  Add attribute.
addEnsemblDriver(EnsemblDriver) - Method in interface org.ensembl.driver.CoordinateSystemAdaptor
  Add an additional driver to retrieve meta information from.
addFirst(Object) - Method in class org.ensembl.util.LocatableList
  Adds a locatable instance to the beginning of this list.
addGenomicAlign(GenomicAlign) - Method in interface org.ensembl.compara.datamodel.GenomicAlignBlock
  Add a GenomicAlign to the block.
addInternalID(Persistent) - Method in class org.ensembl.util.IDList
addLast(Object) - Method in class org.ensembl.util.LocatableList
  Adds a locatable instance to the end of the list.
addOrIncrement(Object) - Method in class org.ensembl.util.FrequencyCounter
  If object is not currently a key in the map it is added as a key pointing to a Counter instance with a value of 1.
addOrIncrementAll(List) - Method in class org.ensembl.util.FrequencyCounter
  Calls addOrIncrement(Object) for each item in list.
addPersistents(List) - Method in class org.ensembl.util.IDList
addRelated(String, int) - Method in interface org.ensembl.datamodel.StableIDEvent
  If relatedStableID is "null" then it is not added but deleted is set to true.
addSynonym(String) - Method in interface org.ensembl.variation.datamodel.Variation
addToMapList(Map, Object, Object) - Static method in class org.ensembl.util.Util
addToMapList(OpenLongObjectHashMap, long, Object) - Static method in class org.ensembl.util.Util
addTranscript(Transcript) - Method in interface org.ensembl.datamodel.Exon
addValidationState(ValidationState) - Method in interface org.ensembl.variation.datamodel.Variation
addVariation(Variation, String) - Method in interface org.ensembl.variation.datamodel.AlleleGroup
  Adds an allele and associated variation to this allele group
addVariation(Variation) - Method in interface org.ensembl.variation.datamodel.VariationGroup
  Add variation to group.
append(AssemblyLocation) - Method in class org.ensembl.datamodel.AssemblyLocation
  Deprecated. Adds _location_ to the end of the location list, this is the same as using setNext(location) if next==null.
append(Location) - Method in class org.ensembl.datamodel.AssemblyLocation
  Deprecated.
append(Location) - Method in class org.ensembl.datamodel.CloneFragmentLocation
append(CloneFragmentLocation) - Method in class org.ensembl.datamodel.CloneFragmentLocation
  Adds _location_ to the end of the location list, this is the same as using setNext(location) if next==null.
append(Location) - Method in class org.ensembl.datamodel.Location
applyEdit(String) - Method in interface org.ensembl.datamodel.SequenceEdit
  Creates a new sequence that is the original with this sequence applied to to it.
arrayCache - Variable in class org.ensembl.util.LongSet
arrayToString(int[][]) - Static method in class org.ensembl.util.StringUtil
assignSeqRegionNameAndCoordinateSystem(Location) - Method in interface org.ensembl.driver.LocationConverter
  Sets the sequence region name and coordinate system on _loc_.

## B

backupAndClearTable(String) - Method in interface org.ensembl.driver.EnsemblDriver
  Make a backup copy of the table and empty the original table.
backupAndClearTables() - Method in interface org.ensembl.driver.EnsemblDriver
  Backs up and clears all tables returned by fetchTableNames().
backupAndClearTables(String[]) - Method in interface org.ensembl.driver.EnsemblDriver
  Backup the tables and empty the originals.
backupTable(String) - Method in interface org.ensembl.driver.EnsemblDriver
  Backup the table.
backupTables() - Method in interface org.ensembl.driver.EnsemblDriver
  Backup all tables returned by fetchTableNames().
backupTables(String[]) - Method in interface org.ensembl.driver.EnsemblDriver
  Backup all the tableNames.
batch(long[], int) - Static method in class org.ensembl.util.Util
  Splits input array into "batches" where each batch length is <=maxBatchSize.
beautifySQL(String) - Static method in class org.ensembl.util.JDBCUtil
  Formats sql for reading.
booleanValue(Properties, String, boolean) - Static method in class org.ensembl.util.PropertiesUtil
briefOrUnset(String) - Static method in class org.ensembl.util.StringUtil
  Converts s into a string representation of at most 10 characters or "unset" if s is null.
buildVersion() - Static method in class org.ensembl.util.Version
  Returns ensj version number if running inside jar, otherwise null.

## C

CLONE_FRAGMENT - Static variable in interface org.ensembl.datamodel.ExternalRef
  Clone fragment type.
CLUSTER - Static variable in class org.ensembl.variation.datamodel.ValidationState
ChainedAssemblyMapper - class org.ensembl.datamodel.ChainedAssemblyMapper.
ChainedAssemblyMapper(CoreDriver, CoordinateSystem, CoordinateSystem, CoordinateSystem) - Constructor for class org.ensembl.datamodel.ChainedAssemblyMapper
Chromosome - interface org.ensembl.datamodel.Chromosome.
ChromosomeBand - interface org.ensembl.datamodel.ChromosomeBand.
CloneFragmentLocation - class org.ensembl.datamodel.CloneFragmentLocation.
  Location on a Contig (Clone Fragment).
CloneFragmentLocation(boolean, int) - Constructor for class org.ensembl.datamodel.CloneFragmentLocation
  Constructs a location with coordinate system = CloneFragmentLocation.DEFAULT_MAP, start=1, end=length+1, strand=unset and whether it is a gap.
CloneFragmentLocation(CoordinateSystem, boolean, int) - Constructor for class org.ensembl.datamodel.CloneFragmentLocation
  Constructs a location with specified coordinate system, start=1, end=length+1, strand=unset and whether it is a gap.
CloneFragmentLocation() - Constructor for class org.ensembl.datamodel.CloneFragmentLocation
  Sets coordinate system to CloneFragmentLocation.DEFAULT_CS.
CloneFragmentLocation(String) - Constructor for class org.ensembl.datamodel.CloneFragmentLocation
  Sets coordinate system to CloneFragmentLocation.DEFAULT_CS.
ComparaDataFactory - interface org.ensembl.compara.datamodel.ComparaDataFactory.
  Abstract Factory for creating ensembl data objects.
ComparaDriver - interface org.ensembl.compara.driver.ComparaDriver.
  Provides adaptors for accessing an ensembl compara database.
ComparaDriverFactory - class org.ensembl.compara.driver.ComparaDriverFactory.
  Factory class that creates ensembl compara driver implementation instances.
ComparaReader - class org.ensembl.compara.driver.ComparaReader.
ComparaReader() - Constructor for class org.ensembl.compara.driver.ComparaReader
ConfigurationException - exception org.ensembl.driver.ConfigurationException.
  Thrown when an illegal configuration is used.
ConfigurationException() - Constructor for class org.ensembl.driver.ConfigurationException
ConfigurationException(String) - Constructor for class org.ensembl.driver.ConfigurationException
ConfigurationException(String, Exception) - Constructor for class org.ensembl.driver.ConfigurationException
ConnectionPoolDataSource - class org.ensembl.util.ConnectionPoolDataSource.
  Connection pooling implementation of a datasource.
ConnectionPoolDataSource(String, String, String, String, int) - Constructor for class org.ensembl.util.ConnectionPoolDataSource
  Creates new instance of the connection pool.
ConnectionPoolDataSource() - Constructor for class org.ensembl.util.ConnectionPoolDataSource
  Creates an unconfigured connection pool.
ConnectionWrapper - class org.ensembl.util.ConnectionWrapper.
  The ConnectionWrapper is a Proxy for an underlying connection and offers additional behaviour relevant for use in a ConnectionPool.
ConnectionWrapper(Connection, ConnectionPoolDataSource) - Constructor for class org.ensembl.util.ConnectionWrapper
CoordinateSystem - class org.ensembl.datamodel.CoordinateSystem.
  A genomic co-ordinate system.
CoordinateSystem() - Constructor for class org.ensembl.datamodel.CoordinateSystem
  Deprecated. use another constructor.
CoordinateSystem(String) - Constructor for class org.ensembl.datamodel.CoordinateSystem
  Creates a new CoordinateSystem object with only the name set.
CoordinateSystem(String, String) - Constructor for class org.ensembl.datamodel.CoordinateSystem
CoordinateSystem(String, String, boolean) - Constructor for class org.ensembl.datamodel.CoordinateSystem
  Deprecated. use another constructor.
CoordinateSystem(String, String, boolean, long) - Constructor for class org.ensembl.datamodel.CoordinateSystem
  Deprecated. use another constructor.
CoordinateSystem(String, String, boolean, long, int, boolean) - Constructor for class org.ensembl.datamodel.CoordinateSystem
  Creates a new CoordinateSystem object.
CoordinateSystemAdaptor - interface org.ensembl.driver.CoordinateSystemAdaptor.
  Provides access to coordinate system and meta data in the datasource(s).
CoordinateSystemMapping - class org.ensembl.datamodel.CoordinateSystemMapping.
  Store information about the mapping between a pair of co-ordinate systems.
CoordinateSystemMapping(CoordinateSystem[]) - Constructor for class org.ensembl.datamodel.CoordinateSystemMapping
  Create a new mapping.
CoreDriver - interface org.ensembl.driver.CoreDriver.
  Provides adaptors for accessing to ensembl core databases.
CoreDriverFactory - class org.ensembl.driver.CoreDriverFactory.
  Factory class that creates ensembl core driver implementation instances.
Counter - class org.ensembl.util.Counter.
  Simple counter class.
Counter(int) - Constructor for class org.ensembl.util.Counter
  Initialises counter.
cacheSeqRegion(String, CoordinateSystem, long, int) - Method in interface org.ensembl.driver.LocationConverter
  Put given combination of things into a cache.
capitaliseFirstLetter(String) - Static method in class org.ensembl.util.StringUtil
  Capitalise first letter.
clear() - Method in class org.ensembl.datamodel.Query
  Deprecated. Resets all values to initial values.
clear() - Method in class org.ensembl.driver.ServerDriver
  Clears the cache.
clear() - Method in class org.ensembl.driver.ServerDriverFactory
clear() - Method in class org.ensembl.registry.Registry
  Removes all name to DriverGroup mappings.
clear() - Method in class org.ensembl.util.LruCache
clear() - Method in class org.ensembl.util.PersistentSet
clearAllCaches() - Method in interface org.ensembl.driver.EnsemblDriver
  Clears all caches.
clearCache() - Method in interface org.ensembl.driver.Adaptor
  Clears any caches being used by the adaptor.
clearChromosome() - Method in class org.ensembl.datamodel.AssemblyLocation
  Deprecated.
clearChromosome() - Method in class org.ensembl.datamodel.CloneFragmentLocation
clearTable(String) - Method in interface org.ensembl.driver.EnsemblDriver
  Empties the table.
clearTables() - Method in interface org.ensembl.driver.EnsemblDriver
  Clears all tables returned by fetchTableNames(); Note: this method might not work with all database servers, it has only been tested with MySQL.
clearTables(String[]) - Method in interface org.ensembl.driver.EnsemblDriver
  Empties all the tables.
clearWarnings() - Method in class org.ensembl.util.ConnectionWrapper
clone() - Method in class org.ensembl.datamodel.Location
  Performs a deep copy.
clone() - Method in class org.ensembl.datamodel.Query
  Deprecated. Performs a deep copy.
close() - Method in class org.ensembl.util.ConnectionWrapper
close(Connection) - Static method in class org.ensembl.util.JDBCUtil
  Convenience method for closing a connection and logging rather than throwing any exceptions thrown.
close(ResultSet) - Static method in class org.ensembl.util.JDBCUtil
  Convenience method for closing a result set and logging rather than throwing any exceptions thrown.
close(Statement) - Static method in class org.ensembl.util.JDBCUtil
  Convenience method for closing a JDBC statement and logging rather than throwing any exceptions thrown.
closeAllConnections() - Method in interface org.ensembl.driver.Adaptor
  Closes all connections opened by the adaptor.
closeAllConnections() - Method in interface org.ensembl.driver.EnsemblDriver
  Closes all connections opened by the driver and it's adapotors.
closeAllConnections() - Method in class org.ensembl.registry.DriverGroup
  Closes open database connections on all drivers.
closeAllConnections() - Method in class org.ensembl.registry.Registry
  Close all the connections on all driver groups.
closeAllConnections() - Method in class org.ensembl.util.ConnectionPoolDataSource
  Close the underlying database connections.
closeAllConnections(DataSource) - Static method in class org.ensembl.util.ConnectionPoolDataSource
  Convenience method for closing connections on instances of this class, handles the fact that the datasource is null and prints a warning if it is not a ConnectionPoolDataSource.
codon2aminoAcid(String) - Static method in class org.ensembl.util.SequenceUtil
  Converts 3 nuceic acids into an amino acid.
commit() - Method in class org.ensembl.util.ConnectionWrapper
compare(Object, Object) - Method in class org.ensembl.util.AscendingInternalIDComparator
compare(String, String) - Static method in class org.ensembl.util.StringUtil
  String comparison which handles null values.
compareTo(Object) - Method in class org.ensembl.datamodel.AssemblyLocation
  Deprecated. Iterate through this location and the other one comparing them.
compareTo(Object) - Method in class org.ensembl.datamodel.CloneFragmentLocation
  Iterate through this location and the other one comparing them.
compareTo(Object) - Method in class org.ensembl.datamodel.CoordinateSystem
  Orders by name then version.
compareTo(Object) - Method in class org.ensembl.datamodel.Location
  Iterate through this location and the other one comparing them.
compareTo(Object) - Method in class org.ensembl.util.Pair
complement() - Method in class org.ensembl.datamodel.Location
  "Complements" strand.
completeInterproIDs(Translation) - Method in interface org.ensembl.driver.TranslationAdaptor
  Retrieves the interproIDs for the translation and sets them on the translation.
configure() - Static method in class org.ensembl.driver.LoggingManager
  Initialise logging system with file DEFAULT_LOGGING_CONF_FILE.
configure(String) - Static method in class org.ensembl.driver.LoggingManager
  Configures logging system with contents of the file filepath.
configure(URL) - Static method in class org.ensembl.driver.LoggingManager
  Configures logging system with contents of URL.
contains(String) - Method in class org.ensembl.driver.ServerDriver
  Returns whether databaseName is in getDatabaseNames().
contains(Persistent) - Method in class org.ensembl.util.IDSet
contains(long) - Method in class org.ensembl.util.LongSet
contains(Object) - Method in class org.ensembl.util.PersistentSet
containsAll(Collection) - Method in class org.ensembl.util.PersistentSet
containsGapNodes() - Method in class org.ensembl.datamodel.Location
  Returns whether this location contains a gap node.
containsPrefix(String) - Method in class org.ensembl.driver.ServerDriver
  Determines if at least one database beginning with the _prefix_ is included in _databaseNames()_.
convert(Location, CoordinateSystem, boolean, boolean, boolean) - Method in interface org.ensembl.driver.LocationConverter
  Create a new location in the target coordinate system that is equivalent to the sourceLocation.
convert(Location, String) - Method in interface org.ensembl.driver.LocationConverter
  Converts location into the target coordinate system.
convert(Location, CoordinateSystem) - Method in interface org.ensembl.driver.LocationConverter
  Converts location into target coordinate system with all gaps and all nodes
convert(Location, String, boolean, boolean, boolean) - Method in interface org.ensembl.driver.LocationConverter
  Converts location to the specified coordinate system.
convertLocationToCoordinateSystemAndGetTheSeqRegionNames(Location, CoordinateSystem) - Method in class org.ensembl.Example
  Converts location into the target coordinate system and prints the results.
convertLocations(List, CoordinateSystem) - Method in interface org.ensembl.driver.FeatureAdaptor
  Converts all feature.location to coordinateSystem.
convertToTopLevel(Location) - Method in interface org.ensembl.driver.LocationConverter
  Fetch the location representing this one in the lowest ranking coordinate system.
copy() - Method in class org.ensembl.datamodel.Location
  Performs a deep copy.
copy() - Method in class org.ensembl.registry.DriverGroup
  Creates a deep copy of this DriverGroup.
copyNode() - Method in class org.ensembl.datamodel.Location
  Performs a deep of the head node.
copyProperty(Properties, String, Properties) - Static method in class org.ensembl.util.PropertiesUtil
  Copy property from src to tgt if not null.
copyProperty(Properties, String, Properties, String) - Static method in class org.ensembl.util.PropertiesUtil
  Copy property from src to tgt if not null.
count - Variable in class org.ensembl.util.Counter
countGenesAndExonsInEachLocation() - Method in class org.ensembl.Example
  Fetch the genes and exons in several locations and print how many there are in each one.
createComparaDriver(String, int, String, String, String) - Static method in class org.ensembl.compara.driver.ComparaDriverFactory
  Creates a core driver connected to the specified database.
createComparaDriver(Properties) - Static method in class org.ensembl.compara.driver.ComparaDriverFactory
  Create a core driver and configure it with the properties object.
createComparaDriver(String) - Static method in class org.ensembl.compara.driver.ComparaDriverFactory
  Create a core driver configured with the parameters in the specified configuration properties file.
createComparaDriverUsingDatabasePrefix(String, int, String, String, String) - Static method in class org.ensembl.compara.driver.ComparaDriverFactory
  Create a core driver connected to the newest database matching the prefix.
createConnection(String, String, String) - Static method in class org.ensembl.util.SimpleDBAccess
createCoreDriver(String, int, String, String, String) - Static method in class org.ensembl.driver.CoreDriverFactory
  Creates a core driver connected to the specified database.
createCoreDriver(Properties) - Static method in class org.ensembl.driver.CoreDriverFactory
  Create a core driver and configure it with the properties object.
createCoreDriver(String) - Static method in class org.ensembl.driver.CoreDriverFactory
  Create a core driver configured with the parameters in the specified configuration properties file.
createCoreDriverUsingDatabasePrefix(String, int, String, String, String) - Static method in class org.ensembl.driver.CoreDriverFactory
  Create a core driver connected to the newest database matching the prefix.
createDataSourceProxy(String) - Method in class org.ensembl.util.ConnectionPoolDataSource
  Creates a proxy for this pool which returns a Datasource whose getConnection() method returns a connection pointing at _defaultConnection_.
createDefaultRegistry() - Static method in class org.ensembl.registry.Registry
  Create a registry pointing at the latest databases on ensembldb.ensembl.org.
createDefaultUserRegistry() - Static method in class org.ensembl.registry.Registry
  Create a registry from the default user registry file returned by getDefaultUserRegistryFile().
createDnaDnaAlignFeature() - Method in interface org.ensembl.compara.datamodel.ComparaDataFactory
createDnaFragment() - Method in interface org.ensembl.compara.datamodel.ComparaDataFactory
createFeaturePair() - Method in interface org.ensembl.compara.datamodel.ComparaDataFactory
createGenomeDB() - Method in interface org.ensembl.compara.datamodel.ComparaDataFactory
createGenomicAlign() - Method in interface org.ensembl.compara.datamodel.ComparaDataFactory
createGenomicAlignBlock() - Method in interface org.ensembl.compara.datamodel.ComparaDataFactory
createHomology() - Method in interface org.ensembl.compara.datamodel.ComparaDataFactory
createLocations() - Static method in class org.ensembl.Example
  Create and then return some ensj locations.
createMember() - Method in interface org.ensembl.compara.datamodel.ComparaDataFactory
createMethodLink() - Method in interface org.ensembl.compara.datamodel.ComparaDataFactory
createMethodLinkSpeciesSet() - Method in interface org.ensembl.compara.datamodel.ComparaDataFactory
createProperties(String[]) - Static method in class org.ensembl.util.PropertiesUtil
  Creates property object from propertyFiles.
createProperties(String) - Static method in class org.ensembl.util.PropertiesUtil
  Creates property object from propertyFile(s).
createProperties(URL) - Static method in class org.ensembl.util.PropertiesUtil
  Creates property object from url.
createStatement() - Method in class org.ensembl.util.ConnectionWrapper
createStatement(int, int) - Method in class org.ensembl.util.ConnectionWrapper
createStatement(int, int, int) - Method in class org.ensembl.util.ConnectionWrapper
createTop(Object) - Method in class org.ensembl.util.ListElement
createValidationState(String) - Static method in class org.ensembl.variation.datamodel.ValidationState
  Factory method for getting instances of this class.
createVariationDriver(String, int, String, String, String) - Static method in class org.ensembl.variation.driver.VariationDriverFactory
  Creates a Variation driver connected to the specified database.
createVariationDriver(Properties) - Static method in class org.ensembl.variation.driver.VariationDriverFactory
  Create a variation driver and configure it with the properties object.
createVariationDriver(String) - Static method in class org.ensembl.variation.driver.VariationDriverFactory
  Create a variation driver configured with the parameters in the specified configuration properties file.
createVariationDriverWithPrefix(String, int, String, String, String) - Static method in class org.ensembl.variation.driver.VariationDriverFactory
  Create a variation driver connected to the newest database matching the prefix.

## D

DEFAULT - Static variable in class org.ensembl.datamodel.AssemblyLocation
  Deprecated.
DEFAULT - Static variable in class org.ensembl.datamodel.CloneFragmentLocation
DEFAULT_CS - Static variable in class org.ensembl.datamodel.AssemblyLocation
  Deprecated.
DEFAULT_CS - Static variable in class org.ensembl.datamodel.CloneFragmentLocation
DEFAULT_LOGGING_CONF_FILE - Static variable in class org.ensembl.driver.LoggingManager
DOUBLEHIT - Static variable in class org.ensembl.variation.datamodel.ValidationState
DOWNSTREAM - Static variable in class org.ensembl.variation.datamodel.AlleleConsequence
  Allele appears upstream of the transcript.
DnaDnaAlignFeature - interface org.ensembl.datamodel.DnaDnaAlignFeature.
DnaDnaAlignFeatureAdaptor - interface org.ensembl.compara.driver.DnaDnaAlignFeatureAdaptor.
DnaDnaAlignment - interface org.ensembl.datamodel.DnaDnaAlignment.
  An alignment between part of a genome and a dna hit
DnaDnaAlignmentAdaptor - interface org.ensembl.driver.DnaDnaAlignmentAdaptor.
  Provides access to DnaDnaAlignments in a datasource.
DnaFragment - interface org.ensembl.compara.datamodel.DnaFragment.
  I am a part of the compara- analysis.
DnaFragmentAdaptor - interface org.ensembl.compara.driver.DnaFragmentAdaptor.
  I am associated with the compara-analyses
DnaProteinAlignment - interface org.ensembl.datamodel.DnaProteinAlignment.
  An alignment between part of a genome and a protein.
DnaProteinAlignmentAdaptor - interface org.ensembl.driver.DnaProteinAlignmentAdaptor.
  Provides access to DnaProteinAlignments in a datasource.
Domain - interface org.ensembl.compara.datamodel.Domain.
  I represent a single species which is part of the compara- analyses.
Driver - interface org.ensembl.driver.Driver.
  Deprecated. Deprecated in version 29.2, use org.ensembl.driver.CoreDriver instead.
DriverGroup - class org.ensembl.registry.DriverGroup.
  All the EnsemblDrivers for a species-release or a compara driver for a release.
DriverGroup() - Constructor for class org.ensembl.registry.DriverGroup
  Create a DriverGroup.
DriverManager - class org.ensembl.driver.DriverManager.
  Utility for creating drivers from a Properties format configuration files.
databaseNames() - Method in class org.ensembl.driver.ServerDriver
databaseNames(DataSource) - Static method in class org.ensembl.util.JDBCUtil
  Returns list of databases (catalogs) in the datasource.
delete(Analysis) - Method in interface org.ensembl.driver.AnalysisAdaptor
delete(long) - Method in interface org.ensembl.driver.AnalysisAdaptor
delete(long) - Method in interface org.ensembl.driver.DnaDnaAlignmentAdaptor
delete(DnaDnaAlignment) - Method in interface org.ensembl.driver.DnaDnaAlignmentAdaptor
delete(long) - Method in interface org.ensembl.driver.DnaProteinAlignmentAdaptor
delete(DnaProteinAlignment) - Method in interface org.ensembl.driver.DnaProteinAlignmentAdaptor
delete(Exon) - Method in interface org.ensembl.driver.ExonAdaptor
  Attempts to remove exon from the data source.
delete(long) - Method in interface org.ensembl.driver.ExonAdaptor
  Attempts to remove exon with the specified internalID from the data source.
delete(long) - Method in interface org.ensembl.driver.ExternalDatabaseAdaptor
delete(ExternalDatabase) - Method in interface org.ensembl.driver.ExternalDatabaseAdaptor
delete(long) - Method in interface org.ensembl.driver.ExternalRefAdaptor
  Deletes ExternalRef, with specified internalID, from datasource, does nothing if externalRef is not in datasource.
delete(ExternalRef) - Method in interface org.ensembl.driver.ExternalRefAdaptor
  Deletes externalRef from datasource, does nothing if externalRef is not in datasource.
delete(Gene) - Method in interface org.ensembl.driver.GeneAdaptor
  Deletes gene with specified internalID plus it's transcripts, translations and exons.
delete(long) - Method in interface org.ensembl.driver.GeneAdaptor
  Deletes gene with specified internalID plus it's transcripts, translations and exons.
delete(Marker) - Method in interface org.ensembl.driver.MarkerAdaptor
  Deletes the marker.
delete(long) - Method in interface org.ensembl.driver.MarkerAdaptor
  Deletes the marker with the specified internalID.
delete(long) - Method in interface org.ensembl.driver.PredictionExonAdaptor
delete(PredictionExon) - Method in interface org.ensembl.driver.PredictionExonAdaptor
delete(long) - Method in interface org.ensembl.driver.PredictionTranscriptAdaptor
delete(PredictionTranscript) - Method in interface org.ensembl.driver.PredictionTranscriptAdaptor
delete(long) - Method in interface org.ensembl.driver.ProteinFeatureAdaptor
delete(ProteinFeature) - Method in interface org.ensembl.driver.ProteinFeatureAdaptor
delete(long) - Method in interface org.ensembl.driver.RepeatConsensusAdaptor
delete(RepeatConsensus) - Method in interface org.ensembl.driver.RepeatConsensusAdaptor
delete(long) - Method in interface org.ensembl.driver.RepeatFeatureAdaptor
delete(RepeatFeature) - Method in interface org.ensembl.driver.RepeatFeatureAdaptor
delete(Sequence) - Method in interface org.ensembl.driver.SequenceAdaptor
delete(long) - Method in interface org.ensembl.driver.SequenceAdaptor
delete(TranslationSnapShot) - Method in interface org.ensembl.driver.StableIDEventAdaptor
  Deletes TranslationSnapshot.
delete(GeneSnapShot) - Method in interface org.ensembl.driver.StableIDEventAdaptor
  Deletes the gene snapshot.
delete(Exon) - Method in interface org.ensembl.driver.SupportingFeatureAdaptor
delete(Transcript) - Method in interface org.ensembl.driver.TranscriptAdaptor
  Deletes transcript plus it's exons and translation from persistent storage.
delete(long) - Method in interface org.ensembl.driver.TranscriptAdaptor
  Deletes transcript with specified internalID plus it's exons and translation from persistent storage.
deleteDatabase() - Method in interface org.ensembl.driver.EnsemblDriver
  Delete the database this driver wraps.
deleteEvents(MappingSession) - Method in interface org.ensembl.driver.StableIDEventAdaptor
  Deletes all stable id events associated with the session.
deleteGeneSnapShots(MappingSession) - Method in interface org.ensembl.driver.StableIDEventAdaptor
  Deletes all GeneSnapShots associated with this session.
deleteSession(MappingSession) - Method in interface org.ensembl.driver.StableIDEventAdaptor
  Deletes session and corresponding stable id events.
deleteTranslationSnapShots(MappingSession) - Method in interface org.ensembl.driver.StableIDEventAdaptor
  Deletes all TranslationSnapShots associated with this session.
deprecated(String) - Static method in class org.ensembl.util.Warnings
dereference(Location) - Method in interface org.ensembl.driver.AssemblyExceptionAdaptor
  Dereferences the request location.
dereference(Location) - Method in interface org.ensembl.driver.LocationConverter
  Dereferences location into component locations.
diff(Location) - Method in class org.ensembl.datamodel.Location
  Convenience method to find the difference between to locations.
diff(SystemUtil.MemoryStatus) - Method in class org.ensembl.util.SystemUtil.MemoryStatus
displayDriversState() - Method in class org.ensembl.Example
  Print details about the drivers' configurations.
dna2protein(String, boolean) - Static method in class org.ensembl.util.SequenceUtil
  Converts string of nuceic acids into string of amino acids.
dna2protein(byte[]) - Static method in class org.ensembl.util.SequenceUtil
dropBottom() - Method in class org.ensembl.util.ListElement
dumpTableToFile(Connection, String, String) - Static method in class org.ensembl.util.Util
  Dump a table's data to a tab-delimited file.

## E

ESSENTIAL_SPLICE_SITE - Static variable in class org.ensembl.variation.datamodel.AlleleConsequence
  Allele hits the 1st or 2nd bases at the beginning or end of an intron.
EnsemblDBLister - class org.ensembl.util.EnsemblDBLister.
  Convenience class that prints the databases available on ensembldb.ensembl.org to stdout.
EnsemblDBLister() - Constructor for class org.ensembl.util.EnsemblDBLister
EnsemblDriver - interface org.ensembl.driver.EnsemblDriver.
  An ensembl driver provides access to an ensembl database through it's adaptors.
Example - class org.ensembl.Example.
  Example code demonstrating how to retrieve data from ensembl databases using ensj.
Example() - Constructor for class org.ensembl.Example
  Creates an instance of Example with core and varition drivers configured.
Exon - interface org.ensembl.datamodel.Exon.
  Exon.
ExonAdaptor - interface org.ensembl.driver.ExonAdaptor.
  Provides access to Exons in the datasource.
ExternalDatabase - interface org.ensembl.datamodel.ExternalDatabase.
ExternalDatabaseAdaptor - interface org.ensembl.driver.ExternalDatabaseAdaptor.
  Provides access to ExternalDatabases in the datasource.
ExternalRef - interface org.ensembl.datamodel.ExternalRef.
  Reference to object outside ensembl database.
ExternalRefAdaptor - interface org.ensembl.driver.ExternalRefAdaptor.
  Provides access to ExternalRefs in the datasource.
environmentDump() - Static method in class org.ensembl.util.SystemUtil
equals(CoordinateSystem) - Method in class org.ensembl.datamodel.CoordinateSystem
  Test for equality with another Coordinate System.
equals(Object) - Method in class org.ensembl.registry.DriverGroup
  Checks if _obj_ is equal to this instance.
equals(Object, Object) - Method in class org.ensembl.util.AscendingInternalIDComparator
equals(Object) - Method in class org.ensembl.util.Pair

## F

FIVE_PRIME_UTR - Static variable in class org.ensembl.variation.datamodel.AlleleConsequence
  Allele affects the 5prime UTR.
FRAMESHIFT_CODING - Static variable in class org.ensembl.variation.datamodel.AlleleConsequence
  Allele causes a frameshift.
FREQ - Static variable in class org.ensembl.variation.datamodel.ValidationState
Family - interface org.ensembl.compara.datamodel.Family.
  I represent a single species which is part of the compara- analyses.
FatalException - exception org.ensembl.compara.driver.FatalException.
FatalException(String) - Constructor for class org.ensembl.compara.driver.FatalException
FatalException(String, Throwable) - Constructor for class org.ensembl.compara.driver.FatalException
Feature - interface org.ensembl.datamodel.Feature.
  Simple genomic feature.
FeatureAdaptor - interface org.ensembl.driver.FeatureAdaptor.
  Provides access to a datatype that is Locatable so can be fetched by location.
FeatureIterator - class org.ensembl.driver.FeatureIterator.
  Provides an iterator over features from a FeatureAdaptor.
FeatureIterator(FeatureAdaptor, int, boolean) - Constructor for class org.ensembl.driver.FeatureIterator
  Create an iterator over all features in the adaptor.
FeatureIterator(FeatureAdaptor, int, boolean, long[]) - Constructor for class org.ensembl.driver.FeatureIterator
  Create an iterator over features with the specified internalIDs.
FeatureIterator(FeatureAdaptor, int, boolean, Location, LocationConverter) - Constructor for class org.ensembl.driver.FeatureIterator
  Create an iterator over features in the adaptor that overlap the specified location.
FeaturePair - interface org.ensembl.datamodel.FeaturePair.
  Feature hit.
FormattedSequencePrintStream - class org.ensembl.util.FormattedSequencePrintStream.
  Extended PrintStream to allow users to print fasta formatted sequence output with an unformatted header, and sequence formatted to a user-specified column width maximum, using a user supplied line ending.
FormattedSequencePrintStream(int, OutputStream) - Constructor for class org.ensembl.util.FormattedSequencePrintStream
  Constructor for a basic FormattedSequencePrintStream, with maxColumn and an underlying OutputStream.
FormattedSequencePrintStream(int, String, OutputStream) - Constructor for class org.ensembl.util.FormattedSequencePrintStream
FormattedSequencePrintStream(int, OutputStream, boolean) - Constructor for class org.ensembl.util.FormattedSequencePrintStream
  Constructor for a FormattedSequencePrintStream, stating whether the underlying PrintStream should be in autoFlush mode, or not.
FormattedSequencePrintStream(int, String, OutputStream, boolean) - Constructor for class org.ensembl.util.FormattedSequencePrintStream
  Constructor for a FormattedSequencePrintStream, setting the autoFlush and the lineEnd string to print when adding a line end to formatted sequence output.
FormattedSequencePrintStream(int, OutputStream, String) - Constructor for class org.ensembl.util.FormattedSequencePrintStream
  Constructor for a FormattedSequencePrintStream, with a specified encoding.
FormattedSequencePrintStream(int, String, OutputStream, boolean, String) - Constructor for class org.ensembl.util.FormattedSequencePrintStream
  Constructor for a FormattedSequencePrintStream, with a specified lineEnd, autoFlush, and encoding.
FrequencyCounter - class org.ensembl.util.FrequencyCounter.
  Convenience class that can be used to count the number of times a key is added.
FrequencyCounter() - Constructor for class org.ensembl.util.FrequencyCounter
FrequencyCounter(int, float) - Constructor for class org.ensembl.util.FrequencyCounter
fastmap(Location) - Method in interface org.ensembl.datamodel.AssemblyMapper
fastmap(Location) - Method in class org.ensembl.datamodel.ChainedAssemblyMapper
fastmap(Location) - Method in class org.ensembl.datamodel.SimpleAssemblyMapper
fetch(String, Location, String) - Method in interface org.ensembl.compara.driver.DnaDnaAlignFeatureAdaptor
  Returns DnaDnaAlignFeature instances for input species, chromosome location and hit species for ALL method-link-types.
fetch(String, Location, String, String) - Method in interface org.ensembl.compara.driver.DnaDnaAlignFeatureAdaptor
  Returns DnaDnaAlignFeature instances for input species, chromosome location and hit species for the specified method-link-type.
fetch(long) - Method in interface org.ensembl.compara.driver.DnaFragmentAdaptor
fetch(GenomeDB, String, String) - Method in interface org.ensembl.compara.driver.DnaFragmentAdaptor
fetch() - Method in interface org.ensembl.compara.driver.GenomeDBAdaptor
fetch(String, String) - Method in interface org.ensembl.compara.driver.GenomeDBAdaptor
fetch(long) - Method in interface org.ensembl.compara.driver.GenomeDBAdaptor
fetch(String) - Method in interface org.ensembl.compara.driver.GenomeDBAdaptor
fetch() - Method in interface org.ensembl.compara.driver.GenomicAlignAdaptor
fetch(long) - Method in interface org.ensembl.compara.driver.GenomicAlignAdaptor
fetch(DnaFragment, GenomeDB, int, int, String) - Method in interface org.ensembl.compara.driver.GenomicAlignAdaptor
fetch(GenomicAlignBlock) - Method in interface org.ensembl.compara.driver.GenomicAlignAdaptor
fetch(long) - Method in interface org.ensembl.compara.driver.GenomicAlignBlockAdaptor
fetch(long[]) - Method in interface org.ensembl.compara.driver.GenomicAlignBlockAdaptor
fetch(MethodLinkSpeciesSet, DnaFragment, int, int) - Method in interface org.ensembl.compara.driver.GenomicAlignBlockAdaptor
fetch(MethodLinkSpeciesSet, Location) - Method in interface org.ensembl.compara.driver.GenomicAlignBlockAdaptor
fetch(long) - Method in interface org.ensembl.compara.driver.HomologyAdaptor
fetch(Member) - Method in interface org.ensembl.compara.driver.HomologyAdaptor
fetch(long) - Method in interface org.ensembl.compara.driver.MemberAdaptor
fetch(String, Location, String, Location) - Method in interface org.ensembl.compara.driver.MemberAdaptor
  Fetches gene-level homology feature pairs given locations on two chromosomes.
fetch(String, Location, String) - Method in interface org.ensembl.compara.driver.MemberAdaptor
  Fetches gene-level homology feature pairs given location on one chromosomes.
fetch(String, String[], String) - Method in interface org.ensembl.compara.driver.MemberAdaptor
  Fetches gene-level homology feature pairs given an input list of stableids
fetch(String, String, String) - Method in interface org.ensembl.compara.driver.MemberAdaptor
  Fetches chromosome-level homology feature pairs for query species, query chromosome and target species.
fetch() - Method in interface org.ensembl.compara.driver.MethodLinkAdaptor
fetch(String) - Method in interface org.ensembl.compara.driver.MethodLinkAdaptor
fetch(long) - Method in interface org.ensembl.compara.driver.MethodLinkAdaptor
fetch() - Method in interface org.ensembl.compara.driver.MethodLinkSpeciesSetAdaptor
fetch(long) - Method in interface org.ensembl.compara.driver.MethodLinkSpeciesSetAdaptor
fetch(MethodLink, GenomeDB[]) - Method in interface org.ensembl.compara.driver.MethodLinkSpeciesSetAdaptor
fetch(MethodLink, GenomeDB) - Method in interface org.ensembl.compara.driver.MethodLinkSpeciesSetAdaptor
fetch(MethodLink) - Method in interface org.ensembl.compara.driver.MethodLinkSpeciesSetAdaptor
fetch(GenomeDB) - Method in interface org.ensembl.compara.driver.MethodLinkSpeciesSetAdaptor
fetch(long) - Method in interface org.ensembl.driver.AnalysisAdaptor
fetch() - Method in interface org.ensembl.driver.AnalysisAdaptor
fetch() - Method in interface org.ensembl.driver.AssemblyExceptionAdaptor
  Retrieve all AssemblyExceptions.
fetch(long) - Method in interface org.ensembl.driver.AssemblyExceptionAdaptor
  Retrieve AssemblyException with specified internalID.
fetch(Location) - Method in interface org.ensembl.driver.AssemblyExceptionAdaptor
  Retrieve AssemblyExceptions that are relevant for given location.
fetch(long) - Method in interface org.ensembl.driver.CoordinateSystemAdaptor
  Fetch a CoordinateSystem by its internalID.
fetch(String, String) - Method in interface org.ensembl.driver.CoordinateSystemAdaptor
  Fetch a CoordinateSystem by name and version.
fetch(long) - Method in interface org.ensembl.driver.DnaDnaAlignmentAdaptor
fetch(Location) - Method in interface org.ensembl.driver.DnaDnaAlignmentAdaptor
fetch(Location, Analysis) - Method in interface org.ensembl.driver.DnaDnaAlignmentAdaptor
fetch(Location, Analysis[]) - Method in interface org.ensembl.driver.DnaDnaAlignmentAdaptor
fetch(Location, String) - Method in interface org.ensembl.driver.DnaDnaAlignmentAdaptor
fetch(String) - Method in interface org.ensembl.driver.DnaDnaAlignmentAdaptor
fetch(Location, String[]) - Method in interface org.ensembl.driver.DnaDnaAlignmentAdaptor
fetch(long) - Method in interface org.ensembl.driver.DnaProteinAlignmentAdaptor
fetch(Location) - Method in interface org.ensembl.driver.DnaProteinAlignmentAdaptor
fetch(Location, Analysis) - Method in interface org.ensembl.driver.DnaProteinAlignmentAdaptor
fetch(Location, Analysis[]) - Method in interface org.ensembl.driver.DnaProteinAlignmentAdaptor
fetch(Location, String) - Method in interface org.ensembl.driver.DnaProteinAlignmentAdaptor
fetch(String) - Method in interface org.ensembl.driver.DnaProteinAlignmentAdaptor
  Fetch all DNAProteinAlignments with the specified logicalName.
fetch(Location, String[]) - Method in interface org.ensembl.driver.DnaProteinAlignmentAdaptor
fetch(long) - Method in interface org.ensembl.driver.ExonAdaptor
fetch(String) - Method in interface org.ensembl.driver.ExonAdaptor
fetch(Query) - Method in interface org.ensembl.driver.ExonAdaptor
  Deprecated. since version 27.0 use other fetch(...) methods.
fetch() - Method in interface org.ensembl.driver.ExternalDatabaseAdaptor
  Fetches all external databases.
fetch(long) - Method in interface org.ensembl.driver.ExternalDatabaseAdaptor
  Fetches ExternalDb for the the given externalDbId
fetch(String) - Method in interface org.ensembl.driver.ExternalDatabaseAdaptor
  Fetches ExternalDb with the specied databaseName.
fetch(long) - Method in interface org.ensembl.driver.ExternalRefAdaptor
  Fetches ExternalRefs with the specified _internalID_.
fetch(long, int) - Method in interface org.ensembl.driver.ExternalRefAdaptor
  Fetches ExternalRefs for the item with the specified _type_ and _internalID_.
fetch(String) - Method in interface org.ensembl.driver.ExternalRefAdaptor
  Fetches ExternalRefs where name appears as either a primaryID, displayID or synonym.
fetch(long[]) - Method in interface org.ensembl.driver.FeatureAdaptor
  Fetch zero or more Features with the specified internalIDs.
fetch(long[], boolean) - Method in interface org.ensembl.driver.FeatureAdaptor
  Fetch zero or more Features with the specified internalIDs.
fetch(Location) - Method in interface org.ensembl.driver.FeatureAdaptor
  Fetches features that overlap with location.
fetch(Location, boolean) - Method in interface org.ensembl.driver.FeatureAdaptor
  Fetches features, optionally including child data, that overlap with location.
fetch(long) - Method in interface org.ensembl.driver.GeneAdaptor
fetch(String) - Method in interface org.ensembl.driver.GeneAdaptor
fetch(Query) - Method in interface org.ensembl.driver.GeneAdaptor
  Deprecated. since version 27.0. Use other fetch(...) methods instead.
fetch(CoordinateSystem, String) - Method in interface org.ensembl.driver.KaryotypeBandAdaptor
fetch(CoordinateSystem, String, String) - Method in interface org.ensembl.driver.KaryotypeBandAdaptor
fetch(long) - Method in interface org.ensembl.driver.MarkerAdaptor
  Location type set to CloneFragmentLocation.
fetch(MarkerFeature) - Method in interface org.ensembl.driver.MarkerAdaptor
  Fetch Marker corresponding to markerFeature
fetch(Location, int) - Method in interface org.ensembl.driver.MarkerFeatureAdaptor
  MarkerFeatures in the specified location matching meeting the other criteria as well.
fetch(Marker) - Method in interface org.ensembl.driver.MarkerFeatureAdaptor
  Fetch MarkerFeatures with the specified Marker.
fetch(long) - Method in interface org.ensembl.driver.MarkerFeatureAdaptor
  Fetch MarkerFeature by internalID
fetch(Location) - Method in interface org.ensembl.driver.MarkerFeatureAdaptor
  Fetch MarkerFeatures by location.
fetch(long) - Method in interface org.ensembl.driver.MiscFeatureAdaptor
fetch(Location, MiscSet) - Method in interface org.ensembl.driver.MiscFeatureAdaptor
  Fetch all MiscFeatures lying in the location and corresponding to the miscSet
fetch(MiscSet) - Method in interface org.ensembl.driver.MiscFeatureAdaptor
  Fetch all MiscFeatures corresponding to the miscSet.
fetch() - Method in interface org.ensembl.driver.MiscSetAdaptor
fetch(long) - Method in interface org.ensembl.driver.MiscSetAdaptor
fetch(String) - Method in interface org.ensembl.driver.MiscSetAdaptor
fetch(long) - Method in interface org.ensembl.driver.OligoArrayAdaptor
  Retrieve OligoArray with specified internal ID.
fetch(String) - Method in interface org.ensembl.driver.OligoArrayAdaptor
  Retrieve OligoArray with specified name.
fetch() - Method in interface org.ensembl.driver.OligoArrayAdaptor
  Fetch all microarrays from the database.
fetch(long) - Method in interface org.ensembl.driver.OligoFeatureAdaptor
  Fetch OligoFeature with specified internalID.
fetch(OligoProbe) - Method in interface org.ensembl.driver.OligoFeatureAdaptor
  Fetches OligoFeatures corresponding the the oligoProbe.
fetch(long) - Method in interface org.ensembl.driver.OligoProbeAdaptor
fetch(OligoArray) - Method in interface org.ensembl.driver.OligoProbeAdaptor
  Returns OligoProbes that appear in the specified array.
fetch(String) - Method in interface org.ensembl.driver.OligoProbeAdaptor
  Fetch Probes from the specified probe set.
fetch(long) - Method in interface org.ensembl.driver.PredictionExonAdaptor
fetch(PredictionTranscript) - Method in interface org.ensembl.driver.PredictionExonAdaptor
fetch(long) - Method in interface org.ensembl.driver.PredictionTranscriptAdaptor
fetch(Location, Analysis) - Method in interface org.ensembl.driver.PredictionTranscriptAdaptor
fetch(Location, Analysis[]) - Method in interface org.ensembl.driver.PredictionTranscriptAdaptor
fetch(Location, String) - Method in interface org.ensembl.driver.PredictionTranscriptAdaptor
fetch(String) - Method in interface org.ensembl.driver.PredictionTranscriptAdaptor
fetch(Location, String[]) - Method in interface org.ensembl.driver.PredictionTranscriptAdaptor
fetch(long) - Method in interface org.ensembl.driver.ProteinFeatureAdaptor
fetch(Translation) - Method in interface org.ensembl.driver.ProteinFeatureAdaptor
fetch(long) - Method in interface org.ensembl.driver.QtlAdaptor
  Fetch Qtl by it's internalID.
fetch(Qtl) - Method in interface org.ensembl.driver.QtlFeatureAdaptor
  Fetch the QtlFeatures related to the qtl.
fetch(long) - Method in interface org.ensembl.driver.RepeatConsensusAdaptor
  Fetches consensus with the specified internalID.
fetch(long) - Method in interface org.ensembl.driver.RepeatFeatureAdaptor
fetch(Location) - Method in interface org.ensembl.driver.RepeatFeatureAdaptor
  Warning: some repeats are stored unstranded (strand=0) which can produce unexpected results.
fetch(Location) - Method in interface org.ensembl.driver.SequenceAdaptor
  Fetches sequence corresponding to location.
fetch(long) - Method in interface org.ensembl.driver.SequenceAdaptor
fetch(long) - Method in interface org.ensembl.driver.SequenceRegionAdaptor
  Fetch a SequenceRegion by its internalID.
fetch(String, CoordinateSystem) - Method in interface org.ensembl.driver.SequenceRegionAdaptor
  Fetch a SequenceRegion by name and co-ordinate system.
fetch(Location) - Method in interface org.ensembl.driver.SequenceRegionAdaptor
  Fetch a SequenceRegion corresponding to a Location.
fetch(long) - Method in interface org.ensembl.driver.SimpleFeatureAdaptor
fetch(Location) - Method in interface org.ensembl.driver.SimpleFeatureAdaptor
fetch(Location, Analysis) - Method in interface org.ensembl.driver.SimpleFeatureAdaptor
fetch(Location, Analysis[]) - Method in interface org.ensembl.driver.SimpleFeatureAdaptor
fetch(Location, String) - Method in interface org.ensembl.driver.SimpleFeatureAdaptor
fetch(String) - Method in interface org.ensembl.driver.SimpleFeatureAdaptor
fetch(Location, String[]) - Method in interface org.ensembl.driver.SimpleFeatureAdaptor
fetch(String) - Method in interface org.ensembl.driver.StableIDEventAdaptor
fetch(String, MappingSession) - Method in interface org.ensembl.driver.StableIDEventAdaptor
fetch(MappingSession) - Method in interface org.ensembl.driver.StableIDEventAdaptor
fetch(Exon) - Method in interface org.ensembl.driver.SupportingFeatureAdaptor
fetch(long) - Method in interface org.ensembl.driver.TranscriptAdaptor
fetch(String) - Method in interface org.ensembl.driver.TranscriptAdaptor
fetch(Query) - Method in interface org.ensembl.driver.TranscriptAdaptor
  Deprecated. use more specific fetch methods
fetch(long) - Method in interface org.ensembl.driver.TranslationAdaptor
  Fetches a translation with the specified id.
fetch(long, boolean) - Method in interface org.ensembl.driver.TranslationAdaptor
  Fetches a translation with the specified id with or without start and end exons preloaded.
fetch(String) - Method in interface org.ensembl.driver.TranslationAdaptor
fetch(Transcript, List) - Method in interface org.ensembl.variation.datamodel.AlleleConsequenceAdaptor
  Creates the AlleleTranscriptConsequences that result from applying the AlleleFeature to the transcript.
fetch(Transcript) - Method in interface org.ensembl.variation.datamodel.AlleleConsequenceAdaptor
  Return the AlleleConsequences for the transcript.
fetch(Location) - Method in interface org.ensembl.variation.driver.AlleleFeatureAdaptor
  Return AlleleFeatures overlapping the location.
fetch(Transcript, int) - Method in interface org.ensembl.variation.driver.AlleleFeatureAdaptor
  Return all the AlleleFeatures hitting the transcript and it's 5prime and 3prime flanking regions.
fetch(long) - Method in interface org.ensembl.variation.driver.AlleleGroupAdaptor
  Fetch Allele group with specified internal ID.
fetch(String) - Method in interface org.ensembl.variation.driver.AlleleGroupAdaptor
  Fetch Allele group with specified name.
fetch(VariationGroup) - Method in interface org.ensembl.variation.driver.AlleleGroupAdaptor
  Fetch all allele groups that are part of the Variation group.
fetch(long) - Method in interface org.ensembl.variation.driver.IndividualAdaptor
  Retrieves an individual via its internal identifier.
fetch(long[]) - Method in interface org.ensembl.variation.driver.IndividualAdaptor
  Fetch Individuals by internal ids.
fetch(String) - Method in interface org.ensembl.variation.driver.IndividualAdaptor
  Retrieves all individuals with the specified name.
fetch(Population) - Method in interface org.ensembl.variation.driver.IndividualAdaptor
  Retrieves all individuals from a specified population
fetch(Individual) - Method in interface org.ensembl.variation.driver.IndividualAdaptor
  Retrieves all individuals which are children of a provided parent individual.
fetch(Individual) - Method in interface org.ensembl.variation.driver.IndividualGenotypeAdaptor
  Retrieves all IndividualGenotypes stored for a particual Individual.
fetch(Location) - Method in interface org.ensembl.variation.driver.LDFeatureAdaptor
  Fetches LDFeatures that overlap with location.
fetch(VariationFeature) - Method in interface org.ensembl.variation.driver.LDFeatureAdaptor
  Fetches LDFeatures that include the VariationFeature.
fetch(long) - Method in interface org.ensembl.variation.driver.PopulationAdaptor
  Fetch population by internal id.
fetch(long[]) - Method in interface org.ensembl.variation.driver.PopulationAdaptor
  Fetch populations by internal id.
fetch(String) - Method in interface org.ensembl.variation.driver.PopulationAdaptor
  Fetch population by name.
fetch(long) - Method in interface org.ensembl.variation.driver.PopulationGenotypeAdaptor
  Retrieves a population genotype via its unique internal identifier.
fetch(Population) - Method in interface org.ensembl.variation.driver.PopulationGenotypeAdaptor
  Retrieves a population genotypes which appear in the specified population.
fetch(long) - Method in interface org.ensembl.variation.driver.TranscriptVariationAdaptor
fetch(VariationFeature) - Method in interface org.ensembl.variation.driver.TranscriptVariationAdaptor
  Retrieves all TranscriptVariation objects associated with provided Ensembl variation features.
fetch(Transcript) - Method in interface org.ensembl.variation.driver.TranscriptVariationAdaptor
  Retrieves all TranscriptVariation objects associated with provided transcript.
fetch(long) - Method in interface org.ensembl.variation.driver.VariationAdaptor
  Fetch variation by internal id.
fetch(long[]) - Method in interface org.ensembl.variation.driver.VariationAdaptor
  Fetch variations by their internal ids.
fetch(String) - Method in interface org.ensembl.variation.driver.VariationAdaptor
  Fetch variation by name.
fetch(long) - Method in interface org.ensembl.variation.driver.VariationFeatureAdaptor
  Fetches the VariationFeature with the specified internal ID.
fetch(Variation) - Method in interface org.ensembl.variation.driver.VariationFeatureAdaptor
  Fetches the VariationFeatures that show where the Variation appears on the genome.
fetch(long) - Method in interface org.ensembl.variation.driver.VariationGroupAdaptor
  Fetch Variation group with specified internal ID.
fetch(String) - Method in interface org.ensembl.variation.driver.VariationGroupAdaptor
  Fetch Variation group with specified name.
fetch(Variation) - Method in interface org.ensembl.variation.driver.VariationGroupAdaptor
  Fetch all variation groups that contain the variation.
fetch(long) - Method in interface org.ensembl.variation.driver.VariationGroupFeatureAdaptor
  Fetches variation group with specified internal ID.
fetchAccessionID(Exon) - Method in interface org.ensembl.driver.ExonAdaptor
  Retrieves accession from persistent store and sets that value on the exon.
fetchAccessionID(Gene) - Method in interface org.ensembl.driver.GeneAdaptor
  Retrieves gene's accession from persistent store and sets gene.accession.
fetchAccessionID(Transcript) - Method in interface org.ensembl.driver.TranscriptAdaptor
  Retrieves transcript's accession from persistent store and sets transcript.accession.
fetchAccessionID(Translation) - Method in interface org.ensembl.driver.TranslationAdaptor
  Retrieves translation's accession from persistent store and sets translation.accession.
fetchAll() - Method in interface org.ensembl.driver.CoordinateSystemAdaptor
  Fetch all the coordinate systems defined for this species.
fetchAll() - Method in interface org.ensembl.driver.FeatureAdaptor
  Retrieves all features from the datasase.
fetchAll(boolean) - Method in interface org.ensembl.driver.FeatureAdaptor
  Retrieves all features from the datasase and if includeChildren is true it might preload it's child data.
fetchAll() - Method in interface org.ensembl.driver.QtlAdaptor
  Fetch all Qtls from database.
fetchAll() - Method in interface org.ensembl.driver.TranslationAdaptor
  Fetch all the translations from the database.
fetchAllByAttributeCode(String) - Method in interface org.ensembl.driver.SequenceRegionAdaptor
  Get all the sequence regions that have an attribute with a particular code set, irrespective of what the value of the attribute is.
fetchAllByAttributeValue(String, String) - Method in interface org.ensembl.driver.SequenceRegionAdaptor
  Fetch all the sequence regions that have an attribute set to a certain value.
fetchAllByCoordinateSystem(CoordinateSystem) - Method in interface org.ensembl.driver.SequenceRegionAdaptor
  Fetch all the sequence regions for a particular co-ordinate system.
fetchAllByFeatureTable(String) - Method in interface org.ensembl.driver.CoordinateSystemAdaptor
  Retrieve a list of the coordinate systems in which features in a particular table are stored.
fetchAllByTranscript(long) - Method in interface org.ensembl.driver.ExonAdaptor
  Fetch all exons associated with the transcript.
fetchAssemblyNames() - Method in interface org.ensembl.driver.LocationConverter
  Assemblies in dataset.
fetchByAttributeType(String) - Method in interface org.ensembl.driver.MiscFeatureAdaptor
  Fetch all MiscFeatures corresponding to the type.
fetchByAttributeTypeAndValue(String, String) - Method in interface org.ensembl.driver.MiscFeatureAdaptor
  Fetch all MiscFeatures corresponding to the type and value.
fetchByBlocks(List) - Method in interface org.ensembl.compara.driver.GenomicAlignAdaptor
fetchByCodePattern(String) - Method in interface org.ensembl.driver.MiscSetAdaptor
  Fetches all MiscSets with a code matching the regular expression.
fetchByCoordSystems(CoordinateSystem, CoordinateSystem) - Method in interface org.ensembl.driver.AssemblyMapperAdaptor
fetchByGeneIDs(long[]) - Method in interface org.ensembl.driver.TranscriptAdaptor
  Get all the transcripts associated with the specified genes.
fetchByGeneIDs(long[], boolean) - Method in interface org.ensembl.driver.TranscriptAdaptor
  Get all the transcripts associated with the specified genes and optionally preload the child transcripts, translations and exons.
fetchByGffFeature(String) - Method in interface org.ensembl.driver.AnalysisAdaptor
fetchByInterproID(String) - Method in interface org.ensembl.driver.GeneAdaptor
fetchByInterproID(String) - Method in interface org.ensembl.driver.TranscriptAdaptor
fetchByInterproID(String) - Method in interface org.ensembl.driver.TranslationAdaptor
fetchByLogicalName(String) - Method in interface org.ensembl.driver.AnalysisAdaptor
fetchByMap(String) - Method in interface org.ensembl.driver.CoordinateSystemAdaptor
  This function supports old style Locations with Maps.
fetchBySourceDatabase(String) - Method in interface org.ensembl.driver.QtlAdaptor
  Fetch all Qtls from database that originally come from the specified database.
fetchBySourceDatabase(String, String) - Method in interface org.ensembl.driver.QtlAdaptor
  Fetch all Qtls from database that originally come from the specified database and have the specified id.
fetchBySynonym(String) - Method in interface org.ensembl.driver.GeneAdaptor
fetchBySynonym(String) - Method in interface org.ensembl.driver.MarkerAdaptor
fetchBySynonym(String) - Method in interface org.ensembl.driver.TranscriptAdaptor
fetchBySynonym(String) - Method in interface org.ensembl.driver.TranslationAdaptor
fetchByTrait(String) - Method in interface org.ensembl.driver.QtlAdaptor
  Fetch all Qtls from database with the specified trait.
fetchByTranscript(long) - Method in interface org.ensembl.driver.TranslationAdaptor
  Fetch a translation by the internal ID of its associated translation.
fetchByTranscript(long, boolean) - Method in interface org.ensembl.driver.TranslationAdaptor
  Fetch a translation by the internal ID of its associated translation with or without including start and end exons.
fetchByTranscripts(long[], boolean) - Method in interface org.ensembl.driver.TranslationAdaptor
  Fetch a translations by the internal IDs of their associated translation.
fetchComplete(CoordinateSystem) - Method in interface org.ensembl.driver.CoordinateSystemAdaptor
  Returns a complete CoordinateSystem maching _cs_.name and _cs_.version.
fetchComplete(Exon) - Method in interface org.ensembl.driver.ExonAdaptor
  This method loads the gene and transcripts into the exon if it corresponds to entries in the database.
fetchComplete(Location) - Method in interface org.ensembl.driver.LocationConverter
  Ensures the location is fully specified by filling in missing values with data from the database.
fetchComplete(Marker) - Method in interface org.ensembl.driver.MarkerAdaptor
  Loads MarkerFeatures into the marker.
fetchComplete(SequenceRegion) - Method in interface org.ensembl.driver.SequenceRegionAdaptor
  Sets the attributes on the seqRegion.
fetchComplete(Transcript) - Method in interface org.ensembl.driver.TranscriptAdaptor
  Loads missing gene and exons into the transcript where these are available in the database.
fetchCompleteGoLinkageType(ExternalRef) - Method in interface org.ensembl.driver.ExternalRefAdaptor
  Fetchs the goLinkageType for the xref and sets it on the xref.
fetchCompleteIdentity(ExternalRef) - Method in interface org.ensembl.driver.ExternalRefAdaptor
  Fetchs the identity query and target for the xref and sets them on the xref.
fetchCompleteSynonyms(ExternalRef) - Method in interface org.ensembl.driver.ExternalRefAdaptor
  Fetches synonyms for specied xref and sets them on the xref.
fetchCount() - Method in interface org.ensembl.driver.FeatureAdaptor
  Fetch the number of features in the database.
fetchCurrent(String) - Method in interface org.ensembl.driver.StableIDEventAdaptor
  Return all StableIDEvents that relate _accession_ to 0 or more stable ids in the current data release.
fetchDatabaseName() - Method in interface org.ensembl.driver.EnsemblDriver
  Returns the database name.
fetchDatabaseNames() - Method in interface org.ensembl.driver.EnsemblDriver
  Lists databases available on this server.
fetchDatabaseSchemaVersion() - Method in interface org.ensembl.driver.EnsemblDriver
  Returns the schema version for the database this driver wraps.
fetchDeletedGeneFromArchive() - Method in class org.ensembl.Example
  Fetches information about a gene from the archive.
fetchExonByInternalID() - Method in class org.ensembl.Example
  Fetch an exon by it's internal id and print it.
fetchFlankingSequence(Variation) - Method in interface org.ensembl.variation.driver.VariationAdaptor
  Loads flanking sequence for variation.
fetchGeneByStableIDAndViewPeptide() - Method in class org.ensembl.Example
  Fetch a gene by it's stable ID and then print the peptide corresponding to its first transcript.
fetchGeneSnapShot(String, int) - Method in interface org.ensembl.driver.StableIDEventAdaptor
  Fetches snapshot from datasource.
fetchGenesByExternalRefs() - Method in class org.ensembl.Example
  Fetch genes corresponding to various external references/identifier such as HUGO ids and Affymetrix probeset names.
fetchGenesByLocation(Location) - Method in class org.ensembl.Example
  This method illustrates several ways to retrieve genes from a specified location.
fetchInternalIDs() - Method in interface org.ensembl.driver.FeatureAdaptor
  Fetch the internalIDs for all features of this type in the database.
fetchInternalIDs(Location) - Method in interface org.ensembl.driver.FeatureAdaptor
  Fetch internalIDs for features in the specified location.
fetchIterator(String) - Method in interface org.ensembl.driver.DnaProteinAlignmentAdaptor
  Fetch an iterator over all DNAProteinAlignments with the specified logicalName.
fetchIterator(long[]) - Method in interface org.ensembl.driver.FeatureAdaptor
  Returns a low memory iterator over Features matching the internalIDs.
fetchIterator(long[], boolean) - Method in interface org.ensembl.driver.FeatureAdaptor
  Returns a low memory iterator over Features matching the internalIDs.
fetchIterator(long[], boolean, int) - Method in interface org.ensembl.driver.FeatureAdaptor
  Returns a low memory iterator over Features matching the internalIDs.
fetchIterator() - Method in interface org.ensembl.driver.FeatureAdaptor
  Returns a low memory footprint iterator over all Features of this type in the database.
fetchIterator(boolean) - Method in interface org.ensembl.driver.FeatureAdaptor
  Returns a low memory footprint iterator over all Features of this type in the database.
fetchIterator(boolean, int) - Method in interface org.ensembl.driver.FeatureAdaptor
  Returns a low memory footprint iterator over all Features of this type in the database.
fetchIterator(Location) - Method in interface org.ensembl.driver.FeatureAdaptor
  Returns a low memory footprint iterator over all Features in the specified location.
fetchIterator(Location, boolean) - Method in interface org.ensembl.driver.FeatureAdaptor
  Returns a low memory footprint iterator over all Features in the specified location with or without child data preloaded.
fetchIterator(Location, boolean, int) - Method in interface org.ensembl.driver.FeatureAdaptor
  Returns a low memory footprint iterator over all Features in the specified location with or without child data preloaded.
fetchIterator(long[]) - Method in interface org.ensembl.driver.OligoProbeAdaptor
  Returns an iterator over OligoProbes that have internalIDs in ids.
fetchKaryotypes(CoordinateSystem, String) - Method in class org.ensembl.Example
  Fetches information about karyotypes (chromosome bands) for the specified chromosome.
fetchKnown(Translation) - Method in interface org.ensembl.driver.TranslationAdaptor
  Retrieves from persistent store whether translation is known and sets translation.known.
fetchKnown(Translation[]) - Method in interface org.ensembl.driver.TranslationAdaptor
  Retrieves from persistent store whether translations are known and for each one sets translation.known.
fetchLDFeatureContainer(VariationFeature) - Method in interface org.ensembl.variation.driver.LDFeatureAdaptor
  Retrieves an LDFeatureContainer that contains all the LDFeatures that refer to the specified VariationFeature.
fetchLDFeatureContainer(Location) - Method in interface org.ensembl.variation.driver.LDFeatureAdaptor
  Retrieves an LDFeatureContainer that contains all the LDFeatures that overlap with the specified location.
fetchMappingSessions() - Method in interface org.ensembl.driver.StableIDEventAdaptor
fetchMetaValues(String) - Method in interface org.ensembl.driver.EnsemblDriver
  Returns zero or more values from the meta table matching the specified meta_key.
fetchPopulations(Individual) - Method in interface org.ensembl.variation.driver.IndividualAdaptor
  Fetch the populations that the individual belongs to.
fetchSequenceLevel() - Method in interface org.ensembl.driver.CoordinateSystemAdaptor
  Fetch the co-ordinate system that represents the sequence level for this species.
fetchSequenceRegionsSuchAsChromosomeOrContig(CoordinateSystem) - Method in class org.ensembl.Example
  Fetches information about the sequence regions.
fetchSubPopulations(Population) - Method in interface org.ensembl.variation.driver.PopulationAdaptor
  Retrieve all sub populations for a given super population.
fetchSuperPopulations(Population) - Method in interface org.ensembl.variation.driver.PopulationAdaptor
  Retrieve all super populations for a given sub population.
fetchSupportingFeatures(long) - Method in interface org.ensembl.driver.TranscriptAdaptor
  Returns supporting features for this transcript.
fetchTableNames() - Method in interface org.ensembl.driver.EnsemblDriver
  Return list of database tables excluding backup tables.
fetchTableNames(boolean) - Method in interface org.ensembl.driver.EnsemblDriver
  Returns list of tables in database with or without backup tables.
fetchTopLevelLocations() - Method in interface org.ensembl.driver.CoordinateSystemAdaptor
  There is one top level location for each sequence region in the highest ranked coordinate system.
fetchTranscriptSnapShot(String, int) - Method in interface org.ensembl.driver.StableIDEventAdaptor
  Fetches transcript snapshot from datasource.
fetchTranslationSnapShot(String, int) - Method in interface org.ensembl.driver.StableIDEventAdaptor
  Fetches translation snapshot from datasource.
fetchVariationsOverlapingGenes() - Method in class org.ensembl.Example
  Fetches all the variations that overlap a particular gene.
fetchVariationsOverlapingLocation() - Method in class org.ensembl.Example
  Fetches all the variations in a specified location from the variation driver.
fetchVersion(Exon) - Method in interface org.ensembl.driver.ExonAdaptor
  Retrieves version from persistent store and sets that value on the exon.
fetchVersion(Transcript) - Method in interface org.ensembl.driver.TranscriptAdaptor
  Retrieves transcript's version from persistent store and sets transcript.version.
fetchVersion(Translation) - Method in interface org.ensembl.driver.TranslationAdaptor
  Retrieves translation's version from persistent store and sets translation.version.
filterDatabaseNames(String) - Method in class org.ensembl.driver.ServerDriver
  Return database names matching the filter string.
filterDatabaseNamesAndReverseSort(String) - Method in class org.ensembl.driver.ServerDriver
  Same as _filterDatabaseNames(String)_ but returns reverse sorted array.
filterOnPrefix(String, Properties) - Static method in class org.ensembl.util.PropertiesUtil
  Filters the input set of properties only allowing those with keys that begin with _prefix_.
finalize() - Method in class org.ensembl.util.ConnectionWrapper
  Closes the wrapped connection.
firstArgumentIsKnownConsensusAndSecondIsKnowQuery(GenomeDB, GenomeDB) - Method in interface org.ensembl.compara.driver.GenomeDBAdaptor
flush() - Method in interface org.ensembl.datamodel.AssemblyMapper
flush() - Method in class org.ensembl.datamodel.ChainedAssemblyMapper
flush() - Method in class org.ensembl.datamodel.SimpleAssemblyMapper
format(LogRecord) - Method in class org.ensembl.util.LogFormatter
format(LogRecord) - Method in class org.ensembl.util.MessageOnlyFormatter
format(long) - Method in class org.ensembl.util.NamedTimer
  Convert time in ms to hours, minutes, seconds.
formatForPrinting(String) - Static method in class org.ensembl.util.StringUtil
formatForPrinting(Object) - Static method in class org.ensembl.util.StringUtil
  Convenience method which automatically calls o.toString() and delegates formatting to sister method.
free - Variable in class org.ensembl.util.SystemUtil.MemoryStatus

## G

GENE - Static variable in interface org.ensembl.datamodel.ExternalRef
  Gene type
GENE - Static variable in interface org.ensembl.datamodel.StableIDEvent
GEORDY - Static variable in class org.ensembl.util.SimpleDBAccess
Gene - interface org.ensembl.datamodel.Gene.
  Gene.
GeneAdaptor - interface org.ensembl.driver.GeneAdaptor.
  Provides access to genes in the datasource.
GeneSnapShot - interface org.ensembl.datamodel.GeneSnapShot.
  Represents part of the state of a gene at some point in time.
GenomeDB - interface org.ensembl.compara.datamodel.GenomeDB.
  I represent a single species which is part of the compara- analyses.
GenomeDBAdaptor - interface org.ensembl.compara.driver.GenomeDBAdaptor.
  I am a part of the compara analysis
GenomicAlign - interface org.ensembl.compara.datamodel.GenomicAlign.
  I am part of the compara-analysis.
GenomicAlignAdaptor - interface org.ensembl.compara.driver.GenomicAlignAdaptor.
  I am a part of the compara analysis
GenomicAlignBlock - interface org.ensembl.compara.datamodel.GenomicAlignBlock.
  I am part of the compara-analysis.
GenomicAlignBlockAdaptor - interface org.ensembl.compara.driver.GenomicAlignBlockAdaptor.
  I am a part of the compara analysis
Genotype - interface org.ensembl.variation.datamodel.Genotype.
  Genotype.
get(Properties) - Method in class org.ensembl.driver.ServerDriverFactory
  Returns a ServerDriver corresponding to the _config_.
get(long) - Method in class org.ensembl.util.IDMap
  Retrieves the item using get(new Long(key)).
get(long) - Method in class org.ensembl.util.LruCache
  Convenience method that converts long to Long for storage.
get(Object) - Method in class org.ensembl.util.LruCache
getAccessionID() - Method in interface org.ensembl.datamodel.Accessioned
  Return the accession (stable id) for this object.
getAccessionID() - Method in class org.ensembl.datamodel.Query
  Deprecated.
getAdaptor(String) - Method in interface org.ensembl.driver.EnsemblDriver
getAdaptors() - Method in interface org.ensembl.driver.EnsemblDriver
getAlignedSequence() - Method in interface org.ensembl.compara.datamodel.GenomicAlign
getAlignmentStrings() - Method in interface org.ensembl.compara.datamodel.GenomicAlignBlock
getAllGenomicAligns() - Method in interface org.ensembl.compara.datamodel.GenomicAlignBlock
  Return genomicAligns.
getAllNonreferenceGenomicAligns() - Method in interface org.ensembl.compara.datamodel.GenomicAlignBlock
getAllUngappedGenomicAlignBlocks() - Method in interface org.ensembl.compara.datamodel.GenomicAlignBlock
getAllele1() - Method in interface org.ensembl.variation.datamodel.Genotype
  One of the alleles that defines this genotype.
getAllele2() - Method in interface org.ensembl.variation.datamodel.Genotype
  One of the alleles that defines this genotype.
getAlleleConsequenceAdaptor() - Method in interface org.ensembl.variation.driver.VariationDriver
  The AlleleConsequence adaptor.
getAlleleFeatureAdaptor() - Method in interface org.ensembl.variation.driver.VariationDriver
  The AlleleFeature adaptor.
getAlleleGroupAdaptor() - Method in interface org.ensembl.variation.driver.VariationDriver
  The allele group adaptor.
getAlleleString() - Method in interface org.ensembl.variation.datamodel.Allele
  The allele string is a string of nucleotide sequence, or a '-' representing the absence of sequence (deletion).
getAlleleString() - Method in interface org.ensembl.variation.datamodel.AlleleFeature
  Return the allele string.
getAlleleString() - Method in interface org.ensembl.variation.datamodel.VariationFeature
  The allele_string is a '/' demimited string representing the alleles associated with this feature's variation.
getAlleles() - Method in interface org.ensembl.variation.datamodel.AlleleGroup
  Retrieves all alleles that are part of this allele group.
getAlleles() - Method in interface org.ensembl.variation.datamodel.Variation
getAlternativeSequence() - Method in interface org.ensembl.datamodel.SequenceEdit
  The replacement sequence used by this edit.
getAminoAcidStart(int) - Method in interface org.ensembl.datamodel.Translation
getAnalysis() - Method in interface org.ensembl.datamodel.Feature
  Get the analysis that created this feature.
getAnalysis() - Method in interface org.ensembl.datamodel.PredictionTranscript
  Analysis which created this prediction.
getAnalysis() - Method in interface org.ensembl.datamodel.ProteinFeature
getAnalysisAdaptor() - Method in interface org.ensembl.driver.CoreDriver
getAnalysisID() - Method in interface org.ensembl.datamodel.Feature
  Get analysisID of the analysis that created this feature.
getArchiveStableID() - Method in interface org.ensembl.datamodel.SnapShot
getArraysContainingThisProbe() - Method in interface org.ensembl.datamodel.OligoProbe
  All microarrays that contain this probe.
getAssembledCoordinateSystem() - Method in class org.ensembl.datamodel.SimpleAssemblyMapper
getAssembly() - Method in interface org.ensembl.compara.datamodel.GenomeDB
getAssemblyExceptionAdaptor() - Method in interface org.ensembl.driver.CoreDriver
getAssemblyMapperAdaptor() - Method in interface org.ensembl.driver.CoreDriver
getAttributeValue(String) - Method in interface org.ensembl.datamodel.SequenceRegion
  Get the value of a particular attribute.
getAttributes() - Method in interface org.ensembl.datamodel.MiscFeature
  Attributes associatted with this feature.
getAttributes(String) - Method in interface org.ensembl.datamodel.MiscFeature
  Get attributes with the specified code
getAttributes() - Method in interface org.ensembl.datamodel.SequenceRegion
getAttributes() - Method in interface org.ensembl.datamodel.Transcript
  Return all attributes associated witht this transcript.
getAttributes(String) - Method in interface org.ensembl.datamodel.Transcript
  Return all Attributes where attribute.code==code.
getAttributes() - Method in interface org.ensembl.datamodel.Translation
  Return all attributes associated witht this translation.
getAttributes(String) - Method in interface org.ensembl.datamodel.Translation
  Return all Attributes where attribute.code==code.
getAutoCommit() - Method in class org.ensembl.util.ConnectionWrapper
getBand() - Method in interface org.ensembl.datamodel.ChromosomeBand
getBand() - Method in interface org.ensembl.datamodel.KaryotypeBand
getBands() - Method in interface org.ensembl.datamodel.Chromosome
getBioType() - Method in interface org.ensembl.datamodel.Gene
  Return the biological type of the gene.
getBioType() - Method in interface org.ensembl.datamodel.Transcript
  Return the biological type of the gene.
getBitFlag() - Method in class org.ensembl.variation.datamodel.ValidationState
  States bit flag.
getCDNALocation() - Method in interface org.ensembl.datamodel.Transcript
  Concatenation of all exon locations.
getCDNAend() - Method in interface org.ensembl.variation.datamodel.TranscriptVariation
  The end position of this variation on the transcript in cdna coordinates.
getCDNAstart() - Method in interface org.ensembl.variation.datamodel.TranscriptVariation
  The start position of this variation on the transcript in CDNA coordinates.
getCatalog() - Method in class org.ensembl.util.ConnectionWrapper
getChildren() - Method in interface org.ensembl.variation.datamodel.Individual
  All children of this individual.
getChrEnd() - Method in interface org.ensembl.compara.datamodel.Member
getChrEnd() - Method in interface org.ensembl.datamodel.ChromosomeBand
getChrName() - Method in interface org.ensembl.compara.datamodel.Member
getChrStart() - Method in interface org.ensembl.compara.datamodel.Member
getChrStart() - Method in interface org.ensembl.datamodel.ChromosomeBand
getChrStrand() - Method in interface org.ensembl.compara.datamodel.Member
getChromosome() - Method in class org.ensembl.datamodel.AssemblyLocation
  Deprecated.
getChromosome() - Method in class org.ensembl.datamodel.CloneFragmentLocation
getChromosomeEnd() - Method in interface org.ensembl.datamodel.AssemblyElement
getChromosomeName() - Method in interface org.ensembl.datamodel.AssemblyElement
getChromosomeStart() - Method in interface org.ensembl.datamodel.AssemblyElement
getCigarString() - Method in interface org.ensembl.compara.datamodel.GenomicAlign
getCigarString() - Method in interface org.ensembl.datamodel.FeaturePair
getClasspath() - Static method in class org.ensembl.util.SystemUtil
getCloneFragmentEnd() - Method in interface org.ensembl.datamodel.AssemblyElement
getCloneFragmentInternalID() - Method in interface org.ensembl.datamodel.AssemblyElement
getCloneFragmentOri() - Method in interface org.ensembl.datamodel.AssemblyElement
getCloneFragmentStart() - Method in interface org.ensembl.datamodel.AssemblyElement
getCode() - Method in interface org.ensembl.datamodel.Attribute
  Code for this attribute
getCode() - Method in interface org.ensembl.datamodel.MiscSet
  Code for this MiscSet.
getCode() - Method in interface org.ensembl.datamodel.SequenceEdit
  Code for this sequence edit.
getCode() - Method in class org.ensembl.variation.datamodel.ValidationState
  States code.
getCodingLocation() - Method in interface org.ensembl.datamodel.Translation
  Concation of the coding part of the coding exons.
getCodingLocations() - Method in interface org.ensembl.datamodel.Translation
  Returns a list of coding locations where each corresponds to the coding part of a coding exon.
getComparaConfig() - Method in class org.ensembl.registry.DriverGroup
  Configuration for the compara driver.
getComparaDriver() - Method in class org.ensembl.registry.DriverGroup
  Returns the compara driver if a compara configuration is set.
getComponentCoordinateSystem() - Method in class org.ensembl.datamodel.SimpleAssemblyMapper
getConfidence() - Method in interface org.ensembl.datamodel.Exon
getConfidence() - Method in interface org.ensembl.datamodel.Gene
  Deprecated. since version 34.1. Use getStatus() instead.
getConfidence() - Method in interface org.ensembl.datamodel.Transcript
  Deprecated. since version 34.1. Use getStatus() instead.
getConfiguration() - Method in interface org.ensembl.driver.EnsemblDriver
getConnection() - Method in interface org.ensembl.driver.EnsemblDriver
getConnection() - Method in class org.ensembl.driver.ServerDriver
getConnection(String) - Method in class org.ensembl.driver.ServerDriver
getConnection() - Method in class org.ensembl.util.ConnectionPoolDataSource
  Gets a connection, either from the pool or a new one is created.
getConnection(String) - Method in class org.ensembl.util.ConnectionPoolDataSource
  Returns a connection to the specified catalog from the pool or by creating a new one.
getConnection(String, String) - Method in class org.ensembl.util.ConnectionPoolDataSource
getConnection(String) - Static method in class org.ensembl.util.SimpleDBAccess
getConnection(int) - Static method in class org.ensembl.util.SimpleDBAccess
getConnection(int, String) - Static method in class org.ensembl.util.SimpleDBAccess
getConsequenceType() - Method in interface org.ensembl.variation.datamodel.TranscriptVariation
  Consequence type of this transcript variation.
getContent() - Method in class org.ensembl.util.ListElement
getCoordSystemName() - Method in interface org.ensembl.compara.datamodel.DnaFragment
getCoordinateSystem() - Method in class org.ensembl.datamodel.Location
getCoordinateSystem() - Method in interface org.ensembl.datamodel.SequenceRegion
getCoordinateSystemAdaptor() - Method in interface org.ensembl.driver.CoreDriver
getCoreConfig() - Method in class org.ensembl.registry.DriverGroup
  Configuration for the core driver.
getCoreDriver() - Method in class org.ensembl.registry.DriverGroup
  Returns the core driver if a core configuration is set.
getCoreDriver() - Method in interface org.ensembl.variation.driver.VariationDriver
  Core driver associated with this variation driver.
getCount(Object) - Method in class org.ensembl.util.FrequencyCounter
  Number of times _o_ has been added to this frequency counter.
getCreated() - Method in interface org.ensembl.datamodel.Analysis
getCreatedDate() - Method in interface org.ensembl.datamodel.Accessioned
  Return the date this object was created.
getCsFirst() - Method in class org.ensembl.datamodel.ChainedAssemblyMapper
getCsLast() - Method in class org.ensembl.datamodel.ChainedAssemblyMapper
getCsMiddle() - Method in class org.ensembl.datamodel.ChainedAssemblyMapper
getCurrent() - Method in class org.ensembl.util.ProgressPrinter
getDPrime() - Method in interface org.ensembl.variation.datamodel.LDFeature
  The D Prime value.
getDataSource() - Method in class org.ensembl.driver.ServerDriver
getDataSource(String) - Method in class org.ensembl.driver.ServerDriver
getDatabase() - Method in interface org.ensembl.datamodel.ArchiveStableID
getDatabase() - Method in interface org.ensembl.datamodel.SubmittedVariation
getDatasource() - Method in interface org.ensembl.driver.EnsemblDriver
  Datasource this driver gets connections from.
getDefaultPopulation() - Method in class org.ensembl.variation.datamodel.LDFeatureContainer
  The default population is the population with the maximum number of LDFeatures.
getDefaultRegistryURLs() - Static method in class org.ensembl.registry.Registry
  Returns the URLs of the configuration files used to initialise the default registry.
getDefaultUserRegistryURL() - Static method in class org.ensembl.registry.Registry
  Returns the URL of the default user registry file.
getDescription() - Method in interface org.ensembl.compara.datamodel.Domain
getDescription() - Method in interface org.ensembl.compara.datamodel.Family
getDescription() - Method in interface org.ensembl.compara.datamodel.Homology
getDescription() - Method in interface org.ensembl.compara.datamodel.Member
getDescription() - Method in interface org.ensembl.datamodel.Attribute
  Description for this attribute.
getDescription() - Method in interface org.ensembl.datamodel.ExternalRef
getDescription() - Method in interface org.ensembl.datamodel.Feature
getDescription() - Method in interface org.ensembl.datamodel.MiscSet
  Description of this MiscSet.
getDescription() - Method in interface org.ensembl.datamodel.OligoProbe
  Probe description.
getDescription() - Method in interface org.ensembl.datamodel.Population
getDescription() - Method in interface org.ensembl.datamodel.SequenceEdit
  Description for this sequence edit.
getDescription() - Method in interface org.ensembl.variation.datamodel.Individual
  Description of the individual.
getDescription() - Method in interface org.ensembl.variation.datamodel.Population
  Population description.
getDescriptionScore() - Method in interface org.ensembl.compara.datamodel.Domain
getDescriptionScore() - Method in interface org.ensembl.compara.datamodel.Family
getDisplayID() - Method in interface org.ensembl.compara.datamodel.GenomicAlign
getDisplayID() - Method in interface org.ensembl.datamodel.ExternalRef
getDisplayName() - Method in interface org.ensembl.datamodel.Feature
getDisplayName() - Method in interface org.ensembl.datamodel.Marker
getDisplayName() - Method in interface org.ensembl.datamodel.MarkerFeature
  This method returns a string that is considered to be the 'display' identifier.
getDisplayName() - Method in interface org.ensembl.datamodel.ProteinFeature
getDisplayName() - Method in interface org.ensembl.datamodel.Transcript
getDn() - Method in interface org.ensembl.compara.datamodel.Homology
getDnaDnaAlignFeatureAdaptor() - Method in interface org.ensembl.compara.driver.ComparaDriver
getDnaDnaAlignmentAdaptor() - Method in interface org.ensembl.driver.CoreDriver
getDnaFragment() - Method in interface org.ensembl.compara.datamodel.GenomicAlign
getDnaFragmentAdaptor() - Method in interface org.ensembl.compara.driver.ComparaDriver
getDnaFragmentId() - Method in interface org.ensembl.compara.datamodel.GenomicAlign
getDnaProteinAlignmentAdaptor() - Method in interface org.ensembl.driver.CoreDriver
getDriver() - Method in class org.ensembl.datamodel.ChainedAssemblyMapper
getDriver() - Method in interface org.ensembl.datamodel.Persistent
  The driver might or might have been set depending on the object's history .
getDrivers() - Method in class org.ensembl.registry.DriverGroup
  Convenience method returning all drivers in the group.
getDs() - Method in interface org.ensembl.compara.datamodel.Homology
getDuration(String) - Method in class org.ensembl.util.NamedTimer
  Retrieve the duration of a previously-stopped timer.
getDuration() - Method in class org.ensembl.util.Timer
getDurationInSecs() - Method in class org.ensembl.util.Timer
getEnd() - Method in interface org.ensembl.compara.datamodel.GenomicAlign
getEnd() - Method in class org.ensembl.datamodel.Location
  End of this location node on the region.
getEnd() - Method in interface org.ensembl.datamodel.SequenceEdit
  The end position of the region replaced by the alternative sequence.
getEndAsFormattedString() - Method in class org.ensembl.datamodel.Location
  Formats end by inserting commas every 3 decimal places.
getEndExon() - Method in interface org.ensembl.datamodel.Translation
getEndExonInternalID() - Method in interface org.ensembl.datamodel.Translation
  Returns endExon internal id.
getEndPhase() - Method in interface org.ensembl.datamodel.Exon
getEnsemblDriver() - Method in class org.ensembl.driver.ServerDriver
getEnsemblDrivers() - Method in interface org.ensembl.driver.CoordinateSystemAdaptor
  All drivers that coordinate systems will be loaded from.
getEvalue() - Method in interface org.ensembl.datamodel.FeaturePair
getEvalue() - Method in interface org.ensembl.datamodel.ProteinFeature
getExonAdaptor() - Method in interface org.ensembl.driver.CoreDriver
getExonCount() - Method in interface org.ensembl.datamodel.PredictionTranscript
  Analysis which created this prediction.
getExons() - Method in interface org.ensembl.datamodel.Gene
getExons() - Method in interface org.ensembl.datamodel.PredictionTranscript
  List of PredictionExons.
getExons() - Method in interface org.ensembl.datamodel.Transcript
getExternalDatabase() - Method in interface org.ensembl.datamodel.ExternalRef
getExternalDatabase() - Method in interface org.ensembl.datamodel.OligoArray
  External database corresponding to this microarray.
getExternalDatabaseAdaptor() - Method in interface org.ensembl.driver.CoreDriver
getExternalDbId() - Method in interface org.ensembl.datamodel.ExternalRef
getExternalEnd() - Method in interface org.ensembl.datamodel.UngappedAlignment
  End position in externalReference dna.
getExternalRef() - Method in interface org.ensembl.datamodel.UngappedAlignment
getExternalRefAdaptor() - Method in interface org.ensembl.driver.CoreDriver
getExternalRefs() - Method in interface org.ensembl.datamodel.Gene
  External refs for this gene, it's transcripts and translations.
getExternalRefs(boolean) - Method in interface org.ensembl.datamodel.Gene
  External refs for this gene and optionally those of it's transcripts and translations.
getExternalRefs() - Method in interface org.ensembl.datamodel.Transcript
  External refs for this transcript and it's translation if is has one.
getExternalRefs(boolean) - Method in interface org.ensembl.datamodel.Transcript
  External refs for this transcript and optionally those of it's translation (if the transcript has one.)
getExternalRefs() - Method in interface org.ensembl.datamodel.Translation
  References to external databases
getExternalStart() - Method in interface org.ensembl.datamodel.UngappedAlignment
  Start in externalReference dna.
getExternalStrand() - Method in interface org.ensembl.datamodel.UngappedAlignment
  Strand in externalReference dna.
getFather() - Method in interface org.ensembl.variation.datamodel.Individual
  Father of this individual.
getFirst() - Method in class org.ensembl.datamodel.CoordinateSystemMapping
getFirstLastMapper() - Method in class org.ensembl.datamodel.ChainedAssemblyMapper
getFirstMiddleMapper() - Method in class org.ensembl.datamodel.ChainedAssemblyMapper
getFirstReg() - Method in class org.ensembl.datamodel.ChainedAssemblyMapper
getFivePrimeFlankingSeq() - Method in interface org.ensembl.variation.datamodel.Variation
getFivePrimeUTR() - Method in interface org.ensembl.datamodel.Transcript
getFivePrimeUTR() - Method in interface org.ensembl.datamodel.Translation
getFlankMarker1() - Method in interface org.ensembl.datamodel.Qtl
  One flanking marker of the interest region, the two flanking markers define the region.
getFlankMarker2() - Method in interface org.ensembl.datamodel.Qtl
  One flanking marker of the interest region, the two flanking markers define the region.
getFrequencies() - Method in interface org.ensembl.datamodel.SubmittedVariation
getFrequency() - Method in interface org.ensembl.variation.datamodel.Allele
  The frequency of the occurance of the allele.
getFrequency() - Method in interface org.ensembl.variation.datamodel.AlleleGroup
  Frequency of the allele group.
getFrequency() - Method in interface org.ensembl.variation.datamodel.PopulationGenotype
  The frequency of occurance of this genotype within its associated population.
getGFFFeature() - Method in interface org.ensembl.datamodel.Analysis
getGFFSource() - Method in interface org.ensembl.datamodel.Analysis
getGap() - Method in class org.ensembl.datamodel.Location
  Deprecated. Since ensj28.3. Use getLength() instead.
getGender() - Method in interface org.ensembl.variation.datamodel.Individual
  Gender.
getGene() - Method in interface org.ensembl.datamodel.Exon
getGene() - Method in interface org.ensembl.datamodel.Transcript
getGeneAdaptor() - Method in interface org.ensembl.driver.CoreDriver
getGeneBuild() - Method in interface org.ensembl.compara.datamodel.GenomeDB
getGeneInternalID() - Method in interface org.ensembl.datamodel.Exon
  Returns gene internal id.
getGeneInternalID() - Method in interface org.ensembl.datamodel.Transcript
  Returns gene internal id.
getGeneMemberId() - Method in interface org.ensembl.compara.datamodel.Member
getGenomeDB() - Method in interface org.ensembl.compara.datamodel.DnaFragment
getGenomeDBAdaptor() - Method in interface org.ensembl.compara.driver.ComparaDriver
getGenomeDbId() - Method in interface org.ensembl.compara.datamodel.Member
getGenomeDbInternalId() - Method in interface org.ensembl.compara.datamodel.DnaFragment
getGenomicAlignAdaptor() - Method in interface org.ensembl.compara.driver.ComparaDriver
getGenomicAlignBlock() - Method in interface org.ensembl.compara.datamodel.GenomicAlign
getGenomicAlignBlockAdaptor() - Method in interface org.ensembl.compara.driver.ComparaDriver
getGenomicAlignBlockInternalID() - Method in interface org.ensembl.compara.datamodel.GenomicAlign
getGoLinkageType() - Method in interface org.ensembl.datamodel.ExternalRef
  Get the linkage_type column on the go_xref table if this is a GO xref.
getGroup(String) - Method in class org.ensembl.registry.Registry
  Returns the specified DriverGroup.
getGroupNames() - Method in class org.ensembl.registry.Registry
  Returns the names for all MetaDrivers.
getGroups() - Method in class org.ensembl.registry.Registry
  Returns all GroupDrivers.
getHitAccession() - Method in interface org.ensembl.datamodel.FeaturePair
getHitDescription() - Method in interface org.ensembl.datamodel.FeaturePair
getHitDisplayName() - Method in interface org.ensembl.datamodel.FeaturePair
getHitLocation() - Method in interface org.ensembl.datamodel.FeaturePair
getHitSequence() - Method in interface org.ensembl.datamodel.FeaturePair
getHitSpecies() - Method in interface org.ensembl.datamodel.DnaDnaAlignFeature
getHoldability() - Method in class org.ensembl.util.ConnectionWrapper
getHomologyAdaptor() - Method in interface org.ensembl.compara.driver.ComparaDriver
getIncludeChildren() - Method in class org.ensembl.datamodel.Query
  Deprecated.
getIncludeSequence() - Method in class org.ensembl.datamodel.Query
  Deprecated.
getIndividual() - Method in interface org.ensembl.variation.datamodel.IndividualGenotype
  Individual associated with this genotype.
getIndividualAdaptor() - Method in interface org.ensembl.variation.driver.VariationDriver
  The individual adaptor.
getIndividualGenotypeAdaptor() - Method in interface org.ensembl.variation.driver.VariationDriver
  The individual genotype adaptor.
getInfoText() - Method in interface org.ensembl.datamodel.ExternalRef
  Info text for the xref.
getInfoType() - Method in interface org.ensembl.datamodel.ExternalRef
  Info type for the xref.
getInternalID() - Method in interface org.ensembl.datamodel.Persistent
getInternalID() - Method in class org.ensembl.datamodel.Query
  Deprecated.
getInternalIDs() - Method in class org.ensembl.datamodel.Query
  Deprecated.
getInterproAccession() - Method in interface org.ensembl.datamodel.ProteinFeature
  Return interpro accession for this protein, can be null.
getInterproDescription() - Method in interface org.ensembl.datamodel.ProteinFeature
  Return interpro description for this protein.
getInterproDisplayName() - Method in interface org.ensembl.datamodel.ProteinFeature
  Get the interpro display name.
getInterproIDs() - Method in interface org.ensembl.datamodel.Gene
  Interpro IDs associated with this gene.
getInterproIDs() - Method in interface org.ensembl.datamodel.Transcript
  Interpro IDs associated with this transcript.
getInterproIDs() - Method in interface org.ensembl.datamodel.Translation
  Interpro IDs associated with this translation.
getKaryotypeBandAdaptor() - Method in interface org.ensembl.driver.CoreDriver
getLDFeatureAdaptor() - Method in interface org.ensembl.variation.driver.VariationDriver
  The LDFeature adaptor.
getLDFeatures() - Method in class org.ensembl.variation.datamodel.LDFeatureContainer
  All LDFeatures held in this container.
getLDFeatures(Population) - Method in class org.ensembl.variation.datamodel.LDFeatureContainer
  Subset of contained LDFeatures that come from the specified population.
getLDFeaturesFromDefaultPopulation() - Method in class org.ensembl.variation.datamodel.LDFeatureContainer
  Subset of contained LDFeatures that come from the default population.
getLast() - Method in class org.ensembl.datamodel.CoordinateSystemMapping
getLastMiddleMapper() - Method in class org.ensembl.datamodel.ChainedAssemblyMapper
getLastReg() - Method in class org.ensembl.datamodel.ChainedAssemblyMapper
getLength() - Method in interface org.ensembl.compara.datamodel.DnaFragment
getLength() - Method in interface org.ensembl.compara.datamodel.GenomicAlignBlock
getLength() - Method in interface org.ensembl.datamodel.Chromosome
getLength() - Method in class org.ensembl.datamodel.Location
  Sum of this nodeLength and any other ones after it in location list.
getLength() - Method in interface org.ensembl.datamodel.OligoProbe
  Length of probe in bases.
getLength() - Method in interface org.ensembl.datamodel.SequenceRegion
getLength() - Method in interface org.ensembl.datamodel.Transcript
  Returns combined length of all exons.
getLengthAsFormattedString() - Method in class org.ensembl.datamodel.Location
  Formats length by inserting commas every 3 decimal places.
getLengthByLocation(Location) - Method in interface org.ensembl.driver.LocationConverter
  Return the length of the used sequence region.
getLnl() - Method in interface org.ensembl.compara.datamodel.Homology
getLocation() - Method in interface org.ensembl.compara.datamodel.DnaFragment
getLocation() - Method in interface org.ensembl.datamodel.KaryotypeBand
getLocation() - Method in interface org.ensembl.datamodel.Locatable
getLocation() - Method in class org.ensembl.datamodel.Query
  Deprecated.
getLocation() - Method in interface org.ensembl.datamodel.UngappedAlignment
  Location in ensembl database.
getLocationConverter() - Method in interface org.ensembl.driver.CoreDriver
getLocator() - Method in interface org.ensembl.compara.datamodel.GenomeDB
getLodScore() - Method in interface org.ensembl.datamodel.Qtl
  A score for the Qtl.
getLogWriter() - Method in class org.ensembl.util.ConnectionPoolDataSource
getLogicalName() - Method in interface org.ensembl.datamodel.Analysis
  Logical name of the analysis.
getLoginTimeout() - Method in class org.ensembl.util.ConnectionPoolDataSource
getLongDescription() - Method in interface org.ensembl.datamodel.Population
getMapWeight() - Method in interface org.ensembl.datamodel.MarkerFeature
  The number of times that this marker has been mapped to the genome.
getMapWeight() - Method in interface org.ensembl.variation.datamodel.VariationFeature
  The map_weight is the number of times this features variation was mapped to the genome.
getMappingPath(CoordinateSystem, CoordinateSystem) - Method in interface org.ensembl.driver.CoordinateSystemAdaptor
  Get the mapping path between two co-ordinate systems, as defined in the meta table.
getMarker() - Method in interface org.ensembl.datamodel.MarkerFeature
getMarkerAdaptor() - Method in interface org.ensembl.driver.CoreDriver
getMarkerFeatureAdaptor() - Method in interface org.ensembl.driver.CoreDriver
getMarkerFeatures() - Method in interface org.ensembl.datamodel.Marker
  MarkerFeatures representing where this marker appears on the genome.
getMax() - Method in class org.ensembl.util.ProgressPrinter
getMaxFeatureLength() - Method in interface org.ensembl.datamodel.MiscSet
  Maximum length of features in this set
getMaxPoolSize() - Method in class org.ensembl.util.ConnectionPoolDataSource
getMaxPrimerDistance() - Method in interface org.ensembl.datamodel.Marker
getMemberAdaptor() - Method in interface org.ensembl.compara.driver.ComparaDriver
getMetaData() - Method in class org.ensembl.util.ConnectionWrapper
getMethodLink() - Method in interface org.ensembl.compara.datamodel.MethodLinkSpeciesSet
getMethodLinkAdaptor() - Method in interface org.ensembl.compara.driver.ComparaDriver
getMethodLinkSpeciesSet() - Method in interface org.ensembl.compara.datamodel.GenomicAlign
getMethodLinkSpeciesSet() - Method in interface org.ensembl.compara.datamodel.GenomicAlignBlock
getMethodLinkSpeciesSetAdaptor() - Method in interface org.ensembl.compara.driver.ComparaDriver
getMethodLinkSpeciesSetId() - Method in interface org.ensembl.compara.datamodel.Domain
getMethodLinkSpeciesSetId() - Method in interface org.ensembl.compara.datamodel.Family
getMethodLinkSpeciesSetId() - Method in interface org.ensembl.compara.datamodel.Homology
getMethodLinkSpeciesSetInternalId() - Method in interface org.ensembl.compara.datamodel.GenomicAlign
getMethodLinkSpeciesSetInternalId() - Method in interface org.ensembl.compara.datamodel.GenomicAlignBlock
getMethodLinkType() - Method in interface org.ensembl.datamodel.DnaDnaAlignFeature
getMin() - Method in class org.ensembl.util.ProgressPrinter
getMinPrimerDistance() - Method in interface org.ensembl.datamodel.Marker
getMisMatchSize() - Method in interface org.ensembl.datamodel.OligoFeature
  The number of bases by which the probe differs from the genomic sequence.
getMiscFeatureAdaptor() - Method in interface org.ensembl.driver.CoreDriver
getMiscSetAdaptor() - Method in interface org.ensembl.driver.CoreDriver
getMiscSets() - Method in interface org.ensembl.datamodel.MiscFeature
  MiscSets associated with this feature.
getModifiedDate() - Method in interface org.ensembl.datamodel.Accessioned
  Return the date the object was last modified.
getMostFrequent() - Method in class org.ensembl.util.FrequencyCounter
  Returns the most frequently added key.
getMother() - Method in interface org.ensembl.variation.datamodel.Individual
  Mother of this individual.
getN() - Method in interface org.ensembl.compara.datamodel.Homology
getName() - Method in interface org.ensembl.compara.datamodel.DnaFragment
getName() - Method in interface org.ensembl.compara.datamodel.GenomeDB
getName() - Method in interface org.ensembl.datamodel.Attribute
  Human readable name for this attribute.
getName() - Method in interface org.ensembl.datamodel.Chromosome
getName() - Method in class org.ensembl.datamodel.CoordinateSystem
  Get the name of this co-ordinate system.
getName() - Method in interface org.ensembl.datamodel.ExternalDatabase
getName() - Method in interface org.ensembl.datamodel.MiscSet
  Name of this MiscSet
getName() - Method in interface org.ensembl.datamodel.OligoArray
  Name of this micro array.
getName() - Method in interface org.ensembl.datamodel.Population
getName() - Method in interface org.ensembl.datamodel.RepeatConsensus
getName() - Method in interface org.ensembl.datamodel.SequenceEdit
  Name of this sequence edit.
getName() - Method in interface org.ensembl.datamodel.SequenceRegion
getName() - Method in interface org.ensembl.variation.datamodel.AlleleGroup
  Name of the allele group.
getName() - Method in interface org.ensembl.variation.datamodel.Individual
getName() - Method in interface org.ensembl.variation.datamodel.Population
  Population name.
getName() - Method in interface org.ensembl.variation.datamodel.Variation
getName() - Method in interface org.ensembl.variation.datamodel.VariationGroup
  name of this variation group
getNameInArray(OligoArray) - Method in interface org.ensembl.datamodel.OligoProbe
  Name of this probe in specified microarray.
getNewDatabase() - Method in interface org.ensembl.datamodel.MappingSession
getNodeCount() - Method in class org.ensembl.datamodel.Location
  Number of nodes in list.
getNodeLength() - Method in class org.ensembl.datamodel.Location
  Length is calculated by end - start + 1.
getNodeLengthAsFormattedString() - Method in class org.ensembl.datamodel.Location
  Formats nodeLength by inserting commas every 3 decimal places.
getObjectXrefID() - Method in interface org.ensembl.datamodel.ExternalRef
getOldDatabase() - Method in interface org.ensembl.datamodel.MappingSession
getOligoArrayAdaptor() - Method in interface org.ensembl.driver.CoreDriver
getOligoFeatureAdaptor() - Method in interface org.ensembl.driver.CoreDriver
getOligoFeatures() - Method in interface org.ensembl.datamodel.OligoProbe
  The places where this probe appears on the genome.
getOligoProbeAdaptor() - Method in interface org.ensembl.driver.CoreDriver
getOligoProbes() - Method in interface org.ensembl.datamodel.OligoArray
  All probes in the array.
getOriginalSequence() - Method in interface org.ensembl.compara.datamodel.GenomicAlign
getParameters() - Method in interface org.ensembl.datamodel.Analysis
  Source database used for analysis.
getPath() - Method in class org.ensembl.datamodel.CoordinateSystemMapping
getPeakMarker() - Method in interface org.ensembl.datamodel.Qtl
  An optional Marker which has the peak probabitity for this traits occurence.
getPeptide() - Method in interface org.ensembl.datamodel.Translation
  Peptide sequence corresponding to the dna sequence returned by getSequence() with or without sequence edits applied.
getPeptide() - Method in interface org.ensembl.datamodel.TranslationSnapShot
getPeptideAlleleString() - Method in interface org.ensembl.variation.datamodel.TranscriptVariation
  The pep allele string is a '/' delimited string of amino acid codes representing the change to the peptide made by this variation.
getPeptideEnd() - Method in interface org.ensembl.datamodel.ProteinFeature
getPeptideStart() - Method in interface org.ensembl.datamodel.ProteinFeature
getPercentageID() - Method in interface org.ensembl.compara.datamodel.GenomicAlignBlock
getPercentageIdentity() - Method in interface org.ensembl.datamodel.FeaturePair
getPercentageIdentity() - Method in interface org.ensembl.datamodel.ProteinFeature
getPhase() - Method in interface org.ensembl.datamodel.Exon
getPopulation() - Method in interface org.ensembl.variation.datamodel.Allele
  The population where this allele appears.
getPopulation() - Method in interface org.ensembl.variation.datamodel.AlleleGroup
  Population associated with this allele group.
getPopulation() - Method in interface org.ensembl.variation.datamodel.LDFeature
  Get Population this linkage disequilibrium appears in.
getPopulation() - Method in interface org.ensembl.variation.datamodel.PopulationGenotype
  Population this genotype appears in.
getPopulationAdaptor() - Method in interface org.ensembl.variation.driver.VariationDriver
  The population adaptor.
getPopulationGenotypeAdaptor() - Method in interface org.ensembl.variation.driver.VariationDriver
  The population genotype adaptor.
getPopulationID() - Method in interface org.ensembl.variation.datamodel.Allele
  Get the internalID of the population this allele belongs to.
getPopulations() - Method in interface org.ensembl.variation.datamodel.Individual
  Populations this individual belongs to.
getPopulations() - Method in class org.ensembl.variation.datamodel.LDFeatureContainer
  Get all the populations present in this instance.
getPopulations(VariationFeature, VariationFeature) - Method in class org.ensembl.variation.datamodel.LDFeatureContainer
  All the populations referenced by LDFeatures in this instance.
getPositionInEndExon() - Method in interface org.ensembl.datamodel.Translation
getPositionInStartExon() - Method in interface org.ensembl.datamodel.Translation
getPostfix() - Method in class org.ensembl.util.ProgressPrinter
  Get the postfix to be printed.
getPredictionExonAdaptor() - Method in interface org.ensembl.driver.CoreDriver
getPredictionTranscriptAdaptor() - Method in interface org.ensembl.driver.CoreDriver
getPrimaryID() - Method in interface org.ensembl.datamodel.ExternalRef
getPriority() - Method in interface org.ensembl.datamodel.ExternalDatabase
getPriority() - Method in interface org.ensembl.datamodel.Marker
getProbe() - Method in interface org.ensembl.datamodel.OligoFeature
  The probe that hits the genome.
getProbeInternalID() - Method in interface org.ensembl.datamodel.OligoFeature
  Database internal ID for the the probe.
getProbeSetName() - Method in interface org.ensembl.datamodel.OligoFeature
  The name of the probe's probeset.
getProbeSetName() - Method in interface org.ensembl.datamodel.OligoProbe
  Name of the probeset this probe belongs to.
getProbeSetSize() - Method in interface org.ensembl.datamodel.OligoArray
  Standard number of probes in a probeset on this array.
getProgram() - Method in interface org.ensembl.datamodel.Analysis
  External program used for analysis.
getProgramFile() - Method in interface org.ensembl.datamodel.Analysis
  External program used for analysis.
getProgramVersion() - Method in interface org.ensembl.datamodel.Analysis
  External program used for analysis.
getProperty(String, String) - Static method in class org.ensembl.util.PropertiesUtil
getProperty(URL, String) - Static method in class org.ensembl.util.PropertiesUtil
getProteinFeatureAdaptor() - Method in interface org.ensembl.driver.CoreDriver
getProteinFeatures() - Method in interface org.ensembl.datamodel.Translation
  Get ProteinFeatures associated with this translation.
getPvalue() - Method in interface org.ensembl.datamodel.PredictionExon
getQtl() - Method in interface org.ensembl.datamodel.QtlFeature
  Qtl this feature is associated with.
getQtlAdaptor() - Method in interface org.ensembl.driver.CoreDriver
getQtlFeatureAdaptor() - Method in interface org.ensembl.driver.CoreDriver
getQtlFeatures() - Method in interface org.ensembl.datamodel.Qtl
  The qtl features associated with this Qtl.
getQtlID() - Method in interface org.ensembl.datamodel.QtlFeature
  Get the internal ID of the QTL this feature represents.
getQualifiedName(OligoArray) - Method in interface org.ensembl.datamodel.OligoProbe
  Return the name of this probe when it's parent is _array_.
getQualifiedNames() - Method in interface org.ensembl.datamodel.OligoProbe
  All the possible names of this probe based on it's parent arrays.
getQueryIdentity() - Method in interface org.ensembl.datamodel.ExternalRef
  Percentage of the ensembl object included in an overlapping region with the external object.
getQueryInternalID() - Method in interface org.ensembl.datamodel.ExternalRef
  Internal ID of the thing this is an external reference for.
getRSquare() - Method in interface org.ensembl.variation.datamodel.LDFeature
  The R Square value.
getRank() - Method in class org.ensembl.datamodel.CoordinateSystem
  Return this coordinate system's rank.
getRank() - Method in interface org.ensembl.datamodel.PredictionExon
getReferenceGenomicAlign() - Method in interface org.ensembl.compara.datamodel.GenomicAlignBlock
getReferenceGenomicAlignInternalID() - Method in interface org.ensembl.compara.datamodel.GenomicAlignBlock
getReferenceSlice() - Method in interface org.ensembl.compara.datamodel.GenomicAlignBlock
getReferenceSliceEnd() - Method in interface org.ensembl.compara.datamodel.GenomicAlignBlock
getReferenceSliceStart() - Method in interface org.ensembl.compara.datamodel.GenomicAlignBlock
getRelatedStableIDs() - Method in interface org.ensembl.datamodel.StableIDEvent
getRelatedVersions(String) - Method in interface org.ensembl.datamodel.StableIDEvent
  Items can relate to not just several other items but also to several versions of those items.
getRepeatConsensus() - Method in interface org.ensembl.datamodel.RepeatFeature
getRepeatConsensusAdaptor() - Method in interface org.ensembl.driver.CoreDriver
getRepeatConsensusInternalID() - Method in interface org.ensembl.datamodel.RepeatFeature
  Returns repeat consensus internal id, this is the same as repeatConsensus.internalID if repeatConsensus is available.
getRepeatFeatureAdaptor() - Method in interface org.ensembl.driver.CoreDriver
getRunnable() - Method in interface org.ensembl.datamodel.Analysis
  Runnable used for analysis.
getRunnableVersion() - Method in interface org.ensembl.datamodel.Analysis
getS() - Method in interface org.ensembl.compara.datamodel.Homology
getSampleCount() - Method in interface org.ensembl.variation.datamodel.LDFeature
  The sample count.
getScore() - Method in interface org.ensembl.compara.datamodel.GenomicAlignBlock
getScore() - Method in interface org.ensembl.datamodel.FeaturePair
getScore() - Method in interface org.ensembl.datamodel.PredictionExon
getScore() - Method in interface org.ensembl.datamodel.ProteinFeature
getScore() - Method in interface org.ensembl.datamodel.SimpleFeature
getSegRegionID() - Method in class org.ensembl.datamodel.Location
  Return the sequence region internal ID this location node is on.
getSeqLeft() - Method in interface org.ensembl.datamodel.Marker
getSeqRegionName() - Method in class org.ensembl.datamodel.Location
getSeqRight() - Method in interface org.ensembl.datamodel.Marker
getSequence() - Method in interface org.ensembl.datamodel.Locatable
  Sequence at this genomic location.
getSequence() - Method in interface org.ensembl.datamodel.RepeatConsensus
  This is not available in old databases, null is returned in such a case.
getSequence() - Method in interface org.ensembl.datamodel.Transcript
getSequence() - Method in interface org.ensembl.datamodel.Translation
  Concatenatation of all exon sequences excluding the UTRs.
getSequenceAdaptor() - Method in interface org.ensembl.driver.CoreDriver
getSequenceEdits() - Method in interface org.ensembl.datamodel.Transcript
  Sequence edits for this transcript.
getSequenceEdits() - Method in interface org.ensembl.datamodel.Translation
  Sequence edits for this translation.
getSequenceId() - Method in interface org.ensembl.compara.datamodel.Member
getSequenceRegion() - Method in class org.ensembl.datamodel.Location
getSequenceRegionAdaptor() - Method in interface org.ensembl.driver.CoreDriver
getServerFactory() - Method in interface org.ensembl.driver.EnsemblDriver
  If two EnsemblDrivers wrap databases on the same database server then setting the same ServerDriverFactory on both will enable them to share connections.
getSession() - Method in interface org.ensembl.datamodel.StableIDEvent
getSimilarityFeatures() - Method in interface org.ensembl.datamodel.Translation
getSimpleFeatureAdaptor() - Method in interface org.ensembl.driver.CoreDriver
getSize() - Method in interface org.ensembl.datamodel.AssemblyMapper
getSize() - Method in class org.ensembl.datamodel.ChainedAssemblyMapper
getSize() - Method in interface org.ensembl.datamodel.Population
getSize() - Method in class org.ensembl.datamodel.SimpleAssemblyMapper
getSize() - Method in class org.ensembl.util.LruCache
getSize() - Method in interface org.ensembl.variation.datamodel.Population
  Population size.
getSource() - Method in interface org.ensembl.datamodel.Gene
getSource() - Method in interface org.ensembl.variation.datamodel.AlleleGroup
  Name of the source database this allele group comes from.
getSource() - Method in interface org.ensembl.variation.datamodel.VariationGroup
  The name of the database this variation group is from
getSourceDatabase() - Method in interface org.ensembl.datamodel.Analysis
  Source database used for analysis.
getSourceDatabaseFile() - Method in interface org.ensembl.datamodel.Analysis
  Source database used for analysis.
getSourceDatabaseName() - Method in interface org.ensembl.datamodel.QtlSynonym
  Name of the database the synonym comes from.
getSourceDatabaseVersion() - Method in interface org.ensembl.datamodel.Analysis
  Source database used for analysis.
getSourceID() - Method in interface org.ensembl.datamodel.QtlSynonym
  Identifier in the source database.
getSourceName() - Method in interface org.ensembl.compara.datamodel.Member
getSpecies() - Method in interface org.ensembl.datamodel.DnaDnaAlignFeature
getSpeciesSet() - Method in interface org.ensembl.compara.datamodel.MethodLinkSpeciesSet
getSpeciesSetdbIDs() - Method in interface org.ensembl.compara.datamodel.MethodLinkSpeciesSet
getSpliceSite() - Method in class org.ensembl.variation.datamodel.AlleleConsequence
  Type of effect on splice site, if any.
getStableID() - Method in interface org.ensembl.datamodel.ArchiveStableID
getStableID() - Method in interface org.ensembl.datamodel.StableIDEvent
getStableIDEventAdaptor() - Method in interface org.ensembl.driver.CoreDriver
getStableIDVersion() - Method in interface org.ensembl.datamodel.StableIDEvent
getStableId() - Method in interface org.ensembl.compara.datamodel.Domain
getStableId() - Method in interface org.ensembl.compara.datamodel.Family
getStableId() - Method in interface org.ensembl.compara.datamodel.Homology
getStableId() - Method in interface org.ensembl.compara.datamodel.Member
getStain() - Method in interface org.ensembl.datamodel.ChromosomeBand
getStain() - Method in interface org.ensembl.datamodel.KaryotypeBand
getStart() - Method in interface org.ensembl.compara.datamodel.GenomicAlign
getStart() - Method in class org.ensembl.datamodel.Location
  Start of this location node on the region.
getStart() - Method in interface org.ensembl.datamodel.SequenceEdit
  The start position of the region replaced by the alternative sequence.
getStartAsFormattedString() - Method in class org.ensembl.datamodel.Location
  Formats start by inserting commas every 3 decimal places.
getStartExon() - Method in interface org.ensembl.datamodel.Translation
getStartExonInternalID() - Method in interface org.ensembl.datamodel.Translation
  Returns startExon internal id.
getStartPhase() - Method in interface org.ensembl.datamodel.PredictionExon
getStatus() - Method in interface org.ensembl.datamodel.ExternalDatabase
getStatus() - Method in interface org.ensembl.datamodel.Gene
  The status of the gene.
getStatus() - Method in interface org.ensembl.datamodel.Transcript
  The status of the transcript.
getStrand() - Method in interface org.ensembl.compara.datamodel.GenomicAlign
getStrand() - Method in class org.ensembl.datamodel.Location
getString() - Method in interface org.ensembl.datamodel.Sequence
getSubPopulations() - Method in interface org.ensembl.variation.datamodel.Population
  Retrieves all populations which are conceptually a sub set of this population.
getSubtype() - Method in interface org.ensembl.compara.datamodel.Homology
getSuperPopulations() - Method in interface org.ensembl.variation.datamodel.Population
  Retrieves all populations which this population is a part of.
getSupportingFeatureAdaptor() - Method in interface org.ensembl.driver.CoreDriver
getSupportingFeatures() - Method in interface org.ensembl.datamodel.Exon
  Supporting features used to build this exon.
getSupportingFeatures() - Method in interface org.ensembl.datamodel.Transcript
  Supporting features used to build this transcript.
getSynonym() - Method in interface org.ensembl.datamodel.SubmittedVariation
getSynonymSources() - Method in interface org.ensembl.variation.datamodel.Variation
getSynonyms() - Method in interface org.ensembl.datamodel.ExternalRef
getSynonyms() - Method in interface org.ensembl.datamodel.Marker
getSynonyms() - Method in interface org.ensembl.variation.datamodel.Variation
getSynoyms() - Method in interface org.ensembl.datamodel.Qtl
  Returns QtlSynonyms.
getTarget() - Method in class org.ensembl.datamodel.AssemblyException
getTargetIdentity() - Method in interface org.ensembl.datamodel.ExternalRef
  Percentage of the external object included in an overlapping region with the ensembl object.
getTaxonId() - Method in interface org.ensembl.compara.datamodel.GenomeDB
getTaxonId() - Method in interface org.ensembl.compara.datamodel.Member
getThreePrimeFlankingSeq() - Method in interface org.ensembl.variation.datamodel.Variation
getThreePrimeUTR() - Method in interface org.ensembl.datamodel.Transcript
getThreePrimeUTR() - Method in interface org.ensembl.datamodel.Translation
getThresholdOnDs() - Method in interface org.ensembl.compara.datamodel.Homology
getTimeStamp() - Static method in class org.ensembl.util.Timer
  Returns a time + date fromated as string.
getTimestamp() - Method in interface org.ensembl.datamodel.MappingSession
getTrait() - Method in interface org.ensembl.datamodel.Qtl
  Phenotype of this Qtl.
getTransactionIsolation() - Method in class org.ensembl.util.ConnectionWrapper
getTranscript() - Method in interface org.ensembl.datamodel.PredictionExon
getTranscript() - Method in interface org.ensembl.datamodel.Translation
getTranscript() - Method in interface org.ensembl.variation.datamodel.TranscriptVariation
  Transcript that is affected by this TranscriptVariation.
getTranscriptAdaptor() - Method in interface org.ensembl.driver.CoreDriver
getTranscriptInternalID() - Method in interface org.ensembl.datamodel.Translation
  Returns transcript internal id.
getTranscriptInternalIDs() - Method in interface org.ensembl.datamodel.Exon
getTranscriptSnapShots() - Method in interface org.ensembl.datamodel.GeneSnapShot
getTranscriptVariationAdaptor() - Method in interface org.ensembl.variation.driver.VariationDriver
  The transcript variation adaptor.
getTranscripts() - Method in interface org.ensembl.datamodel.Exon
getTranscripts() - Method in interface org.ensembl.datamodel.Gene
getTranslation() - Method in interface org.ensembl.datamodel.ProteinFeature
getTranslation() - Method in interface org.ensembl.datamodel.Transcript
getTranslationAdaptor() - Method in interface org.ensembl.driver.CoreDriver
getTranslationEnd() - Method in interface org.ensembl.datamodel.ProteinFeature
getTranslationEnd() - Method in interface org.ensembl.variation.datamodel.TranscriptVariation
  The end position of this variation on the translation of the associated transcript in peptide coordinates.
getTranslationInternalID() - Method in interface org.ensembl.datamodel.ProteinFeature
  Returns translation internal id, this is the same as translation.internalID if translation is available.
getTranslationInternalID() - Method in interface org.ensembl.datamodel.Transcript
  Returns translation internal id.
getTranslationSnapShot() - Method in interface org.ensembl.datamodel.TranscriptSnapShot
getTranslationStart() - Method in interface org.ensembl.datamodel.ProteinFeature
getTranslationStart() - Method in interface org.ensembl.variation.datamodel.TranscriptVariation
  the start position of this variation on the translation of the associated transcript in peptide coordinates.
getType() - Method in interface org.ensembl.compara.datamodel.MethodLink
getType() - Method in interface org.ensembl.datamodel.AssemblyElement
getType() - Method in class org.ensembl.datamodel.AssemblyException
getType() - Method in interface org.ensembl.datamodel.Gene
  Deprecated. since ensj34.2 use getBioType() instead.
getType() - Method in interface org.ensembl.datamodel.Marker
getType() - Method in interface org.ensembl.datamodel.OligoArray
  Type of array.
getType() - Method in class org.ensembl.datamodel.Query
  Deprecated.
getType() - Method in interface org.ensembl.datamodel.RepeatConsensus
getType() - Method in interface org.ensembl.datamodel.StableIDEvent
  Type of event; gene, transcript or translaton.
getType() - Method in interface org.ensembl.driver.Adaptor
getType() - Method in class org.ensembl.variation.datamodel.AlleleConsequence
  Type of consequence.
getType() - Method in interface org.ensembl.variation.datamodel.VariationGroup
  Type of this group.
getTypeMap() - Method in class org.ensembl.util.ConnectionWrapper
getUngappedAlignments() - Method in interface org.ensembl.datamodel.DnaDnaAlignFeature
getUniqueOligoFeatureLocations() - Method in interface org.ensembl.datamodel.OligoProbe
  Locations where this probe hits the genome.
getValidationStates() - Method in interface org.ensembl.variation.datamodel.Variation
getValue() - Method in interface org.ensembl.datamodel.Attribute
  Value of this attribute
getVariation() - Method in interface org.ensembl.variation.datamodel.AlleleFeature
  Variation this allele belongs to.
getVariation() - Method in interface org.ensembl.variation.datamodel.Genotype
  Variation.
getVariation() - Method in interface org.ensembl.variation.datamodel.VariationFeature
  The variation associated with this feature.
getVariationAdaptor() - Method in interface org.ensembl.variation.driver.VariationDriver
  The variation adaptor.
getVariationConfig() - Method in class org.ensembl.registry.DriverGroup
  Configuration for the variation driver.
getVariationDriver() - Method in interface org.ensembl.driver.CoreDriver
  Get the sister variation driver.
getVariationDriver() - Method in class org.ensembl.registry.DriverGroup
  Returns the variation driver if available.
getVariationFeature() - Method in interface org.ensembl.variation.datamodel.TranscriptVariation
  VariationFeature associated with this transcript variation.
getVariationFeature1() - Method in interface org.ensembl.variation.datamodel.LDFeature
  First VariationFeature.
getVariationFeature2() - Method in interface org.ensembl.variation.datamodel.LDFeature
  Second VariationFeature.
getVariationFeatureAdaptor() - Method in interface org.ensembl.variation.driver.VariationDriver
  The variation feature adaptor.
getVariationGroup() - Method in interface org.ensembl.variation.datamodel.AlleleGroup
  VariationGroup associated with this allele group.
getVariationGroup() - Method in interface org.ensembl.variation.datamodel.VariationGroupFeature
  Get the variation group associated with the feature.
getVariationGroupAdaptor() - Method in interface org.ensembl.variation.driver.VariationDriver
  The variation group adaptor.
getVariationGroupFeatureAdaptor() - Method in interface org.ensembl.variation.driver.VariationDriver
  The variation group feature adaptor.
getVariationGroupID(long) - Method in interface org.ensembl.variation.datamodel.AlleleGroup
  Get the internalID of the VariationGroup associated with this allele group.
getVariationGroupName() - Method in interface org.ensembl.variation.datamodel.VariationGroupFeature
  Get the name of the variation group associated with the feature.
getVariationInternalID() - Method in interface org.ensembl.variation.datamodel.AlleleFeature
  Variation this allele belongs to.
getVariationInternalID() - Method in interface org.ensembl.variation.datamodel.VariationFeature
  The internal id of the variation associated with this feature.
getVariationName() - Method in interface org.ensembl.variation.datamodel.VariationFeature
  Name of the variation associated with the feature.
getVariations() - Method in interface org.ensembl.variation.datamodel.AlleleGroup
  Retrieves all variations that are associated with the alleles that comprise this allele group.
getVariations() - Method in class org.ensembl.variation.datamodel.LDFeatureContainer
  All the variations associated to LDFeatures in this instance.
getVariations(Population) - Method in class org.ensembl.variation.datamodel.LDFeatureContainer
  Variations associated with the population.
getVariations() - Method in interface org.ensembl.variation.datamodel.VariationGroup
  Variations which make up this group.
getVariationsFromDefaultPopulation() - Method in class org.ensembl.variation.datamodel.LDFeatureContainer
  All Variations associated with the default population.
getVersion() - Method in interface org.ensembl.compara.datamodel.Member
getVersion() - Method in interface org.ensembl.datamodel.Accessioned
  Return the version of this object.
getVersion() - Method in interface org.ensembl.datamodel.ArchiveStableID
getVersion() - Method in class org.ensembl.datamodel.CoordinateSystem
  Get the version of this co-ordinate system.
getVersion() - Method in interface org.ensembl.datamodel.ExternalDatabase
getVersion() - Method in interface org.ensembl.datamodel.ExternalRef
getWarnings() - Method in class org.ensembl.util.ConnectionWrapper

## H

HAPMAP - Static variable in class org.ensembl.variation.datamodel.ValidationState
Homology - interface org.ensembl.compara.datamodel.Homology.
  I represent a single species which is part of the compara- analyses.
HomologyAdaptor - interface org.ensembl.compara.driver.HomologyAdaptor.
  I am associated with the compara-analyses
hasAttributes() - Method in interface org.ensembl.datamodel.SequenceRegion
hasConfigs() - Method in class org.ensembl.registry.DriverGroup
  Convenience method that returns whether at least one of the _configs_ is set.
hasNext() - Method in class org.ensembl.datamodel.AssemblyLocation
  Deprecated.
hasNext() - Method in class org.ensembl.datamodel.CloneFragmentLocation
hasNext() - Method in class org.ensembl.datamodel.Location
hasNext() - Method in class org.ensembl.driver.FeatureIterator
  Returns whether there is another item to be returned via next().
hasNext() - Method in class org.ensembl.driver.LocationFeatureIterator
  Returns whether there is another item to be returned via next().
hasNext() - Method in class org.ensembl.util.ArrayIterator
hasReferences(Location) - Method in interface org.ensembl.driver.AssemblyExceptionAdaptor
  Determines whether loc includes references to other locations.
hashCode() - Method in class org.ensembl.datamodel.CoordinateSystem
  Generate a hash code since we're overriding equals().
hashCode() - Method in class org.ensembl.registry.DriverGroup
  Hash code for this instance.
hashCode() - Method in class org.ensembl.util.Pair
haveRegisteredAssembled(String, int) - Method in class org.ensembl.datamodel.SimpleAssemblyMapper
haveRegisteredComponent(String) - Method in class org.ensembl.datamodel.SimpleAssemblyMapper
highestVersionedDatabaseName(String) - Method in class org.ensembl.driver.ServerDriver
  Searches the database names in the cache for the one that begins with _prefix_ and has the highest version.

## I

IDList - class org.ensembl.util.IDList.
  List of persistent internal ids.
IDList(List) - Constructor for class org.ensembl.util.IDList
IDMap - class org.ensembl.util.IDMap.
  A fast hash map providing internalID -> Persistent object mapping.
IDMap(Iterator) - Constructor for class org.ensembl.util.IDMap
  Adds all the persistent objects returned by the iterator using their internalIDs as the keys.
IDMap(List) - Constructor for class org.ensembl.util.IDMap
  Adds all the persistent objects in the list using their internalIDs as the keys.
IDMap(Persistent[]) - Constructor for class org.ensembl.util.IDMap
  Creates a map conainting all the persistent objects keyed on their internalIDs.
IDMap() - Constructor for class org.ensembl.util.IDMap
IDSet - class org.ensembl.util.IDSet.
  Convenience class for managing sets of ids taken from Persistent item's internal ids.
IDSet() - Constructor for class org.ensembl.util.IDSet
IDSet(long[]) - Constructor for class org.ensembl.util.IDSet
IDSet(IDSet) - Constructor for class org.ensembl.util.IDSet
  Create a copy of _s_.
IDSet(Collection) - Constructor for class org.ensembl.util.IDSet
  Creates a set from a collection of Persistent objects.
IDSet(Iterator) - Constructor for class org.ensembl.util.IDSet
  Creates a set from a iterator over Persistent objects.
INTRONIC - Static variable in class org.ensembl.variation.datamodel.AlleleConsequence
  Allele appears within an intron.
Individual - interface org.ensembl.variation.datamodel.Individual.
  This is a class representing a single individual.
IndividualAdaptor - interface org.ensembl.variation.driver.IndividualAdaptor.
  This adaptor provides database connectivity for Individual objects.
IndividualGenotype - interface org.ensembl.variation.datamodel.IndividualGenotype.
  The genotype of a single diploid individual at a specific locus.
IndividualGenotypeAdaptor - interface org.ensembl.variation.driver.IndividualGenotypeAdaptor.
  This adaptor provides database connectivity for IndividualGenotype objects.
InvalidLocationException - exception org.ensembl.datamodel.InvalidLocationException.
  Represents the fact that an attempt was made to create or use an invalid location.
InvalidLocationException(String) - Constructor for class org.ensembl.datamodel.InvalidLocationException
InvalidLocationException() - Constructor for class org.ensembl.datamodel.InvalidLocationException
idToLocation(long, int, int, int) - Method in interface org.ensembl.driver.LocationConverter
  Make a location from the sequence region internal id, start, end strand are passed into its constructor
idToLocation(long) - Method in interface org.ensembl.driver.LocationConverter
  Make a location from the sequence region internal id, with start =1, end = sequence regon length and strand = 0.
increment() - Method in class org.ensembl.util.Counter
  Increments count by 1;
indexOfFirstDigit(String) - Static method in class org.ensembl.util.StringUtil
initialise(Properties) - Method in interface org.ensembl.driver.EnsemblDriver
  Initialises the driver and it's adaptor with the configuration.
isAccessionIDSet() - Method in class org.ensembl.datamodel.Query
  Deprecated.
isChromosomeSet() - Method in class org.ensembl.datamodel.AssemblyLocation
  Deprecated.
isChromosomeSet() - Method in class org.ensembl.datamodel.CloneFragmentLocation
isCloneFragmentInternalIDSet() - Method in class org.ensembl.datamodel.CloneFragmentLocation
isClosed() - Method in class org.ensembl.util.ConnectionWrapper
isComplete() - Method in class org.ensembl.datamodel.CoordinateSystem
  The coordinate system is complete if all attributes are set.
isComplete() - Method in class org.ensembl.datamodel.Location
  The location is complete if it species a region unambiguously.
isCompleted() - Method in interface org.ensembl.datamodel.Gene
isConfigured() - Static method in class org.ensembl.driver.LoggingManager
isConnected() - Method in interface org.ensembl.driver.EnsemblDriver
  Deprecated. Since ensj 30.3. Use testConnection() instead.
isCoordinateSystemSet() - Method in class org.ensembl.datamodel.Location
isCreated() - Method in interface org.ensembl.datamodel.StableIDEvent
isDefault() - Method in class org.ensembl.datamodel.CoordinateSystem
  Whether this is the default co-ordinate system for the species.
isDefaultAssembly() - Method in interface org.ensembl.compara.datamodel.GenomeDB
isDefaultUserRegistryAvailable() - Static method in class org.ensembl.registry.Registry
  Convenience method that checks whether the default user registry is available.
isDeleted() - Method in interface org.ensembl.datamodel.StableIDEvent
isEmpty() - Method in class org.ensembl.util.PersistentSet
isEndSet() - Method in class org.ensembl.datamodel.Location
isGap() - Method in class org.ensembl.datamodel.Location
  Return whether this node is a gap.
isInernalIDsSet() - Method in class org.ensembl.datamodel.Query
  Deprecated.
isInternalIDSet() - Method in class org.ensembl.datamodel.Query
  Deprecated.
isKnown() - Method in interface org.ensembl.datamodel.ExternalDatabase
  Determines if external database is known.
isKnown() - Method in interface org.ensembl.datamodel.Gene
  Whether this is a known Gene.
isKnown() - Method in interface org.ensembl.datamodel.Transcript
  Whether this is a known transcript.
isKnown() - Method in interface org.ensembl.datamodel.Translation
  Whether this is a known translation.
isLocationSet() - Method in class org.ensembl.datamodel.Query
  Deprecated.
isMerged() - Method in interface org.ensembl.datamodel.StableIDEvent
isProbeInArray(OligoArray) - Method in interface org.ensembl.datamodel.OligoProbe
  Whether this probe appears in the array.
isReadOnly() - Method in class org.ensembl.util.ConnectionWrapper
isSeqRegionNameSet() - Method in class org.ensembl.datamodel.Location
isSequenceEditsEnabled() - Method in interface org.ensembl.datamodel.Transcript
  Whether sequence edits are enabled.
isSequenceLevel() - Method in class org.ensembl.datamodel.CoordinateSystem
  Check if this co-ordinate system is the sequence-level co-ordinate system for this species.
isSplicable() - Method in interface org.ensembl.datamodel.Gene
isSplit() - Method in interface org.ensembl.datamodel.StableIDEvent
isStartSet() - Method in class org.ensembl.datamodel.Location
isStrandSet() - Method in class org.ensembl.datamodel.Location
iterator() - Method in class org.ensembl.util.PersistentSet

## J

JDBCUtil - class org.ensembl.util.JDBCUtil.
  Utility functions for working with JDBC.
JDBCUtil() - Constructor for class org.ensembl.util.JDBCUtil

## K

KAKA - Static variable in class org.ensembl.util.SimpleDBAccess
KaryotypeBand - interface org.ensembl.datamodel.KaryotypeBand.
KaryotypeBandAdaptor - interface org.ensembl.driver.KaryotypeBandAdaptor.
keys() - Method in class org.ensembl.util.LruCache

## L

LDFeature - interface org.ensembl.variation.datamodel.LDFeature.
  A linkage disequilibrium between two VariationFeatures.
LDFeatureAdaptor - interface org.ensembl.variation.driver.LDFeatureAdaptor.
  Provides database access for retrieving LDFeatures as either a simple List or wrapped in an optimised LDFeaturesContainer.
LDFeatureContainer - class org.ensembl.variation.datamodel.LDFeatureContainer.
  A container for LDFeatures (linkage disequilibrium features) that provides various methods for filtering and accessing the the contained data.
LDFeatureContainer(List) - Constructor for class org.ensembl.variation.datamodel.LDFeatureContainer
  Create a container for the specified LD features.
LENGTH_ORDER - Static variable in class org.ensembl.util.StringUtil
  Comparator which orders strings by length.
ListElement - class org.ensembl.util.ListElement.
ListElement() - Constructor for class org.ensembl.util.ListElement
ListElement(Object, ListElement, ListElement) - Constructor for class org.ensembl.util.ListElement
Locatable - interface org.ensembl.datamodel.Locatable.
  Genome feature with a location on genome.
LocatableList - class org.ensembl.util.LocatableList.
  Container for locatables that offers a convenient means of retrieving an array of the locatable's internalIDs where the locatables are sorted by genomic location.
LocatableList() - Constructor for class org.ensembl.util.LocatableList
Location - class org.ensembl.datamodel.Location.
  A Location is an 'address' of regions on sequences.
Location(CoordinateSystem, String, int, int) - Constructor for class org.ensembl.datamodel.Location
  Default values: strand = 0, gap = false.
Location(String, String, int, int) - Constructor for class org.ensembl.datamodel.Location
  Both strands of the sequence region from _start_ to _end_ in the default version of the specified coordinate system.
Location(String, String, int, int, int) - Constructor for class org.ensembl.datamodel.Location
  The strand of the sequence region from _start_ to _end_ in the default version of the specified coordinate system.
Location(String) - Constructor for class org.ensembl.datamodel.Location
  Location object is initialized to the value of the specified string.
Location(CoordinateSystem, String, int, int, int, boolean) - Constructor for class org.ensembl.datamodel.Location
Location(CoordinateSystem, String, int, int, int) - Constructor for class org.ensembl.datamodel.Location
Location(long, int, int, int) - Constructor for class org.ensembl.datamodel.Location
  Create a location as a range on a sequence region defined by it's internalID.
Location(CoordinateSystem) - Constructor for class org.ensembl.datamodel.Location
  Location representing the whole coordinate system.
Location(CoordinateSystem, String) - Constructor for class org.ensembl.datamodel.Location
  The whole of the sequence region in the default version of the specified coordinate system.
Location(String, String) - Constructor for class org.ensembl.datamodel.Location
  The whole of the sequence region in the default version of the specified coordinate system.
Location(CoordinateSystem, SequenceRegion) - Constructor for class org.ensembl.datamodel.Location
Location(CoordinateSystem, boolean, int) - Constructor for class org.ensembl.datamodel.Location
  Constructs a location with map=CloneFragmentLocation.DEFAULT_CS, start=1, end=length+1, strand=unset and whether it is a gap.
Location(Location[]) - Constructor for class org.ensembl.datamodel.Location
  Create a list location by appending copies of the items in _locations_.
LocationConverter - interface org.ensembl.driver.LocationConverter.
  Converts locations between different coordinate systems.
LocationFeatureIterator - class org.ensembl.driver.LocationFeatureIterator.
LocationFeatureIterator(FeatureAdaptor, int, boolean, Location, LocationConverter) - Constructor for class org.ensembl.driver.LocationFeatureIterator
LockableGeneAdaptor - interface org.ensembl.driver.LockableGeneAdaptor.
  When the implementing class overrides store() the intention is that it will succeed only if the gene is locked by the 'current' user and that the lock is released before any other user can modify the gene.
LogFormatter - class org.ensembl.util.LogFormatter.
  Custom class for formatting log messages.
LogFormatter() - Constructor for class org.ensembl.util.LogFormatter
LoggingManager - class org.ensembl.driver.LoggingManager.
  Utility class to simplify logging system configuration.
LoggingUtil - class org.ensembl.util.LoggingUtil.
  Convenience functions for interacting with the logging system.
LongList - class org.ensembl.util.LongList.
  Dynamic list of longs.
LongList() - Constructor for class org.ensembl.util.LongList
LongList(long[]) - Constructor for class org.ensembl.util.LongList
LongSet - class org.ensembl.util.LongSet.
  Set for storing unique longs.
LongSet() - Constructor for class org.ensembl.util.LongSet
  Create an empty set.
LongSet(Collection) - Constructor for class org.ensembl.util.LongSet
  Creates a set of Longs from _s_.
LongSet(Collection, Class) - Constructor for class org.ensembl.util.LongSet
  Creates a set of Longs from various collections.
LongSet(long[]) - Constructor for class org.ensembl.util.LongSet
  Creates a set of Longs ids.
LruCache - class org.ensembl.util.LruCache.
LruCache(int) - Constructor for class org.ensembl.util.LruCache
last() - Method in class org.ensembl.datamodel.Location
  Last node in location list.
left - Variable in class org.ensembl.util.Pair
leftInt - Variable in class org.ensembl.util.Pair
lengthDiff() - Method in interface org.ensembl.datamodel.SequenceEdit
  The difference in length caused by applying this edit to a sequence.
list - Variable in class org.ensembl.util.LongList
listSeqRegionNames(Location) - Method in class org.ensembl.datamodel.ChainedAssemblyMapper
listSeqRegionNames(Location) - Method in class org.ensembl.datamodel.SimpleAssemblyMapper
listSize() - Method in class org.ensembl.util.LruCache
listToInternalIDArray(List) - Static method in class org.ensembl.util.PersistentUtil
load(Properties) - Static method in class org.ensembl.driver.DriverManager
  Creates an instance of the driver specified by the ensembl_driver parameter in the configuration and calls driver.initialise(configuration).
load(String) - Static method in class org.ensembl.driver.DriverManager
  Creates an instance of the driver specified by the ensembl_driver parameter in the configuration and calls driver.initialise(configuration).
load(Registry) - Method in interface org.ensembl.registry.RegistryLoader
  Loads DriverGroups into _registry_.
load(Registry) - Method in class org.ensembl.registry.RegistryLoaderIni
  Adds a copy of all loaded DriverGroups keyed on name and alias to the _registry_.
load(Registry) - Method in class org.ensembl.registry.RegistryLoaderJython
  Runs the script with _registry_ available in the environment.
loadDriver(Properties) - Static method in class org.ensembl.driver.DriverManager
  Creates an instance of the driver specified by the ensembl_driver parameter in the configuration and calls driver.initialise(configuration).
loadDriver(String) - Static method in class org.ensembl.driver.DriverManager
  Creates an instance of the driver specified by the ensembl_driver parameter in the configuration and calls driver.initialise(configuration).
loadEnsemblDriver(Properties) - Static method in class org.ensembl.driver.DriverManager
  Creates an instance of the driver specified by the ensembl_driver parameter in the configuration and calls driver.initialise(configuration).
loadEnsemblDriver(String) - Static method in class org.ensembl.driver.DriverManager
  Creates an instance of the driver specified by the ensembl_driver parameter in the configuration and calls driver.initialise(configuration).
loadVariationDriver(Properties) - Static method in class org.ensembl.driver.DriverManager
  Creates an instance of the driver specified by the ensembl_driver parameter in the configuration and calls driver.initialise(configuration).
loadVariationDriver(String) - Static method in class org.ensembl.driver.DriverManager
  Creates an instance of the driver specified by the ensembl_driver parameter in the configuration and calls driver.initialise(configuration).
locationToIds(Location) - Method in interface org.ensembl.driver.LocationConverter
  Convenience function to get all ids from non gap nodes of the location.
lock(Gene) - Method in interface org.ensembl.driver.LockableGeneAdaptor

## M

Mailer - class org.ensembl.util.Mailer.
  Simple class to allow SMTP email to be sent.
Mailer(String) - Constructor for class org.ensembl.util.Mailer
MappingSession - interface org.ensembl.datamodel.MappingSession.
Marker - interface org.ensembl.datamodel.Marker.
  Marker.
MarkerAdaptor - interface org.ensembl.driver.MarkerAdaptor.
  Provides access to Markers in the datasource.
MarkerFeature - interface org.ensembl.datamodel.MarkerFeature.
  Represents a marker feature in the EnsEMBL database.
MarkerFeatureAdaptor - interface org.ensembl.driver.MarkerFeatureAdaptor.
Member - interface org.ensembl.compara.datamodel.Member.
  I represent a single species which is part of the compara- analyses.
MemberAdaptor - interface org.ensembl.compara.driver.MemberAdaptor.
  I am associated with the compara-analyses
MessageOnlyFormatter - class org.ensembl.util.MessageOnlyFormatter.
  Custom class for formatting log messages, just prints the log message.
MessageOnlyFormatter() - Constructor for class org.ensembl.util.MessageOnlyFormatter
MethodLink - interface org.ensembl.compara.datamodel.MethodLink.
  I represent a type of dna-dna alignment
MethodLinkAdaptor - interface org.ensembl.compara.driver.MethodLinkAdaptor.
  I am a part of the compara analysis
MethodLinkSpeciesSet - interface org.ensembl.compara.datamodel.MethodLinkSpeciesSet.
  I represent a type of analysis which could be applied between the elements of a set of genomes and the actual set which had it applied.
MethodLinkSpeciesSetAdaptor - interface org.ensembl.compara.driver.MethodLinkSpeciesSetAdaptor.
  I am a part of the compara analysis
MethodNotSupportedException - exception org.ensembl.util.MethodNotSupportedException.
  This exception is thrown as a warning from a method which has not been implemented for normal use and for which there are no plans to implement it in future.
MethodNotSupportedException() - Constructor for class org.ensembl.util.MethodNotSupportedException
MethodNotSupportedException(String) - Constructor for class org.ensembl.util.MethodNotSupportedException
MiscFeature - interface org.ensembl.datamodel.MiscFeature.
  MiscFeatures are extremely general features with a location and an arbitrary group of attributes.
MiscFeatureAdaptor - interface org.ensembl.driver.MiscFeatureAdaptor.
  Adaptor for retrieving MiscFeatures.
MiscSet - interface org.ensembl.datamodel.MiscSet.
  MiscSets represent classsifications or groupings of MiscFeatures.
MiscSetAdaptor - interface org.ensembl.driver.MiscSetAdaptor.
main(String[]) - Static method in class org.ensembl.Example
  Prints some debug information before printing the output from the example methods in this class.
main(String[]) - Static method in class org.ensembl.compara.driver.ComparaReader
main(String[]) - Static method in class org.ensembl.datamodel.ChainedAssemblyMapper
main(String[]) - Static method in class org.ensembl.util.EnsemblDBLister
main(String[]) - Static method in class org.ensembl.util.JDBCUtil
main(String[]) - Static method in class org.ensembl.util.SimpleDBAccess
main(String[]) - Static method in class org.ensembl.util.SystemUtil
main(String[]) - Static method in class org.ensembl.util.Timer
main(String[]) - Static method in class org.ensembl.util.Version
  Prints ensj version.
makeEnsemblGeneLink(String) - Static method in class org.ensembl.util.Util
  Create a link to the ensembl.org page for a particular gene.
map(Location) - Method in interface org.ensembl.datamodel.AssemblyMapper
map(Location) - Method in class org.ensembl.datamodel.ChainedAssemblyMapper
map(Location) - Method in class org.ensembl.datamodel.SimpleAssemblyMapper
mapper - Variable in class org.ensembl.datamodel.SimpleAssemblyMapper
memoryStatus() - Static method in class org.ensembl.util.SystemUtil
  Memory usage for JVM, useful for debugging.
memoryStatus(boolean) - Static method in class org.ensembl.util.SystemUtil
  Memory usage for JVM, useful for debugging.
mergeAdjacentNodes() - Method in class org.ensembl.datamodel.Location
  Merges nodes in this location that are adjacent on a sequence.
moveTop(ListElement) - Method in class org.ensembl.util.ListElement

## N

NON_SYNONYMOUS_CODING - Static variable in class org.ensembl.variation.datamodel.AlleleConsequence
  Allele affects the peptide.
NamedTimer - class org.ensembl.util.NamedTimer.
  A class that can support multiple named timers.
NamedTimer() - Constructor for class org.ensembl.util.NamedTimer
NonFatalException - exception org.ensembl.compara.driver.NonFatalException.
NonFatalException(String) - Constructor for class org.ensembl.compara.driver.NonFatalException
NonFatalException(String, Throwable) - Constructor for class org.ensembl.compara.driver.NonFatalException
NotImplementedYetException - exception org.ensembl.util.NotImplementedYetException.
  This exception is thrown as a warning from a part of the code which has not been implemented yet, but will be in future.
NotImplementedYetException() - Constructor for class org.ensembl.util.NotImplementedYetException
NotImplementedYetException(String) - Constructor for class org.ensembl.util.NotImplementedYetException
nameToId(String, CoordinateSystem) - Method in interface org.ensembl.driver.LocationConverter
  Convert to an internal id, request from database if not in cache
namesToIds(String[], CoordinateSystem) - Method in interface org.ensembl.driver.LocationConverter
  Convert a number of names in the same coordinate system into an array of internal ids.
nativeSQL(String) - Method in class org.ensembl.util.ConnectionWrapper
next() - Method in class org.ensembl.datamodel.AssemblyLocation
  Deprecated.
next() - Method in class org.ensembl.datamodel.CloneFragmentLocation
next() - Method in class org.ensembl.datamodel.Location
next() - Method in class org.ensembl.driver.FeatureIterator
  Returns the next element in the iteration.
next() - Method in class org.ensembl.driver.LocationFeatureIterator
  Returns the next element in the iteration.
next() - Method in class org.ensembl.util.ArrayIterator
nextAL() - Method in class org.ensembl.datamodel.AssemblyLocation
  Deprecated.
nextCFL() - Method in class org.ensembl.datamodel.CloneFragmentLocation

## O

OligoArray - interface org.ensembl.datamodel.OligoArray.
  An microarray chip which contains probes.
OligoArrayAdaptor - interface org.ensembl.driver.OligoArrayAdaptor.
  Adaptor for retrieving microarrays.
OligoFeature - interface org.ensembl.datamodel.OligoFeature.
  The location where an OligoProbe hits the genome.
OligoFeatureAdaptor - interface org.ensembl.driver.OligoFeatureAdaptor.
  Adaptor for retrieving OligoFeatures from a database.
OligoProbe - interface org.ensembl.datamodel.OligoProbe.
  An oligo spot from one or more microarrays.
OligoProbeAdaptor - interface org.ensembl.driver.OligoProbeAdaptor.
  Adaptor for retrieving AffyProbes from the database.
org.ensembl - package org.ensembl
  Java library for accessing Ensembl core, compara and variation (SNP) databases.
org.ensembl.compara.datamodel - package org.ensembl.compara.datamodel
  Data types that are unique to ensembl compara databases such as Homology and GenomicAlign.
org.ensembl.compara.driver - package org.ensembl.compara.driver
  Compara adaptors.
org.ensembl.datamodel - package org.ensembl.datamodel
  Data types that appear in the core ensembl databases such as Genes, Exons and Karyotypes and various support classes such as Location.
org.ensembl.driver - package org.ensembl.driver
  Driver and adaptors for accessing ensembl core databases.
org.ensembl.registry - package org.ensembl.registry
  The Registry makes it easy to access to multiple ensembl databases.
org.ensembl.util - package org.ensembl.util
  Utility classes.
org.ensembl.variation.datamodel - package org.ensembl.variation.datamodel
  Data types that are unique to ensembl variation databases such as Variation, Allele and Genotype.
org.ensembl.variation.driver - package org.ensembl.variation.driver
  Driver and adaptors for accessing ensembl variation databases.
overlapSize(Location, boolean) - Method in class org.ensembl.datamodel.Location
  Finds the number of bases this location shares with the other location.
overlapSize(Location) - Method in class org.ensembl.datamodel.Location
  Calls `overlapSize(location,true)`.
overlaps(Location) - Method in class org.ensembl.datamodel.AssemblyLocation
  Deprecated. Checks if locations overlap each other, ignores strand.
overlaps(Location) - Method in class org.ensembl.datamodel.CloneFragmentLocation
  Checks if locations overlap each other, ignores strand.
overlaps(Location, boolean) - Method in class org.ensembl.datamodel.Location
  Checks if locations overlap each other.
overlaps(Location) - Method in class org.ensembl.datamodel.Location
  Calls `overlaps(location,false)`.

## P

PORT_FORWARD_TO_ACARI - Static variable in class org.ensembl.util.SimpleDBAccess
Pair - class org.ensembl.util.Pair.
  A simple "record" data structure representing a pair of strings.
Pair(String, String) - Constructor for class org.ensembl.util.Pair
  leftInt and rightInt default to 0.
Pair(String, int, String, int, String) - Constructor for class org.ensembl.util.Pair
Persistent - interface org.ensembl.datamodel.Persistent.
  Capable of storing in persistent storage.
PersistentSet - class org.ensembl.util.PersistentSet.
  Manages a set of persistent objects.
PersistentSet() - Constructor for class org.ensembl.util.PersistentSet
PersistentUtil - class org.ensembl.util.PersistentUtil.
PersistentUtil() - Constructor for class org.ensembl.util.PersistentUtil
Population - interface org.ensembl.datamodel.Population.
Population - interface org.ensembl.variation.datamodel.Population.
  A group of individuals.
PopulationAdaptor - interface org.ensembl.variation.driver.PopulationAdaptor.
  Adaptor for retrieving variation populations.
PopulationGenotype - interface org.ensembl.variation.datamodel.PopulationGenotype.
  A genotype that is present in a population.
PopulationGenotypeAdaptor - interface org.ensembl.variation.driver.PopulationGenotypeAdaptor.
  This adaptor provides database connectivity for PopulationGenotype objects.
PredictionExon - interface org.ensembl.datamodel.PredictionExon.
  Predicted exon which lacks a gene and UTRs.
PredictionExonAdaptor - interface org.ensembl.driver.PredictionExonAdaptor.
PredictionTranscript - interface org.ensembl.datamodel.PredictionTranscript.
  Transcript consisting of PredictionExons.
PredictionTranscriptAdaptor - interface org.ensembl.driver.PredictionTranscriptAdaptor.
  Provides access to PredictionTranscripts in the datasource.
ProgressPrinter - class org.ensembl.util.ProgressPrinter.
  Simple class to print & update a console percentage progress meter.
ProgressPrinter(int, int, String) - Constructor for class org.ensembl.util.ProgressPrinter
  Create a new ProgressPrinter.
PropertiesUtil - class org.ensembl.util.PropertiesUtil.
  Convenience class offering methods for easily accessing property files stored as files available via file system or URL.
PropertiesUtil() - Constructor for class org.ensembl.util.PropertiesUtil
ProteinFeature - interface org.ensembl.datamodel.ProteinFeature.
  An alignment between a part of the genome and a peptide.
ProteinFeatureAdaptor - interface org.ensembl.driver.ProteinFeatureAdaptor.
  Provides access to ProteinFeatures in the datasource.
parseInt(String) - Static method in class org.ensembl.util.StringUtil
  Converts string to int.
poolSize() - Method in class org.ensembl.util.ConnectionPoolDataSource
prepareCall(String) - Method in class org.ensembl.util.ConnectionWrapper
prepareCall(String, int, int) - Method in class org.ensembl.util.ConnectionWrapper
prepareCall(String, int, int, int) - Method in class org.ensembl.util.ConnectionWrapper
prepareStatement(String) - Method in class org.ensembl.util.ConnectionWrapper
prepareStatement(String, int) - Method in class org.ensembl.util.ConnectionWrapper
prepareStatement(String, int, int) - Method in class org.ensembl.util.ConnectionWrapper
prepareStatement(String, int, int, int) - Method in class org.ensembl.util.ConnectionWrapper
prepareStatement(String, int[]) - Method in class org.ensembl.util.ConnectionWrapper
prepareStatement(String, String[]) - Method in class org.ensembl.util.ConnectionWrapper
printSequence(char) - Method in class org.ensembl.util.FormattedSequencePrintStream
  Write out a char of sequence, with formatting.
printSequence(char[]) - Method in class org.ensembl.util.FormattedSequencePrintStream
  Write out a char[] object of sequence, with formatting.
printSequence(String) - Method in class org.ensembl.util.FormattedSequencePrintStream
  Write out a String of sequence.
printUpdate(int) - Method in class org.ensembl.util.ProgressPrinter
put(long, Object) - Method in class org.ensembl.util.IDMap
  Stores the object using new Long(key) as it's key.
put(Persistent) - Method in class org.ensembl.util.IDMap
  Stores the persistent object using it's internalID as the key.
put(Object, long) - Method in class org.ensembl.util.LruCache
  Convenience method that converts long to Long for storage.
put(Object, Object) - Method in class org.ensembl.util.LruCache
put(Object, Object, Object) - Method in class org.ensembl.util.LruCache
put(Object, Object, Object, Object) - Method in class org.ensembl.util.LruCache
putAll(Iterator) - Method in class org.ensembl.util.IDMap
  Stores the persistent objects using their internalIDs as the keys.
putAll(List) - Method in class org.ensembl.util.IDMap
  Adds all the persistent objects using their internalIDs as the keys.
putAll(Persistent[]) - Method in class org.ensembl.util.IDMap
  Adds all the persistent objects using their internalIDs as the keys.

## Q

Qtl - interface org.ensembl.datamodel.Qtl.
  Represents a quantitative trait locus (Qtl) in the EnsEMBL database.
QtlAdaptor - interface org.ensembl.driver.QtlAdaptor.
  Retrieves Qtls from the database.
QtlFeature - interface org.ensembl.datamodel.QtlFeature.
  A QtlFeature represent a region where the Qtl appears in the Ensembl database.
QtlFeatureAdaptor - interface org.ensembl.driver.QtlFeatureAdaptor.
  Retrieves QtlFeatures from the database.
QtlSynonym - interface org.ensembl.datamodel.QtlSynonym.
  Synonym for a Qtl.
Query - class org.ensembl.datamodel.Query.
  Deprecated. since version 27.0
Query() - Constructor for class org.ensembl.datamodel.Query
  Deprecated. Lazy loading is off by default.
Query(long) - Constructor for class org.ensembl.datamodel.Query
  Deprecated.
Query(long[]) - Constructor for class org.ensembl.datamodel.Query
  Deprecated.
Query(long, boolean) - Constructor for class org.ensembl.datamodel.Query
  Deprecated.
Query(long, boolean, Location) - Constructor for class org.ensembl.datamodel.Query
  Deprecated.
Query(Location) - Constructor for class org.ensembl.datamodel.Query
  Deprecated.
Query(Location, boolean) - Constructor for class org.ensembl.datamodel.Query
  Deprecated.
Query(String) - Constructor for class org.ensembl.datamodel.Query
  Deprecated.
Query(String, boolean) - Constructor for class org.ensembl.datamodel.Query
  Deprecated.
Query(String, boolean, Location) - Constructor for class org.ensembl.datamodel.Query
  Deprecated.

## R

Registry - class org.ensembl.registry.Registry.
  A Registry provide convenient programatic access to multiple ensembl databases through DriverGroups.
Registry() - Constructor for class org.ensembl.registry.Registry
  Create an empty registry.
Registry(RegistryLoader) - Constructor for class org.ensembl.registry.Registry
  Create a registry with DriverGroups loaded from loader.
RegistryLoader - interface org.ensembl.registry.RegistryLoader.
  Interface for classes that can load DriverGroups into a registry.
RegistryLoaderIni - class org.ensembl.registry.RegistryLoaderIni.
  Loads a registry with DriverGroups defined in "ini" style configuration files.
RegistryLoaderIni(InputStream, String) - Constructor for class org.ensembl.registry.RegistryLoaderIni
  Loads DriverGroups for configuration defined in _srcConfig_.
RegistryLoaderIni(byte[], String) - Constructor for class org.ensembl.registry.RegistryLoaderIni
  Loads DriverGroups for configuration stored in byte array.
RegistryLoaderIni(String, ServerDriverFactory) - Constructor for class org.ensembl.registry.RegistryLoaderIni
  Loads DriverGroups for configuration at _url_ Providing a serverDriverFactory that is used in other parts of your code can lead to faster performance as the caches only need to be populated once.
RegistryLoaderIni(String[], ServerDriverFactory, boolean) - Constructor for class org.ensembl.registry.RegistryLoaderIni
  Load driver groups defined in the _urls_.
RegistryLoaderIni(String) - Constructor for class org.ensembl.registry.RegistryLoaderIni
  Loads DriverGroups for configuration at _url_.
RegistryLoaderIni(URL) - Constructor for class org.ensembl.registry.RegistryLoaderIni
  Loads DriverGroups defined in the configuration file _url_.
RegistryLoaderJython - class org.ensembl.registry.RegistryLoaderJython.
  Runs a jython script that can load DriverGroups into a registry.
RegistryLoaderJython(InputStream, String) - Constructor for class org.ensembl.registry.RegistryLoaderJython
  Loads DriverGroups for configuration defined in _srcConfig_.
RegistryLoaderJython(byte[], String) - Constructor for class org.ensembl.registry.RegistryLoaderJython
  Loads the script stored in byte array.
RegistryLoaderJython(String) - Constructor for class org.ensembl.registry.RegistryLoaderJython
  Loads the script stored at _url_.
RegistryLoaderJython(URL) - Constructor for class org.ensembl.registry.RegistryLoaderJython
  Loads DriverGroups for configuration at _url_.
RepeatConsensus - interface org.ensembl.datamodel.RepeatConsensus.
  Repeat sequence.
RepeatConsensusAdaptor - interface org.ensembl.driver.RepeatConsensusAdaptor.
  Provides access to RepeatConsensus' in the datasource.
RepeatFeature - interface org.ensembl.datamodel.RepeatFeature.
  Repetitive sequence on genome.
RepeatFeatureAdaptor - interface org.ensembl.driver.RepeatFeatureAdaptor.
  Provides access to RepeatFeatures in the datasource.
RuntimeAdaptorException - exception org.ensembl.driver.RuntimeAdaptorException.
  Thrown when an problem occurs executing a method on an adaptor.
RuntimeAdaptorException() - Constructor for class org.ensembl.driver.RuntimeAdaptorException
RuntimeAdaptorException(String) - Constructor for class org.ensembl.driver.RuntimeAdaptorException
RuntimeAdaptorException(Exception) - Constructor for class org.ensembl.driver.RuntimeAdaptorException
RuntimeAdaptorException(String, Exception) - Constructor for class org.ensembl.driver.RuntimeAdaptorException
readObject(String) - Static method in class org.ensembl.util.SerialUtil
  Read an object from a previously serialised file.
readObject(File) - Static method in class org.ensembl.util.SerialUtil
readTextFile(String) - Static method in class org.ensembl.util.StringUtil
  Read a text file into a String.
registerAssembled(String, int) - Method in class org.ensembl.datamodel.SimpleAssemblyMapper
  Mark the given assembly chunk as registered in this AssemblyMapper.
registerAssembled(SimpleAssemblyMapper, String, int, int) - Method in interface org.ensembl.driver.AssemblyMapperAdaptor
registerChained(ChainedAssemblyMapper, String, String, List) - Method in interface org.ensembl.driver.AssemblyMapperAdaptor
registerComponent(String) - Method in class org.ensembl.datamodel.SimpleAssemblyMapper
registerComponent(SimpleAssemblyMapper, String) - Method in interface org.ensembl.driver.AssemblyMapperAdaptor
registerLocation(Location) - Method in class org.ensembl.datamodel.ChainedAssemblyMapper
relative(int) - Method in class org.ensembl.datamodel.Location
  Creates a new 1 base pair location relative to this location where newLocation.start = newLocation.end = this.start + offset.
relative(int, int) - Method in class org.ensembl.datamodel.Location
  Creates a new location relative to this location where start=this.start+offset, and end=this.start+length-1.
release(Gene) - Method in interface org.ensembl.driver.LockableGeneAdaptor
release(Connection) - Method in class org.ensembl.util.ConnectionPoolDataSource
  Returns the connection to the pool.
releaseSavepoint(Savepoint) - Method in class org.ensembl.util.ConnectionWrapper
remove() - Method in class org.ensembl.driver.FeatureIterator
  Not supported.
remove() - Method in class org.ensembl.driver.LocationFeatureIterator
  Not supported.
remove(String) - Method in class org.ensembl.registry.Registry
  Removes the mapping from _name_ to it's associated DriverGroup.
remove() - Method in class org.ensembl.util.ArrayIterator
remove(Object) - Method in class org.ensembl.util.PersistentSet
removeAdaptor(Adaptor) - Method in interface org.ensembl.driver.EnsemblDriver
removeAdaptor(String) - Method in interface org.ensembl.driver.EnsemblDriver
removeAll(Collection) - Method in class org.ensembl.util.PersistentSet
removeAllAdaptors() - Method in interface org.ensembl.driver.EnsemblDriver
removeAttribute(Attribute) - Method in interface org.ensembl.datamodel.Transcript
  Remove attribute if present in attributes.
removeAttribute(Attribute) - Method in interface org.ensembl.datamodel.Translation
  Remove attribute if present in attributes.
removeEnsemblDriver(EnsemblDriver) - Method in interface org.ensembl.driver.CoordinateSystemAdaptor
  Removes additional datasource.
removeGapNodes() - Method in class org.ensembl.datamodel.Location
  Returns a location derived by removing all gap nodes from this location, null if only gaps present.
removePrefixFromKeys(Properties, String) - Static method in class org.ensembl.util.PropertiesUtil
  Removes "prefix\\." from the beginning of all keys in _src_.
removePrefixFromKeys(Properties, String, String) - Static method in class org.ensembl.util.PropertiesUtil
  Removes _prefix_+separator from the beginning of all keys in _src_.
removeRelated(String) - Method in interface org.ensembl.datamodel.StableIDEvent
removeValue(Object) - Method in class org.ensembl.util.LruCache
removeValueByKey(Object) - Method in class org.ensembl.util.LruCache
replaceSubSequence(String, Location, String, Location) - Static method in class org.ensembl.util.SequenceUtil
  Replace a sub sequence from sourceSeq with replacementSeq.
rereference(Location, SequenceRegion) - Method in interface org.ensembl.driver.AssemblyExceptionAdaptor
  Refereferences the source locations.
rereference(Location, SequenceRegion) - Method in interface org.ensembl.driver.LocationConverter
  References locations into the same sequence region specified by target location.
resetColumnCount() - Method in class org.ensembl.util.FormattedSequencePrintStream
  sets the columnCount to 0, to signal that a new output of sequence has begun
resetInternalIDs(List) - Static method in class org.ensembl.util.PersistentUtil
  Resets the internalID for all items to 0.
restoreTable(String) - Method in interface org.ensembl.driver.EnsemblDriver
  Restores the table from a backup table.
restoreTables() - Method in interface org.ensembl.driver.EnsemblDriver
  Restores all the tables returned by fetchTableNames().
restoreTables(String[]) - Method in interface org.ensembl.driver.EnsemblDriver
  Restores all the tables from their respective backups.
result - Variable in class org.ensembl.util.LongList
retainAll(Collection) - Method in class org.ensembl.util.PersistentSet
reverse() - Method in class org.ensembl.datamodel.AssemblyLocation
  Deprecated.
reverse() - Method in class org.ensembl.datamodel.CloneFragmentLocation
  Deprecated. use complement, reverse is not biological meaningful
reverseComplement() - Method in interface org.ensembl.compara.datamodel.GenomicAlign
reverseComplement() - Method in interface org.ensembl.compara.datamodel.GenomicAlignBlock
reverseComplement(String) - Static method in class org.ensembl.util.SequenceUtil
  Reverses the string and complements each base.
reverseComplement(byte[]) - Static method in class org.ensembl.util.SequenceUtil
right - Variable in class org.ensembl.util.Pair
rightInt - Variable in class org.ensembl.util.Pair
rollback() - Method in class org.ensembl.util.ConnectionWrapper
rollback(Savepoint) - Method in class org.ensembl.util.ConnectionWrapper
runtimeResourceLocation(String) - Static method in class org.ensembl.util.SystemUtil
  Attempts to resolve the src to a URL.

## S

SPLICE_SITE - Static variable in class org.ensembl.variation.datamodel.AlleleConsequence
  Allele hits the 3rd, 4th, 5th, 6th, 7th or 8th bases at the start or end of an intron OR the 1st or 2nd bases of an exon (adjacent to an intron).
STOP_GAINED - Static variable in class org.ensembl.variation.datamodel.AlleleConsequence
  Allele causes a new stop codon.
STOP_LOST - Static variable in class org.ensembl.variation.datamodel.AlleleConsequence
  Allele causes the loss of a stop codon.
SUBMITTER - Static variable in class org.ensembl.variation.datamodel.ValidationState
SYNONYMOUS_CODING - Static variable in class org.ensembl.variation.datamodel.AlleleConsequence
  Allele does not affect the peptide.
Sequence - interface org.ensembl.datamodel.Sequence.
  Genomic DNA sequence.
SequenceAdaptor - interface org.ensembl.driver.SequenceAdaptor.
  Provides access to Sequence in the datasource.
SequenceEdit - interface org.ensembl.datamodel.SequenceEdit.
  A sequence modification action.
SequenceRegion - interface org.ensembl.datamodel.SequenceRegion.
  Represents a region of sequence, which could be from any co-ordinate system.
SequenceRegionAdaptor - interface org.ensembl.driver.SequenceRegionAdaptor.
  Adaptor for SequenceRegion objects.
SequenceUtil - class org.ensembl.util.SequenceUtil.
  Utility functions for dealing with sequence data.
SequenceUtil() - Constructor for class org.ensembl.util.SequenceUtil
SerialUtil - class org.ensembl.util.SerialUtil.
SerialUtil() - Constructor for class org.ensembl.util.SerialUtil
ServerDriver - class org.ensembl.driver.ServerDriver.
  Driver providing access to an ensembl database server.
ServerDriver(Properties) - Constructor for class org.ensembl.driver.ServerDriver
  Lazy loading cache of database names.
ServerDriverFactory - class org.ensembl.driver.ServerDriverFactory.
  Factory for producing, or retrieving from a cached, ServerDrivers.
ServerDriverFactory() - Constructor for class org.ensembl.driver.ServerDriverFactory
SimpleAssemblyMapper - class org.ensembl.datamodel.SimpleAssemblyMapper.
SimpleAssemblyMapper(CoreDriver, CoordinateSystem, CoordinateSystem) - Constructor for class org.ensembl.datamodel.SimpleAssemblyMapper
SimpleDBAccess - class org.ensembl.util.SimpleDBAccess.
SimpleDBAccess() - Constructor for class org.ensembl.util.SimpleDBAccess
SimpleFeature - interface org.ensembl.datamodel.SimpleFeature.
SimpleFeatureAdaptor - interface org.ensembl.driver.SimpleFeatureAdaptor.
  Provides access to SimpleFeatures in the datasource.
SnapShot - interface org.ensembl.datamodel.SnapShot.
  A partial representation of a data element's state at some point in time.
StableIDEvent - interface org.ensembl.datamodel.StableIDEvent.
StableIDEventAdaptor - interface org.ensembl.driver.StableIDEventAdaptor.
  Provides access to StableIDEvents in the datasource.
StringUtil - class org.ensembl.util.StringUtil.
  String Utility methods.
StringUtil() - Constructor for class org.ensembl.util.StringUtil
SubmittedVariation - interface org.ensembl.datamodel.SubmittedVariation.
SupportingFeatureAdaptor - interface org.ensembl.driver.SupportingFeatureAdaptor.
  Provides access to SupportingFeatures in the datasource.
SystemUtil - class org.ensembl.util.SystemUtil.
SystemUtil() - Constructor for class org.ensembl.util.SystemUtil
SystemUtil.MemoryStatus - class org.ensembl.util.SystemUtil.MemoryStatus.
SystemUtil.MemoryStatus(long, long, long) - Constructor for class org.ensembl.util.SystemUtil.MemoryStatus
sameInternalID(Persistent) - Method in interface org.ensembl.datamodel.Persistent
sendMail(String[], String, String, String) - Method in class org.ensembl.util.Mailer
sendMail(String, String, String, String) - Method in class org.ensembl.util.Mailer
setAccessionID(String) - Method in interface org.ensembl.datamodel.Accessioned
  Set the accession (stable id) for this object.
setAccessionID(String) - Method in class org.ensembl.datamodel.Query
  Deprecated.
setAlignedSequence(String) - Method in interface org.ensembl.compara.datamodel.GenomicAlign
setAlleleString(String) - Method in interface org.ensembl.variation.datamodel.Allele
  Sets the allele string.
setAlleleString(String) - Method in interface org.ensembl.variation.datamodel.VariationFeature
  Set the allele string.
setAnalysis(Analysis) - Method in interface org.ensembl.datamodel.Feature
  Set the analysis that created this feature.
setAnalysis(Analysis) - Method in interface org.ensembl.datamodel.PredictionTranscript
  Analysis which created this prediction.
setAnalysis(Analysis) - Method in interface org.ensembl.datamodel.ProteinFeature
setAnalysisID(long) - Method in interface org.ensembl.datamodel.Feature
  Set the analysisID of the analysis that created this feature.
setAssembly(String) - Method in interface org.ensembl.compara.datamodel.GenomeDB
setAutoCommit(boolean) - Method in class org.ensembl.util.ConnectionWrapper
setBand(String) - Method in interface org.ensembl.datamodel.ChromosomeBand
setBand(String) - Method in interface org.ensembl.datamodel.KaryotypeBand
setBands(List) - Method in interface org.ensembl.datamodel.Chromosome
setBioType(String) - Method in interface org.ensembl.datamodel.Gene
  Set the biological type of the gene.
setBioType(String) - Method in interface org.ensembl.datamodel.Transcript
  Set the biological type of the gene.
setCatalog(String) - Method in class org.ensembl.util.ConnectionWrapper
setChrEnd(int) - Method in interface org.ensembl.compara.datamodel.Member
setChrEnd(int) - Method in interface org.ensembl.datamodel.ChromosomeBand
setChrName(String) - Method in interface org.ensembl.compara.datamodel.Member
setChrStart(int) - Method in interface org.ensembl.compara.datamodel.Member
setChrStart(int) - Method in interface org.ensembl.datamodel.ChromosomeBand
setChrStrand(int) - Method in interface org.ensembl.compara.datamodel.Member
setChromosome(String) - Method in class org.ensembl.datamodel.AssemblyLocation
  Deprecated. Note: if you include 'chr' at the beginning of the chromosome name it will be removed.
setChromosome(String) - Method in class org.ensembl.datamodel.CloneFragmentLocation
setChromosomeEnd(int) - Method in interface org.ensembl.datamodel.AssemblyElement
setChromosomeName(String) - Method in interface org.ensembl.datamodel.AssemblyElement
setChromosomeStart(int) - Method in interface org.ensembl.datamodel.AssemblyElement
setCigarString(String) - Method in interface org.ensembl.compara.datamodel.GenomicAlign
setCigarString(String) - Method in interface org.ensembl.datamodel.FeaturePair
setCloneFragmentEnd(int) - Method in interface org.ensembl.datamodel.AssemblyElement
setCloneFragmentInternalID(long) - Method in interface org.ensembl.datamodel.AssemblyElement
setCloneFragmentOri(int) - Method in interface org.ensembl.datamodel.AssemblyElement
setCloneFragmentStart(int) - Method in interface org.ensembl.datamodel.AssemblyElement
setCode(String) - Method in interface org.ensembl.datamodel.Attribute
  Code for this attribute.
setCode(String) - Method in interface org.ensembl.datamodel.MiscSet
  Code for this MiscSet.
setComparaConfig(Properties) - Method in class org.ensembl.registry.DriverGroup
  Configuration for the compara driver.
setCompleted(boolean) - Method in interface org.ensembl.datamodel.Gene
setConfidence(double) - Method in interface org.ensembl.datamodel.Exon
setCoordSystemName(String) - Method in interface org.ensembl.compara.datamodel.DnaFragment
setCoordinateSystem(CoordinateSystem, LocationConverter) - Method in interface org.ensembl.datamodel.Locatable
  Converts location to the specified coordinateSystem using the specified locationConverter.
setCoordinateSystem(CoordinateSystem) - Method in class org.ensembl.datamodel.Location
setCoordinateSystem(CoordinateSystem) - Method in interface org.ensembl.datamodel.SequenceRegion
setCoreConfig(Properties) - Method in class org.ensembl.registry.DriverGroup
  Configuration for the core driver.
setCoreDriver(CoreDriver) - Method in interface org.ensembl.variation.driver.VariationDriver
  Core driver associated with this variation driver.
setCreated(Timestamp) - Method in interface org.ensembl.datamodel.Analysis
setCreated(boolean) - Method in interface org.ensembl.datamodel.StableIDEvent
setCreatedDate(Date) - Method in interface org.ensembl.datamodel.Accessioned
  Set the date the object was created .
setCurrent(int) - Method in class org.ensembl.util.ProgressPrinter
setDatabase(String) - Method in interface org.ensembl.datamodel.SubmittedVariation
setDefault(boolean) - Method in class org.ensembl.datamodel.CoordinateSystem
  Deprecated. set this value in the appropriate constructor instead
setDefaultAssembly(boolean) - Method in interface org.ensembl.compara.datamodel.GenomeDB
setDeleted(boolean) - Method in interface org.ensembl.datamodel.StableIDEvent
setDescription(String) - Method in interface org.ensembl.compara.datamodel.Domain
setDescription(String) - Method in interface org.ensembl.compara.datamodel.Family
setDescription(String) - Method in interface org.ensembl.compara.datamodel.Homology
setDescription(String) - Method in interface org.ensembl.compara.datamodel.Member
setDescription(String) - Method in interface org.ensembl.datamodel.Attribute
  Description for this attribute.
setDescription(String) - Method in interface org.ensembl.datamodel.ExternalRef
setDescription(String) - Method in interface org.ensembl.datamodel.Feature
setDescription(String) - Method in interface org.ensembl.datamodel.MiscSet
  Description of this MiscSet.
setDescription(String) - Method in interface org.ensembl.datamodel.Population
setDescription(String) - Method in interface org.ensembl.variation.datamodel.Population
  Set the population description.
setDescriptionScore(double) - Method in interface org.ensembl.compara.datamodel.Domain
setDescriptionScore(double) - Method in interface org.ensembl.compara.datamodel.Family
setDisplayID(String) - Method in interface org.ensembl.datamodel.ExternalRef
setDisplayName(String) - Method in interface org.ensembl.datamodel.Feature
setDisplayName(String) - Method in interface org.ensembl.datamodel.Marker
setDisplayName(String) - Method in interface org.ensembl.datamodel.MarkerFeature
setDisplayName(String) - Method in interface org.ensembl.datamodel.ProteinFeature
setDisplayName(String) - Method in interface org.ensembl.datamodel.Transcript
setDn(double) - Method in interface org.ensembl.compara.datamodel.Homology
setDnaFragment(DnaFragment) - Method in interface org.ensembl.compara.datamodel.GenomicAlign
setDnaFragmentId(long) - Method in interface org.ensembl.compara.datamodel.GenomicAlign
setDriver(CoreDriver) - Method in class org.ensembl.datamodel.ChainedAssemblyMapper
setDriver(CoreDriver) - Method in interface org.ensembl.datamodel.Persistent
setDs(double) - Method in interface org.ensembl.compara.datamodel.Homology
setEnd(int) - Method in interface org.ensembl.compara.datamodel.GenomicAlign
setEnd(int) - Method in class org.ensembl.datamodel.Location
  Sets the end attribute.
setEndExon(Exon) - Method in interface org.ensembl.datamodel.Translation
setEndExonInternalID(long) - Method in interface org.ensembl.datamodel.Translation
  Returns endExon internal id.
setEndPhase(int) - Method in interface org.ensembl.datamodel.Exon
setEvalue(double) - Method in interface org.ensembl.datamodel.FeaturePair
setEvalue(double) - Method in interface org.ensembl.datamodel.ProteinFeature
setExonCount(int) - Method in interface org.ensembl.datamodel.PredictionTranscript
  Number of exons.
setExons(List) - Method in interface org.ensembl.datamodel.PredictionTranscript
setExons(List) - Method in interface org.ensembl.datamodel.Transcript
setExternalDatabase(ExternalDatabase) - Method in interface org.ensembl.datamodel.ExternalRef
setExternalDbId(long) - Method in interface org.ensembl.datamodel.ExternalRef
setExternalEnd(int) - Method in interface org.ensembl.datamodel.UngappedAlignment
  End position in externalReference dna.
setExternalRef(ExternalRef) - Method in interface org.ensembl.datamodel.UngappedAlignment
setExternalRefs(List) - Method in interface org.ensembl.datamodel.Translation
setExternalStart(int) - Method in interface org.ensembl.datamodel.UngappedAlignment
  Start in externalReference dna.
setExternalStrand(int) - Method in interface org.ensembl.datamodel.UngappedAlignment
  Strand in externalReference dna.
setFivePrimeFlankingSeq(String) - Method in interface org.ensembl.variation.datamodel.Variation
setFlankMarker1(Marker) - Method in interface org.ensembl.datamodel.Qtl
  One flanking marker of the interest region, the two flanking markers define the region.
setFlankMarker2(Marker) - Method in interface org.ensembl.datamodel.Qtl
  One flanking marker of the interest region, the two flanking markers define the region.
setFrequencies(List) - Method in interface org.ensembl.datamodel.SubmittedVariation
setFrequency(double) - Method in interface org.ensembl.variation.datamodel.Allele
  Set the frequency.
setGFFFeature(String) - Method in interface org.ensembl.datamodel.Analysis
setGFFSource(String) - Method in interface org.ensembl.datamodel.Analysis
setGap(boolean) - Method in class org.ensembl.datamodel.Location
setGene(Gene) - Method in interface org.ensembl.datamodel.Exon
  Sets gene and geneInternalID.
setGene(Gene) - Method in interface org.ensembl.datamodel.Transcript
  Sets gene and geneInternalID.
setGeneBuild(String) - Method in interface org.ensembl.compara.datamodel.GenomeDB
setGeneInternalID(long) - Method in interface org.ensembl.datamodel.Exon
  Sets gene internal id, also sets the gene.internalID if gene is available.
setGeneInternalID(long) - Method in interface org.ensembl.datamodel.Transcript
  Sets gene internal id, also sets the gene.internalID if gene is available.
setGeneMemberId(long) - Method in interface org.ensembl.compara.datamodel.Member
setGenomeDB(GenomeDB) - Method in interface org.ensembl.compara.datamodel.DnaFragment
setGenomeDbId(long) - Method in interface org.ensembl.compara.datamodel.Member
setGenomeDbInternalId(long) - Method in interface org.ensembl.compara.datamodel.DnaFragment
setGenomicAlignBlock(GenomicAlignBlock) - Method in interface org.ensembl.compara.datamodel.GenomicAlign
setGenomicAlignBlockInternalID(long) - Method in interface org.ensembl.compara.datamodel.GenomicAlign
setGoLinkageType(String) - Method in interface org.ensembl.datamodel.ExternalRef
  Set the linkage_type column on the go_xref table if this is a GO xref.
setHitAccession(String) - Method in interface org.ensembl.datamodel.FeaturePair
setHitDescription(String) - Method in interface org.ensembl.datamodel.FeaturePair
setHitDisplayName(String) - Method in interface org.ensembl.datamodel.FeaturePair
setHitLocation(Location) - Method in interface org.ensembl.datamodel.FeaturePair
setHitSequence(Sequence) - Method in interface org.ensembl.datamodel.FeaturePair
setHitSpecies(String) - Method in interface org.ensembl.datamodel.DnaDnaAlignFeature
setHoldability(int) - Method in class org.ensembl.util.ConnectionWrapper
setIncludeChildren(boolean) - Method in class org.ensembl.datamodel.Query
  Deprecated.
setIncludeSequence(boolean) - Method in class org.ensembl.datamodel.Query
  Deprecated.
setInfoText(String) - Method in interface org.ensembl.datamodel.ExternalRef
  Set the Info text for the xref.
setInfoType(String) - Method in interface org.ensembl.datamodel.ExternalRef
  Set the Info type for the xref.
setInternalID(long) - Method in interface org.ensembl.datamodel.Persistent
setInternalID(long) - Method in class org.ensembl.datamodel.Query
  Deprecated.
setInternalIDs(long[]) - Method in class org.ensembl.datamodel.Query
  Deprecated.
setInterproAccession(String) - Method in interface org.ensembl.datamodel.ProteinFeature
  Set the interpro accession for this protein.
setInterproDescription(String) - Method in interface org.ensembl.datamodel.ProteinFeature
  Set the interpro description for this protein.
setInterproDisplayName(String) - Method in interface org.ensembl.datamodel.ProteinFeature
  Set the interpro display name.
setInterproIDs(String[]) - Method in interface org.ensembl.datamodel.Translation
  Interpro IDs associated with this translation.
setKnown(boolean) - Method in interface org.ensembl.datamodel.Translation
  Sets whether this is a known translation.
setLength(int) - Method in interface org.ensembl.compara.datamodel.DnaFragment
setLength(int) - Method in interface org.ensembl.compara.datamodel.GenomicAlignBlock
setLength(long) - Method in interface org.ensembl.datamodel.Chromosome
setLength(long) - Method in interface org.ensembl.datamodel.SequenceRegion
setLnl(double) - Method in interface org.ensembl.compara.datamodel.Homology
setLocation(Location) - Method in interface org.ensembl.compara.datamodel.DnaFragment
setLocation(Location) - Method in interface org.ensembl.datamodel.Exon
setLocation(Location) - Method in interface org.ensembl.datamodel.Gene
setLocation(Location) - Method in interface org.ensembl.datamodel.KaryotypeBand
setLocation(Location) - Method in interface org.ensembl.datamodel.Locatable
setLocation(Location) - Method in interface org.ensembl.datamodel.PredictionExon
setLocation(Location) - Method in class org.ensembl.datamodel.Query
  Deprecated.
setLocation(Location) - Method in interface org.ensembl.datamodel.UngappedAlignment
  Location in ensembl database.
setLocator(String) - Method in interface org.ensembl.compara.datamodel.GenomeDB
setLodScore(float) - Method in interface org.ensembl.datamodel.Qtl
  A score for the Qtl.
setLogWriter(PrintWriter) - Method in class org.ensembl.util.ConnectionPoolDataSource
setLogicalName(String) - Method in interface org.ensembl.datamodel.Analysis
setLoginTimeout(int) - Method in class org.ensembl.util.ConnectionPoolDataSource
setLongDescription(String) - Method in interface org.ensembl.datamodel.Population
setMapWeight(int) - Method in interface org.ensembl.datamodel.MarkerFeature
  The number of times that this marker has been mapped to the genome.
setMapWeight(int) - Method in interface org.ensembl.variation.datamodel.VariationFeature
setMarker(Marker) - Method in interface org.ensembl.datamodel.MarkerFeature
setMarkerFeatures(List) - Method in interface org.ensembl.datamodel.Marker
  MarkerFeatures representing where this marker appears on the genome.
setMax(int) - Method in class org.ensembl.util.ProgressPrinter
setMaxFeatureLength(int) - Method in interface org.ensembl.datamodel.MiscSet
  Maximum length of features in this set
setMaxPrimerDistance(int) - Method in interface org.ensembl.datamodel.Marker
setMethodLink(MethodLink) - Method in interface org.ensembl.compara.datamodel.MethodLinkSpeciesSet
setMethodLinkSpeciesSet(MethodLinkSpeciesSet) - Method in interface org.ensembl.compara.datamodel.GenomicAlign
setMethodLinkSpeciesSet(MethodLinkSpeciesSet) - Method in interface org.ensembl.compara.datamodel.GenomicAlignBlock
setMethodLinkSpeciesSetId(long) - Method in interface org.ensembl.compara.datamodel.Domain
setMethodLinkSpeciesSetId(long) - Method in interface org.ensembl.compara.datamodel.Family
setMethodLinkSpeciesSetId(long) - Method in interface org.ensembl.compara.datamodel.Homology
setMethodLinkSpeciesSetInternalId(long) - Method in interface org.ensembl.compara.datamodel.GenomicAlign
setMethodLinkSpeciesSetInternalId(long) - Method in interface org.ensembl.compara.datamodel.GenomicAlignBlock
setMethodLinkType(String) - Method in interface org.ensembl.datamodel.DnaDnaAlignFeature
setMin(int) - Method in class org.ensembl.util.ProgressPrinter
setMinPrimerDistance(int) - Method in interface org.ensembl.datamodel.Marker
setModifiedDate(Date) - Method in interface org.ensembl.datamodel.Accessioned
  Set the date the object was last modified.
setN(double) - Method in interface org.ensembl.compara.datamodel.Homology
setName(String) - Method in interface org.ensembl.compara.datamodel.DnaFragment
setName(String) - Method in interface org.ensembl.compara.datamodel.GenomeDB
setName(String) - Method in interface org.ensembl.datamodel.Attribute
  Human readable name for this attribute
setName(String) - Method in interface org.ensembl.datamodel.Chromosome
setName(String) - Method in class org.ensembl.datamodel.CoordinateSystem
  Deprecated. set this value in the appropriate constructor instead
setName(String) - Method in interface org.ensembl.datamodel.ExternalDatabase
setName(String) - Method in interface org.ensembl.datamodel.MiscSet
  Name of this MiscSet
setName(String) - Method in interface org.ensembl.datamodel.Population
setName(String) - Method in interface org.ensembl.datamodel.RepeatConsensus
setName(String) - Method in interface org.ensembl.datamodel.SequenceRegion
setName(String) - Method in interface org.ensembl.variation.datamodel.Population
  Set the population name.
setName(String) - Method in interface org.ensembl.variation.datamodel.Variation
setName(String) - Method in interface org.ensembl.variation.datamodel.VariationGroup
  Set the name of this variation group.
setNewDatabase(String) - Method in interface org.ensembl.datamodel.MappingSession
setNext(AssemblyLocation) - Method in class org.ensembl.datamodel.AssemblyLocation
  Deprecated.
setNext(CloneFragmentLocation) - Method in class org.ensembl.datamodel.CloneFragmentLocation
setNext(Location) - Method in class org.ensembl.datamodel.Location
setObjectXrefID(long) - Method in interface org.ensembl.datamodel.ExternalRef
setOldDatabase(String) - Method in interface org.ensembl.datamodel.MappingSession
setOrUnset(Object) - Static method in class org.ensembl.util.StringUtil
setOriginalSequence(String) - Method in interface org.ensembl.compara.datamodel.GenomicAlign
setParameters(String) - Method in interface org.ensembl.datamodel.Analysis
setPeakMarker(Marker) - Method in interface org.ensembl.datamodel.Qtl
  An optional Marker which has the peak probablitity for this traits occurence.
setPeptide(String) - Method in interface org.ensembl.datamodel.Translation
setPeptideEnd(int) - Method in interface org.ensembl.datamodel.ProteinFeature
setPeptideStart(int) - Method in interface org.ensembl.datamodel.ProteinFeature
setPercentageID(double) - Method in interface org.ensembl.compara.datamodel.GenomicAlignBlock
setPercentageIdentity(double) - Method in interface org.ensembl.datamodel.FeaturePair
setPercentageIdentity(double) - Method in interface org.ensembl.datamodel.ProteinFeature
setPhase(int) - Method in interface org.ensembl.datamodel.Exon
setPopulation(Population) - Method in interface org.ensembl.variation.datamodel.Allele
  Set the population where the allele appears.
setPopulationID(long) - Method in interface org.ensembl.variation.datamodel.Allele
  Set the internalID of the population this allele belongs to.
setPositionInEndExon(int) - Method in interface org.ensembl.datamodel.Translation
setPositionInStartExon(int) - Method in interface org.ensembl.datamodel.Translation
setPostfix(String) - Method in class org.ensembl.util.ProgressPrinter
  Set the postfix to be printed.
setPrimaryID(String) - Method in interface org.ensembl.datamodel.ExternalRef
setPriority(int) - Method in interface org.ensembl.datamodel.ExternalDatabase
setPriority(int) - Method in interface org.ensembl.datamodel.Marker
setProgram(String) - Method in interface org.ensembl.datamodel.Analysis
setProgramFile(String) - Method in interface org.ensembl.datamodel.Analysis
setProgramVersion(String) - Method in interface org.ensembl.datamodel.Analysis
setPvalue(double) - Method in interface org.ensembl.datamodel.PredictionExon
setQtl(Qtl) - Method in interface org.ensembl.datamodel.QtlFeature
  Qtl this feature is associated with.
setQtlFeatures(List) - Method in interface org.ensembl.datamodel.Qtl
  The qtl features associated with this Qtl.
setQtlID(long) - Method in interface org.ensembl.datamodel.QtlFeature
  Set the internal ID of the QTL this feature represents.
setQueryIdentity(int) - Method in interface org.ensembl.datamodel.ExternalRef
setQueryInternalID(long) - Method in interface org.ensembl.datamodel.ExternalRef
setRank(int) - Method in class org.ensembl.datamodel.CoordinateSystem
  Deprecated. set this value in the appropriate constructor instead
setRank(int) - Method in interface org.ensembl.datamodel.PredictionExon
setReadOnly(boolean) - Method in class org.ensembl.util.ConnectionWrapper
setReferenceGenomicAlign(GenomicAlign) - Method in interface org.ensembl.compara.datamodel.GenomicAlignBlock
setReferenceGenomicAlignInternalID(long) - Method in interface org.ensembl.compara.datamodel.GenomicAlignBlock
setReferenceSlice(Location) - Method in interface org.ensembl.compara.datamodel.GenomicAlignBlock
setReferenceSliceEnd(int) - Method in interface org.ensembl.compara.datamodel.GenomicAlignBlock
setReferenceSliceStart(int) - Method in interface org.ensembl.compara.datamodel.GenomicAlignBlock
setRepeatConsensus(RepeatConsensus) - Method in interface org.ensembl.datamodel.RepeatFeature
setRepeatConsensusInternalID(long) - Method in interface org.ensembl.datamodel.RepeatFeature
  Sets repeatConsensus internal id, also sets the repeatConsensus.internalID if repeatConsensus is available.
setRootLoggerHandlersLevels(Level) - Static method in class org.ensembl.util.LoggingUtil
  Set the logging level for all the handlers on the root logger instance For a log message to be printed it's level must be >= the logger's level AND >= the handlers level.
setRootLoggerHandlersLevels(Level, Class) - Static method in class org.ensembl.util.LoggingUtil
  Set the logging level for all the handlers of the specified type on the root logger instance For a log message to be printed it's level must be >= the logger's level AND >= the handlers level.
setRootLoggerHandlersLevelsToALL() - Static method in class org.ensembl.util.LoggingUtil
  Calls setRootLoggerHandlersLevels(Level.ALL).
setRootLoggerHandlersLevelsToCONFIG() - Static method in class org.ensembl.util.LoggingUtil
  Calls setRootLoggerHandlersLevels(Level.CONFIG).
setRootLoggerHandlersLevelsToFINE() - Static method in class org.ensembl.util.LoggingUtil
  Calls setRootLoggerHandlersLevels(Level.FINE).
setRootLoggerHandlersLevelsToFINER() - Static method in class org.ensembl.util.LoggingUtil
  Calls setRootLoggerHandlersLevels(Level.FINER).
setRootLoggerHandlersLevelsToFINEST() - Static method in class org.ensembl.util.LoggingUtil
  Calls setRootLoggerHandlersLevels(Level.FINEST).
setRootLoggerHandlersLevelsToINFO() - Static method in class org.ensembl.util.LoggingUtil
  Calls setRootLoggerHandlersLevels(Level.INFO).
setRootLoggerHandlersLevelsToSEVERE() - Static method in class org.ensembl.util.LoggingUtil
  Calls setRootLoggerHandlersLevels(Level.SEVERE).
setRootLoggerHandlersLevelsToWARNING() - Static method in class org.ensembl.util.LoggingUtil
  Calls setRootLoggerHandlersLevels(Level.WARNING).
setRunnable(String) - Method in interface org.ensembl.datamodel.Analysis
setRunnableVersion(String) - Method in interface org.ensembl.datamodel.Analysis
setS(double) - Method in interface org.ensembl.compara.datamodel.Homology
setSavepoint() - Method in class org.ensembl.util.ConnectionWrapper
setSavepoint(String) - Method in class org.ensembl.util.ConnectionWrapper
setScore(double) - Method in interface org.ensembl.compara.datamodel.GenomicAlignBlock
setScore(double) - Method in interface org.ensembl.datamodel.FeaturePair
setScore(double) - Method in interface org.ensembl.datamodel.PredictionExon
setScore(double) - Method in interface org.ensembl.datamodel.ProteinFeature
setScore(double) - Method in interface org.ensembl.datamodel.SimpleFeature
setSegRegionID(long) - Method in class org.ensembl.datamodel.Location
  Set the sequence region internal ID this location node is on.
setSeqLeft(String) - Method in interface org.ensembl.datamodel.Marker
setSeqRegionName(String) - Method in class org.ensembl.datamodel.Location
setSeqRight(String) - Method in interface org.ensembl.datamodel.Marker
setSequence(Sequence) - Method in interface org.ensembl.datamodel.Exon
setSequence(Sequence) - Method in interface org.ensembl.datamodel.Gene
setSequence(Sequence) - Method in interface org.ensembl.datamodel.Locatable
setSequence(Sequence) - Method in interface org.ensembl.datamodel.RepeatConsensus
setSequence(Sequence) - Method in interface org.ensembl.datamodel.Transcript
setSequence(Sequence) - Method in interface org.ensembl.datamodel.Translation
setSequenceEditsEnabled(boolean) - Method in interface org.ensembl.datamodel.Transcript
  Set whether sequence edits should be applied to sequence.
setSequenceId(long) - Method in interface org.ensembl.compara.datamodel.Member
setSequenceLevel(boolean) - Method in class org.ensembl.datamodel.CoordinateSystem
  Deprecated. set this value in the appropriate constructor instead
setSequenceRegion(SequenceRegion) - Method in class org.ensembl.datamodel.Location
setServerDriverFactory(ServerDriverFactory) - Method in interface org.ensembl.driver.EnsemblDriver
  If two EnsemblDrivers wrap databases on the same database server then setting the same ServerDriverFactory on both will enable them to share connections.
setSession(MappingSession) - Method in interface org.ensembl.datamodel.StableIDEvent
setSize(int) - Method in interface org.ensembl.datamodel.Population
setSize(int) - Method in interface org.ensembl.variation.datamodel.Population
  Set the population size.
setSource(String) - Method in interface org.ensembl.datamodel.Gene
setSource(String) - Method in interface org.ensembl.variation.datamodel.VariationGroup
setSourceDatabase(String) - Method in interface org.ensembl.datamodel.Analysis
setSourceDatabaseFile(String) - Method in interface org.ensembl.datamodel.Analysis
setSourceDatabaseName(String) - Method in interface org.ensembl.datamodel.QtlSynonym
  Name of the database the synonym comes from.
setSourceDatabaseVersion(String) - Method in interface org.ensembl.datamodel.Analysis
setSourceID(String) - Method in interface org.ensembl.datamodel.QtlSynonym
  Identifier in the source database.
setSourceName(String) - Method in interface org.ensembl.compara.datamodel.Member
setSpecies(String) - Method in interface org.ensembl.datamodel.DnaDnaAlignFeature
setSpeciesSet(Set) - Method in interface org.ensembl.compara.datamodel.MethodLinkSpeciesSet
setSpeciesSetDBIDs(Set) - Method in interface org.ensembl.compara.datamodel.MethodLinkSpeciesSet
setSplicable(boolean) - Method in interface org.ensembl.datamodel.Gene
setStableID(String) - Method in interface org.ensembl.datamodel.StableIDEvent
setStableIDVersion(int) - Method in interface org.ensembl.datamodel.StableIDEvent
setStableId(String) - Method in interface org.ensembl.compara.datamodel.Domain
setStableId(String) - Method in interface org.ensembl.compara.datamodel.Family
setStableId(String) - Method in interface org.ensembl.compara.datamodel.Homology
setStableId(String) - Method in interface org.ensembl.compara.datamodel.Member
setStain(String) - Method in interface org.ensembl.datamodel.ChromosomeBand
setStain(String) - Method in interface org.ensembl.datamodel.KaryotypeBand
setStart(int) - Method in interface org.ensembl.compara.datamodel.GenomicAlign
setStart(int) - Method in class org.ensembl.datamodel.Location
  Sets the start.
setStartExon(Exon) - Method in interface org.ensembl.datamodel.Translation
setStartExonInternalID(long) - Method in interface org.ensembl.datamodel.Translation
  Sets startExon internal id, also sets the startExon.internalID if startExon is available.
setStartPhase(int) - Method in interface org.ensembl.datamodel.PredictionExon
setStatus(String) - Method in interface org.ensembl.datamodel.ExternalDatabase
setStatus(String) - Method in interface org.ensembl.datamodel.Gene
  Set the status this the gene.
setStatus(String) - Method in interface org.ensembl.datamodel.Transcript
  Set the status of the transcript.
setStrand(int) - Method in interface org.ensembl.compara.datamodel.GenomicAlign
setStrand(int) - Method in class org.ensembl.datamodel.Location
  Sets the strand.
setString(String) - Method in interface org.ensembl.datamodel.Sequence
setSubtype(String) - Method in interface org.ensembl.compara.datamodel.Homology
setSynonym(String) - Method in interface org.ensembl.datamodel.SubmittedVariation
setSynonyms(List) - Method in interface org.ensembl.datamodel.ExternalRef
setSynonyms(List) - Method in interface org.ensembl.datamodel.Marker
setSynoyms(List) - Method in interface org.ensembl.datamodel.Qtl
  Set QtlSynonyms.
setTargetIdentity(int) - Method in interface org.ensembl.datamodel.ExternalRef
setTaxonId(int) - Method in interface org.ensembl.compara.datamodel.GenomeDB
setTaxonId(long) - Method in interface org.ensembl.compara.datamodel.Member
setThreePrimeFlankingSeq(String) - Method in interface org.ensembl.variation.datamodel.Variation
setThresholdOnDs(double) - Method in interface org.ensembl.compara.datamodel.Homology
setTimestamp(String) - Method in interface org.ensembl.datamodel.MappingSession
setTrait(String) - Method in interface org.ensembl.datamodel.Qtl
  Phenotype of this Qtl.
setTransactionIsolation(int) - Method in class org.ensembl.util.ConnectionWrapper
setTranscript(PredictionTranscript) - Method in interface org.ensembl.datamodel.PredictionExon
setTranscript(Transcript) - Method in interface org.ensembl.datamodel.Translation
setTranscriptInternalID(long) - Method in interface org.ensembl.datamodel.Translation
  Sets transcript internal id, also sets the transcript.internalID if transcript is available.
setTranscripts(List) - Method in interface org.ensembl.datamodel.Exon
  Sets transcripts and transcriptInternalIDs.
setTranscriptsAndExons(List, List) - Method in interface org.ensembl.datamodel.Gene
setTranslation(Translation) - Method in interface org.ensembl.datamodel.ProteinFeature
setTranslation(Translation) - Method in interface org.ensembl.datamodel.Transcript
  Sets translation and translationInternalID.
setTranslationEnd(int) - Method in interface org.ensembl.datamodel.ProteinFeature
setTranslationInternalID(long) - Method in interface org.ensembl.datamodel.ProteinFeature
  Sets translation internal id, also sets the translation.internalID if translation is available.
setTranslationInternalID(long) - Method in interface org.ensembl.datamodel.Transcript
  Sets translation internal id, also sets the translation.internalID if translation is available.
setTranslationStart(int) - Method in interface org.ensembl.datamodel.ProteinFeature
setType(String) - Method in interface org.ensembl.compara.datamodel.MethodLink
setType(String) - Method in interface org.ensembl.datamodel.AssemblyElement
setType(String) - Method in interface org.ensembl.datamodel.Marker
setType(String) - Method in class org.ensembl.datamodel.Query
  Deprecated.
setType(String) - Method in interface org.ensembl.datamodel.RepeatConsensus
setType(String) - Method in interface org.ensembl.datamodel.StableIDEvent
  Type of event; gene, transcript or translaton.
setType(String) - Method in interface org.ensembl.variation.datamodel.VariationGroup
  Set the type of this group.
setTypeMap(Map) - Method in class org.ensembl.util.ConnectionWrapper
setUngappedAlignments(List) - Method in interface org.ensembl.datamodel.DnaDnaAlignFeature
setValue(String) - Method in interface org.ensembl.datamodel.Attribute
  Value of this attribute.
setVariation(Variation) - Method in interface org.ensembl.variation.datamodel.VariationFeature
setVariationConfig(Properties) - Method in class org.ensembl.registry.DriverGroup
  Configuration for the variation driver.
setVariationDriver(VariationDriver) - Method in interface org.ensembl.driver.CoreDriver
  Sets the variation driver on the driver.
setVariationInternalID(long) - Method in interface org.ensembl.variation.datamodel.VariationFeature
setVariationName(String) - Method in interface org.ensembl.variation.datamodel.VariationFeature
setVersion(int) - Method in interface org.ensembl.compara.datamodel.Member
setVersion(int) - Method in interface org.ensembl.datamodel.Accessioned
  Set the version of this object.
setVersion(String) - Method in class org.ensembl.datamodel.CoordinateSystem
  Deprecated. set this value in the appropriate constructor instead
setVersion(String) - Method in interface org.ensembl.datamodel.ExternalDatabase
setVersion(String) - Method in interface org.ensembl.datamodel.ExternalRef
showExternalRefsForAGene() - Method in class org.ensembl.Example
  Fetches a gene from the database and prints a summary of it's external refs if it has any.
size() - Method in class org.ensembl.datamodel.Location
  Returns number of elements in location list.
size() - Method in class org.ensembl.util.ListElement
size - Variable in class org.ensembl.util.LongList
size() - Method in class org.ensembl.util.LongList
size() - Method in class org.ensembl.util.PersistentSet
sizeOrUnset(Collection) - Static method in class org.ensembl.util.StringUtil
start(String) - Method in class org.ensembl.util.NamedTimer
  Start the timer.
start() - Method in class org.ensembl.util.Timer
stop(String) - Method in class org.ensembl.util.NamedTimer
  Stop a timer.
stop() - Method in class org.ensembl.util.Timer
store(GenomeDB) - Method in interface org.ensembl.compara.driver.GenomeDBAdaptor
store(GenomicAlign) - Method in interface org.ensembl.compara.driver.GenomicAlignAdaptor
store(MethodLink) - Method in interface org.ensembl.compara.driver.MethodLinkAdaptor
store(MethodLinkSpeciesSet) - Method in interface org.ensembl.compara.driver.MethodLinkSpeciesSetAdaptor
store(Analysis) - Method in interface org.ensembl.driver.AnalysisAdaptor
  Stores analysis.
store(CoordinateSystem) - Method in interface org.ensembl.driver.CoordinateSystemAdaptor
  Store the CoordinateSystem in the approriate data source and set the internalID.
store(DnaDnaAlignment) - Method in interface org.ensembl.driver.DnaDnaAlignmentAdaptor
  Stores the feature in the approriate data source.
store(DnaProteinAlignment) - Method in interface org.ensembl.driver.DnaProteinAlignmentAdaptor
  Stores feature.
store(Exon) - Method in interface org.ensembl.driver.ExonAdaptor
  Stores new exon in the data source.
store(ExternalDatabase) - Method in interface org.ensembl.driver.ExternalDatabaseAdaptor
store(ExternalRef) - Method in interface org.ensembl.driver.ExternalRefAdaptor
  Stores ExternalRef.
store(Gene) - Method in interface org.ensembl.driver.GeneAdaptor
  Store the gene in the approriate data source.
store(Marker) - Method in interface org.ensembl.driver.MarkerAdaptor
  Store the marker in the data source.
store(PredictionExon) - Method in interface org.ensembl.driver.PredictionExonAdaptor
store(PredictionTranscript) - Method in interface org.ensembl.driver.PredictionTranscriptAdaptor
store(ProteinFeature) - Method in interface org.ensembl.driver.ProteinFeatureAdaptor
store(RepeatConsensus) - Method in interface org.ensembl.driver.RepeatConsensusAdaptor
  Stores consensus.
store(RepeatFeature) - Method in interface org.ensembl.driver.RepeatFeatureAdaptor
store(Sequence) - Method in interface org.ensembl.driver.SequenceAdaptor
  Store the Sequence in data source.
store(Feature) - Method in interface org.ensembl.driver.SimpleFeatureAdaptor
  Attempts to store the feature in the approriate data source.
store(Feature, Connection) - Method in interface org.ensembl.driver.SimpleFeatureAdaptor
  Attempts to store the feature in the approriate data source.
store(StableIDEvent) - Method in interface org.ensembl.driver.StableIDEventAdaptor
store(Pair[], MappingSession) - Method in interface org.ensembl.driver.StableIDEventAdaptor
  Store unpacked StableIDPairs with session in database.
store(TranslationSnapShot, MappingSession) - Method in interface org.ensembl.driver.StableIDEventAdaptor
  Store the translation snapshot.
store(TranslationSnapShot[], MappingSession) - Method in interface org.ensembl.driver.StableIDEventAdaptor
  Store the translation snapshots.
store(GeneSnapShot, MappingSession) - Method in interface org.ensembl.driver.StableIDEventAdaptor
  Store the gene snapshot.
store(GeneSnapShot[], MappingSession) - Method in interface org.ensembl.driver.StableIDEventAdaptor
  Stores the genes.
store(StableIDEvent[]) - Method in interface org.ensembl.driver.StableIDEventAdaptor
  Stores stable id events, and there session, in database.
store(MappingSession) - Method in interface org.ensembl.driver.StableIDEventAdaptor
  If the session is new then it is added to the database.
store(Exon, List) - Method in interface org.ensembl.driver.SupportingFeatureAdaptor
  Stores links between exon and supporting features.
store(Transcript) - Method in interface org.ensembl.driver.TranscriptAdaptor
  Stores transcript plus it's exons and translation in persistent storage.
storeObjectExternalRefLink(long, int, long) - Method in interface org.ensembl.driver.ExternalRefAdaptor
  Stores a link between an ensembl object and an externalRef.
stringInArray(String, String[], boolean) - Static method in class org.ensembl.util.StringUtil
  Check if a String is in an array of Strings.
stringOrUnset(String) - Static method in class org.ensembl.util.StringUtil
stringToProperties(String, String) - Static method in class org.ensembl.util.PropertiesUtil
  Convenience method for creating a properties object from a string.
stringToURL(String) - Static method in class org.ensembl.util.PropertiesUtil
  Attempts to convert file location into a URL corresponding to a file in the local filesystem or in the classpath.
subSequence(int, int) - Method in interface org.ensembl.datamodel.Sequence

## T

THREE_PRIME_UTR - Static variable in class org.ensembl.variation.datamodel.AlleleConsequence
  Allele affects the 3prim UTR.
TRANSCRIPT - Static variable in interface org.ensembl.datamodel.ExternalRef
  Transcript type.
TRANSCRIPT - Static variable in interface org.ensembl.datamodel.StableIDEvent
TRANSLATION - Static variable in interface org.ensembl.datamodel.ExternalRef
  Translation type
TRANSLATION - Static variable in interface org.ensembl.datamodel.StableIDEvent
TYPE - Static variable in interface org.ensembl.compara.driver.DnaDnaAlignFeatureAdaptor
TYPE - Static variable in interface org.ensembl.compara.driver.DnaFragmentAdaptor
TYPE - Static variable in interface org.ensembl.compara.driver.GenomeDBAdaptor
TYPE - Static variable in interface org.ensembl.compara.driver.GenomicAlignAdaptor
TYPE - Static variable in interface org.ensembl.compara.driver.GenomicAlignBlockAdaptor
TYPE - Static variable in interface org.ensembl.compara.driver.HomologyAdaptor
TYPE - Static variable in interface org.ensembl.compara.driver.MemberAdaptor
TYPE - Static variable in interface org.ensembl.compara.driver.MethodLinkAdaptor
TYPE - Static variable in interface org.ensembl.compara.driver.MethodLinkSpeciesSetAdaptor
TYPE - Static variable in interface org.ensembl.driver.AnalysisAdaptor
  Name of the default AnalysisAdaptor available from a driver.
TYPE - Static variable in interface org.ensembl.driver.AssemblyExceptionAdaptor
TYPE - Static variable in interface org.ensembl.driver.AssemblyMapperAdaptor
TYPE - Static variable in interface org.ensembl.driver.CoordinateSystemAdaptor
  Name of the default CoordinateSystemAdaptor available from a driver.
TYPE - Static variable in interface org.ensembl.driver.DnaDnaAlignmentAdaptor
  Name of the default DnaDnaAlignmentAdaptor available from a driver.
TYPE - Static variable in interface org.ensembl.driver.DnaProteinAlignmentAdaptor
  Name of the default DnaProteinAlignmentAdaptor available from a driver.
TYPE - Static variable in interface org.ensembl.driver.ExonAdaptor
  Name of the default ExonAdaptor available from a driver.
TYPE - Static variable in interface org.ensembl.driver.ExternalDatabaseAdaptor
  Name of the default ExternalDatabaseAdaptor available from a driver.
TYPE - Static variable in interface org.ensembl.driver.ExternalRefAdaptor
  Name of the default ExternalEefAdaptor available from a driver.
TYPE - Static variable in interface org.ensembl.driver.GeneAdaptor
  Name of the default GeneAdaptor available from a driver.
TYPE - Static variable in interface org.ensembl.driver.KaryotypeBandAdaptor
  Name of the default KaryotypeAdaptor available from a driver.
TYPE - Static variable in interface org.ensembl.driver.LocationConverter
  Name of the default LocationConverteravailable from a driver.
TYPE - Static variable in interface org.ensembl.driver.MarkerAdaptor
  Name of the default MarkerAdaptor available from a driver.
TYPE - Static variable in interface org.ensembl.driver.MarkerFeatureAdaptor
TYPE - Static variable in interface org.ensembl.driver.MiscFeatureAdaptor
TYPE - Static variable in interface org.ensembl.driver.MiscSetAdaptor
TYPE - Static variable in interface org.ensembl.driver.OligoArrayAdaptor
TYPE - Static variable in interface org.ensembl.driver.OligoFeatureAdaptor
TYPE - Static variable in interface org.ensembl.driver.OligoProbeAdaptor
TYPE - Static variable in interface org.ensembl.driver.PredictionExonAdaptor
TYPE - Static variable in interface org.ensembl.driver.PredictionTranscriptAdaptor
TYPE - Static variable in interface org.ensembl.driver.ProteinFeatureAdaptor
  Name of the default ProteinFeatureAdaptor available from a driver.
TYPE - Static variable in interface org.ensembl.driver.QtlAdaptor
  Adaptor type.
TYPE - Static variable in interface org.ensembl.driver.QtlFeatureAdaptor
  Adaptor type.
TYPE - Static variable in interface org.ensembl.driver.RepeatConsensusAdaptor
  Name of the default RepeatConsensusAdaptor available from a driver.
TYPE - Static variable in interface org.ensembl.driver.RepeatFeatureAdaptor
  Name of the default RepeatFeatureAdaptor available from a driver.
TYPE - Static variable in interface org.ensembl.driver.SequenceAdaptor
  Name of the default SequenceAdaptor available from a driver.
TYPE - Static variable in interface org.ensembl.driver.SequenceRegionAdaptor
  Name of the default SequenceRegionAdaptor available from a driver.
TYPE - Static variable in interface org.ensembl.driver.SimpleFeatureAdaptor
  Name of the default SimpleFeatureAdaptor available from a driver.
TYPE - Static variable in interface org.ensembl.driver.StableIDEventAdaptor
  Name of the default StableIDEventAdaptor available from a driver.
TYPE - Static variable in interface org.ensembl.driver.SupportingFeatureAdaptor
  Name of the default SupportingFeatureAdaptor available from a driver.
TYPE - Static variable in interface org.ensembl.driver.TranscriptAdaptor
  Name of the default TranscriptAdaptor available from a driver.
TYPE - Static variable in interface org.ensembl.driver.TranslationAdaptor
  Name of the default TranslationAdaptor available from a driver.
TYPE - Static variable in interface org.ensembl.variation.datamodel.AlleleConsequenceAdaptor
TYPE - Static variable in interface org.ensembl.variation.driver.AlleleFeatureAdaptor
TYPE - Static variable in interface org.ensembl.variation.driver.AlleleGroupAdaptor
TYPE - Static variable in interface org.ensembl.variation.driver.IndividualAdaptor
TYPE - Static variable in interface org.ensembl.variation.driver.IndividualGenotypeAdaptor
TYPE - Static variable in interface org.ensembl.variation.driver.LDFeatureAdaptor
TYPE - Static variable in interface org.ensembl.variation.driver.PopulationAdaptor
TYPE - Static variable in interface org.ensembl.variation.driver.PopulationGenotypeAdaptor
TYPE - Static variable in interface org.ensembl.variation.driver.TranscriptVariationAdaptor
TYPE - Static variable in interface org.ensembl.variation.driver.VariationAdaptor
TYPE - Static variable in interface org.ensembl.variation.driver.VariationFeatureAdaptor
  Name of the default variation feature adaptor available from a driver.
TYPE - Static variable in interface org.ensembl.variation.driver.VariationGroupAdaptor
TYPE - Static variable in interface org.ensembl.variation.driver.VariationGroupFeatureAdaptor
Timer - class org.ensembl.util.Timer.
  Event timer.
Timer(boolean) - Constructor for class org.ensembl.util.Timer
Timer() - Constructor for class org.ensembl.util.Timer
  Creates timer in non-paranoid mode.
Transcript - interface org.ensembl.datamodel.Transcript.
  Transcript.
TranscriptAdaptor - interface org.ensembl.driver.TranscriptAdaptor.
  Provides access to Transcripts in the datasource.
TranscriptAlleleHelper - class org.ensembl.datamodel.TranscriptAlleleHelper.
  Denormalised representation of the transcript optimised for answering questions about variations.
TranscriptAlleleHelper(Transcript) - Constructor for class org.ensembl.datamodel.TranscriptAlleleHelper
  Denormalise relevant information from transcript.
TranscriptSnapShot - interface org.ensembl.datamodel.TranscriptSnapShot.
  Represents part of the state of a transcript at some point in time.
TranscriptVariation - interface org.ensembl.variation.datamodel.TranscriptVariation.
  A TranscriptVariation object represents a variation feature which is in close proximity to an Ensembl transcript.
TranscriptVariationAdaptor - interface org.ensembl.variation.driver.TranscriptVariationAdaptor.
  This adaptor provides database connectivity for TranscriptVariation objects.
Translation - interface org.ensembl.datamodel.Translation.
  Translation.
TranslationAdaptor - interface org.ensembl.driver.TranslationAdaptor.
  Provides access to Translations in the datasource.
TranslationSnapShot - interface org.ensembl.datamodel.TranslationSnapShot.
  Represents part of the state of a translation at some point in time.
testConnection() - Method in interface org.ensembl.driver.EnsemblDriver
  Checks whether a connection can be made to the database.
throwableToStackTraceString(Throwable) - Static method in class org.ensembl.util.Util
toAlleleConsequences(List) - Method in class org.ensembl.datamodel.TranscriptAlleleHelper
  Converts one or more alleleFeatures into alleleConsequences.
toAlleleConsequences(AlleleFeature) - Method in class org.ensembl.datamodel.TranscriptAlleleHelper
  Converts an alleleFeature into zero or more alleleConsequences.
toArray() - Method in class org.ensembl.util.LongList
toArray() - Method in class org.ensembl.util.PersistentSet
toArray(Object[]) - Method in class org.ensembl.util.PersistentSet
toCommaSeparatedString() - Method in class org.ensembl.util.IDList
toCommaSeparatedString() - Method in class org.ensembl.util.LongList
  Comma separated list of items in list.
toList() - Method in class org.ensembl.util.PersistentSet
toSortedInternalIDArray() - Method in class org.ensembl.util.LocatableList
  Sorts locatable's by genomic location and returns an array of the locatable's internalIDs.
toString() - Method in class org.ensembl.datamodel.AssemblyException
toString() - Method in class org.ensembl.datamodel.AssemblyLocation
  Deprecated.
toString() - Method in class org.ensembl.datamodel.CloneFragmentLocation
toString() - Method in class org.ensembl.datamodel.CoordinateSystem
  Return a string representation of this object
toString() - Method in class org.ensembl.datamodel.CoordinateSystemMapping
toString() - Method in class org.ensembl.datamodel.Location
  Converts all nodes into a string.
toString(boolean, boolean) - Method in class org.ensembl.datamodel.Location
  Converts this node into a string.
toString(boolean, boolean, boolean) - Method in class org.ensembl.datamodel.Location
  Converts this node into a string.
toString() - Method in class org.ensembl.datamodel.Query
  Deprecated.
toString() - Method in class org.ensembl.datamodel.TranscriptAlleleHelper
toString(String) - Method in class org.ensembl.datamodel.TranscriptAlleleHelper
toString() - Method in class org.ensembl.registry.DriverGroup
toString() - Method in class org.ensembl.registry.Registry
toString() - Method in class org.ensembl.util.ConnectionPoolDataSource
toString() - Method in class org.ensembl.util.ConnectionWrapper
toString(ResultSet) - Static method in class org.ensembl.util.JDBCUtil
toString(int) - Method in class org.ensembl.util.ListElement
toString() - Method in class org.ensembl.util.ListElement
toString() - Method in class org.ensembl.util.LruCache
toString() - Method in class org.ensembl.util.Pair
toString() - Method in class org.ensembl.util.PersistentSet
toString(Properties) - Static method in class org.ensembl.util.PropertiesUtil
  Sorts pairs by key name and prints one name = value pair per line.
toString(long[]) - Static method in class org.ensembl.util.StringUtil
  Convenience method for converting an array of longs into a string of numbers separated by commas.
toString(long[], boolean) - Static method in class org.ensembl.util.StringUtil
  Convenience method for converting an array of longs into a string of numbers separated by commas.
toString(int[]) - Static method in class org.ensembl.util.StringUtil
toString(String[]) - Static method in class org.ensembl.util.StringUtil
toString(Collection) - Static method in class org.ensembl.util.StringUtil
toString(Collection, String) - Static method in class org.ensembl.util.StringUtil
toString(Object[]) - Static method in class org.ensembl.util.StringUtil
toString(Object[], String) - Static method in class org.ensembl.util.StringUtil
toString() - Method in class org.ensembl.util.SystemUtil.MemoryStatus
toString(Object[]) - Static method in class org.ensembl.util.SystemUtil
  Converts each element in the array to a string via element.toString() and creates a formated string containing all the strings.
toString(int[]) - Static method in class org.ensembl.util.SystemUtil
  Converts array into a string representation.
toString() - Method in class org.ensembl.util.Timer
  Returns duration in seconds.
toString() - Method in class org.ensembl.variation.datamodel.AlleleConsequence
toString() - Method in class org.ensembl.variation.datamodel.ValidationState
toStringMb() - Method in class org.ensembl.util.SystemUtil.MemoryStatus
to_longArray() - Method in class org.ensembl.util.LongSet
to_longArray(boolean) - Method in class org.ensembl.util.LongSet
to_longArray(Collection) - Static method in class org.ensembl.util.LongSet
  Creates an Array from a collection of Longs.
total - Variable in class org.ensembl.util.SystemUtil.MemoryStatus
transform(int, int) - Method in class org.ensembl.datamodel.Location
  Transforms this location into another by changing the start and end positions.
transformNode(int, int) - Method in class org.ensembl.datamodel.Location
  Resizes location node taking into account the strand and ignoring rest of location list if present.
translate() - Method in interface org.ensembl.datamodel.PredictionTranscript
  Translate the prediction transcript
type - Variable in class org.ensembl.util.Pair

## U

UPSTREAM - Static variable in class org.ensembl.variation.datamodel.AlleleConsequence
  Allele appears upstream of the transcript.
UngappedAlignment - interface org.ensembl.datamodel.UngappedAlignment.
  Alignment to external reference.
Util - class org.ensembl.util.Util.
  General utilities that don't fit elsewhere.
Util() - Constructor for class org.ensembl.util.Util
update(int) - Method in class org.ensembl.util.ProgressPrinter
  Update the current value.
used - Variable in class org.ensembl.util.SystemUtil.MemoryStatus

## V

ValidationState - class org.ensembl.variation.datamodel.ValidationState.
  Possible Validation states of a Variation.
Variation - interface org.ensembl.variation.datamodel.Variation.
  A nucleotide variation such as a SNP.
VariationAdaptor - interface org.ensembl.variation.driver.VariationAdaptor.
  The point of this class is ...
VariationDriver - interface org.ensembl.variation.driver.VariationDriver.
  The point of this class is ...
VariationDriverFactory - class org.ensembl.variation.driver.VariationDriverFactory.
  Factory class that creates ensembl Variation driver implementation instances.
VariationFeature - interface org.ensembl.variation.datamodel.VariationFeature.
  This is a an occurrence of a nucleotide variation in the genome.
VariationFeatureAdaptor - interface org.ensembl.variation.driver.VariationFeatureAdaptor.
  Adaptor for retrieving VariationFeatures.
VariationGroup - interface org.ensembl.variation.datamodel.VariationGroup.
  Grouping of variations (aka haplotype set).
VariationGroupAdaptor - interface org.ensembl.variation.driver.VariationGroupAdaptor.
  Retrieves Variation groups from an ensembl database.
VariationGroupFeature - interface org.ensembl.variation.datamodel.VariationGroupFeature.
  The point of this class is....
VariationGroupFeatureAdaptor - interface org.ensembl.variation.driver.VariationGroupFeatureAdaptor.
  This adaptor provides database connectivity for VariationGroupFeature objects.
Version - class org.ensembl.util.Version.
  Program and function to report ensj build version.
Version() - Constructor for class org.ensembl.util.Version
valueOf(String) - Static method in class org.ensembl.datamodel.AssemblyLocation
  Deprecated.
valueOf(String) - Static method in class org.ensembl.datamodel.CloneFragmentLocation
values() - Method in class org.ensembl.util.LruCache

## W

Warnings - class org.ensembl.util.Warnings.
  Utility class for issuing warnings.
Warnings() - Constructor for class org.ensembl.util.Warnings
writeObject(Object, String) - Static method in class org.ensembl.util.SerialUtil
  Write an object to a file.
writeObject(Object, File) - Static method in class org.ensembl.util.SerialUtil
writeSequence(byte) - Method in class org.ensembl.util.FormattedSequencePrintStream
  Write out a byte of sequence, with formatting.
writeSequence(byte[]) - Method in class org.ensembl.util.FormattedSequencePrintStream
  write an entire byte[] object containing sequence, with formatting.
writeSequence(byte[], int, int) - Method in class org.ensembl.util.FormattedSequencePrintStream
  write a portion of a byte[] object containing sequence, with formatting.
writeToFile(Properties, String, String) - Static method in class org.ensembl.util.PropertiesUtil
  Write some properties to file.

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