uk.ac.roslin.ensembl.dao.database.coreaccess

Class DBAssemblyDAO

java.lang.Object

uk.ac.roslin.ensembl.dao.database.DBBaseDAO

uk.ac.roslin.ensembl.dao.database.coreaccess.DBCoreObjectDAO

uk.ac.roslin.ensembl.dao.database.coreaccess.DBAssemblyDAO

All Implemented Interfaces:

AssemblyDAO

public class DBAssemblyDAO
extends DBCoreObjectDAO
implements AssemblyDAO

Author:

paterson

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
class	DBAssemblyDAO.PARMappingHandler

Field Summary

Fields inherited from class uk.ac.roslin.ensembl.dao.database.coreaccess.DBCoreObjectDAO

collFactory, singleSpecies, species, ssFactory

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

configuration, daoFactory

Constructor Summary

Constructors

Constructor and Description
DBAssemblyDAO()
DBAssemblyDAO(DAOCollectionCoreFactory factory)
DBAssemblyDAO(DAOSingleSpeciesCoreFactory factory)

Method Summary

Methods

Modifier and Type	Method and Description
MappingSet	getComponentMappingsByStartStop(DNASequence assembledSequence, Integer begin, Integer stop)
MappingSet	getPARMappingsByStartStop(Chromosome chr, Integer begin, Integer stop)

Methods inherited from class uk.ac.roslin.ensembl.dao.database.coreaccess.DBCoreObjectDAO

getDAOFactory, getSpecies, isSingleSpecies, setFactory, setFactory

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

getFactory, setConfiguration, setFactory

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

DBAssemblyDAO

public DBAssemblyDAO()

DBAssemblyDAO

public DBAssemblyDAO(DAOSingleSpeciesCoreFactory factory)

DBAssemblyDAO

public DBAssemblyDAO(DAOCollectionCoreFactory factory)

Method Detail

getComponentMappingsByStartStop

public MappingSet getComponentMappingsByStartStop(DNASequence assembledSequence,
                                         Integer begin,
                                         Integer stop)
                                           throws DAOException

Specified by:

getComponentMappingsByStartStop in interface AssemblyDAO

Throws:

DAOException

getPARMappingsByStartStop

public MappingSet getPARMappingsByStartStop(Chromosome chr,
                                   Integer begin,
                                   Integer stop)
                                     throws DAOException

Specified by:

getPARMappingsByStartStop in interface AssemblyDAO

Throws:

DAOException