Ensembl Datasource Aware Module v1.09
© Roslin Institute 2010. GNU General Public License, version3
Ensembl Datasource Aware Module
v1.09

uk.ac.roslin.ensembl.datasourceaware.core
Class DAFeature

java.lang.Object
  extended by uk.ac.roslin.ensembl.datasourceaware.DAObject
      extended by uk.ac.roslin.ensembl.datasourceaware.core.DACoreObject
          extended by 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

Nested Class Summary
static class DAFeature.Status
           
 
Nested classes/interfaces inherited from class uk.ac.roslin.ensembl.datasourceaware.DAObject
DAObject.DAComparator
 
Field Summary
protected  Date creationDate
           
protected  Boolean current
           
protected  String description
           
protected  String displayName
           
protected  DAXRef displayXRef
           
protected  Set<uk.ac.roslin.ensembl.model.ObjectType> mappedObjectTypes
           
protected  uk.ac.roslin.ensembl.model.MappingSet mappings
           
protected  Date modificationDate
           
protected  HashMap<uk.ac.roslin.ensembl.model.ObjectType,uk.ac.roslin.ensembl.model.MappingSet> objectTypeMappings
           
protected  List<DAXRef> xrefs
           
 
Fields inherited from class uk.ac.roslin.ensembl.datasourceaware.core.DACoreObject
comparaFactories, species
 
Fields inherited from class uk.ac.roslin.ensembl.datasourceaware.DAObject
daComparator, daoFactory, dbVersion, id, registry, schemaVersion
 
Constructor Summary
DAFeature()
           
DAFeature(uk.ac.roslin.ensembl.dao.factory.DAOCoreFactory factory)
           
 
Method Summary
 void addMappedObjectType(uk.ac.roslin.ensembl.model.ObjectType mappedType)
           
 Boolean addMapping(uk.ac.roslin.ensembl.model.Mapping mapping)
           
 void addXRefs(List<DAXRef> xrefs)
           
 void clearAllMappings()
           
 uk.ac.roslin.ensembl.model.MappingSet getAnnotationLevelMappings()
           
 uk.ac.roslin.ensembl.model.MappingSet getBuildLevelMappings()
           
 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.
 Date getCreationDate()
           
 String getDescription()
           
 String getDisplayName()
           
 DAXRef getDisplayXRef()
           
 uk.ac.roslin.ensembl.model.MappingSet getMappings()
           
 uk.ac.roslin.ensembl.model.MappingSet getMappings(uk.ac.roslin.ensembl.model.ObjectType targetType)
           
 Date getModificationDate()
           
 String getStatus()
           
 uk.ac.roslin.ensembl.model.MappingSet getTopLevelMappings()
           
 List<DAXRef> getXRefs()
           
 Boolean isCurrent()
           
 Boolean isObjectTypeMapped(uk.ac.roslin.ensembl.model.ObjectType mappedType)
           
 void setCreationDate(Date creationDate)
           
 void setCurrent(Boolean current)
           
 void setDescription(String description)
           
 void setDisplayName(String displayName)
           
 void setDisplayXRef(DAXRef xref)
           
 void setModificationDate(Date modificationDate)
           
 void setStatus(String status)
           
 
Methods inherited from class uk.ac.roslin.ensembl.datasourceaware.core.DACoreObject
getAssembly, getComparaDivision, getComparaFactory, getComparaFactory, getDaoFactory, getSpecies, setDBVersion, setSpecies
 
Methods inherited from class uk.ac.roslin.ensembl.datasourceaware.DAObject
getDBVersion, getHashID, getId, getRegistry, getSchemaVersion, setDaoFactory, setId, 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, getType, setId
 

Field Detail

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
Constructor Detail

DAFeature

public DAFeature()

DAFeature

public DAFeature(uk.ac.roslin.ensembl.dao.factory.DAOCoreFactory factory)
Method Detail

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

Ensembl Datasource Aware Module v1.09
© Roslin Institute 2010. GNU General Public License, version3