uk.ac.roslin.ensembl.dao.database

Class DBCollectionSpecies

java.lang.Object

uk.ac.roslin.ensembl.dao.database.DBSpecies

uk.ac.roslin.ensembl.dao.database.DBCollectionSpecies

All Implemented Interfaces:

Comparable, CollectionSpecies, Species

public class DBCollectionSpecies
extends DBSpecies
implements CollectionSpecies

Field Summary

Fields

Modifier and Type	Field and Description
protected TreeMap<String,Integer>	versionIDmap

Fields inherited from class uk.ac.roslin.ensembl.dao.database.DBSpecies

aliases, allChromosomesRetrieved, allFragmentsRetrieved, assemblyAccessionsByVersion, assemblyNamesByVersion, chromosomes, commonName, comparaNameByVersion, databaseStyleSpeciesName, dbStyleNameByVersion, dbVersions, ensemblStablePrefix, fragments, highestDBRelease, mostRecentEnsemblSchemaVersion, registry, schemaVersions, shortName, speciesBinomial, taxonomyID, urlName

Constructor Summary

Constructors

Constructor and Description
DBCollectionSpecies()
DBCollectionSpecies(DBCollectionCoreDatabase database)

Method Summary

Methods

Modifier and Type	Method and Description
void	addDatabase(Database database)
void	addDatabases(TreeSet<? extends Database> databases)
int	compareTo(Object o)
boolean	equals(Object o)
String	getAssemblyAccession(String dbVersion)
String	getAssemblyName(String dbVersion)
DAChromosome	getChromosomeByName(String name, String dbVersion)
TreeMap<String,DAChromosome>	getChromosomes(String dbVersion)
String	getComparaName(String version)
DBCollectionDatabase	getDatabaseByTypeAndVersion(DatabaseType type, String version)
TreeSet<DBCollectionDatabase>	getDatabases()
TreeSet<DBCollectionDatabase>	getDatabasesByType(DatabaseType type)
TreeSet<DBCollectionDatabase>	getDatabasesByVersion(String version)
Integer	getDBSpeciesID() Deprecated.
Integer	getDBSpeciesID(String version)
DAAssembledDNASequence	getFragmentByName(String name, String dbVersion)
TreeMap<String,DAAssembledDNASequence>	getFragments(String dbVersion)
DAGene	getGeneByStableID(String stableID, String dbVersion)
List<DAGene>	getGenesForExactName(String name, String dbVersion)
List<DAGene>	getGenesForVegaID(String vegaID, String dbVersion) Method returns a List of Genes that have been mapped to the given Vega Identifier.
DBCollectionCoreDatabase	getMostRecentCoreDatabase()
DATranscript	getTranscriptByStableID(String stableID, String dbVersion)
List<DATranscript>	getTranscriptsForCcdsID(String ccdsID, String dbVersion) Method returns a List of Transcripts that have been mapped to the given CCDS Identifier (This may be the CCDS accession or the CCDS accession.schemaVersion).
List<DATranscript>	getTranscriptsForVegaID(String vegaID, String dbVersion) Method returns a List of Transcripts that have been mapped to the given Vega Identifier.
DATranslation	getTranslationByStableID(String stableID, String dbVersion)
List<DATranslation>	getTranslationsForVegaID(String vegaID, String dbVersion) Method returns a List of Translations that have been mapped to the given Vega Identifier.
int	hashCode()
void	setAssemblyExceptions(String version)
void	setIDForVersion(Integer ID, String version)
void	setMostRecentCoreDatabase(DBCollectionCoreDatabase currentCoreDatabase)
void	setProperty(HashMap row)

Methods inherited from class uk.ac.roslin.ensembl.dao.database.DBSpecies

getAliases, getAssemblyAccessionStem, getAssemblyAccessionStem, getCachedChromosome, getCachedFragment, getChromosomeByName, getChromosomes, getCommonName, getComparaDivision, getDatabaseStyleName, getDatabaseStyleSpeciesName, getDBVersions, getDisplayName, getEnsemblStablePrefix, getFragmentByName, getFragments, getGeneByStableID, getGenesForExactName, getGenesForNameBeginning, getGenesForNameBeginning, getGenesForVegaID, getHighestDBRelease, getSchemaVersions, getShortName, getSpeciesBinomial, getTaxonomyID, getTranscriptByStableID, getTranscriptsForCcdsID, getTranscriptsForVegaID, getTranslationByStableID, getTranslationsForVegaID, getUrlName, isInPanCompara, setAssemblyAccession, setAssemblyName, setCommonName, setComparaDivision, setComparaDivision, setComparaName, setDatabaseStyleSpeciesName, setDatabaseStyleSpeciesName, setEnsemblStablePrefix, setShortName, setSpeciesBinomial, setTaxonomyID, setUrlName, toString

Methods inherited from class java.lang.Object

clone, finalize, getClass, notify, notifyAll, wait, wait, wait

Methods inherited from interface uk.ac.roslin.ensembl.model.core.Species

getAliases, getAssemblyAccessionStem, getAssemblyAccessionStem, getChromosomeByName, getChromosomes, getCommonName, getComparaDivision, getDatabaseStyleName, getDBVersions, getDisplayName, getEnsemblStablePrefix, getFragmentByName, getFragments, getGeneByStableID, getGenesForExactName, getGenesForNameBeginning, getGenesForNameBeginning, getGenesForVegaID, getHighestDBRelease, getSchemaVersions, getShortName, getSpeciesBinomial, getTaxonomyID, getTranscriptByStableID, getTranscriptsForCcdsID, getTranscriptsForVegaID, getTranslationByStableID, getTranslationsForVegaID, isInPanCompara

Field Detail

versionIDmap

protected TreeMap<String,Integer> versionIDmap

Constructor Detail

DBCollectionSpecies

public DBCollectionSpecies()

DBCollectionSpecies

public DBCollectionSpecies(DBCollectionCoreDatabase database)
                    throws ConfigurationException

Throws:

ConfigurationException

Method Detail

setIDForVersion

public void setIDForVersion(Integer ID,
                   String version)

setProperty

public void setProperty(HashMap row)

Specified by:

setProperty in interface Species

Overrides:

setProperty in class DBSpecies

getDBSpeciesID

public Integer getDBSpeciesID(String version)

Specified by:

getDBSpeciesID in interface Species

Overrides:

getDBSpeciesID in class DBSpecies

getDBSpeciesID

@Deprecated
public Integer getDBSpeciesID()

Deprecated.

Overrides:

getDBSpeciesID in class DBSpecies

compareTo

public int compareTo(Object o)

Specified by:

compareTo in interface Comparable

hashCode

public int hashCode()

Overrides:

hashCode in class Object

equals

public boolean equals(Object o)

Overrides:

equals in class Object

getMostRecentCoreDatabase

public DBCollectionCoreDatabase getMostRecentCoreDatabase()

Specified by:

getMostRecentCoreDatabase in interface Species

Overrides:

getMostRecentCoreDatabase in class DBSpecies

setMostRecentCoreDatabase

public void setMostRecentCoreDatabase(DBCollectionCoreDatabase currentCoreDatabase)

getDatabases

public TreeSet<DBCollectionDatabase> getDatabases()

Specified by:

getDatabases in interface Species

Overrides:

getDatabases in class DBSpecies

addDatabases

public void addDatabases(TreeSet<? extends Database> databases)

Specified by:

addDatabases in interface Species

Overrides:

addDatabases in class DBSpecies

addDatabase

public void addDatabase(Database database)

Specified by:

addDatabase in interface Species

Overrides:

addDatabase in class DBSpecies

getDatabasesByType

public TreeSet<DBCollectionDatabase> getDatabasesByType(DatabaseType type)

Specified by:

getDatabasesByType in interface Species

Overrides:

getDatabasesByType in class DBSpecies

getDatabasesByVersion

public TreeSet<DBCollectionDatabase> getDatabasesByVersion(String version)

Specified by:

getDatabasesByVersion in interface Species

Overrides:

getDatabasesByVersion in class DBSpecies

getDatabaseByTypeAndVersion

public DBCollectionDatabase getDatabaseByTypeAndVersion(DatabaseType type,
                                               String version)

Specified by:

getDatabaseByTypeAndVersion in interface Species

Overrides:

getDatabaseByTypeAndVersion in class DBSpecies

getChromosomeByName

public DAChromosome getChromosomeByName(String name,
                               String dbVersion)
                                 throws DAOException

Specified by:

getChromosomeByName in interface Species

Overrides:

getChromosomeByName in class DBSpecies

Throws:

DAOException

getChromosomes

public TreeMap<String,DAChromosome> getChromosomes(String dbVersion)
                                            throws DAOException

Specified by:

getChromosomes in interface Species

Overrides:

getChromosomes in class DBSpecies

Throws:

DAOException

getFragmentByName

public DAAssembledDNASequence getFragmentByName(String name,
                                       String dbVersion)
                                         throws DAOException

Specified by:

getFragmentByName in interface Species

Overrides:

getFragmentByName in class DBSpecies

Throws:

DAOException

getFragments

public TreeMap<String,DAAssembledDNASequence> getFragments(String dbVersion)
                                                    throws DAOException

Specified by:

getFragments in interface Species

Overrides:

getFragments in class DBSpecies

Throws:

DAOException

getTranscriptsForCcdsID

public List<DATranscript> getTranscriptsForCcdsID(String ccdsID,
                                         String dbVersion)
                                           throws DAOException

Method returns a List of Transcripts that have been mapped to the given CCDS Identifier (This may be the CCDS accession or the CCDS accession.schemaVersion). There may be more than one Ensembl Transcript returned. CCDS currently curates consensus canonical transcripts for human and mouse. Calling this method on EnsemblGenomes (invertebrate) species will return an empty list by default via the wrapped TranscriptDAO method).

Specified by:

getTranscriptsForCcdsID in interface Species

Overrides:

getTranscriptsForCcdsID in class DBSpecies

Parameters:

ccdsID -

dbVersion -

Throws:

DAOException

getTranscriptsForVegaID

public List<DATranscript> getTranscriptsForVegaID(String vegaID,
                                         String dbVersion)
                                           throws DAOException

Method returns a List of Transcripts that have been mapped to the given Vega Identifier. (there may be more than one Ensembl Transcript). Vega currently curates gene, transcript and protein annotations for a human and and a few key regions of other vertebrate species. Calling this method on EnsemblGenomes (invertebrate) species will return an empty list by default Via the wrapped TranscriptDAO method).

Specified by:

getTranscriptsForVegaID in interface Species

Overrides:

getTranscriptsForVegaID in class DBSpecies

Parameters:

vegaID -

dbVersion -

Throws:

DAOException

getTranslationsForVegaID

public List<DATranslation> getTranslationsForVegaID(String vegaID,
                                           String dbVersion)
                                             throws DAOException

Method returns a List of Translations that have been mapped to the given Vega Identifier. (there may be more than one Ensembl Translation). Vega currently curates gene, transcript and protein annotations for a human and and a few key regions of other vertebrate species. Calling this method on EnsemblGenomes (invertebrate) species will return an empty list by default Via the wrapped TranslationDAO method).

Specified by:

getTranslationsForVegaID in interface Species

Overrides:

getTranslationsForVegaID in class DBSpecies

Parameters:

vegaID -

dbVersion -

Throws:

DAOException

getGenesForVegaID

public List<DAGene> getGenesForVegaID(String vegaID,
                             String dbVersion)
                               throws DAOException

Method returns a List of Genes that have been mapped to the given Vega Identifier. (there may be more than one Ensembl Gene). Vega currently curates gene, transcript and protein annotations for a human and and a few key regions of other vertebrate species. Calling this method on EnsemblGenomes (invertebrate) species will return an empty list by default Via the wrapped GeneDAO method).

Specified by:

getGenesForVegaID in interface Species

Overrides:

getGenesForVegaID in class DBSpecies

Parameters:

vegaID -

dbVersion -

Throws:

DAOException

getGeneByStableID

public DAGene getGeneByStableID(String stableID,
                       String dbVersion)
                         throws DAOException

Specified by:

getGeneByStableID in interface Species

Overrides:

getGeneByStableID in class DBSpecies

Throws:

DAOException

getTranscriptByStableID

public DATranscript getTranscriptByStableID(String stableID,
                                   String dbVersion)
                                     throws DAOException

Specified by:

getTranscriptByStableID in interface Species

Overrides:

getTranscriptByStableID in class DBSpecies

Throws:

DAOException

getTranslationByStableID

public DATranslation getTranslationByStableID(String stableID,
                                     String dbVersion)
                                       throws DAOException

Specified by:

getTranslationByStableID in interface Species

Overrides:

getTranslationByStableID in class DBSpecies

Throws:

DAOException

getAssemblyName

public String getAssemblyName(String dbVersion)

Specified by:

getAssemblyName in interface Species

Overrides:

getAssemblyName in class DBSpecies

getAssemblyAccession

public String getAssemblyAccession(String dbVersion)

Specified by:

getAssemblyAccession in interface Species

Overrides:

getAssemblyAccession in class DBSpecies

setAssemblyExceptions

public void setAssemblyExceptions(String version)
                           throws DAOException

Specified by:

setAssemblyExceptions in interface Species

Overrides:

setAssemblyExceptions in class DBSpecies

Throws:

DAOException

getGenesForExactName

public List<DAGene> getGenesForExactName(String name,
                                String dbVersion)
                                  throws DAOException

Specified by:

getGenesForExactName in interface Species

Overrides:

getGenesForExactName in class DBSpecies

Throws:

DAOException

getComparaName

public String getComparaName(String version)

Specified by:

getComparaName in interface Species

Overrides:

getComparaName in class DBSpecies