uk.ac.roslin.ensembl.dao.database

Class DBSingleSpeciesCoreDatabase

java.lang.Object

uk.ac.roslin.ensembl.dao.database.DBDatabase

uk.ac.roslin.ensembl.dao.database.DBSingleSpeciesDatabase

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

All Implemented Interfaces:

Comparable<Database>, CoreDatabase, Database, DatabaseWithExternalDBs, SingleSpeciesCoreDatabase, SingleSpeciesDatabase

public class DBSingleSpeciesCoreDatabase
extends DBSingleSpeciesDatabase
implements SingleSpeciesCoreDatabase

Author:

paterson

Field Summary

Fields

Modifier and Type	Field and Description
protected String	assemblyAccession
protected String	assemblyName
protected String	comparaName

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

dbSpeciesName, originalDBName, originalDBSpeciesName, species

Constructor Summary

Constructors

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

Method Summary

Methods

Modifier and Type	Method and Description
void	addFeatureCS(String featureType, Integer csID, Integer maxLength)
HashMap<Integer,DAAnalysis>	getAnalyses() Analyses are cached at the Database level
String	getAssemblyAccession()
String	getAssemblyName()
DACoordinateSystem	getBuildCoordSystem(String featureType)
String	getBuildLevel(String featureType)
HashMap<FeatureType,String>	getBuildLevels()
DAChromosome	getChromosomeByName(String name)
DACoordinateSystem	getChromosomeLevelCoordSystem()
List<DAChromosome>	getChromosomes() Note that Chromosomes are not cached by the Database object - but by the Species Object
String	getComparaName()
List<DACoordinateSystem>	getCoordinateSystems()
DBDAOSingleSpeciesCoreFactory	getCoreFactory()
DACoordinateSystem	getCSByID(Integer id)
Set<DACoordinateSystem>	getCSForFeature(ObjectType featureType)
ExternalDB	getExternalDB(Integer id)
List<FeatureType>	getFeaturesForCS(CoordinateSystem coordSys)
DAAssembledDNASequence	getFragmentByName(String name) a Fragment is TopLevelAssembledDNASequence ( where there are no chromosomes )
List<DAAssembledDNASequence>	getFragments() Fragments are TopLevelAssembledDNASequences
Integer	getMaxLengthForFeature(ObjectType featureType, CoordinateSystem cs)
DACoordinateSystem	getSequenceLevelCoordSystem()
DACoordinateSystem	getTopLevelCoordSystem()
void	initializeExternalDBs()
void	lazyLoadMetadata()
void	setAssemblyAccession(String value)
void	setAssemblyName(String value)
void	setBuildLevel(String featureKey, String level)
void	setComparaName(String value)
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.DBSingleSpeciesDatabase

getdBName, getDbSpeciesName, getOriginalDBName, getOriginalDBSpeciesName, getRenamedDBName, getSpecies, isDBRenamed, setDbSpeciesName, setSpecies

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

compareTo, getBuild, getdBClassifier, 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.SingleSpeciesDatabase

getDbSpeciesName, getSpecies, setDbSpeciesName, setSpecies

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

Field Detail

assemblyName

protected String assemblyName

assemblyAccession

protected String assemblyAccession

comparaName

protected String comparaName

Constructor Detail

DBSingleSpeciesCoreDatabase

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

Throws:

ConfigurationException

Method Detail

getCoreFactory

public DBDAOSingleSpeciesCoreFactory getCoreFactory()

Specified by:

getCoreFactory in interface SingleSpeciesCoreDatabase

getCSByID

public DACoordinateSystem getCSByID(Integer id)
                             throws DAOException

Specified by:

getCSByID in interface SingleSpeciesCoreDatabase

Throws:

DAOException

getCoordinateSystems

public List<DACoordinateSystem> getCoordinateSystems()
                                              throws DAOException

Throws:

DAOException

getTopLevelCoordSystem

public DACoordinateSystem getTopLevelCoordSystem()
                                          throws DAOException

Specified by:

getTopLevelCoordSystem in interface SingleSpeciesCoreDatabase

Throws:

DAOException

getChromosomeLevelCoordSystem

public DACoordinateSystem getChromosomeLevelCoordSystem()
                                                 throws DAOException

Specified by:

getChromosomeLevelCoordSystem in interface SingleSpeciesCoreDatabase

Throws:

DAOException

getSequenceLevelCoordSystem

public DACoordinateSystem getSequenceLevelCoordSystem()
                                               throws DAOException

Specified by:

getSequenceLevelCoordSystem in interface SingleSpeciesCoreDatabase

Throws:

DAOException

getChromosomeByName

public DAChromosome getChromosomeByName(String name)
                                 throws DAOException

Specified by:

getChromosomeByName in interface SingleSpeciesCoreDatabase

Throws:

DAOException

getFragmentByName

public DAAssembledDNASequence getFragmentByName(String name)
                                         throws DAOException

a Fragment is TopLevelAssembledDNASequence ( where there are no chromosomes )

Specified by:

getFragmentByName in interface SingleSpeciesCoreDatabase

Parameters:

name -

Throws:

DAOException

getChromosomes

public List<DAChromosome> getChromosomes()
                                  throws DAOException

Note that Chromosomes are not cached by the Database object - but by the Species Object

Specified by:

getChromosomes in interface SingleSpeciesCoreDatabase

Throws:

DAOException

getFragments

public List<DAAssembledDNASequence> getFragments()
                                          throws DAOException

Fragments are TopLevelAssembledDNASequences

Specified by:

getFragments in interface SingleSpeciesCoreDatabase

Throws:

DAOException

getCSForFeature

public Set<DACoordinateSystem> getCSForFeature(ObjectType featureType)
                                        throws DAOException

Specified by:

getCSForFeature in interface SingleSpeciesCoreDatabase

Throws:

DAOException

getFeaturesForCS

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

Specified by:

getFeaturesForCS in interface SingleSpeciesCoreDatabase

Throws:

DAOException

getMaxLengthForFeature

public Integer getMaxLengthForFeature(ObjectType featureType,
                             CoordinateSystem cs)
                               throws DAOException

Specified by:

getMaxLengthForFeature in interface SingleSpeciesCoreDatabase

Throws:

DAOException

addFeatureCS

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

Specified by:

addFeatureCS in interface SingleSpeciesCoreDatabase

setBuildLevel

public void setBuildLevel(String featureKey,
                 String level)

Specified by:

setBuildLevel in interface SingleSpeciesCoreDatabase

getBuildLevel

public String getBuildLevel(String featureType)
                     throws DAOException

Specified by:

getBuildLevel in interface SingleSpeciesCoreDatabase

Throws:

DAOException

getBuildCoordSystem

public DACoordinateSystem getBuildCoordSystem(String featureType)
                                       throws DAOException

Specified by:

getBuildCoordSystem in interface SingleSpeciesCoreDatabase

Throws:

DAOException

getBuildLevels

public HashMap<FeatureType,String> getBuildLevels()

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

getAssemblyName

public String getAssemblyName()

Specified by:

getAssemblyName in interface SingleSpeciesCoreDatabase

getComparaName

public String getComparaName()

Specified by:

getComparaName in interface SingleSpeciesCoreDatabase

getAssemblyAccession

public String getAssemblyAccession()

Specified by:

getAssemblyAccession in interface SingleSpeciesCoreDatabase

lazyLoadMetadata

public void lazyLoadMetadata()
                      throws DAOException

Throws:

DAOException

setAssemblyName

public void setAssemblyName(String value)

Specified by:

setAssemblyName in interface SingleSpeciesCoreDatabase

setAssemblyAccession

public void setAssemblyAccession(String value)

Specified by:

setAssemblyAccession in interface SingleSpeciesCoreDatabase

setComparaName

public void setComparaName(String value)

Specified by:

setComparaName in interface SingleSpeciesCoreDatabase