Ensembl Data Access Module v1.09
© Roslin Institute 2010. GNU General Public License, version3
uk.ac.roslin.ensembl.dao.database
Class DBSingleSpeciesCoreDatabase
java.lang.Object
uk.ac.roslin.ensembl.dao.database.DBDatabase
uk.ac.roslin.ensembl.dao.database.DBSingleSpeciesDatabase
uk.ac.roslin.ensembl.dao.database.DBSingleSpeciesCoreDatabase
- All Implemented Interfaces:
- Comparable<uk.ac.roslin.ensembl.model.database.Database>, uk.ac.roslin.ensembl.model.database.CoreDatabase, uk.ac.roslin.ensembl.model.database.Database, uk.ac.roslin.ensembl.model.database.SingleSpeciesCoreDatabase, uk.ac.roslin.ensembl.model.database.SingleSpeciesDatabase
public class DBSingleSpeciesCoreDatabase
- extends DBSingleSpeciesDatabase
- implements uk.ac.roslin.ensembl.model.database.SingleSpeciesCoreDatabase
- Author:
- paterson
Constructor Summary |
DBSingleSpeciesCoreDatabase(String db_name,
uk.ac.roslin.ensembl.config.EnsemblDBType type,
uk.ac.roslin.ensembl.model.database.Registry registry)
|
Methods inherited from class uk.ac.roslin.ensembl.dao.database.DBDatabase |
compareTo, getBuild, getdBName, getDBVersion, getIntDBVersion, getIntSchemaVersion, getNewSqlSession, getRegistry, getSchemaVersion, getType, setBuild, setdBName, setDBVersion, setIntDBVersion, setIntSchemaVersion, setRegistry, setSchemaVersion, setType, toString |
Methods inherited from interface uk.ac.roslin.ensembl.model.database.SingleSpeciesDatabase |
getAssembly, getDbSpeciesName, getSpecies, setDbSpeciesName, setSpecies |
Methods inherited from interface uk.ac.roslin.ensembl.model.database.Database |
getBuild, getdBName, getDBVersion, getIntDBVersion, getIntSchemaVersion, getNewSqlSession, getRegistry, getSchemaVersion, getType |
DBSingleSpeciesCoreDatabase
public DBSingleSpeciesCoreDatabase(String db_name,
uk.ac.roslin.ensembl.config.EnsemblDBType type,
uk.ac.roslin.ensembl.model.database.Registry registry)
throws uk.ac.roslin.ensembl.exception.ConfigurationException
- Throws:
uk.ac.roslin.ensembl.exception.ConfigurationException
getCoreFactory
public DBDAOSingleSpeciesCoreFactory getCoreFactory()
- Specified by:
getCoreFactory
in interface uk.ac.roslin.ensembl.model.database.SingleSpeciesCoreDatabase
getCSByID
public uk.ac.roslin.ensembl.datasourceaware.core.DACoordinateSystem getCSByID(Integer id)
throws uk.ac.roslin.ensembl.exception.DAOException
- Specified by:
getCSByID
in interface uk.ac.roslin.ensembl.model.database.SingleSpeciesCoreDatabase
- Throws:
uk.ac.roslin.ensembl.exception.DAOException
getTopLevelCoordSystem
public uk.ac.roslin.ensembl.datasourceaware.core.DACoordinateSystem getTopLevelCoordSystem()
throws uk.ac.roslin.ensembl.exception.DAOException
- Specified by:
getTopLevelCoordSystem
in interface uk.ac.roslin.ensembl.model.database.SingleSpeciesCoreDatabase
- Throws:
uk.ac.roslin.ensembl.exception.DAOException
getChromosomeLevelCoordSystem
public uk.ac.roslin.ensembl.datasourceaware.core.DACoordinateSystem getChromosomeLevelCoordSystem()
throws uk.ac.roslin.ensembl.exception.DAOException
- Specified by:
getChromosomeLevelCoordSystem
in interface uk.ac.roslin.ensembl.model.database.SingleSpeciesCoreDatabase
- Throws:
uk.ac.roslin.ensembl.exception.DAOException
getSequenceLevelCoordSystem
public uk.ac.roslin.ensembl.datasourceaware.core.DACoordinateSystem getSequenceLevelCoordSystem()
throws uk.ac.roslin.ensembl.exception.DAOException
- Specified by:
getSequenceLevelCoordSystem
in interface uk.ac.roslin.ensembl.model.database.SingleSpeciesCoreDatabase
- Throws:
uk.ac.roslin.ensembl.exception.DAOException
getChromosomeByName
public uk.ac.roslin.ensembl.datasourceaware.core.DAChromosome getChromosomeByName(String name)
throws uk.ac.roslin.ensembl.exception.DAOException
- Specified by:
getChromosomeByName
in interface uk.ac.roslin.ensembl.model.database.SingleSpeciesCoreDatabase
- Throws:
uk.ac.roslin.ensembl.exception.DAOException
getChromosomes
public List<uk.ac.roslin.ensembl.datasourceaware.core.DAChromosome> getChromosomes()
throws uk.ac.roslin.ensembl.exception.DAOException
- Specified by:
getChromosomes
in interface uk.ac.roslin.ensembl.model.database.SingleSpeciesCoreDatabase
- Throws:
uk.ac.roslin.ensembl.exception.DAOException
getCSForFeature
public Set<uk.ac.roslin.ensembl.datasourceaware.core.DACoordinateSystem> getCSForFeature(uk.ac.roslin.ensembl.model.ObjectType featureType)
throws uk.ac.roslin.ensembl.exception.DAOException
- Specified by:
getCSForFeature
in interface uk.ac.roslin.ensembl.model.database.SingleSpeciesCoreDatabase
- Throws:
uk.ac.roslin.ensembl.exception.DAOException
getFeaturesForCS
public List<uk.ac.roslin.ensembl.config.FeatureType> getFeaturesForCS(uk.ac.roslin.ensembl.model.core.CoordinateSystem coordSys)
throws uk.ac.roslin.ensembl.exception.DAOException
- Specified by:
getFeaturesForCS
in interface uk.ac.roslin.ensembl.model.database.SingleSpeciesCoreDatabase
- Throws:
uk.ac.roslin.ensembl.exception.DAOException
getMaxLengthForFeature
public Integer getMaxLengthForFeature(uk.ac.roslin.ensembl.model.ObjectType featureType,
uk.ac.roslin.ensembl.model.core.CoordinateSystem cs)
throws uk.ac.roslin.ensembl.exception.DAOException
- Specified by:
getMaxLengthForFeature
in interface uk.ac.roslin.ensembl.model.database.SingleSpeciesCoreDatabase
- Throws:
uk.ac.roslin.ensembl.exception.DAOException
addFeatureCS
public void addFeatureCS(String featureType,
Integer csID,
Integer maxLength)
- Specified by:
addFeatureCS
in interface uk.ac.roslin.ensembl.model.database.SingleSpeciesCoreDatabase
setBuildLevel
public void setBuildLevel(String featureKey,
String level)
- Specified by:
setBuildLevel
in interface uk.ac.roslin.ensembl.model.database.SingleSpeciesCoreDatabase
getBuildLevel
public String getBuildLevel(String featureType)
throws uk.ac.roslin.ensembl.exception.DAOException
- Specified by:
getBuildLevel
in interface uk.ac.roslin.ensembl.model.database.SingleSpeciesCoreDatabase
- Throws:
uk.ac.roslin.ensembl.exception.DAOException
getBuildCoordSystem
public uk.ac.roslin.ensembl.datasourceaware.core.DACoordinateSystem getBuildCoordSystem(String featureType)
throws uk.ac.roslin.ensembl.exception.DAOException
- Specified by:
getBuildCoordSystem
in interface uk.ac.roslin.ensembl.model.database.SingleSpeciesCoreDatabase
- Throws:
uk.ac.roslin.ensembl.exception.DAOException
getBuildLevels
public HashMap<uk.ac.roslin.ensembl.config.FeatureType,String> getBuildLevels()
Ensembl Data Access Module v1.09
© Roslin Institute 2010. GNU General Public License, version3