uk.ac.roslin.ensembl.model.core

Interface Species

All Known Subinterfaces:

CollectionSpecies

All Known Implementing Classes:

DBCollectionSpecies, DBSpecies

public interface Species

Author:

paterson

Method Summary

Methods

Modifier and Type	Method and Description
void	addDatabase(Database database)
void	addDatabases(TreeSet<? extends Database> databases)
TreeSet<String>	getAliases()
String	getAssemblyAccession(String dbVersion)
String	getAssemblyAccessionStem()
String	getAssemblyAccessionStem(String dbVersion)
String	getAssemblyName(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(String version)
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	getDisplayName()
String	getEnsemblStablePrefix()
AssembledDNASequence	getFragmentByName(String name)
AssembledDNASequence	getFragmentByName(String name, String dbVersion)
TreeMap<String,? extends AssembledDNASequence>	getFragments()
TreeMap<String,? extends AssembledDNASequence>	getFragments(String dbVersion)
Gene	getGeneByStableID(String stableID)
Gene	getGeneByStableID(String stableID, String dbVersion)
List<? extends Gene>	getGenesForExactName(String name)
List<? extends Gene>	getGenesForExactName(String name, String dbVersion)
List<? extends Gene>	getGenesForNameBeginning(String name)
List<? extends Gene>	getGenesForNameBeginning(String name, String dbVersion)
List<? extends Gene>	getGenesForVegaID(String vegaID)
List<? extends Gene>	getGenesForVegaID(String vegaID, String dbVersion)
Integer	getHighestDBRelease()
CoreDatabase	getMostRecentCoreDatabase()
TreeSet<String>	getSchemaVersions()
String	getShortName()
String	getSpeciesBinomial()
String	getTaxonomyID()
Transcript	getTranscriptByStableID(String stableID)
Transcript	getTranscriptByStableID(String stableID, String dbVersion)
List<? extends Transcript>	getTranscriptsForCcdsID(String ccdsID)
List<? extends Transcript>	getTranscriptsForCcdsID(String ccdsID, String dbVersion)
List<? extends Transcript>	getTranscriptsForVegaID(String vegaID)
List<? extends Transcript>	getTranscriptsForVegaID(String vegaID, String dbVersion)
Translation	getTranslationByStableID(String stableID)
Translation	getTranslationByStableID(String stableID, String dbVersion)
List<? extends Translation>	getTranslationsForVegaID(String vegaID)
List<? extends Translation>	getTranslationsForVegaID(String vegaID, String dbVersion)
boolean	isInPanCompara(String dbVersion)
void	setAssemblyExceptions(String dbVersion)
void	setProperty(HashMap row)

Method Detail

getAliases

TreeSet<String> getAliases()

getCommonName

String getCommonName()

getSpeciesBinomial

String getSpeciesBinomial()

getDatabaseStyleName

String getDatabaseStyleName()

getComparaName

String getComparaName(String version)

getShortName

String getShortName()

getDisplayName

String getDisplayName()

setProperty

void setProperty(HashMap row)

getMostRecentCoreDatabase

CoreDatabase getMostRecentCoreDatabase()

getHighestDBRelease

Integer getHighestDBRelease()

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

getFragmentByName

AssembledDNASequence getFragmentByName(String name)
                                       throws DAOException

Throws:

DAOException

getFragmentByName

AssembledDNASequence getFragmentByName(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

getFragments

TreeMap<String,? extends AssembledDNASequence> getFragments()
                                                            throws DAOException

Throws:

DAOException

getFragments

TreeMap<String,? extends AssembledDNASequence> getFragments(String dbVersion)
                                                            throws DAOException

Throws:

DAOException

getSchemaVersions

TreeSet<String> getSchemaVersions()

getDBVersions

TreeSet<String> getDBVersions()

getGenesForVegaID

List<? extends Gene> getGenesForVegaID(String vegaID)
                                       throws DAOException

Throws:

DAOException

getGenesForVegaID

List<? extends Gene> getGenesForVegaID(String vegaID,
                                     String dbVersion)
                                       throws DAOException

Throws:

DAOException

getTranscriptsForVegaID

List<? extends Transcript> getTranscriptsForVegaID(String vegaID)
                                                   throws DAOException

Throws:

DAOException

getTranscriptsForVegaID

List<? extends Transcript> getTranscriptsForVegaID(String vegaID,
                                                 String dbVersion)
                                                   throws DAOException

Throws:

DAOException

getTranscriptsForCcdsID

List<? extends Transcript> getTranscriptsForCcdsID(String ccdsID)
                                                   throws DAOException

Throws:

DAOException

getTranscriptsForCcdsID

List<? extends Transcript> getTranscriptsForCcdsID(String ccdsID,
                                                 String dbVersion)
                                                   throws DAOException

Throws:

DAOException

getTranslationsForVegaID

List<? extends Translation> getTranslationsForVegaID(String vegaID)
                                                     throws DAOException

Throws:

DAOException

getTranslationsForVegaID

List<? extends Translation> getTranslationsForVegaID(String vegaID,
                                                   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

getTranscriptByStableID

Transcript getTranscriptByStableID(String stableID)
                                   throws DAOException

Throws:

DAOException

getTranscriptByStableID

Transcript getTranscriptByStableID(String stableID,
                                 String dbVersion)
                                   throws DAOException

Throws:

DAOException

getTranslationByStableID

Translation getTranslationByStableID(String stableID)
                                     throws DAOException

Throws:

DAOException

getTranslationByStableID

Translation getTranslationByStableID(String stableID,
                                   String dbVersion)
                                     throws DAOException

Throws:

DAOException

getGenesForExactName

List<? extends Gene> getGenesForExactName(String name)
                                          throws DAOException

Throws:

DAOException

getGenesForExactName

List<? extends Gene> getGenesForExactName(String name,
                                        String dbVersion)
                                          throws DAOException

Throws:

DAOException

getGenesForNameBeginning

List<? extends Gene> getGenesForNameBeginning(String name)
                                              throws DAOException

Throws:

DAOException

getGenesForNameBeginning

List<? extends Gene> getGenesForNameBeginning(String name,
                                            String dbVersion)
                                              throws DAOException

Throws:

DAOException

getComparaDivision

EnsemblComparaDivision getComparaDivision()

getAssemblyAccessionStem

String getAssemblyAccessionStem()

getAssemblyAccessionStem

String getAssemblyAccessionStem(String dbVersion)

getAssemblyName

String getAssemblyName(String dbVersion)

getAssemblyAccession

String getAssemblyAccession(String dbVersion)

setAssemblyExceptions

void setAssemblyExceptions(String dbVersion)
                           throws DAOException

Throws:

DAOException

isInPanCompara

boolean isInPanCompara(String dbVersion)