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 DBCollectionSpecies

java.lang.Object
  extended by uk.ac.roslin.ensembl.dao.database.DBSpecies
      extended by uk.ac.roslin.ensembl.dao.database.DBCollectionSpecies
All Implemented Interfaces:
Comparable<uk.ac.roslin.ensembl.model.core.CollectionSpecies>, uk.ac.roslin.ensembl.model.core.CollectionSpecies, uk.ac.roslin.ensembl.model.core.Species

public class DBCollectionSpecies
extends DBSpecies
implements uk.ac.roslin.ensembl.model.core.CollectionSpecies


Field Summary
 
Fields inherited from class uk.ac.roslin.ensembl.dao.database.DBSpecies
aliases, commonName, comparaName, databaseStyleSpeciesName, ensemblStablePrefix, mostRecentDBRelease, mostRecentEnsemblSchemaVersion, registry, shortName, speciesBinomial, taxonomyID
 
Constructor Summary
DBCollectionSpecies()
           
DBCollectionSpecies(DBCollectionDatabase database)
           
 
Method Summary
 void addDatabase(uk.ac.roslin.ensembl.model.database.Database database)
           
 void addDatabases(TreeSet<? extends uk.ac.roslin.ensembl.model.database.Database> databases)
           
 int compareTo(uk.ac.roslin.ensembl.model.core.CollectionSpecies o)
           
 String getAssembly()
           
 String getAssembly(String dbVersion)
           
 uk.ac.roslin.ensembl.datasourceaware.core.DAChromosome getChromosomeByName(String name, String dbVersion)
           
 TreeMap<String,uk.ac.roslin.ensembl.datasourceaware.core.DAChromosome> getChromosomes(String dbVersion)
           
 DBCollectionCoreDatabase getCurrentCoreDatabase()
           
 DBCollectionDatabase getDatabaseByTypeAndVersion(uk.ac.roslin.ensembl.model.database.DatabaseType type, String version)
           
 TreeSet<DBCollectionDatabase> getDatabases()
           
 TreeSet<DBCollectionDatabase> getDatabasesByType(uk.ac.roslin.ensembl.model.database.DatabaseType type)
           
 TreeSet<DBCollectionDatabase> getDatabasesByVersion(String version)
           
 Integer getDBSpeciesID(String version)
           
 uk.ac.roslin.ensembl.datasourceaware.core.DAGene getGeneByID(Integer id, String dbVersion)
           
 uk.ac.roslin.ensembl.datasourceaware.core.DAGene getGeneByStableID(String stableID, String dbVersion)
           
 void setCurrentCoreDatabase(DBCollectionCoreDatabase currentCoreDatabase)
           
 void setDatabase(DBCollectionDatabase database)
           
 void setIDForVersion(Integer ID, String version)
           
 void setProperty(HashMap row)
           
 
Methods inherited from class uk.ac.roslin.ensembl.dao.database.DBSpecies
getAliases, getCachedChromosome, getChromosomeByName, getChromosomes, getCommonName, getComparaDivision, getComparaName, getDatabaseStyleName, getDBSpeciesID, getDBVersions, getEnsemblStablePrefix, getGeneByID, getGeneByStableID, getSchemaVersions, getShortName, getSpeciesBinomial, getTaxonomyID, getVersions, setCommonName, setComparaDivision, setComparaName, setDatabaseStyleSpeciesName, setEnsemblStablePrefix, setShortName, setSpeciesBinomial, setTaxonomyID, 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.core.Species
getAliases, getChromosomeByName, getChromosomes, getCommonName, getComparaDivision, getComparaName, getDatabaseStyleName, getDBVersions, getEnsemblStablePrefix, getGeneByID, getGeneByStableID, getSchemaVersions, getShortName, getSpeciesBinomial, getTaxonomyID
 

Constructor Detail

DBCollectionSpecies

public DBCollectionSpecies()

DBCollectionSpecies

public DBCollectionSpecies(DBCollectionDatabase database)
                    throws uk.ac.roslin.ensembl.exception.ConfigurationException
Throws:
uk.ac.roslin.ensembl.exception.ConfigurationException
Method Detail

setDatabase

public void setDatabase(DBCollectionDatabase database)
                 throws uk.ac.roslin.ensembl.exception.ConfigurationException
Throws:
uk.ac.roslin.ensembl.exception.ConfigurationException

setIDForVersion

public void setIDForVersion(Integer ID,
                            String version)

setProperty

public void setProperty(HashMap row)
Specified by:
setProperty in interface uk.ac.roslin.ensembl.model.core.Species
Overrides:
setProperty in class DBSpecies

getDBSpeciesID

public Integer getDBSpeciesID(String version)
Specified by:
getDBSpeciesID in interface uk.ac.roslin.ensembl.model.core.Species
Overrides:
getDBSpeciesID in class DBSpecies

compareTo

public int compareTo(uk.ac.roslin.ensembl.model.core.CollectionSpecies o)
Specified by:
compareTo in interface Comparable<uk.ac.roslin.ensembl.model.core.CollectionSpecies>

getCurrentCoreDatabase

public DBCollectionCoreDatabase getCurrentCoreDatabase()
Specified by:
getCurrentCoreDatabase in interface uk.ac.roslin.ensembl.model.core.Species
Overrides:
getCurrentCoreDatabase in class DBSpecies

setCurrentCoreDatabase

public void setCurrentCoreDatabase(DBCollectionCoreDatabase currentCoreDatabase)

getDatabases

public TreeSet<DBCollectionDatabase> getDatabases()
Specified by:
getDatabases in interface uk.ac.roslin.ensembl.model.core.Species
Overrides:
getDatabases in class DBSpecies

addDatabases

public void addDatabases(TreeSet<? extends uk.ac.roslin.ensembl.model.database.Database> databases)
Specified by:
addDatabases in interface uk.ac.roslin.ensembl.model.core.Species
Overrides:
addDatabases in class DBSpecies

addDatabase

public void addDatabase(uk.ac.roslin.ensembl.model.database.Database database)
Specified by:
addDatabase in interface uk.ac.roslin.ensembl.model.core.Species
Overrides:
addDatabase in class DBSpecies

getDatabasesByType

public TreeSet<DBCollectionDatabase> getDatabasesByType(uk.ac.roslin.ensembl.model.database.DatabaseType type)
Specified by:
getDatabasesByType in interface uk.ac.roslin.ensembl.model.core.Species
Overrides:
getDatabasesByType in class DBSpecies

getDatabasesByVersion

public TreeSet<DBCollectionDatabase> getDatabasesByVersion(String version)
Specified by:
getDatabasesByVersion in interface uk.ac.roslin.ensembl.model.core.Species
Overrides:
getDatabasesByVersion in class DBSpecies

getDatabaseByTypeAndVersion

public DBCollectionDatabase getDatabaseByTypeAndVersion(uk.ac.roslin.ensembl.model.database.DatabaseType type,
                                                        String version)
Specified by:
getDatabaseByTypeAndVersion in interface uk.ac.roslin.ensembl.model.core.Species
Overrides:
getDatabaseByTypeAndVersion in class DBSpecies

getChromosomeByName

public uk.ac.roslin.ensembl.datasourceaware.core.DAChromosome getChromosomeByName(String name,
                                                                                  String dbVersion)
                                                                           throws uk.ac.roslin.ensembl.exception.DAOException
Specified by:
getChromosomeByName in interface uk.ac.roslin.ensembl.model.core.Species
Overrides:
getChromosomeByName in class DBSpecies
Throws:
uk.ac.roslin.ensembl.exception.DAOException

getChromosomes

public TreeMap<String,uk.ac.roslin.ensembl.datasourceaware.core.DAChromosome> getChromosomes(String dbVersion)
                                                                                      throws uk.ac.roslin.ensembl.exception.DAOException
Specified by:
getChromosomes in interface uk.ac.roslin.ensembl.model.core.Species
Overrides:
getChromosomes in class DBSpecies
Throws:
uk.ac.roslin.ensembl.exception.DAOException

getGeneByID

public uk.ac.roslin.ensembl.datasourceaware.core.DAGene getGeneByID(Integer id,
                                                                    String dbVersion)
                                                             throws uk.ac.roslin.ensembl.exception.DAOException
Specified by:
getGeneByID in interface uk.ac.roslin.ensembl.model.core.Species
Overrides:
getGeneByID in class DBSpecies
Throws:
uk.ac.roslin.ensembl.exception.DAOException

getGeneByStableID

public uk.ac.roslin.ensembl.datasourceaware.core.DAGene getGeneByStableID(String stableID,
                                                                          String dbVersion)
                                                                   throws uk.ac.roslin.ensembl.exception.DAOException
Specified by:
getGeneByStableID in interface uk.ac.roslin.ensembl.model.core.Species
Overrides:
getGeneByStableID in class DBSpecies
Throws:
uk.ac.roslin.ensembl.exception.DAOException

getAssembly

public String getAssembly()
Specified by:
getAssembly in interface uk.ac.roslin.ensembl.model.core.Species
Overrides:
getAssembly in class DBSpecies

getAssembly

public String getAssembly(String dbVersion)
Specified by:
getAssembly in interface uk.ac.roslin.ensembl.model.core.Species
Overrides:
getAssembly in class DBSpecies

Ensembl Data Access Module
v1.09

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