Package org.ensembl.driver

Driver and adaptors for accessing ensembl core databases.

See:
Description

Interface Summary

Adaptor	Provides access to some datatype in some datasource.
AffyArrayAdaptor	Adaptor for retrieving AffyArrays.
AffyFeatureAdaptor	Adaptor for retrieving AffyFeatures from a database.
AffyProbeAdaptor	Adaptor for retrieving AffyProbes from the database.
AnalysisAdaptor	Provides access to Analyses in the datasource.
AssemblyExceptionAdaptor	Adaptor for retrieving and handling AssemblyExceptions which are used to represent PARs and haplotypes.
AssemblyMapperAdaptor
CoordinateSystemAdaptor	Provides access to coordinate system and meta data in the datasource(s).
CoreDriver	Provides adaptors for accessing to ensembl core databases.
DnaDnaAlignmentAdaptor	Provides access to DnaDnaAlignments in a datasource.
DnaProteinAlignmentAdaptor	Provides access to DnaProteinAlignments in a datasource.
Driver	Deprecated. Deprecated in version 29.2, use org.ensembl.driver.CoreDriver instead.
EnsemblDriver	An ensembl driver provides access to an ensembl database through it's adaptors.
ExonAdaptor	Provides access to Exons in the datasource.
ExternalDatabaseAdaptor	Provides access to ExternalDatabases in the datasource.
ExternalRefAdaptor	Provides access to ExternalRefs in the datasource.
FeatureAdaptor	Provides access to a datatype that is Locatable so can be fetched by location.
GeneAdaptor	Provides access to genes in the datasource.
KaryotypeBandAdaptor
LocationConverter	Converts locations between different coordinate systems.
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.
MarkerAdaptor	Provides access to Markers in the datasource.
MarkerFeatureAdaptor
MiscFeatureAdaptor	Adaptor for retrieving MiscFeatures.
MiscSetAdaptor
PredictionExonAdaptor
PredictionTranscriptAdaptor	Provides access to PredictionTranscripts in the datasource.
ProteinFeatureAdaptor	Provides access to ProteinFeatures in the datasource.
QtlAdaptor	Retrieves Qtls from the database.
QtlFeatureAdaptor	Retrieves QtlFeatures from the database.
RepeatConsensusAdaptor	Provides access to RepeatConsensus' in the datasource.
RepeatFeatureAdaptor	Provides access to RepeatFeatures in the datasource.
SequenceAdaptor	Provides access to Sequence in the datasource.
SequenceRegionAdaptor	Adaptor for SequenceRegion objects.
SimpleFeatureAdaptor	Provides access to SimpleFeatures in the datasource.
StableIDEventAdaptor	Provides access to StableIDEvents in the datasource.
SupportingFeatureAdaptor	Provides access to SupportingFeatures in the datasource.
TranscriptAdaptor	Provides access to Transcripts in the datasource.
TranslationAdaptor	Provides access to Translations in the datasource.

Class Summary

CoreDriverFactory	Factory class that creates ensembl core driver implementation instances.
DriverManager	Utility for creating drivers from a Properties format configuration files.
FeatureIterator	Provides an iterator over features from a FeatureAdaptor.
LoggingManager	Utility class to simplify logging system configuration.
ServerDriver	Driver providing access to an ensembl database server.
ServerDriverFactory	Factory for producing, or retrieving from a cached, ServerDrivers.

Exception Summary

AdaptorException	Thrown when a problem occurs running code in ensj.
ConfigurationException	Thrown when an illegal configuration is used.
RuntimeAdaptorException	Thrown when an problem occurs executing a method on an adaptor.

Package org.ensembl.driver Description

Driver and adaptors for accessing ensembl core databases.

The Driver and adaptors specify interfaces which can be implemented to provide access to specific datasources.

Implementations for other datasources such as flat files or an Oracle database could also be added by implementing relevant adaptors and, where necessary, a driver. This provides an extensible means for seamlessly loading 3rd party data into native Ensembl datatypes as well as supporting instances of ensembl data in non-mysql databases.