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 DBCollectionCoreDatabase

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

Field Summary
 
Fields inherited from class uk.ac.roslin.ensembl.dao.database.DBCollectionDatabase
assemblyMap, collection, collectionName
 
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.DBCollectionDatabase
getAssembly, getCollection, getCollectionName, setCollection, setCollectionName
 
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.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
 
Methods inherited from interface java.lang.Comparable
compareTo
 

Constructor Detail

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
Method Detail

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

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