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<Database>, CollectionCoreDatabase, CollectionDatabase, CoreDatabase, Database, DatabaseWithExternalDBs

public class DBCollectionCoreDatabase
extends DBCollectionDatabase
implements CollectionCoreDatabase

Author:

paterson

Field Summary

Fields inherited from class uk.ac.roslin.ensembl.dao.database.DBCollectionDatabase

collection, collectionName

Constructor Summary

Constructors

Constructor and Description
DBCollectionCoreDatabase(String db_name, EnsemblDBType type, Registry registry)

Method Summary

Methods

Modifier and Type	Method and Description
void	addFeatureCS(String featureType, Integer csID, Integer maxLength, Species sp)
HashMap<Integer,DAAnalysis>	getAnalyses() Analyses are cached at the Database level
String	getAssemblyAccession(CollectionSpecies species) Returns the AssemblyAccession value for this species.
String	getAssemblyName(CollectionSpecies species) Returns the AssemblyName value for this species.
DACoordinateSystem	getBuildCoordSystem(Species species, String featureType)
String	getBuildLevel(Species species, String featureKey)
HashMap<FeatureType,String>	getBuildLevels(CollectionSpecies species)
DAChromosome	getChromosomeByName(Species species, String name)
DACoordinateSystem	getChromosomeLevelCS(Species species)
List<DAChromosome>	getChromosomes(Species species)
DBDAOCollectionCoreFactory	getCoreFactory(Species sp)
DACoordinateSystem	getCSByID(Species species, Integer id)
Set<DACoordinateSystem>	getCSForFeature(Species sp, ObjectType feature)
ExternalDB	getExternalDB(Integer id)
List<FeatureType>	getFeaturesForCS(Species sp, CoordinateSystem coordSys)
DAAssembledDNASequence	getFragmentByName(Species species, String name)
List<DAAssembledDNASequence>	getFragments(Species species)
Integer	getMaxLengthForFeature(Species sp, ObjectType feature, CoordinateSystem cs)
DACoordinateSystem	getSequenceLevelCS(Species species)
DACoordinateSystem	getTopLevelCS(Species species)
void	initializeExternalDBs()
void	setBuildLevels(Species species, HashMap<String,String> keyedValues)
ExternalDB	validateExternalDB(ExternalDB db) Validates a givenExternalDB object, to return a pre-existing version id present.

Methods inherited from class uk.ac.roslin.ensembl.dao.database.DBCollectionDatabase

getCollection, getCollectionName, setCollection, setCollectionName

Methods inherited from class uk.ac.roslin.ensembl.dao.database.DBDatabase

compareTo, getBuild, getdBClassifier, getdBName, getDBVersion, getIntDBVersion, getIntSchemaVersion, getNewSqlSession, getRegistry, getSchemaVersion, getSessionFactory, 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

getCollection, getCollectionName, setCollection, setCollectionName

Methods inherited from interface uk.ac.roslin.ensembl.model.database.Database

getBuild, getdBClassifier, getdBName, getDBVersion, getIntDBVersion, getIntSchemaVersion, getNewSqlSession, getRegistry, getSchemaVersion, getType

Methods inherited from interface java.lang.Comparable

compareTo

Constructor Detail

DBCollectionCoreDatabase

public DBCollectionCoreDatabase(String db_name,
                        EnsemblDBType type,
                        Registry registry)
                         throws ConfigurationException

Throws:

ConfigurationException

Method Detail

getCoreFactory

public DBDAOCollectionCoreFactory getCoreFactory(Species sp)

Specified by:

getCoreFactory in interface CollectionCoreDatabase

getChromosomeLevelCS

public DACoordinateSystem getChromosomeLevelCS(Species species)
                                        throws DAOException

Specified by:

getChromosomeLevelCS in interface CollectionCoreDatabase

Throws:

DAOException

getSequenceLevelCS

public DACoordinateSystem getSequenceLevelCS(Species species)
                                      throws DAOException

Specified by:

getSequenceLevelCS in interface CollectionCoreDatabase

Throws:

DAOException

getTopLevelCS

public DACoordinateSystem getTopLevelCS(Species species)
                                 throws DAOException

Specified by:

getTopLevelCS in interface CollectionCoreDatabase

Throws:

DAOException

setBuildLevels

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

Specified by:

setBuildLevels in interface CollectionCoreDatabase

getBuildLevel

public String getBuildLevel(Species species,
                   String featureKey)
                     throws DAOException

Specified by:

getBuildLevel in interface CollectionCoreDatabase

Throws:

DAOException

getBuildLevels

public HashMap<FeatureType,String> getBuildLevels(CollectionSpecies species)

addFeatureCS

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

Specified by:

addFeatureCS in interface CollectionCoreDatabase

getCSForFeature

public Set<DACoordinateSystem> getCSForFeature(Species sp,
                                      ObjectType feature)
                                        throws DAOException

Specified by:

getCSForFeature in interface CollectionCoreDatabase

Throws:

DAOException

getFeaturesForCS

public List<FeatureType> getFeaturesForCS(Species sp,
                                 CoordinateSystem coordSys)
                                   throws DAOException

Specified by:

getFeaturesForCS in interface CollectionCoreDatabase

Throws:

DAOException

getMaxLengthForFeature

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

Specified by:

getMaxLengthForFeature in interface CollectionCoreDatabase

Throws:

DAOException

getBuildCoordSystem

public DACoordinateSystem getBuildCoordSystem(Species species,
                                     String featureType)
                                       throws DAOException

Specified by:

getBuildCoordSystem in interface CollectionCoreDatabase

Throws:

DAOException

getCSByID

public DACoordinateSystem getCSByID(Species species,
                           Integer id)
                             throws DAOException

Specified by:

getCSByID in interface CollectionCoreDatabase

Throws:

DAOException

getChromosomeByName

public DAChromosome getChromosomeByName(Species species,
                               String name)
                                 throws DAOException

Specified by:

getChromosomeByName in interface CollectionCoreDatabase

Throws:

DAOException

getChromosomes

public List<DAChromosome> getChromosomes(Species species)
                                  throws DAOException

Specified by:

getChromosomes in interface CollectionCoreDatabase

Throws:

DAOException

getFragmentByName

public DAAssembledDNASequence getFragmentByName(Species species,
                                       String name)
                                         throws DAOException

Specified by:

getFragmentByName in interface CollectionCoreDatabase

Throws:

DAOException

getFragments

public List<DAAssembledDNASequence> getFragments(Species species)
                                          throws DAOException

Specified by:

getFragments in interface CollectionCoreDatabase

Throws:

DAOException

getAnalyses

public HashMap<Integer,DAAnalysis> getAnalyses()
                                        throws DAOException

Analyses are cached at the Database level

Specified by:

getAnalyses in interface CoreDatabase

Throws:

DAOException

validateExternalDB

public ExternalDB validateExternalDB(ExternalDB db)

Validates a givenExternalDB object, to return a pre-existing version id present.

Specified by:

validateExternalDB in interface DatabaseWithExternalDBs

Parameters:

db -

initializeExternalDBs

public void initializeExternalDBs()

Specified by:

initializeExternalDBs in interface DatabaseWithExternalDBs

getExternalDB

public ExternalDB getExternalDB(Integer id)

Specified by:

getExternalDB in interface DatabaseWithExternalDBs

getAssemblyAccession

public String getAssemblyAccession(CollectionSpecies species)

Returns the AssemblyAccession value for this species. (This method is maintained purely for equivalence to the SingelSpecies Database, lazy loading is not performed by the CollectionDatabase as this property should be filled in on initialisation).

Specified by:

getAssemblyAccession in interface CollectionCoreDatabase

Parameters:

species -

Returns:

getAssemblyName

public String getAssemblyName(CollectionSpecies species)

Returns the AssemblyName value for this species. (This method is maintained purely for equivalence to the SingelSpecies Database, lazy loading is not performed by the CollectionDatabase as this property should be filled in on initialisation).

Specified by:

getAssemblyName in interface CollectionCoreDatabase

Parameters:

species -

Returns: