Ensembl Datasource Aware Module v1.09
© Roslin Institute 2010. GNU General Public License, version3
uk.ac.roslin.ensembl.datasourceaware.core
Class DAFeature
java.lang.Object
uk.ac.roslin.ensembl.datasourceaware.DAObject
uk.ac.roslin.ensembl.datasourceaware.core.DACoreObject
uk.ac.roslin.ensembl.datasourceaware.core.DAFeature
- All Implemented Interfaces:
- Serializable, uk.ac.roslin.ensembl.model.core.CoreObject, uk.ac.roslin.ensembl.model.core.Feature, uk.ac.roslin.ensembl.model.IdentifiableObject, uk.ac.roslin.ensembl.model.MappableObject
- Direct Known Subclasses:
- DAExon, DAGene, DATranscript
public abstract class DAFeature
- extends DACoreObject
- implements uk.ac.roslin.ensembl.model.core.Feature
- Author:
- tpaterso
- See Also:
- Serialized Form
Constructor Summary |
DAFeature()
|
DAFeature(uk.ac.roslin.ensembl.dao.factory.DAOCoreFactory factory)
|
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, getType, setId |
mappings
protected uk.ac.roslin.ensembl.model.MappingSet mappings
objectTypeMappings
protected HashMap<uk.ac.roslin.ensembl.model.ObjectType,uk.ac.roslin.ensembl.model.MappingSet> objectTypeMappings
mappedObjectTypes
protected Set<uk.ac.roslin.ensembl.model.ObjectType> mappedObjectTypes
creationDate
protected Date creationDate
modificationDate
protected Date modificationDate
description
protected String description
displayXRef
protected DAXRef displayXRef
xrefs
protected List<DAXRef> xrefs
displayName
protected String displayName
current
protected Boolean current
DAFeature
public DAFeature()
DAFeature
public DAFeature(uk.ac.roslin.ensembl.dao.factory.DAOCoreFactory factory)
getMappings
public uk.ac.roslin.ensembl.model.MappingSet getMappings()
- Specified by:
getMappings
in interface uk.ac.roslin.ensembl.model.MappableObject
getMappings
public uk.ac.roslin.ensembl.model.MappingSet getMappings(uk.ac.roslin.ensembl.model.ObjectType targetType)
- Specified by:
getMappings
in interface uk.ac.roslin.ensembl.model.MappableObject
addMapping
public Boolean addMapping(uk.ac.roslin.ensembl.model.Mapping mapping)
- Specified by:
addMapping
in interface uk.ac.roslin.ensembl.model.MappableObject
addMappedObjectType
public void addMappedObjectType(uk.ac.roslin.ensembl.model.ObjectType mappedType)
- Specified by:
addMappedObjectType
in interface uk.ac.roslin.ensembl.model.core.Feature
isObjectTypeMapped
public Boolean isObjectTypeMapped(uk.ac.roslin.ensembl.model.ObjectType mappedType)
- Specified by:
isObjectTypeMapped
in interface uk.ac.roslin.ensembl.model.core.Feature
getTopLevelMappings
public uk.ac.roslin.ensembl.model.MappingSet getTopLevelMappings()
throws uk.ac.roslin.ensembl.exception.DAOException
- Throws:
uk.ac.roslin.ensembl.exception.DAOException
getChromosomeMapping
public uk.ac.roslin.ensembl.model.Mapping getChromosomeMapping(uk.ac.roslin.ensembl.model.core.Chromosome chr)
- 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 resinitialize method this may be called.
- Specified by:
getChromosomeMapping
in interface uk.ac.roslin.ensembl.model.core.Feature
- Parameters:
chr
-
- Returns:
- a single Mapping
getAnnotationLevelMappings
public uk.ac.roslin.ensembl.model.MappingSet getAnnotationLevelMappings()
throws uk.ac.roslin.ensembl.exception.DAOException
- Throws:
uk.ac.roslin.ensembl.exception.DAOException
getBuildLevelMappings
public uk.ac.roslin.ensembl.model.MappingSet getBuildLevelMappings()
throws uk.ac.roslin.ensembl.exception.DAOException
- Throws:
uk.ac.roslin.ensembl.exception.DAOException
clearAllMappings
public void clearAllMappings()
- Specified by:
clearAllMappings
in interface uk.ac.roslin.ensembl.model.MappableObject
getDescription
public String getDescription()
setDescription
public void setDescription(String description)
getCreationDate
public Date getCreationDate()
setCreationDate
public void setCreationDate(Date creationDate)
getModificationDate
public Date getModificationDate()
setModificationDate
public void setModificationDate(Date modificationDate)
getDisplayXRef
public DAXRef getDisplayXRef()
setDisplayXRef
public void setDisplayXRef(DAXRef xref)
getXRefs
public List<DAXRef> getXRefs()
addXRefs
public void addXRefs(List<DAXRef> xrefs)
getStatus
public String getStatus()
setStatus
public void setStatus(String status)
getDisplayName
public String getDisplayName()
setDisplayName
public void setDisplayName(String displayName)
isCurrent
public Boolean isCurrent()
- Specified by:
isCurrent
in interface uk.ac.roslin.ensembl.model.core.Feature
setCurrent
public void setCurrent(Boolean current)
Ensembl Datasource Aware Module v1.09
© Roslin Institute 2010. GNU General Public License, version3