uk.ac.roslin.ensembl.model.database

Interface SingleSpeciesCoreDatabase

All Superinterfaces:

Comparable<Database>, CoreDatabase, Database, DatabaseWithExternalDBs, SingleSpeciesDatabase

All Known Implementing Classes:

DBSingleSpeciesCoreDatabase

public interface SingleSpeciesCoreDatabase
extends SingleSpeciesDatabase, CoreDatabase

Author:

tpaterso

Method Summary

Methods

Modifier and Type	Method and Description
void	addFeatureCS(String featureType, Integer csID, Integer maxLength)
String	getAssemblyAccession()
String	getAssemblyName()
CoordinateSystem	getBuildCoordSystem(String featureType)
String	getBuildLevel(String featureType)
Chromosome	getChromosomeByName(String name)
CoordinateSystem	getChromosomeLevelCoordSystem()
List<? extends Chromosome>	getChromosomes()
String	getComparaName()
Object	getCoreFactory()
CoordinateSystem	getCSByID(Integer id)
Set<? extends CoordinateSystem>	getCSForFeature(ObjectType featureType)
List<? extends ObjectType>	getFeaturesForCS(CoordinateSystem coordSys)
AssembledDNASequence	getFragmentByName(String name)
List<? extends AssembledDNASequence>	getFragments()
Integer	getMaxLengthForFeature(ObjectType featureType, CoordinateSystem cs)
CoordinateSystem	getSequenceLevelCoordSystem()
CoordinateSystem	getTopLevelCoordSystem()
void	setAssemblyAccession(String value)
void	setAssemblyName(String value)
void	setBuildLevel(String featureKey, String level)
void	setComparaName(String comparaName)

Methods inherited from interface uk.ac.roslin.ensembl.model.database.SingleSpeciesDatabase

getDbSpeciesName, getSpecies, setDbSpeciesName, setSpecies

Methods inherited from interface uk.ac.roslin.ensembl.model.database.CoreDatabase

getAnalyses

Methods inherited from interface uk.ac.roslin.ensembl.model.database.DatabaseWithExternalDBs

getExternalDB, initializeExternalDBs, validateExternalDB

Methods inherited from interface uk.ac.roslin.ensembl.model.database.Database

getBuild, getdBClassifier, getdBName, getDBVersion, getIntDBVersion, getIntSchemaVersion, getNewSqlSession, getRegistry, getSchemaVersion, getType

Methods inherited from interface java.lang.Comparable

compareTo

Method Detail

getCoreFactory

Object getCoreFactory()

getTopLevelCoordSystem

CoordinateSystem getTopLevelCoordSystem()
                                        throws DAOException

Throws:

DAOException

getChromosomeLevelCoordSystem

CoordinateSystem getChromosomeLevelCoordSystem()
                                               throws DAOException

Throws:

DAOException

getSequenceLevelCoordSystem

CoordinateSystem getSequenceLevelCoordSystem()
                                             throws DAOException

Throws:

DAOException

getCSByID

CoordinateSystem getCSByID(Integer id)
                           throws DAOException

Throws:

DAOException

getBuildCoordSystem

CoordinateSystem getBuildCoordSystem(String featureType)
                                     throws DAOException

Throws:

DAOException

getCSForFeature

Set<? extends CoordinateSystem> getCSForFeature(ObjectType featureType)
                                                throws DAOException

Throws:

DAOException

getChromosomeByName

Chromosome getChromosomeByName(String name)
                               throws DAOException

Throws:

DAOException

getChromosomes

List<? extends Chromosome> getChromosomes()
                                          throws DAOException

Throws:

DAOException

getFragmentByName

AssembledDNASequence getFragmentByName(String name)
                                       throws DAOException

Throws:

DAOException

getFragments

List<? extends AssembledDNASequence> getFragments()
                                                  throws DAOException

Throws:

DAOException

setBuildLevel

void setBuildLevel(String featureKey,
                 String level)

getBuildLevel

String getBuildLevel(String featureType)
                     throws DAOException

Throws:

DAOException

getFeaturesForCS

List<? extends ObjectType> getFeaturesForCS(CoordinateSystem coordSys)
                                            throws DAOException

Throws:

DAOException

getMaxLengthForFeature

Integer getMaxLengthForFeature(ObjectType featureType,
                             CoordinateSystem cs)
                               throws DAOException

Throws:

DAOException

addFeatureCS

void addFeatureCS(String featureType,
                Integer csID,
                Integer maxLength)

getAssemblyName

String getAssemblyName()

getComparaName

String getComparaName()

getAssemblyAccession

String getAssemblyAccession()

setAssemblyName

void setAssemblyName(String value)

setAssemblyAccession

void setAssemblyAccession(String value)

setComparaName

void setComparaName(String comparaName)