Ensembl Data Access Module v1.09
© Roslin Institute 2010. GNU General Public License, version3
Ensembl Data Access Module
v1.09

uk.ac.roslin.ensembl.dao.database
Class DBSingleSpeciesCoreDatabase

java.lang.Object
  extended by uk.ac.roslin.ensembl.dao.database.DBDatabase
      extended by uk.ac.roslin.ensembl.dao.database.DBSingleSpeciesDatabase
          extended by 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

Field Summary
 
Fields inherited from class uk.ac.roslin.ensembl.dao.database.DBSingleSpeciesDatabase
assembly, dbSpeciesName, species
 
Constructor Summary
DBSingleSpeciesCoreDatabase(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.datasourceaware.core.DACoordinateSystem getBuildCoordSystem(String featureType)
           
 String getBuildLevel(String featureType)
           
 HashMap<uk.ac.roslin.ensembl.config.FeatureType,String> getBuildLevels()
           
 uk.ac.roslin.ensembl.datasourceaware.core.DAChromosome getChromosomeByName(String name)
           
 uk.ac.roslin.ensembl.datasourceaware.core.DACoordinateSystem getChromosomeLevelCoordSystem()
           
 List<uk.ac.roslin.ensembl.datasourceaware.core.DAChromosome> getChromosomes()
           
 DBDAOSingleSpeciesCoreFactory getCoreFactory()
           
 uk.ac.roslin.ensembl.datasourceaware.core.DACoordinateSystem getCSByID(Integer id)
           
 Set<uk.ac.roslin.ensembl.datasourceaware.core.DACoordinateSystem> getCSForFeature(uk.ac.roslin.ensembl.model.ObjectType featureType)
           
 List<uk.ac.roslin.ensembl.config.FeatureType> getFeaturesForCS(uk.ac.roslin.ensembl.model.core.CoordinateSystem coordSys)
           
 Integer getMaxLengthForFeature(uk.ac.roslin.ensembl.model.ObjectType featureType, uk.ac.roslin.ensembl.model.core.CoordinateSystem cs)
           
 uk.ac.roslin.ensembl.datasourceaware.core.DACoordinateSystem getSequenceLevelCoordSystem()
           
 uk.ac.roslin.ensembl.datasourceaware.core.DACoordinateSystem getTopLevelCoordSystem()
           
 void setBuildLevel(String featureKey, String level)
           
 
Methods inherited from class uk.ac.roslin.ensembl.dao.database.DBSingleSpeciesDatabase
getAssembly, getDbSpeciesName, getSpecies, lazyLoadAssembly, setDbSpeciesName, setSpecies
 
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 class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait
 
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
 
Methods inherited from interface java.lang.Comparable
compareTo
 

Constructor Detail

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
Method Detail

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

Ensembl Data Access Module v1.09
© Roslin Institute 2010. GNU General Public License, version3