Ensembl Model v1.09
© Roslin Institute 2010. GNU General Public License, version3
Ensembl Model
v1.09

uk.ac.roslin.ensembl.model.core
Interface Species

All Known Subinterfaces:
CollectionSpecies

public interface Species

Author:
paterson

Method Summary
 void addDatabase(Database database)
           
 void addDatabases(TreeSet<? extends Database> databases)
           
 TreeSet<String> getAliases()
           
 String getAssembly()
           
 String getAssembly(String dbVersion)
           
 Chromosome getChromosomeByName(String name)
           
 Chromosome getChromosomeByName(String name, String dbVersion)
           
 TreeMap<String,? extends Chromosome> getChromosomes()
           
 TreeMap<String,? extends Chromosome> getChromosomes(String dbVersion)
           
 String getCommonName()
           
 EnsemblComparaDivision getComparaDivision()
           
 String getComparaName()
           
 CoreDatabase getCurrentCoreDatabase()
           
 Database getDatabaseByTypeAndVersion(DatabaseType type, String version)
           
 TreeSet<? extends Database> getDatabases()
           
 TreeSet<? extends Database> getDatabasesByType(DatabaseType type)
           
 TreeSet<? extends Database> getDatabasesByVersion(String version)
           
 String getDatabaseStyleName()
           
 Integer getDBSpeciesID(String version)
           
 TreeSet<String> getDBVersions()
           
 String getEnsemblStablePrefix()
           
 Gene getGeneByID(Integer id)
           
 Gene getGeneByID(Integer id, String dbVersion)
           
 Gene getGeneByStableID(String stableID)
           
 Gene getGeneByStableID(String stableID, String dbVersion)
           
 TreeSet<String> getSchemaVersions()
           
 String getShortName()
           
 String getSpeciesBinomial()
           
 String getTaxonomyID()
           
 void setProperty(HashMap row)
           
 

Method Detail

getAliases

TreeSet<String> getAliases()

getCommonName

String getCommonName()

getSpeciesBinomial

String getSpeciesBinomial()

getDatabaseStyleName

String getDatabaseStyleName()

getComparaName

String getComparaName()

getShortName

String getShortName()

setProperty

void setProperty(HashMap row)

getCurrentCoreDatabase

CoreDatabase getCurrentCoreDatabase()

getTaxonomyID

String getTaxonomyID()

getDBSpeciesID

Integer getDBSpeciesID(String version)

getEnsemblStablePrefix

String getEnsemblStablePrefix()

getDatabases

TreeSet<? extends Database> getDatabases()

addDatabases

void addDatabases(TreeSet<? extends Database> databases)

addDatabase

void addDatabase(Database database)

getDatabasesByType

TreeSet<? extends Database> getDatabasesByType(DatabaseType type)

getDatabasesByVersion

TreeSet<? extends Database> getDatabasesByVersion(String version)

getDatabaseByTypeAndVersion

Database getDatabaseByTypeAndVersion(DatabaseType type,
                                     String version)

getChromosomeByName

Chromosome getChromosomeByName(String name)
                               throws DAOException
Throws:
DAOException

getChromosomeByName

Chromosome getChromosomeByName(String name,
                               String dbVersion)
                               throws DAOException
Throws:
DAOException

getChromosomes

TreeMap<String,? extends Chromosome> getChromosomes()
                                                    throws DAOException
Throws:
DAOException

getChromosomes

TreeMap<String,? extends Chromosome> getChromosomes(String dbVersion)
                                                    throws DAOException
Throws:
DAOException

getSchemaVersions

TreeSet<String> getSchemaVersions()

getDBVersions

TreeSet<String> getDBVersions()

getGeneByID

Gene getGeneByID(Integer id)
                 throws DAOException
Throws:
DAOException

getGeneByID

Gene getGeneByID(Integer id,
                 String dbVersion)
                 throws DAOException
Throws:
DAOException

getGeneByStableID

Gene getGeneByStableID(String stableID)
                       throws DAOException
Throws:
DAOException

getGeneByStableID

Gene getGeneByStableID(String stableID,
                       String dbVersion)
                       throws DAOException
Throws:
DAOException

getComparaDivision

EnsemblComparaDivision getComparaDivision()

getAssembly

String getAssembly()

getAssembly

String getAssembly(String dbVersion)

Ensembl Model
v1.09

Ensembl Model v1.09
© Roslin Institute 2010. GNU General Public License, version3