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 DBSpecies

java.lang.Object
  extended by uk.ac.roslin.ensembl.dao.database.DBSpecies
All Implemented Interfaces:
uk.ac.roslin.ensembl.model.core.Species
Direct Known Subclasses:
DBCollectionSpecies

public class DBSpecies
extends Object
implements uk.ac.roslin.ensembl.model.core.Species


Field Summary
protected  TreeSet<String> aliases
           
protected  String commonName
           
protected  String comparaName
           
protected  String databaseStyleSpeciesName
           
protected  String ensemblStablePrefix
           
protected  String mostRecentDBRelease
           
protected  String mostRecentEnsemblSchemaVersion
           
protected  uk.ac.roslin.ensembl.model.database.Registry registry
           
protected  String shortName
           
protected  String speciesBinomial
           
protected  String taxonomyID
           
 
Constructor Summary
DBSpecies()
           
DBSpecies(DBSingleSpeciesCoreDatabase 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)
           
 TreeSet<String> getAliases()
           
 String getAssembly()
           
 String getAssembly(String dbVersion)
           
 uk.ac.roslin.ensembl.datasourceaware.core.DAChromosome getCachedChromosome(uk.ac.roslin.ensembl.datasourceaware.core.DAChromosome chr_in)
           
 uk.ac.roslin.ensembl.datasourceaware.core.DAChromosome getChromosomeByName(String name)
           
 uk.ac.roslin.ensembl.datasourceaware.core.DAChromosome getChromosomeByName(String name, String dbVersion)
           
 TreeMap<String,uk.ac.roslin.ensembl.datasourceaware.core.DAChromosome> getChromosomes()
           
 TreeMap<String,uk.ac.roslin.ensembl.datasourceaware.core.DAChromosome> getChromosomes(String dbVersion)
           
 String getCommonName()
           
 uk.ac.roslin.ensembl.config.EnsemblComparaDivision getComparaDivision()
           
 String getComparaName()
           
 uk.ac.roslin.ensembl.model.database.CoreDatabase getCurrentCoreDatabase()
           
 DBDatabase getDatabaseByTypeAndVersion(uk.ac.roslin.ensembl.model.database.DatabaseType type, String version)
           
 TreeSet<? extends DBDatabase> getDatabases()
           
 TreeSet<? extends DBDatabase> getDatabasesByType(uk.ac.roslin.ensembl.model.database.DatabaseType type)
           
 TreeSet<? extends DBDatabase> getDatabasesByVersion(String version)
           
 String getDatabaseStyleName()
           
 Integer getDBSpeciesID()
           
 Integer getDBSpeciesID(String version)
           
 TreeSet<String> getDBVersions()
           
 String getEnsemblStablePrefix()
           
 uk.ac.roslin.ensembl.datasourceaware.core.DAGene getGeneByID(Integer id)
           
 uk.ac.roslin.ensembl.datasourceaware.core.DAGene getGeneByID(Integer id, String dbVersion)
           
 uk.ac.roslin.ensembl.datasourceaware.core.DAGene getGeneByStableID(String stableID)
           
 uk.ac.roslin.ensembl.datasourceaware.core.DAGene getGeneByStableID(String stableID, String dbVersion)
           
 TreeSet<String> getSchemaVersions()
           
 String getShortName()
           
 String getSpeciesBinomial()
           
 String getTaxonomyID()
           
 TreeSet<String> getVersions()
           
 void setCommonName(String commonName)
           
 void setComparaDivision(String speciesDivision)
           
 void setComparaName(String comparaName)
           
 void setDatabaseStyleSpeciesName(String dbSpeciesName)
           
 void setEnsemblStablePrefix(String ensemblStablePrefix)
           
 void setProperty(HashMap row)
           
 void setShortName(String name)
           
 void setSpeciesBinomial(String speciesBinomial)
           
 void setTaxonomyID(String taxonomyID)
           
 String toString()
           
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait
 

Field Detail

databaseStyleSpeciesName

protected String databaseStyleSpeciesName

speciesBinomial

protected String speciesBinomial

commonName

protected String commonName

comparaName

protected String comparaName

shortName

protected String shortName

mostRecentEnsemblSchemaVersion

protected String mostRecentEnsemblSchemaVersion

mostRecentDBRelease

protected String mostRecentDBRelease

taxonomyID

protected String taxonomyID

ensemblStablePrefix

protected String ensemblStablePrefix

aliases

protected TreeSet<String> aliases

registry

protected uk.ac.roslin.ensembl.model.database.Registry registry
Constructor Detail

DBSpecies

public DBSpecies()

DBSpecies

public DBSpecies(DBSingleSpeciesCoreDatabase database)
Method Detail

getVersions

public TreeSet<String> getVersions()

getAliases

public TreeSet<String> getAliases()
Specified by:
getAliases in interface uk.ac.roslin.ensembl.model.core.Species

setProperty

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

getCurrentCoreDatabase

public uk.ac.roslin.ensembl.model.database.CoreDatabase getCurrentCoreDatabase()
Specified by:
getCurrentCoreDatabase in interface uk.ac.roslin.ensembl.model.core.Species

getCommonName

public String getCommonName()
Specified by:
getCommonName in interface uk.ac.roslin.ensembl.model.core.Species

getShortName

public String getShortName()
Specified by:
getShortName in interface uk.ac.roslin.ensembl.model.core.Species

setShortName

public void setShortName(String name)

getDatabaseStyleName

public String getDatabaseStyleName()
Specified by:
getDatabaseStyleName in interface uk.ac.roslin.ensembl.model.core.Species

getDatabases

public TreeSet<? extends DBDatabase> getDatabases()
Specified by:
getDatabases in interface uk.ac.roslin.ensembl.model.core.Species

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

addDatabase

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

getEnsemblStablePrefix

public String getEnsemblStablePrefix()
Specified by:
getEnsemblStablePrefix in interface uk.ac.roslin.ensembl.model.core.Species

getSpeciesBinomial

public String getSpeciesBinomial()
Specified by:
getSpeciesBinomial in interface uk.ac.roslin.ensembl.model.core.Species

getTaxonomyID

public String getTaxonomyID()
Specified by:
getTaxonomyID in interface uk.ac.roslin.ensembl.model.core.Species

getDatabasesByType

public TreeSet<? extends DBDatabase> getDatabasesByType(uk.ac.roslin.ensembl.model.database.DatabaseType type)
Specified by:
getDatabasesByType in interface uk.ac.roslin.ensembl.model.core.Species

getDatabasesByVersion

public TreeSet<? extends DBDatabase> getDatabasesByVersion(String version)
Specified by:
getDatabasesByVersion in interface uk.ac.roslin.ensembl.model.core.Species

getDatabaseByTypeAndVersion

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

setCommonName

public void setCommonName(String commonName)

setEnsemblStablePrefix

public void setEnsemblStablePrefix(String ensemblStablePrefix)

setSpeciesBinomial

public void setSpeciesBinomial(String speciesBinomial)

setTaxonomyID

public void setTaxonomyID(String taxonomyID)

getDBSpeciesID

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

getDBSpeciesID

public Integer getDBSpeciesID()

getComparaName

public String getComparaName()
Specified by:
getComparaName in interface uk.ac.roslin.ensembl.model.core.Species

setComparaName

public void setComparaName(String comparaName)

getChromosomes

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

getChromosomeByName

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

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
Throws:
uk.ac.roslin.ensembl.exception.DAOException

getGeneByID

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

getGeneByStableID

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

getSchemaVersions

public TreeSet<String> getSchemaVersions()
Specified by:
getSchemaVersions in interface uk.ac.roslin.ensembl.model.core.Species

getDBVersions

public TreeSet<String> getDBVersions()
Specified by:
getDBVersions in interface uk.ac.roslin.ensembl.model.core.Species

setDatabaseStyleSpeciesName

public void setDatabaseStyleSpeciesName(String dbSpeciesName)

toString

public String toString()
Overrides:
toString in class Object

getCachedChromosome

public uk.ac.roslin.ensembl.datasourceaware.core.DAChromosome getCachedChromosome(uk.ac.roslin.ensembl.datasourceaware.core.DAChromosome chr_in)

getComparaDivision

public uk.ac.roslin.ensembl.config.EnsemblComparaDivision getComparaDivision()
Specified by:
getComparaDivision in interface uk.ac.roslin.ensembl.model.core.Species

setComparaDivision

public void setComparaDivision(String speciesDivision)

getAssembly

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

getAssembly

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

Ensembl Data Access Module
v1.09

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