Ensembl Data Access Module v1.09
© Roslin Institute 2010. GNU General Public License, version3
uk.ac.roslin.ensembl.dao.database
Class DBCollectionSpecies
java.lang.Object
uk.ac.roslin.ensembl.dao.database.DBSpecies
uk.ac.roslin.ensembl.dao.database.DBCollectionSpecies
- All Implemented Interfaces:
- Comparable<uk.ac.roslin.ensembl.model.core.CollectionSpecies>, uk.ac.roslin.ensembl.model.core.CollectionSpecies, uk.ac.roslin.ensembl.model.core.Species
public class DBCollectionSpecies
- extends DBSpecies
- implements uk.ac.roslin.ensembl.model.core.CollectionSpecies
Fields inherited from class uk.ac.roslin.ensembl.dao.database.DBSpecies |
aliases, commonName, comparaName, databaseStyleSpeciesName, ensemblStablePrefix, mostRecentDBRelease, mostRecentEnsemblSchemaVersion, registry, shortName, speciesBinomial, taxonomyID |
Methods inherited from class uk.ac.roslin.ensembl.dao.database.DBSpecies |
getAliases, getCachedChromosome, getChromosomeByName, getChromosomes, getCommonName, getComparaDivision, getComparaName, getDatabaseStyleName, getDBSpeciesID, getDBVersions, getEnsemblStablePrefix, getGeneByID, getGeneByStableID, getSchemaVersions, getShortName, getSpeciesBinomial, getTaxonomyID, getVersions, setCommonName, setComparaDivision, setComparaName, setDatabaseStyleSpeciesName, setEnsemblStablePrefix, setShortName, setSpeciesBinomial, setTaxonomyID, toString |
Methods inherited from interface uk.ac.roslin.ensembl.model.core.Species |
getAliases, getChromosomeByName, getChromosomes, getCommonName, getComparaDivision, getComparaName, getDatabaseStyleName, getDBVersions, getEnsemblStablePrefix, getGeneByID, getGeneByStableID, getSchemaVersions, getShortName, getSpeciesBinomial, getTaxonomyID |
DBCollectionSpecies
public DBCollectionSpecies()
DBCollectionSpecies
public DBCollectionSpecies(DBCollectionDatabase database)
throws uk.ac.roslin.ensembl.exception.ConfigurationException
- Throws:
uk.ac.roslin.ensembl.exception.ConfigurationException
setDatabase
public void setDatabase(DBCollectionDatabase database)
throws uk.ac.roslin.ensembl.exception.ConfigurationException
- Throws:
uk.ac.roslin.ensembl.exception.ConfigurationException
setIDForVersion
public void setIDForVersion(Integer ID,
String version)
setProperty
public void setProperty(HashMap row)
- Specified by:
setProperty
in interface uk.ac.roslin.ensembl.model.core.Species
- Overrides:
setProperty
in class DBSpecies
getDBSpeciesID
public Integer getDBSpeciesID(String version)
- Specified by:
getDBSpeciesID
in interface uk.ac.roslin.ensembl.model.core.Species
- Overrides:
getDBSpeciesID
in class DBSpecies
compareTo
public int compareTo(uk.ac.roslin.ensembl.model.core.CollectionSpecies o)
- Specified by:
compareTo
in interface Comparable<uk.ac.roslin.ensembl.model.core.CollectionSpecies>
getCurrentCoreDatabase
public DBCollectionCoreDatabase getCurrentCoreDatabase()
- Specified by:
getCurrentCoreDatabase
in interface uk.ac.roslin.ensembl.model.core.Species
- Overrides:
getCurrentCoreDatabase
in class DBSpecies
setCurrentCoreDatabase
public void setCurrentCoreDatabase(DBCollectionCoreDatabase currentCoreDatabase)
getDatabases
public TreeSet<DBCollectionDatabase> getDatabases()
- Specified by:
getDatabases
in interface uk.ac.roslin.ensembl.model.core.Species
- Overrides:
getDatabases
in class DBSpecies
addDatabases
public void addDatabases(TreeSet<? extends uk.ac.roslin.ensembl.model.database.Database> databases)
- Specified by:
addDatabases
in interface uk.ac.roslin.ensembl.model.core.Species
- Overrides:
addDatabases
in class DBSpecies
addDatabase
public void addDatabase(uk.ac.roslin.ensembl.model.database.Database database)
- Specified by:
addDatabase
in interface uk.ac.roslin.ensembl.model.core.Species
- Overrides:
addDatabase
in class DBSpecies
getDatabasesByType
public TreeSet<DBCollectionDatabase> getDatabasesByType(uk.ac.roslin.ensembl.model.database.DatabaseType type)
- Specified by:
getDatabasesByType
in interface uk.ac.roslin.ensembl.model.core.Species
- Overrides:
getDatabasesByType
in class DBSpecies
getDatabasesByVersion
public TreeSet<DBCollectionDatabase> getDatabasesByVersion(String version)
- Specified by:
getDatabasesByVersion
in interface uk.ac.roslin.ensembl.model.core.Species
- Overrides:
getDatabasesByVersion
in class DBSpecies
getDatabaseByTypeAndVersion
public DBCollectionDatabase getDatabaseByTypeAndVersion(uk.ac.roslin.ensembl.model.database.DatabaseType type,
String version)
- Specified by:
getDatabaseByTypeAndVersion
in interface uk.ac.roslin.ensembl.model.core.Species
- Overrides:
getDatabaseByTypeAndVersion
in class DBSpecies
getChromosomeByName
public uk.ac.roslin.ensembl.datasourceaware.core.DAChromosome getChromosomeByName(String name,
String dbVersion)
throws uk.ac.roslin.ensembl.exception.DAOException
- Specified by:
getChromosomeByName
in interface uk.ac.roslin.ensembl.model.core.Species
- Overrides:
getChromosomeByName
in class DBSpecies
- Throws:
uk.ac.roslin.ensembl.exception.DAOException
getChromosomes
public TreeMap<String,uk.ac.roslin.ensembl.datasourceaware.core.DAChromosome> getChromosomes(String dbVersion)
throws uk.ac.roslin.ensembl.exception.DAOException
- Specified by:
getChromosomes
in interface uk.ac.roslin.ensembl.model.core.Species
- Overrides:
getChromosomes
in class DBSpecies
- Throws:
uk.ac.roslin.ensembl.exception.DAOException
getGeneByID
public uk.ac.roslin.ensembl.datasourceaware.core.DAGene getGeneByID(Integer id,
String dbVersion)
throws uk.ac.roslin.ensembl.exception.DAOException
- Specified by:
getGeneByID
in interface uk.ac.roslin.ensembl.model.core.Species
- Overrides:
getGeneByID
in class DBSpecies
- Throws:
uk.ac.roslin.ensembl.exception.DAOException
getGeneByStableID
public uk.ac.roslin.ensembl.datasourceaware.core.DAGene getGeneByStableID(String stableID,
String dbVersion)
throws uk.ac.roslin.ensembl.exception.DAOException
- Specified by:
getGeneByStableID
in interface uk.ac.roslin.ensembl.model.core.Species
- Overrides:
getGeneByStableID
in class DBSpecies
- Throws:
uk.ac.roslin.ensembl.exception.DAOException
getAssembly
public String getAssembly()
- Specified by:
getAssembly
in interface uk.ac.roslin.ensembl.model.core.Species
- Overrides:
getAssembly
in class DBSpecies
getAssembly
public String getAssembly(String dbVersion)
- Specified by:
getAssembly
in interface uk.ac.roslin.ensembl.model.core.Species
- Overrides:
getAssembly
in class DBSpecies
Ensembl Data Access Module v1.09
© Roslin Institute 2010. GNU General Public License, version3