Uses of Class
uk.ac.roslin.ensembl.exception.DAOException

Packages that use DAOException

Package	Description
uk.ac.roslin.ensembl.dao
uk.ac.roslin.ensembl.dao.compara
uk.ac.roslin.ensembl.dao.coreaccess
uk.ac.roslin.ensembl.dao.database
uk.ac.roslin.ensembl.dao.database.compara
uk.ac.roslin.ensembl.dao.database.coreaccess
uk.ac.roslin.ensembl.dao.database.factory
uk.ac.roslin.ensembl.dao.database.variation
uk.ac.roslin.ensembl.dao.factory
uk.ac.roslin.ensembl.dao.variation
uk.ac.roslin.ensembl.datasourceaware.core
uk.ac.roslin.ensembl.demo
uk.ac.roslin.ensembl.model.core
uk.ac.roslin.ensembl.model.database

Uses of DAOException in uk.ac.roslin.ensembl.dao

Methods in uk.ac.roslin.ensembl.dao that throw DAOException

Modifier and Type	Method and Description
List<String>	DatabaseDAO.getAllCoreDatabasesForVersion(int dbVersion)
TreeSet<String>	XRefDAO.getAllSynonyms(XRefed object)
List<? extends XRef>	XRefDAO.getAllXRefs(IdentifiableObject feature)
HashMap<Integer,? extends Analysis>	AnalysisDAO.getAnalyses()
CollectionOfSpecies	DatabaseDAO.getCollectionSpeciesProperties(CollectionCoreDatabase database)
List<String>	DatabaseDAO.getDatabases()
Species	DatabaseDAO.getSpeciesProperties(SingleSpeciesCoreDatabase database)
TreeSet<String>	XRefDAO.getSynonyms(XRef xref)

Uses of DAOException in uk.ac.roslin.ensembl.dao.compara

Methods in uk.ac.roslin.ensembl.dao.compara that throw DAOException

Modifier and Type	Method and Description
List<? extends HomologyPairRelationship>	HomologyDAO.getHomologiesForGene(Gene g) Specification of Data Access method to retrieve all of the homologies (i.e. to all species) for a given gene with a stableID.
List<? extends HomologyPairRelationship>	HomologyDAO.getHomologiesForGenesBySpecies(List<? extends Gene> genes, Species target_sp, String chrName) Specification of Data Access method to retrieve all of the homologies in the specified target species for a List of genes with stableIDs.
HashMap<? extends DNASequence,? extends MappingSet>	HomologyDAO.getRegionsOfConservedSynteny(DNASequence source, Coordinate range, Species target) Specification of Data Access method to retrieve all of the regions on DNASequences for the specified target species, holding genes with homologies to genes found in the given region of the source query sequence.
HashMap<? extends DNASequence,? extends MappingSet>	HomologyDAO.getRegionsOfConservedSynteny(DNASequence source, Coordinate range, Species target, String chrName) Specification of Data Access method to retrieve any potential region of conserved synteny on a given Chromosome/fragment for the specified target species, holding genes with homologies to genes found in the given region of the source query sequence.

Uses of DAOException in uk.ac.roslin.ensembl.dao.coreaccess

Methods in uk.ac.roslin.ensembl.dao.coreaccess that throw DAOException

Modifier and Type	Method and Description
Gene	GeneDAO.addGeneByIDOnParent(Integer id, DNASequence parent)
Gene	GeneDAO.addGeneByStableIDOnParent(String stableID, DNASequence parent)
Chromosome	ChromosomeDAO.getChromosomeByName(String name)
List<? extends Chromosome>	ChromosomeDAO.getChromosomes()
MappingSet	AssemblyDAO.getComponentMappingsByStartStop(DNASequence assembledSequence, Integer start, Integer stop)
List<? extends CoordinateSystem>	CoordinateSystemDAO.getCoordinateSystems()
Exon	ExonDAO.getExonByID(Integer id)
Exon	ExonDAO.getExonByStableID(String stableID)
List<? extends Exon>	ExonDAO.getExonsForTranscript(Transcript transcript)
AssembledDNASequence	ChromosomeDAO.getFragmentByName(String name)
List<? extends AssembledDNASequence>	ChromosomeDAO.getFragments()
String	DNASequenceDAO.getFullSequence(EnsemblDNASequenceReader reader)
Gene	GeneDAO.getGeneByID(Integer id)
Gene	GeneDAO.getGeneByStableID(String stableId)
List<? extends Mapping>	GeneDAO.getGeneMappingsOnRegion(DNASequence region, Coordinate coords)
List<? extends Gene>	GeneDAO.getGenesByExactName(String name)
List<? extends Gene>	GeneDAO.getGenesByNameBeginning(String name)
List<? extends Gene>	GeneDAO.getGenesForVegaID(String id)
MappingSet	AssemblyDAO.getPARMappingsByStartStop(Chromosome chr, Integer start, Integer stop)
List<? extends ProteinFeature>	ProteinFeatureDAO.getProteinFeaturesByTranslationID(int translationID)
DNASequence	DNASequenceDAO.getSequenceByID(Integer id)
String	DNASequenceDAO.getSequenceByStartStop(EnsemblDNASequenceReader reader, Integer start, Integer stop)
Chromosome	ChromosomeDAO.getSexLinkedChromosome(Chromosome chr)
Transcript	TranscriptDAO.getTranscriptByID(Integer id)
Transcript	TranscriptDAO.getTranscriptByStableID(String stableID)
List<? extends Transcript>	TranscriptDAO.getTranscriptsForCcdsID(String id) Returns a list of Ensembl Transcripts matching the query CCDS ID string.
List<? extends Transcript>	TranscriptDAO.getTranscriptsForGene(Gene gene)
List<? extends Transcript>	TranscriptDAO.getTranscriptsForVegaID(String id) Returns a list of Ensembl Transcripts matching the query VegaID string.
Translation	TranslationDAO.getTranslationByID(Integer id)
Translation	TranslationDAO.getTranslationByStableID(String stableID)
List<? extends Translation>	TranslationDAO.getTranslationsForTranscript(Transcript transcript)
List<? extends Translation>	TranslationDAO.getTranslationsForVegaID(String id)
DNASequence	DNASequenceDAO.getValidatedSequence(DNASequence seq)
List<? extends DNASequence>	DNASequenceDAO.getValidatedSequences(List<? extends DNASequence> sequences)
void	ReInitializationDAO.reInitialize(IdentifiableObject object)
void	ChromosomeDAO.setAssemblyExceptions(TreeMap<String,? extends Chromosome> chrs)
void	CoordinateSystemDAO.setFeatureCS()

Uses of DAOException in uk.ac.roslin.ensembl.dao.database

Methods in uk.ac.roslin.ensembl.dao.database that throw DAOException

Modifier and Type	Method and Description
static DBRegistry	DBRegistry.createRegistryForConfiguration(RegistryConfiguration conf)
static DBRegistry	DBRegistry.createRegistryForDataSource(DBConnection.DataSource type)
static DBRegistry	DBRegistry.createRegistryForDataSourceAtReleaseVersion(DBConnection.DataSource type, Integer release)
static DBRegistry	DBRegistry.createRegistryForDataSourceCurrentRelease(DBConnection.DataSource type)
static DBRegistry	DBRegistry.createUninitializedRegistryForConfiguration(RegistryConfiguration conf)
static DBRegistry	DBRegistry.createUninitializedRegistryForDataSource(DBConnection.DataSource type)
TreeSet<String>	DBXRefDAO.getAllSynonyms(XRefed object)
List<DAXRef>	DBXRefDAO.getAllXRefs(IdentifiableObject feature)
HashMap<Integer,DAAnalysis>	DBSingleSpeciesCoreDatabase.getAnalyses() Analyses are cached at the Database level
HashMap<Integer,DAAnalysis>	DBCollectionCoreDatabase.getAnalyses() Analyses are cached at the Database level
HashMap<Integer,DAAnalysis>	DBAnalysisDAO.getAnalyses()
DACoordinateSystem	DBCollectionCoreDatabase.getBuildCoordSystem(Species species, String featureType)
DACoordinateSystem	DBSingleSpeciesCoreDatabase.getBuildCoordSystem(String featureType)
String	DBCollectionCoreDatabase.getBuildLevel(Species species, String featureKey)
String	DBSingleSpeciesCoreDatabase.getBuildLevel(String featureType)
DAChromosome	DBCollectionCoreDatabase.getChromosomeByName(Species species, String name)
DAChromosome	DBSpecies.getChromosomeByName(String name)
DAChromosome	DBSingleSpeciesCoreDatabase.getChromosomeByName(String name)
DAChromosome	DBSpecies.getChromosomeByName(String name, String dbVersion)
DAChromosome	DBCollectionSpecies.getChromosomeByName(String name, String dbVersion)
DACoordinateSystem	DBSingleSpeciesCoreDatabase.getChromosomeLevelCoordSystem()
DACoordinateSystem	DBCollectionCoreDatabase.getChromosomeLevelCS(Species species)
TreeMap<String,DAChromosome>	DBSpecies.getChromosomes()
List<DAChromosome>	DBSingleSpeciesCoreDatabase.getChromosomes() Note that Chromosomes are not cached by the Database object - but by the Species Object
List<DAChromosome>	DBCollectionCoreDatabase.getChromosomes(Species species)
TreeMap<String,DAChromosome>	DBSpecies.getChromosomes(String dbVersion)
TreeMap<String,DAChromosome>	DBCollectionSpecies.getChromosomes(String dbVersion)
List<DACoordinateSystem>	DBSingleSpeciesCoreDatabase.getCoordinateSystems()
DACoordinateSystem	DBSingleSpeciesCoreDatabase.getCSByID(Integer id)
DACoordinateSystem	DBCollectionCoreDatabase.getCSByID(Species species, Integer id)
Set<DACoordinateSystem>	DBSingleSpeciesVariationDatabase.getCSForFeature(ObjectType featureType)
Set<DACoordinateSystem>	DBSingleSpeciesCoreDatabase.getCSForFeature(ObjectType featureType)
Set<DACoordinateSystem>	DBCollectionCoreDatabase.getCSForFeature(Species sp, ObjectType feature)
List<FeatureType>	DBSingleSpeciesVariationDatabase.getFeaturesForCS(CoordinateSystem coordSys)
List<FeatureType>	DBSingleSpeciesCoreDatabase.getFeaturesForCS(CoordinateSystem coordSys)
List<FeatureType>	DBCollectionCoreDatabase.getFeaturesForCS(Species sp, CoordinateSystem coordSys)
DAAssembledDNASequence	DBCollectionCoreDatabase.getFragmentByName(Species species, String name)
DAAssembledDNASequence	DBSpecies.getFragmentByName(String name)
DAAssembledDNASequence	DBSingleSpeciesCoreDatabase.getFragmentByName(String name) a Fragment is TopLevelAssembledDNASequence ( where there are no chromosomes )
DAAssembledDNASequence	DBSpecies.getFragmentByName(String name, String dbVersion)
DAAssembledDNASequence	DBCollectionSpecies.getFragmentByName(String name, String dbVersion)
TreeMap<String,DAAssembledDNASequence>	DBSpecies.getFragments()
List<DAAssembledDNASequence>	DBSingleSpeciesCoreDatabase.getFragments() Fragments are TopLevelAssembledDNASequences
List<DAAssembledDNASequence>	DBCollectionCoreDatabase.getFragments(Species species)
TreeMap<String,DAAssembledDNASequence>	DBSpecies.getFragments(String dbVersion)
TreeMap<String,DAAssembledDNASequence>	DBCollectionSpecies.getFragments(String dbVersion)
DAGene	DBSpecies.getGeneByStableID(String stableID)
DAGene	DBSpecies.getGeneByStableID(String stableID, String dbVersion)
DAGene	DBCollectionSpecies.getGeneByStableID(String stableID, String dbVersion)
List<DAGene>	DBSpecies.getGenesForExactName(String name)
List<DAGene>	DBSpecies.getGenesForExactName(String name, String dbVersion)
List<DAGene>	DBCollectionSpecies.getGenesForExactName(String name, String dbVersion)
List<DAGene>	DBSpecies.getGenesForNameBeginning(String name)
List<DAGene>	DBSpecies.getGenesForNameBeginning(String name, String dbVersion)
List<DAGene>	DBSpecies.getGenesForVegaID(String vegaID) Method returns a List of Genes that have been mapped to the given Vega Identifier.
List<DAGene>	DBSpecies.getGenesForVegaID(String vegaID, String dbVersion) Method returns a List of Genes that have been mapped to the given Vega Identifier.
List<DAGene>	DBCollectionSpecies.getGenesForVegaID(String vegaID, String dbVersion) Method returns a List of Genes that have been mapped to the given Vega Identifier.
int	DBRegistry.getHighestEnsemblSchemaVersion()
int	DBRegistry.getHighestReleaseVersion()
Integer	DBSingleSpeciesVariationDatabase.getMaxLengthForFeature(ObjectType featureType, CoordinateSystem cs)
Integer	DBSingleSpeciesCoreDatabase.getMaxLengthForFeature(ObjectType featureType, CoordinateSystem cs)
Integer	DBCollectionCoreDatabase.getMaxLengthForFeature(Species sp, ObjectType feature, CoordinateSystem cs)
org.apache.ibatis.session.SqlSession	DBDatabase.getNewSqlSession()
DACoordinateSystem	DBSingleSpeciesCoreDatabase.getSequenceLevelCoordSystem()
DACoordinateSystem	DBCollectionCoreDatabase.getSequenceLevelCS(Species species)
protected org.apache.ibatis.session.SqlSessionFactory	DBDatabase.getSessionFactory()
TreeSet<String>	DBXRefDAO.getSynonyms(XRef xref)
DACoordinateSystem	DBSingleSpeciesCoreDatabase.getTopLevelCoordSystem()
DACoordinateSystem	DBCollectionCoreDatabase.getTopLevelCS(Species species)
DATranscript	DBSpecies.getTranscriptByStableID(String stableID)
DATranscript	DBSpecies.getTranscriptByStableID(String stableID, String dbVersion)
DATranscript	DBCollectionSpecies.getTranscriptByStableID(String stableID, String dbVersion)
List<DATranscript>	DBSpecies.getTranscriptsForCcdsID(String ccdsID)
List<DATranscript>	DBSpecies.getTranscriptsForCcdsID(String ccdsID, String dbVersion) Method returns a List of Transcripts that have been mapped to the given CCDS Identifier (This may be the CCDS accession or the CCDS accession.version).
List<DATranscript>	DBCollectionSpecies.getTranscriptsForCcdsID(String ccdsID, String dbVersion) Method returns a List of Transcripts that have been mapped to the given CCDS Identifier (This may be the CCDS accession or the CCDS accession.schemaVersion).
List<DATranscript>	DBSpecies.getTranscriptsForVegaID(String vegaID) Method returns a List of Transcripts that have been mapped to the given Vega Identifier.
List<DATranscript>	DBSpecies.getTranscriptsForVegaID(String vegaID, String dbVersion) Method returns a List of Transcripts that have been mapped to the given Vega Identifier.
List<DATranscript>	DBCollectionSpecies.getTranscriptsForVegaID(String vegaID, String dbVersion) Method returns a List of Transcripts that have been mapped to the given Vega Identifier.
DATranslation	DBSpecies.getTranslationByStableID(String stableID)
DATranslation	DBSpecies.getTranslationByStableID(String stableID, String dbVersion)
DATranslation	DBCollectionSpecies.getTranslationByStableID(String stableID, String dbVersion)
List<DATranslation>	DBSpecies.getTranslationsForVegaID(String vegaID) Method returns a List of Translations that have been mapped to the given Vega Identifier.
List<DATranslation>	DBSpecies.getTranslationsForVegaID(String vegaID, String dbVersion) Method returns a List of Translations that have been mapped to the given Vega Identifier.
List<DATranslation>	DBCollectionSpecies.getTranslationsForVegaID(String vegaID, String dbVersion) Method returns a List of Translations that have been mapped to the given Vega Identifier.
void	DBRegistry.initialize(Integer release) private initialisation method for the registry which connects to ensembl via a DBDatasourceDAO and retrieves details on all the current tables and creates database objects of the appropriate type for each.
void	DBSingleSpeciesCoreDatabase.lazyLoadMetadata()
void	DBXRefDAO.reInitialize(IdentifiableObject xref) Uses the xref_id of an xref to fill in missing data that would have been present if the the xref had initially been made by a call to getXRefs on the identifiable object.
void	DBSpecies.setAssemblyExceptions(String version)
void	DBCollectionSpecies.setAssemblyExceptions(String version)
void	DBRegistry.setConfiguration(DBConnection.DataSource type)
void	DBRegistry.setConfiguration(RegistryConfiguration conf)
void	DBRegistry.setSpeciesMetadata(CoreDatabase db) should only be called for non current singlespecies core databases

Constructors in uk.ac.roslin.ensembl.dao.database that throw DAOException

Constructor and Description
DBAnalysisDAO(DAOFactory factory)
DBBaseDAO(DAOFactory inFactory) Constructor for (subclasses of) this class.
DBBaseDAO(Properties inConfiguration) Constructor for (subclasses of) this class.
DBXRefDAO(DAOFactory factory)

Uses of DAOException in uk.ac.roslin.ensembl.dao.database.compara

Methods in uk.ac.roslin.ensembl.dao.database.compara that throw DAOException

Modifier and Type	Method and Description
List<DAHomologyPairRelationship>	DBHomologyDAO.getHomologiesForGene(Gene g) Data Access method to retrieve all of the homologies (i.e. to all species) for a given gene with a stableID.
List<DAHomologyPairRelationship>	DBHomologyDAO.getHomologiesForGenesBySpecies(List<? extends Gene> genes, Species target_sp, String chrName) Data Access method to retrieve all of the homologies in the specified target species for a List of genes with stableIDs.
HashMap<DADNASequence,MappingSet>	DBHomologyDAO.getRegionsOfConservedSynteny(DNASequence source, Coordinate range, Species target) Data Access method to retrieve all of the regions on DNASequences for the specified target species, holding genes with homologies to genes found in the given region of the source query sequence.
HashMap<DADNASequence,MappingSet>	DBHomologyDAO.getRegionsOfConservedSynteny(DNASequence source, Coordinate range, Species target, String chrName) Data Access method to retrieve any potential region of conserved synteny on a given Chromosome/fragment for the specified target species, holding genes with homologies to genes found in the given region of the source query sequence.

Constructors in uk.ac.roslin.ensembl.dao.database.compara that throw DAOException

Constructor and Description
DBHomologyDAO(DAOComparaFactory factory)

Uses of DAOException in uk.ac.roslin.ensembl.dao.database.coreaccess

Methods in uk.ac.roslin.ensembl.dao.database.coreaccess that throw DAOException

Modifier and Type	Method and Description
DAGene	DBGeneDAO.addGeneByIDOnParent(Integer id, DNASequence parent)
DAGene	DBGeneDAO.addGeneByStableIDOnParent(String stableID, DNASequence parent) The gene returned has mapping to a sequence region - and the id for the coordinate system that this region belongs to
DAChromosome	DBChromosomeDAO.getChromosomeByName(String name)
List<DAChromosome>	DBChromosomeDAO.getChromosomes()
MappingSet	DBAssemblyDAO.getComponentMappingsByStartStop(DNASequence assembledSequence, Integer begin, Integer stop)
List<DACoordinateSystem>	DBCoordinateSystemDAO.getCoordinateSystems()
DAExon	DBExonDAO.getExonByID(Integer id)
DAExon	DBExonDAO.getExonByStableID(String stableID)
List<DAExon>	DBExonDAO.getExonsForTranscript(Transcript transcript)
DAAssembledDNASequence	DBChromosomeDAO.getFragmentByName(String name)
List<DAAssembledDNASequence>	DBChromosomeDAO.getFragments()
String	DBDNASequenceDAO.getFullSequence(EnsemblDNASequenceReader reader)
DAGene	DBGeneDAO.getGeneByID(Integer id)
DAGene	DBGeneDAO.getGeneByStableID(String stableID)
List<Mapping>	DBGeneDAO.getGeneMappingsOnRegion(DNASequence region, Coordinate coords)
List<DAGene>	DBGeneDAO.getGenesByExactName(String name)
List<DAGene>	DBGeneDAO.getGenesByNameBeginning(String name)
List<DAGene>	DBGeneDAO.getGenesForVegaID(String id) Returns a list of Ensembl Genes matching the query VegaID string.
MappingSet	DBAssemblyDAO.getPARMappingsByStartStop(Chromosome chr, Integer begin, Integer stop)
List<DAProteinFeature>	DBProteinFeatureDAO.getProteinFeaturesByTranslationID(int translationID)
DADNASequence	DBDNASequenceDAO.getSequenceByID(Integer id)
String	DBDNASequenceDAO.getSequenceByStartStop(EnsemblDNASequenceReader reader, Integer start, Integer stop)
DAChromosome	DBChromosomeDAO.getSexLinkedChromosome(Chromosome chr)
DATranscript	DBTranscriptDAO.getTranscriptByID(Integer id)
DATranscript	DBTranscriptDAO.getTranscriptByStableID(String stableID)
List<DATranscript>	DBTranscriptDAO.getTranscriptsForCcdsID(String id) Returns a list of Ensembl Transcripts matching the query CCDS ID string.
List<DATranscript>	DBTranscriptDAO.getTranscriptsForGene(Gene gene)
List<DATranscript>	DBTranscriptDAO.getTranscriptsForVegaID(String id) Returns a list of Ensembl Transcripts matching the query VegaID string.
DATranslation	DBTranslationDAO.getTranslationByID(Integer id)
DATranslation	DBTranslationDAO.getTranslationByStableID(String stableID)
List<DATranslation>	DBTranslationDAO.getTranslationsForTranscript(Transcript transcript)
List<DATranslation>	DBTranslationDAO.getTranslationsForVegaID(String id) Returns a list of Ensembl Translations matching the query VegaID string.
DADNASequence	DBDNASequenceDAO.getValidatedSequence(DNASequence seq)
List<? extends DNASequence>	DBDNASequenceDAO.getValidatedSequences(List<? extends DNASequence> in_sequences)
void	DBTranscriptDAO.TranscriptRowHandler.handleResult()
void	DBGeneDAO.GeneMappingRowHandler.handleResult()
void	DBGeneDAO.MappingRowHandler.handleResult()
void	DBExonDAO.ExonRowHandler.handleResult()
void	DBDNASequenceDAO.SequenceRowHandler.handleResult()
void	DBChromosomeDAO.AssemblyExceptionRowHandler.handleResult()
void	DBAssemblyDAO.PARMappingHandler.handleResult()
void	DBTranslationDAO.reInitialize(IdentifiableObject object)
void	DBTranscriptDAO.reInitialize(IdentifiableObject object) Uses the stableid of an object to fill in missing data
void	DBGeneDAO.reInitialize(IdentifiableObject object) Uses the stableid of an object to fill in missing data that would have been present if the the gene had intially been made by a call to getGeneByStableID or getGeneByID.
void	DBExonDAO.reInitialize(IdentifiableObject object) Uses the stableid of an object to fill in missing data
void	DBChromosomeDAO.setAssemblyExceptions(TreeMap<String,? extends Chromosome> chrs)
void	DBCoordinateSystemDAO.setFeatureCS()

Constructors in uk.ac.roslin.ensembl.dao.database.coreaccess that throw DAOException

Constructor and Description
DBExonDAO(DAOCollectionCoreFactory factory)
DBExonDAO(DAOSingleSpeciesCoreFactory factory)
DBGeneDAO(DAOCollectionCoreFactory factory)
DBGeneDAO(DAOSingleSpeciesCoreFactory factory)
DBTranscriptDAO(DAOCollectionCoreFactory factory)
DBTranscriptDAO(DAOSingleSpeciesCoreFactory factory)

Uses of DAOException in uk.ac.roslin.ensembl.dao.database.factory

Methods in uk.ac.roslin.ensembl.dao.database.factory that throw DAOException

Modifier and Type	Method and Description
DBAnalysisDAO	DBDAOSingleSpeciesFuncgenFactory.getAnalysisDAO()
DBAnalysisDAO	DBDAOSingleSpeciesCoreFactory.getAnalysisDAO()
DBAnalysisDAO	DBDAOCollectionFuncgenFactory.getAnalysisDAO()
DBAnalysisDAO	DBDAOCollectionCoreFactory.getAnalysisDAO()
DBAssemblyDAO	DBDAOSingleSpeciesCoreFactory.getAssemblyDAO()
DBAssemblyDAO	DBDAOCollectionCoreFactory.getAssemblyDAO()
DBChromosomeDAO	DBDAOSingleSpeciesCoreFactory.getChromosomeDAO()
DBChromosomeDAO	DBDAOCollectionCoreFactory.getChromosomeDAO()
DBCoordinateSystemDAO	DBDAOSingleSpeciesCoreFactory.getCoordinateSystemDAO()
DBCoordinateSystemDAO	DBDAOCollectionCoreFactory.getCoordinateSystemDAO()
DBExonDAO	DBDAOSingleSpeciesCoreFactory.getExonDAO()
DBExonDAO	DBDAOCollectionCoreFactory.getExonDAO()
DBGeneDAO	DBDAOSingleSpeciesCoreFactory.getGeneDAO()
DBGeneDAO	DBDAOCollectionCoreFactory.getGeneDAO()
DBHomologyDAO	DBDAOComparaFactory.getHomologyDAO()
org.apache.ibatis.session.SqlSession	DBDAOSingleSpeciesVariationFactory.getNewSqlSession()
org.apache.ibatis.session.SqlSession	DBDAOSingleSpeciesCoreFactory.getNewSqlSession()
org.apache.ibatis.session.SqlSession	DBDAOFactory.getNewSqlSession()
org.apache.ibatis.session.SqlSession	DBDAOCollectionCoreFactory.getNewSqlSession()
DBProteinFeatureDAO	DBDAOSingleSpeciesCoreFactory.getProteinFeatureDAO()
DBProteinFeatureDAO	DBDAOCollectionCoreFactory.getProteinFeatureDAO()
DBDNASequenceDAO	DBDAOSingleSpeciesCoreFactory.getSequenceDAO()
DBDNASequenceDAO	DBDAOCollectionCoreFactory.getSequenceDAO()
DBTranscriptDAO	DBDAOSingleSpeciesCoreFactory.getTranscriptDAO()
DBTranscriptDAO	DBDAOCollectionCoreFactory.getTranscriptDAO()
DBTranslationDAO	DBDAOSingleSpeciesCoreFactory.getTranslationDAO()
DBTranslationDAO	DBDAOCollectionCoreFactory.getTranslationDAO()
DBVariationDAO	DBDAOSingleSpeciesVariationFactory.getVariationDAO()
DBXRefDAO	DBDAOSingleSpeciesCoreFactory.getXRefDAO()
DBXRefDAO	DBDAOCollectionCoreFactory.getXRefDAO()
void	DBDAOFactory.setDatabase(Database db)

Constructors in uk.ac.roslin.ensembl.dao.database.factory that throw DAOException

Constructor and Description
DBDAOCollectionCoreFactory(CollectionDatabase database, CollectionSpecies species)
DBDAOCollectionFactory(CollectionDatabase database, CollectionSpecies species)
DBDAOCollectionFuncgenFactory(CollectionDatabase database, CollectionSpecies species)
DBDAOCollectionVariationFactory(CollectionDatabase database, CollectionSpecies species)
DBDAOComparaFactory(ComparisonDatabase database)
DBDAOFactory(Database database)
DBDAOSingleSpeciesCoreFactory(SingleSpeciesDatabase database)
DBDAOSingleSpeciesFactory(SingleSpeciesDatabase database)
DBDAOSingleSpeciesFuncgenFactory(SingleSpeciesDatabase database)
DBDAOSingleSpeciesVariationFactory(SingleSpeciesDatabase database)
DBDAOSpeciesFactory(CollectionDatabase database, CollectionSpecies species)
DBDAOSpeciesFactory(SingleSpeciesDatabase database)

Uses of DAOException in uk.ac.roslin.ensembl.dao.database.variation

Methods in uk.ac.roslin.ensembl.dao.database.variation that throw DAOException

Modifier and Type	Method and Description
DAVariation	DBVariationDAO.getUniquelyMappedVariation(String variationName)
List<DAVariation>	DBVariationDAO.getUniquelyMappedVariations(List<String> variationNames)
List<VariationMapping>	DBVariationDAO.getVariationMappingsOnRegion(DNASequence region, Coordinate coords)
List<DAVariation>	DBVariationDAO.getVariationsOnRegion(DNASequence region, Coordinate coords)

Constructors in uk.ac.roslin.ensembl.dao.database.variation that throw DAOException

Constructor and Description
DBVariationDAO(DAOVariationFactory factory)

Uses of DAOException in uk.ac.roslin.ensembl.dao.factory

Methods in uk.ac.roslin.ensembl.dao.factory that throw DAOException

Modifier and Type	Method and Description
AnalysisDAO	DAOFactoryWithAnalyses.getAnalysisDAO()
AssemblyDAO	DAOCoreFactory.getAssemblyDAO()
ChromosomeDAO	DAOCoreFactory.getChromosomeDAO()
CoordinateSystemDAO	DAOCoreFactory.getCoordinateSystemDAO()
ExonDAO	DAOCoreFactory.getExonDAO()
GeneDAO	DAOCoreFactory.getGeneDAO()
HomologyDAO	DAOComparaFactory.getHomologyDAO()
org.apache.ibatis.session.SqlSession	DAOFactory.getNewSqlSession()
ProteinFeatureDAO	DAOCoreFactory.getProteinFeatureDAO()
DNASequenceDAO	DAOCoreFactory.getSequenceDAO()
TranscriptDAO	DAOCoreFactory.getTranscriptDAO()
TranslationDAO	DAOCoreFactory.getTranslationDAO()
VariationDAO	DAOVariationFactory.getVariationDAO()
XRefDAO	DAOCoreFactory.getXRefDAO()

Uses of DAOException in uk.ac.roslin.ensembl.dao.variation

Methods in uk.ac.roslin.ensembl.dao.variation that throw DAOException

Modifier and Type	Method and Description
Variation	VariationDAO.getUniquelyMappedVariation(String variationName)
List<? extends Variation>	VariationDAO.getUniquelyMappedVariations(List<String> variationNames)
List<? extends Mapping>	VariationDAO.getVariationMappingsOnRegion(DNASequence region, Coordinate coords)
List<? extends Variation>	VariationDAO.getVariationsOnRegion(DNASequence region, Coordinate coords)

Uses of DAOException in uk.ac.roslin.ensembl.datasourceaware.core

Methods in uk.ac.roslin.ensembl.datasourceaware.core that throw DAOException

Modifier and Type	Method and Description
Integer	DATranscript.convertChromosomeToProcessedTranscriptPosition(Integer chromosomePosition) Converts an Integer position on the TopLevel-annotated Target (typically the Chromosome) to the position on the processed (spliced) Transcript.
Integer	DATranscript.convertPrimaryToProcessedTranscriptPosition(Integer primaryTranscriptPosition) Returns the mapped position on the Processed transcript equivalent to the given position on the Primary (unprocessed) transcript
Integer	DATranscript.convertProcessedToPrimaryTranscriptPosition(Integer processedTranscriptPosition) Returns the mapped position on the Primary transcript equivalent to the given position on the processed transcript
Integer	DATranscript.convertProcessedTranscriptPositionToChromosome(Integer processedTranscriptPosition) Converts an Integer position on the processed (spliced) transcript to the position on the TopLevel-annotated Target (typically the Chromosome).
MappingSet	DAFeature.getAnnotationLevelMappings()
MappingSet	DAChromosome.getAssemblyExceptions(AssemblyExceptionType type) Returns a MappingSet of AssemblyExceptions of the indicated AssemblyExceptionType.
MappingSet	DAFeature.getBuildLevelMappings()
Coordinate	DATranslation.getChromosomePositionFromAA(Integer aminoAcidPosition) Returns the mapped chromosomal coordinates of an amino acid position.
Integer	DATranslation.getChromosomePositionFromBASE(Integer translationBase) Returns the mapped chromosomal position of a translation (nucleotide) position.
List<DAGene>	DADNASequence.getGenesOnRegion(Coordinate coord) Returns a List of Genes on the specified Coordinate region.
List<DAGene>	DADNASequence.getGenesOnRegion(Integer start, Integer stop) Returns a List of Genes on the specified Region.
List<DAGene>	DADNASequence.getGenesOnRegion(Integer start, Integer stop, Coordinate.Strand strand) Returns a List of Genes on the specified Region.
MappingSet	DAAssembly.getMappings() Returns the MappingSet 'componentMappings' of all of the mappings of all of the DNASequences that make up this assembly.
String	DAAssembly.getPaddedReverseComplementSequenceAsString(Integer start, Integer stop) Returns a String representation of the reverse complement of theassembly sequence for the given range.
String	DAAssembly.getPaddedSequenceAsString(Integer start, Integer stop) Returns a String representation of the assembly sequence for the given range.
DADNASequence	DATranscript.getProcessedTranscript() Returns a DADNASequence object representing the processed (spliced exons) version of this Transcript.
Integer	DATranscript.getProcessedTranscriptLength() Returns the length of the processed (spliced exons) version of this Transcript.
Coordinate	DATranslation.getProcessedTranscriptPositionFromAA(Integer aminoAcidPosition) Returns the mapped coordinates of an amino acid position on the (spliced) processed transcript that provides this translation.
Integer	DATranslation.getProcessedTranscriptPositionFromBASE(Integer translationBase) Returns the mapped position of a translation (nucleotide) position on the (spliced) processed transcript that provides this translation.
RNASequence	DATranscript.getProcessedTranscriptRNASequence() Returns an RNASequence object representing the Processed (RNA spliced) Transcript.
String	DATranscript.getProcessedTranscriptRNASequenceAsString() Returns a String representing the RNA sequence of the Processed (RNA spliced) Transcript.
String	DATranscript.getProcessedTranscriptRNASequenceAsString(Integer start, Integer stop) Returns a String representing the RNA sequence of the Processed (RNA spliced) Transcript, for the given range.
HashMap<DADNASequence,MappingSet>	DADNASequence.getRegionsOfConservedSynteny(Coordinate range, Species target) Specifies method to retrieve all potential regions of conserved synteny (i.e. multiple chromosome regions) in the specified target Species
HashMap<DADNASequence,MappingSet>	DADNASequence.getRegionsOfConservedSynteny(Coordinate range, Species target, String chrName) Method to retrieve a single potential region of conserved synteny for the named chromosome in the specified target Species.
String	DAAssembly.getReverseComplementSequenceAsString(Integer start, Integer stop) Returns a String representation of the reverse complement of the assembly sequence for the given range.
String	DAAssembly.getSequenceAsString(Integer start, Integer stop) Returns a String representation of the assembly sequence for the given range.
MappingSet	DAAssembly.getStitchedMappings() Returns the MappingSet 'stitchedComponentMappings' of all of the mappings of all of the DNASequences that make up this assembly, that have been 'edited', i.e. stitched together into a single continuous gap free assembly.
MappingSet	DAAssembly.getStitchedMappings(Integer start, Integer stop) For a given range, returns a subset of the MappingSet 'stitchedComponentMappings' of all of the mappings of all of the DNASequences that make up this assembly, that have been 'edited', i.e. stitched together into a single continuous gap free assembly.
MappingSet	DAFeature.getTopLevelMappings()
Coordinate	DAFeature.getTopLevelTargetCoordinates()
DADNASequence	DAFeature.getTopLevelTargetSequence()
List<? extends Mapping>	DADNASequence.getVariationMappingsOnRegion(Coordinate coord) Returns List of Mappings of Variations on specified Coordinate Region.
List<? extends Mapping>	DADNASequence.getVariationMappingsOnRegion(Integer start, Integer stop) Returns List of Mappings of Variations on specified Coordinate Region.
List<DAVariation>	DADNASequence.getVariationsOnRegion(Coordinate coord) Returns list of Variations on specified Coordinate Region.
List<DAVariation>	DADNASequence.getVariationsOnRegion(Integer start, Integer stop) Returns list of Variations on specified Region.
protected void	DAFeature.inititializeTopLevel() This method is used to initialize the 'topLevelCS', the 'topLevelTargetCoordinates' and the 'topLevelTargetSequence' fields.
protected MappingSet	DAAssembly.stitchComponents() Protected method to join together (stitch) all of the component sub-sequences of the assembly, together with GapSequences to form a single continuous ungapped assembly, held in the MappingSet 'stitchedComponentMappings';

Uses of DAOException in uk.ac.roslin.ensembl.demo

Methods in uk.ac.roslin.ensembl.demo that throw DAOException

Modifier and Type	Method and Description
void	RegistryFactory.testBacteria()
void	RegistryFactory.testEnsembl()
void	RegistryFactory.testGenomes()

Uses of DAOException in uk.ac.roslin.ensembl.model.core

Methods in uk.ac.roslin.ensembl.model.core that throw DAOException

Modifier and Type	Method and Description
Chromosome	Species.getChromosomeByName(String name)
Chromosome	Species.getChromosomeByName(String name, String dbVersion)
TreeMap<String,? extends Chromosome>	Species.getChromosomes()
TreeMap<String,? extends Chromosome>	Species.getChromosomes(String dbVersion)
AssembledDNASequence	Species.getFragmentByName(String name)
AssembledDNASequence	Species.getFragmentByName(String name, String dbVersion)
TreeMap<String,? extends AssembledDNASequence>	Species.getFragments()
TreeMap<String,? extends AssembledDNASequence>	Species.getFragments(String dbVersion)
Gene	Species.getGeneByStableID(String stableID)
Gene	Species.getGeneByStableID(String stableID, String dbVersion)
List<? extends Gene>	Species.getGenesForExactName(String name)
List<? extends Gene>	Species.getGenesForExactName(String name, String dbVersion)
List<? extends Gene>	Species.getGenesForNameBeginning(String name)
List<? extends Gene>	Species.getGenesForNameBeginning(String name, String dbVersion)
List<? extends Gene>	Species.getGenesForVegaID(String vegaID)
List<? extends Gene>	Species.getGenesForVegaID(String vegaID, String dbVersion)
List<? extends Gene>	DNASequence.getGenesOnRegion(Coordinate coord)
List<? extends Gene>	DNASequence.getGenesOnRegion(Integer start, Integer stop)
List<? extends Gene>	DNASequence.getGenesOnRegion(Integer start, Integer stop, Coordinate.Strand strand)
MappingSet	Assembly.getMappings()
HashMap<? extends DNASequence,MappingSet>	DNASequence.getRegionsOfConservedSynteny(Coordinate range, Species target) Specifies method to retrieve all potential regions of conserved synteny (i.e. multiple chromosome regions) in the specified target Species
HashMap<? extends DNASequence,MappingSet>	DNASequence.getRegionsOfConservedSynteny(Coordinate range, Species target, String chrName) Specifies method to retrieve a single potential region of conserved synteny for the named chromosome in the specified target Species.
MappingSet	Assembly.getStitchedMappings()
Transcript	Species.getTranscriptByStableID(String stableID)
Transcript	Species.getTranscriptByStableID(String stableID, String dbVersion)
List<? extends Transcript>	Species.getTranscriptsForCcdsID(String ccdsID)
List<? extends Transcript>	Species.getTranscriptsForCcdsID(String ccdsID, String dbVersion)
List<? extends Transcript>	Species.getTranscriptsForVegaID(String vegaID)
List<? extends Transcript>	Species.getTranscriptsForVegaID(String vegaID, String dbVersion)
Translation	Species.getTranslationByStableID(String stableID)
Translation	Species.getTranslationByStableID(String stableID, String dbVersion)
List<? extends Translation>	Species.getTranslationsForVegaID(String vegaID)
List<? extends Translation>	Species.getTranslationsForVegaID(String vegaID, String dbVersion)
List<? extends Mapping>	DNASequence.getVariationMappingsOnRegion(Coordinate coord)
List<? extends Mapping>	DNASequence.getVariationMappingsOnRegion(Integer start, Integer stop)
List<? extends Variation>	DNASequence.getVariationsOnRegion(Coordinate coord)
List<? extends Variation>	DNASequence.getVariationsOnRegion(Integer start, Integer stop)
void	Species.setAssemblyExceptions(String dbVersion)

Uses of DAOException in uk.ac.roslin.ensembl.model.database

Methods in uk.ac.roslin.ensembl.model.database that throw DAOException

Modifier and Type	Method and Description
HashMap<Integer,? extends Analysis>	CoreDatabase.getAnalyses()
CoordinateSystem	CollectionCoreDatabase.getBuildCoordSystem(Species species, String featureType)
CoordinateSystem	SingleSpeciesCoreDatabase.getBuildCoordSystem(String featureType)
String	CollectionCoreDatabase.getBuildLevel(Species species, String featureKey)
String	SingleSpeciesCoreDatabase.getBuildLevel(String featureType)
Chromosome	CollectionCoreDatabase.getChromosomeByName(Species species, String name)
Chromosome	SingleSpeciesCoreDatabase.getChromosomeByName(String name)
CoordinateSystem	SingleSpeciesCoreDatabase.getChromosomeLevelCoordSystem()
CoordinateSystem	CollectionCoreDatabase.getChromosomeLevelCS(Species species)
List<? extends Chromosome>	SingleSpeciesCoreDatabase.getChromosomes()
List<? extends Chromosome>	CollectionCoreDatabase.getChromosomes(Species species)
CoordinateSystem	SingleSpeciesCoreDatabase.getCSByID(Integer id)
CoordinateSystem	CollectionCoreDatabase.getCSByID(Species species, Integer id)
Set<? extends CoordinateSystem>	SingleSpeciesCoreDatabase.getCSForFeature(ObjectType featureType)
Set<? extends CoordinateSystem>	CollectionCoreDatabase.getCSForFeature(Species sp, ObjectType feature)
List<? extends ObjectType>	SingleSpeciesCoreDatabase.getFeaturesForCS(CoordinateSystem coordSys)
List<? extends ObjectType>	CollectionCoreDatabase.getFeaturesForCS(Species sp, CoordinateSystem coordSys)
AssembledDNASequence	CollectionCoreDatabase.getFragmentByName(Species species, String name)
AssembledDNASequence	SingleSpeciesCoreDatabase.getFragmentByName(String name)
List<? extends AssembledDNASequence>	SingleSpeciesCoreDatabase.getFragments()
List<? extends AssembledDNASequence>	CollectionCoreDatabase.getFragments(Species species)
int	Registry.getHighestEnsemblSchemaVersion()
int	Registry.getHighestReleaseVersion()
Integer	SingleSpeciesCoreDatabase.getMaxLengthForFeature(ObjectType featureType, CoordinateSystem cs)
Integer	CollectionCoreDatabase.getMaxLengthForFeature(Species sp, ObjectType feature, CoordinateSystem cs)
Object	Database.getNewSqlSession()
CoordinateSystem	SingleSpeciesCoreDatabase.getSequenceLevelCoordSystem()
CoordinateSystem	CollectionCoreDatabase.getSequenceLevelCS(Species species)
CoordinateSystem	SingleSpeciesCoreDatabase.getTopLevelCoordSystem()
CoordinateSystem	CollectionCoreDatabase.getTopLevelCS(Species species)
void	Registry.setSpeciesMetadata(CoreDatabase database)