Ensembl Data Access Module v1.09
© Roslin Institute 2010. GNU General Public License, version3
uk.ac.roslin.ensembl.dao.database
Class DBCollectionCoreDatabase
java.lang.Object
uk.ac.roslin.ensembl.dao.database.DBDatabase
uk.ac.roslin.ensembl.dao.database.DBCollectionDatabase
uk.ac.roslin.ensembl.dao.database.DBCollectionCoreDatabase
- All Implemented Interfaces:
- Comparable<uk.ac.roslin.ensembl.model.database.Database>, uk.ac.roslin.ensembl.model.database.CollectionCoreDatabase, uk.ac.roslin.ensembl.model.database.CollectionDatabase, uk.ac.roslin.ensembl.model.database.CoreDatabase, uk.ac.roslin.ensembl.model.database.Database
public class DBCollectionCoreDatabase
- extends DBCollectionDatabase
- implements uk.ac.roslin.ensembl.model.database.CollectionCoreDatabase
- Author:
- paterson
Constructor Summary |
DBCollectionCoreDatabase(String db_name,
uk.ac.roslin.ensembl.config.EnsemblDBType type,
uk.ac.roslin.ensembl.model.database.Registry registry)
|
Method Summary |
void |
addFeatureCS(String featureType,
Integer csID,
Integer maxLength,
uk.ac.roslin.ensembl.model.core.Species sp)
|
uk.ac.roslin.ensembl.datasourceaware.core.DACoordinateSystem |
getBuildCoordSystem(uk.ac.roslin.ensembl.model.core.Species species,
String featureType)
|
String |
getBuildLevel(uk.ac.roslin.ensembl.model.core.Species species,
String featureKey)
|
HashMap<uk.ac.roslin.ensembl.config.FeatureType,String> |
getBuildLevels(uk.ac.roslin.ensembl.model.core.CollectionSpecies species)
|
uk.ac.roslin.ensembl.datasourceaware.core.DAChromosome |
getChromosomeByName(uk.ac.roslin.ensembl.model.core.Species species,
String name)
|
uk.ac.roslin.ensembl.datasourceaware.core.DACoordinateSystem |
getChromosomeLevelCS(uk.ac.roslin.ensembl.model.core.Species species)
|
List<uk.ac.roslin.ensembl.datasourceaware.core.DAChromosome> |
getChromosomes(uk.ac.roslin.ensembl.model.core.Species species)
|
DBDAOCollectionCoreFactory |
getCoreFactory(uk.ac.roslin.ensembl.model.core.Species sp)
|
uk.ac.roslin.ensembl.datasourceaware.core.DACoordinateSystem |
getCSByID(uk.ac.roslin.ensembl.model.core.Species species,
Integer id)
|
Set<uk.ac.roslin.ensembl.datasourceaware.core.DACoordinateSystem> |
getCSForFeature(uk.ac.roslin.ensembl.model.core.Species sp,
uk.ac.roslin.ensembl.model.ObjectType feature)
|
List<uk.ac.roslin.ensembl.config.FeatureType> |
getFeaturesForCS(uk.ac.roslin.ensembl.model.core.Species sp,
uk.ac.roslin.ensembl.model.core.CoordinateSystem coordSys)
|
Integer |
getMaxLengthForFeature(uk.ac.roslin.ensembl.model.core.Species sp,
uk.ac.roslin.ensembl.model.ObjectType feature,
uk.ac.roslin.ensembl.model.core.CoordinateSystem cs)
|
uk.ac.roslin.ensembl.datasourceaware.core.DACoordinateSystem |
getSequenceLevelCS(uk.ac.roslin.ensembl.model.core.Species species)
|
uk.ac.roslin.ensembl.datasourceaware.core.DACoordinateSystem |
getTopLevelCS(uk.ac.roslin.ensembl.model.core.Species species)
|
void |
setBuildLevels(uk.ac.roslin.ensembl.model.core.Species species,
HashMap<String,String> keyedValues)
|
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.CollectionDatabase |
getAssembly, getCollection, getCollectionName, setCollection, setCollectionName |
Methods inherited from interface uk.ac.roslin.ensembl.model.database.Database |
getBuild, getdBName, getDBVersion, getIntDBVersion, getIntSchemaVersion, getNewSqlSession, getRegistry, getSchemaVersion, getType |
DBCollectionCoreDatabase
public DBCollectionCoreDatabase(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 DBDAOCollectionCoreFactory getCoreFactory(uk.ac.roslin.ensembl.model.core.Species sp)
- Specified by:
getCoreFactory
in interface uk.ac.roslin.ensembl.model.database.CollectionCoreDatabase
getChromosomeLevelCS
public uk.ac.roslin.ensembl.datasourceaware.core.DACoordinateSystem getChromosomeLevelCS(uk.ac.roslin.ensembl.model.core.Species species)
throws uk.ac.roslin.ensembl.exception.DAOException
- Specified by:
getChromosomeLevelCS
in interface uk.ac.roslin.ensembl.model.database.CollectionCoreDatabase
- Throws:
uk.ac.roslin.ensembl.exception.DAOException
getSequenceLevelCS
public uk.ac.roslin.ensembl.datasourceaware.core.DACoordinateSystem getSequenceLevelCS(uk.ac.roslin.ensembl.model.core.Species species)
throws uk.ac.roslin.ensembl.exception.DAOException
- Specified by:
getSequenceLevelCS
in interface uk.ac.roslin.ensembl.model.database.CollectionCoreDatabase
- Throws:
uk.ac.roslin.ensembl.exception.DAOException
getTopLevelCS
public uk.ac.roslin.ensembl.datasourceaware.core.DACoordinateSystem getTopLevelCS(uk.ac.roslin.ensembl.model.core.Species species)
throws uk.ac.roslin.ensembl.exception.DAOException
- Specified by:
getTopLevelCS
in interface uk.ac.roslin.ensembl.model.database.CollectionCoreDatabase
- Throws:
uk.ac.roslin.ensembl.exception.DAOException
setBuildLevels
public void setBuildLevels(uk.ac.roslin.ensembl.model.core.Species species,
HashMap<String,String> keyedValues)
- Specified by:
setBuildLevels
in interface uk.ac.roslin.ensembl.model.database.CollectionCoreDatabase
getBuildLevel
public String getBuildLevel(uk.ac.roslin.ensembl.model.core.Species species,
String featureKey)
throws uk.ac.roslin.ensembl.exception.DAOException
- Specified by:
getBuildLevel
in interface uk.ac.roslin.ensembl.model.database.CollectionCoreDatabase
- Throws:
uk.ac.roslin.ensembl.exception.DAOException
getBuildLevels
public HashMap<uk.ac.roslin.ensembl.config.FeatureType,String> getBuildLevels(uk.ac.roslin.ensembl.model.core.CollectionSpecies species)
addFeatureCS
public void addFeatureCS(String featureType,
Integer csID,
Integer maxLength,
uk.ac.roslin.ensembl.model.core.Species sp)
- Specified by:
addFeatureCS
in interface uk.ac.roslin.ensembl.model.database.CollectionCoreDatabase
getCSForFeature
public Set<uk.ac.roslin.ensembl.datasourceaware.core.DACoordinateSystem> getCSForFeature(uk.ac.roslin.ensembl.model.core.Species sp,
uk.ac.roslin.ensembl.model.ObjectType feature)
throws uk.ac.roslin.ensembl.exception.DAOException
- Specified by:
getCSForFeature
in interface uk.ac.roslin.ensembl.model.database.CollectionCoreDatabase
- Throws:
uk.ac.roslin.ensembl.exception.DAOException
getFeaturesForCS
public List<uk.ac.roslin.ensembl.config.FeatureType> getFeaturesForCS(uk.ac.roslin.ensembl.model.core.Species sp,
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.CollectionCoreDatabase
- Throws:
uk.ac.roslin.ensembl.exception.DAOException
getMaxLengthForFeature
public Integer getMaxLengthForFeature(uk.ac.roslin.ensembl.model.core.Species sp,
uk.ac.roslin.ensembl.model.ObjectType feature,
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.CollectionCoreDatabase
- Throws:
uk.ac.roslin.ensembl.exception.DAOException
getBuildCoordSystem
public uk.ac.roslin.ensembl.datasourceaware.core.DACoordinateSystem getBuildCoordSystem(uk.ac.roslin.ensembl.model.core.Species species,
String featureType)
throws uk.ac.roslin.ensembl.exception.DAOException
- Specified by:
getBuildCoordSystem
in interface uk.ac.roslin.ensembl.model.database.CollectionCoreDatabase
- Throws:
uk.ac.roslin.ensembl.exception.DAOException
getCSByID
public uk.ac.roslin.ensembl.datasourceaware.core.DACoordinateSystem getCSByID(uk.ac.roslin.ensembl.model.core.Species species,
Integer id)
throws uk.ac.roslin.ensembl.exception.DAOException
- Specified by:
getCSByID
in interface uk.ac.roslin.ensembl.model.database.CollectionCoreDatabase
- Throws:
uk.ac.roslin.ensembl.exception.DAOException
getChromosomeByName
public uk.ac.roslin.ensembl.datasourceaware.core.DAChromosome getChromosomeByName(uk.ac.roslin.ensembl.model.core.Species species,
String name)
throws uk.ac.roslin.ensembl.exception.DAOException
- Specified by:
getChromosomeByName
in interface uk.ac.roslin.ensembl.model.database.CollectionCoreDatabase
- Throws:
uk.ac.roslin.ensembl.exception.DAOException
getChromosomes
public List<uk.ac.roslin.ensembl.datasourceaware.core.DAChromosome> getChromosomes(uk.ac.roslin.ensembl.model.core.Species species)
throws uk.ac.roslin.ensembl.exception.DAOException
- Specified by:
getChromosomes
in interface uk.ac.roslin.ensembl.model.database.CollectionCoreDatabase
- Throws:
uk.ac.roslin.ensembl.exception.DAOException
Ensembl Data Access Module v1.09
© Roslin Institute 2010. GNU General Public License, version3