Ensembl Model v1.09
© Roslin Institute 2010. GNU General Public License, version3
Ensembl Model
v1.09

uk.ac.roslin.ensembl.model.database
Interface SingleSpeciesCoreDatabase

All Superinterfaces:
Comparable<Database>, CoreDatabase, Database, SingleSpeciesDatabase

public interface SingleSpeciesCoreDatabase
extends SingleSpeciesDatabase, CoreDatabase

Author:
tpaterso

Method Summary
 void addFeatureCS(String featureType, Integer csID, Integer maxLength)
           
 CoordinateSystem getBuildCoordSystem(String featureType)
           
 String getBuildLevel(String featureType)
           
 Chromosome getChromosomeByName(String name)
           
 CoordinateSystem getChromosomeLevelCoordSystem()
           
 List<? extends Chromosome> getChromosomes()
           
 Object getCoreFactory()
           
 CoordinateSystem getCSByID(Integer id)
           
 Set<? extends CoordinateSystem> getCSForFeature(ObjectType featureType)
           
 List<? extends ObjectType> getFeaturesForCS(CoordinateSystem coordSys)
           
 Integer getMaxLengthForFeature(ObjectType featureType, CoordinateSystem cs)
           
 CoordinateSystem getSequenceLevelCoordSystem()
           
 CoordinateSystem getTopLevelCoordSystem()
           
 void setBuildLevel(String featureKey, String level)
           
 
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
 

Method Detail

getCoreFactory

Object getCoreFactory()

getTopLevelCoordSystem

CoordinateSystem getTopLevelCoordSystem()
                                        throws DAOException
Throws:
DAOException

getChromosomeLevelCoordSystem

CoordinateSystem getChromosomeLevelCoordSystem()
                                               throws DAOException
Throws:
DAOException

getSequenceLevelCoordSystem

CoordinateSystem getSequenceLevelCoordSystem()
                                             throws DAOException
Throws:
DAOException

getCSByID

CoordinateSystem getCSByID(Integer id)
                           throws DAOException
Throws:
DAOException

getBuildCoordSystem

CoordinateSystem getBuildCoordSystem(String featureType)
                                     throws DAOException
Throws:
DAOException

getCSForFeature

Set<? extends CoordinateSystem> getCSForFeature(ObjectType featureType)
                                                throws DAOException
Throws:
DAOException

getChromosomeByName

Chromosome getChromosomeByName(String name)
                               throws DAOException
Throws:
DAOException

getChromosomes

List<? extends Chromosome> getChromosomes()
                                          throws DAOException
Throws:
DAOException

setBuildLevel

void setBuildLevel(String featureKey,
                   String level)

getBuildLevel

String getBuildLevel(String featureType)
                     throws DAOException
Throws:
DAOException

getFeaturesForCS

List<? extends ObjectType> getFeaturesForCS(CoordinateSystem coordSys)
                                            throws DAOException
Throws:
DAOException

getMaxLengthForFeature

Integer getMaxLengthForFeature(ObjectType featureType,
                               CoordinateSystem cs)
                               throws DAOException
Throws:
DAOException

addFeatureCS

void addFeatureCS(String featureType,
                  Integer csID,
                  Integer maxLength)

Ensembl Model
v1.09

Ensembl Model v1.09
© Roslin Institute 2010. GNU General Public License, version3