uk.ac.roslin.ensembl.datasourceaware.variation

Class DAVariation

java.lang.Object

uk.ac.roslin.ensembl.datasourceaware.DAObject

uk.ac.roslin.ensembl.datasourceaware.variation.DAVariation

All Implemented Interfaces:

Serializable, Feature, IdentifiableObject, MappableObject, Variation

public class DAVariation
extends DAObject
implements Variation

Author:

tpaterso

See Also:

Serialized Form

Nested Class Summary

Nested classes/interfaces inherited from class uk.ac.roslin.ensembl.datasourceaware.DAObject

DAObject.DAComparator

Field Summary

Fields

Modifier and Type	Field and Description
protected String	ancestralAllele
protected Boolean	flipped
protected Set<ObjectType>	mappedObjectTypes
protected MappingSet	mappings
protected String	name
protected HashMap<ObjectType,MappingSet>	objectTypeMappings
protected int	occurrences
protected Boolean	somatic
protected String	synonym
protected List<String>	synonyms
protected VariationType	varType
protected DAVariationXRef	xref

Fields inherited from class uk.ac.roslin.ensembl.datasourceaware.DAObject

daComparator, daoFactory, dbVersion, id, registry, schemaVersion

Constructor Summary

Constructors

Constructor and Description
DAVariation()
DAVariation(DAOVariationFactory factory)

Method Summary

Methods

Modifier and Type	Method and Description
void	addMappedObjectType(ObjectType mappedType)
Boolean	addMapping(Mapping mapping)
void	checkInitialized() This is a hack to classigy the loaded mapping by type, because MyBatis apparently sets 'mappings' by reflection, not with the setter, so objectTypeMappings is not initialized by the MyBatis call.
void	clearAllMappings()
List<String>	getAllSynonyms()
String	getAncestralAllele()
Mapping	getChromosomeMapping() Utility method to pull back a unique chromosomal mapping of this Feature.
Mapping	getChromosomeMapping(Chromosome chr) Utility method to pull back a single mapping of this Feature on a Given chromosome.
MappingSet	getChromosomeMappings() Method to return all chromosomal mappings for this feature.
DAOVariationFactory	getDaoFactory()
MappingSet	getLoadedMappings()
MappingSet	getLoadedMappings(ObjectType targetType)
MappingSet	getMappings()
String	getName()
int	getOccurrences()
String	getSynonym()
VariationType	getType()
DAVariationXRef	getXRef()
Boolean	isCurrent()
Boolean	isFlipped()
Boolean	isObjectTypeMapped(ObjectType mappedType)
Boolean	isSomatic()
void	setAncestralAllele(String ancestralAllele)
void	setFlipped(Boolean flipped)
void	setMappings(MappingSet mappings)
void	setName(String name)
void	setOccurrences(int count)
void	setSomatic(Boolean somatic)
void	setSynonym(String altname)
void	setVarType(VariationType varType)
void	setXRef(DAVariationXRef xref)

Methods inherited from class uk.ac.roslin.ensembl.datasourceaware.DAObject

getDBVersion, getHashID, getId, getRegistry, getSchemaVersion, isLazyloadAllowed, setDaoFactory, setId, setLazyloadAllowed, setRegistry

Methods inherited from class java.lang.Object

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

Methods inherited from interface uk.ac.roslin.ensembl.model.IdentifiableObject

getDBVersion, getHashID, getId, getSchemaVersion, setId

Field Detail

mappings

protected MappingSet mappings

objectTypeMappings

protected HashMap<ObjectType,MappingSet> objectTypeMappings

mappedObjectTypes

protected Set<ObjectType> mappedObjectTypes

name

protected String name

synonym

protected String synonym

synonyms

protected List<String> synonyms

ancestralAllele

protected String ancestralAllele

xref

protected DAVariationXRef xref

varType

protected VariationType varType

somatic

protected Boolean somatic

flipped

protected Boolean flipped

occurrences

protected int occurrences

Constructor Detail

DAVariation

public DAVariation()

DAVariation

public DAVariation(DAOVariationFactory factory)

Method Detail

checkInitialized

public void checkInitialized()

This is a hack to classigy the loaded mapping by type, because MyBatis apparently sets 'mappings' by reflection, not with the setter, so objectTypeMappings is not initialized by the MyBatis call.

getDaoFactory

public DAOVariationFactory getDaoFactory()

Overrides:

getDaoFactory in class DAObject

getType

public VariationType getType()

Specified by:

getType in interface IdentifiableObject

setVarType

public void setVarType(VariationType varType)

addMappedObjectType

public void addMappedObjectType(ObjectType mappedType)

Specified by:

addMappedObjectType in interface Feature

isObjectTypeMapped

public Boolean isObjectTypeMapped(ObjectType mappedType)

Specified by:

isObjectTypeMapped in interface Feature

isCurrent

public Boolean isCurrent()

Specified by:

isCurrent in interface Feature

getChromosomeMapping

public Mapping getChromosomeMapping(Chromosome chr)
                             throws NonUniqueException

Utility method to pull back a single mapping of this Feature on a Given chromosome. This should be the mapping stored at initialisation. If the Feature has implemented a reinitialize method this may be called.

Specified by:

getChromosomeMapping in interface Feature

Parameters:

chr -

Returns:

a single Mapping

Throws:

NonUniqueException - if more than one mapping for the chromosome

getChromosomeMapping

public Mapping getChromosomeMapping()
                             throws NonUniqueException

Utility method to pull back a unique chromosomal mapping of this Feature. This should be the mapping stored at initialisation. If the Feature has implemented a reinitialize method this may be called.

Specified by:

getChromosomeMapping in interface Feature

Returns:

a single Mapping

Throws:

NonUniqueException - if more than one mapping for the chromosome

getChromosomeMappings

public MappingSet getChromosomeMappings()

Method to return all chromosomal mappings for this feature. In most circumstances there should be only one mapping. If the Feature has implemented a re-initialize method this may be called.

Specified by:

getChromosomeMappings in interface Feature

Returns:

MappingSet ordered set of chromosomal mappings

getLoadedMappings

public MappingSet getLoadedMappings(ObjectType targetType)

Specified by:

getLoadedMappings in interface MappableObject

getLoadedMappings

public MappingSet getLoadedMappings()

Specified by:

getLoadedMappings in interface MappableObject

getMappings

public MappingSet getMappings()

addMapping

public Boolean addMapping(Mapping mapping)

Specified by:

addMapping in interface MappableObject

setMappings

public void setMappings(MappingSet mappings)

clearAllMappings

public void clearAllMappings()

Specified by:

clearAllMappings in interface MappableObject

getName

public String getName()

Specified by:

getName in interface Variation

setName

public void setName(String name)

Specified by:

setName in interface Variation

getXRef

public DAVariationXRef getXRef()

Specified by:

getXRef in interface Variation

setXRef

public void setXRef(DAVariationXRef xref)

isSomatic

public Boolean isSomatic()

Specified by:

isSomatic in interface Variation

setSomatic

public void setSomatic(Boolean somatic)

isFlipped

public Boolean isFlipped()

Specified by:

isFlipped in interface Variation

setFlipped

public void setFlipped(Boolean flipped)

getAncestralAllele

public String getAncestralAllele()

Specified by:

getAncestralAllele in interface Variation

setAncestralAllele

public void setAncestralAllele(String ancestralAllele)

getOccurrences

public int getOccurrences()

Specified by:

getOccurrences in interface Variation

setOccurrences

public void setOccurrences(int count)

getSynonym

public String getSynonym()

Specified by:

getSynonym in interface Variation

getAllSynonyms

public List<String> getAllSynonyms()

Specified by:

getAllSynonyms in interface Variation

setSynonym

public void setSynonym(String altname)

Specified by:

setSynonym in interface Variation