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

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

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

public interface CollectionCoreDatabase
extends CollectionDatabase, CoreDatabase

Author:
tpaterso

Method Summary
 void addFeatureCS(String featureType, Integer csID, Integer maxLength, Species sp)
           
 CoordinateSystem getBuildCoordSystem(Species species, String featureType)
           
 String getBuildLevel(Species species, String featureKey)
           
 Chromosome getChromosomeByName(Species species, String name)
           
 CoordinateSystem getChromosomeLevelCS(Species species)
           
 List<? extends Chromosome> getChromosomes(Species species)
           
 Object getCoreFactory(Species species)
           
 CoordinateSystem getCSByID(Species species, Integer id)
           
 Set<? extends CoordinateSystem> getCSForFeature(Species sp, ObjectType feature)
           
 List<? extends ObjectType> getFeaturesForCS(Species sp, CoordinateSystem coordSys)
           
 Integer getMaxLengthForFeature(Species sp, ObjectType feature, CoordinateSystem cs)
           
 CoordinateSystem getSequenceLevelCS(Species species)
           
 CoordinateSystem getTopLevelCS(Species species)
           
 void setBuildLevels(Species species, HashMap<String,String> keyedValues)
           
 
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
 

Method Detail

getCoreFactory

Object getCoreFactory(Species species)

getChromosomeLevelCS

CoordinateSystem getChromosomeLevelCS(Species species)
                                      throws DAOException
Throws:
DAOException

getSequenceLevelCS

CoordinateSystem getSequenceLevelCS(Species species)
                                    throws DAOException
Throws:
DAOException

getTopLevelCS

CoordinateSystem getTopLevelCS(Species species)
                               throws DAOException
Throws:
DAOException

getCSByID

CoordinateSystem getCSByID(Species species,
                           Integer id)
                           throws DAOException
Throws:
DAOException

getBuildCoordSystem

CoordinateSystem getBuildCoordSystem(Species species,
                                     String featureType)
                                     throws DAOException
Throws:
DAOException

getCSForFeature

Set<? extends CoordinateSystem> getCSForFeature(Species sp,
                                                ObjectType feature)
                                                throws DAOException
Throws:
DAOException

setBuildLevels

void setBuildLevels(Species species,
                    HashMap<String,String> keyedValues)

getBuildLevel

String getBuildLevel(Species species,
                     String featureKey)
                     throws DAOException
Throws:
DAOException

getFeaturesForCS

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

getMaxLengthForFeature

Integer getMaxLengthForFeature(Species sp,
                               ObjectType feature,
                               CoordinateSystem cs)
                               throws DAOException
Throws:
DAOException

addFeatureCS

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

getChromosomeByName

Chromosome getChromosomeByName(Species species,
                               String name)
                               throws DAOException
Throws:
DAOException

getChromosomes

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

Ensembl Model
v1.09

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