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

Class DBChromosomeDAO

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.DBChromosomeDAO

All Implemented Interfaces:

ChromosomeDAO

public class DBChromosomeDAO
extends DBCoreObjectDAO
implements ChromosomeDAO

Author:

paterson

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
class	DBChromosomeDAO.AssemblyExceptionRowHandler

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
DBChromosomeDAO()
DBChromosomeDAO(DAOCollectionCoreFactory factory)
DBChromosomeDAO(DAOSingleSpeciesCoreFactory factory)

Method Summary

Methods

Modifier and Type	Method and Description
DAChromosome	getChromosomeByName(String name)
List<DAChromosome>	getChromosomes()
DAAssembledDNASequence	getFragmentByName(String name)
List<DAAssembledDNASequence>	getFragments()
DAChromosome	getSexLinkedChromosome(Chromosome chr)
void	setAssemblyExceptions(TreeMap<String,? extends Chromosome> chrs)

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

DBChromosomeDAO

public DBChromosomeDAO()

DBChromosomeDAO

public DBChromosomeDAO(DAOSingleSpeciesCoreFactory factory)

DBChromosomeDAO

public DBChromosomeDAO(DAOCollectionCoreFactory factory)

Method Detail

getChromosomeByName

public DAChromosome getChromosomeByName(String name)
                                 throws DAOException

Specified by:

getChromosomeByName in interface ChromosomeDAO

Throws:

DAOException

getFragmentByName

public DAAssembledDNASequence getFragmentByName(String name)
                                         throws DAOException

Specified by:

getFragmentByName in interface ChromosomeDAO

Throws:

DAOException

getChromosomes

public List<DAChromosome> getChromosomes()
                                  throws DAOException

Specified by:

getChromosomes in interface ChromosomeDAO

Throws:

DAOException

getFragments

public List<DAAssembledDNASequence> getFragments()
                                          throws DAOException

Specified by:

getFragments in interface ChromosomeDAO

Throws:

DAOException

getSexLinkedChromosome

public DAChromosome getSexLinkedChromosome(Chromosome chr)
                                    throws DAOException

Specified by:

getSexLinkedChromosome in interface ChromosomeDAO

Throws:

DAOException

setAssemblyExceptions

public void setAssemblyExceptions(TreeMap<String,? extends Chromosome> chrs)
                           throws DAOException

Specified by:

setAssemblyExceptions in interface ChromosomeDAO

Throws:

DAOException