uk.ac.roslin.ensembl.model.database

Interface CollectionCoreDatabase

All Superinterfaces:

CollectionDatabase, Comparable<Database>, CoreDatabase, Database, DatabaseWithExternalDBs

All Known Implementing Classes:

DBCollectionCoreDatabase

public interface CollectionCoreDatabase
extends CollectionDatabase, CoreDatabase

Author:

tpaterso

Method Summary

Methods

Modifier and Type	Method and Description
void	addFeatureCS(String featureType, Integer csID, Integer maxLength, Species sp)
String	getAssemblyAccession(CollectionSpecies species)
String	getAssemblyName(CollectionSpecies species)
CoordinateSystem	getBuildCoordSystem(Species species, String featureType)
String	getBuildLevel(Species species, String featureKey)
Chromosome	getChromosomeByName(Species species, String name)
CoordinateSystem	getChromosomeLevelCS(Species species)
List<? extends Chromosome>	getChromosomes(Species species)
Object	getCoreFactory(Species species)
CoordinateSystem	getCSByID(Species species, Integer id)
Set<? extends CoordinateSystem>	getCSForFeature(Species sp, ObjectType feature)
List<? extends ObjectType>	getFeaturesForCS(Species sp, CoordinateSystem coordSys)
AssembledDNASequence	getFragmentByName(Species species, String name)
List<? extends AssembledDNASequence>	getFragments(Species species)
Integer	getMaxLengthForFeature(Species sp, ObjectType feature, CoordinateSystem cs)
CoordinateSystem	getSequenceLevelCS(Species species)
CoordinateSystem	getTopLevelCS(Species species)
void	setBuildLevels(Species species, HashMap<String,String> keyedValues)

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

getCollection, getCollectionName, setCollection, setCollectionName

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(Species species)

getChromosomeLevelCS

CoordinateSystem getChromosomeLevelCS(Species species)
                                      throws DAOException

Throws:

DAOException

getSequenceLevelCS

CoordinateSystem getSequenceLevelCS(Species species)
                                    throws DAOException

Throws:

DAOException

getTopLevelCS

CoordinateSystem getTopLevelCS(Species species)
                               throws DAOException

Throws:

DAOException

getCSByID

CoordinateSystem getCSByID(Species species,
                         Integer id)
                           throws DAOException

Throws:

DAOException

getBuildCoordSystem

CoordinateSystem getBuildCoordSystem(Species species,
                                   String featureType)
                                     throws DAOException

Throws:

DAOException

getCSForFeature

Set<? extends CoordinateSystem> getCSForFeature(Species sp,
                                              ObjectType feature)
                                                throws DAOException

Throws:

DAOException

setBuildLevels

void setBuildLevels(Species species,
                  HashMap<String,String> keyedValues)

getBuildLevel

String getBuildLevel(Species species,
                   String featureKey)
                     throws DAOException

Throws:

DAOException

getFeaturesForCS

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

Throws:

DAOException

getMaxLengthForFeature

Integer getMaxLengthForFeature(Species sp,
                             ObjectType feature,
                             CoordinateSystem cs)
                               throws DAOException

Throws:

DAOException

addFeatureCS

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

getChromosomeByName

Chromosome getChromosomeByName(Species species,
                             String name)
                               throws DAOException

Throws:

DAOException

getChromosomes

List<? extends Chromosome> getChromosomes(Species species)
                                          throws DAOException

Throws:

DAOException

getFragmentByName

AssembledDNASequence getFragmentByName(Species species,
                                     String name)
                                       throws DAOException

Throws:

DAOException

getFragments

List<? extends AssembledDNASequence> getFragments(Species species)
                                                  throws DAOException

Throws:

DAOException

getAssemblyName

String getAssemblyName(CollectionSpecies species)

getAssemblyAccession

String getAssemblyAccession(CollectionSpecies species)