Ensembl Data Access Module v1.09
© Roslin Institute 2010. GNU General Public License, version3
uk.ac.roslin.ensembl.dao.database
Class DBSpecies
java.lang.Object
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
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
DBSpecies
public DBSpecies()
DBSpecies
public DBSpecies(DBSingleSpeciesCoreDatabase database)
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
© Roslin Institute 2010. GNU General Public License, version3