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, CoreObject, Feature, IdentifiableObject, MappableObject, StableID

Direct Known Subclasses:

DAAnalyzedFeature, DAExon

public abstract class DAFeature
extends DACoreObject
implements Feature

Author:

tpaterso

See Also:

Serialized Form

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	DAFeature.Status

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

DAObject.DAComparator

Field Summary

Fields

Modifier and Type	Field and Description
protected Boolean	current
protected String	description
protected String	displayName
protected DAXRef	displayXRef
protected boolean	initialized
protected Integer	length
protected Set<ObjectType>	mappedObjectTypes
protected MappingSet	mappings
protected HashMap<ObjectType,MappingSet>	objectTypeMappings
protected DAFeature.Status	status
protected DADNASequence	thisSequence

Fields inherited from class uk.ac.roslin.ensembl.datasourceaware.core.DACoreObject

comparaFactories, creationDate, modificationDate, species, stableID, version

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

daComparator, daoFactory, dbVersion, id, registry, schemaVersion

Constructor Summary

Constructors

Constructor and Description
DAFeature()
DAFeature(DAOCoreFactory factory)

Method Summary

Methods

Modifier and Type	Method and Description
void	addMappedObjectType(ObjectType mappedType)
Boolean	addMapping(Mapping mapping)
void	clearAllMappings()
Integer	convertChromosomePositionToFeature(Integer chromosomePosition) Converts an Integer position on the TopLevel-annotated Target (typically the Chromosome) to the position on this feature.
Coordinate	convertToTargetCoordinate(Integer start, Integer stop) Converts a given range (relative to the annotation start site) to the Coordinates on the annotated target TopLevel (genomic) sequence.
Integer	convertToTargetPosition(Integer query) Converts an Integer relative to the annotation start site to the position on the annotated TopLevel target (genomic) sequence.
MappingSet	getAnnotationLevelMappings()
MappingSet	getBuildLevelMappings()
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.
Date	getCreationDate()
String	getDescription()
String	getDisplayName()
String	getFlankingTargetSequenceAsString(Integer start, Integer stop) Retrieves the String representation of the target (genomic) sequence that this feature is annotated upon, for the given range.
Integer	getId()
Integer	getLength() Returns the length of this feature, as calculated from its mapped coordinates on the top level annotated sequence (typically the chromosome).
MappingSet	getLoadedMappings()
MappingSet	getLoadedMappings(ObjectType targetType)
Date	getModificationDate()
String	getPaddedFlankingTargetSequenceAsString(Integer start, Integer stop) Retrieves the String representation of the target (genomic) sequence that this feature is annotated upon, for the given range.
RNASequence	getRNASequence() Returns an RNASequence object trancribed from the DNASequence representing the extent of this annotation.
String	getRNASequenceAsString() Returns a string representation of the RNASequence object trancribed from the DNASequence representing the extent of this annotation.
String	getRNASequenceAsString(Integer start, Integer stop) Returns a string representation for the given range of the RNASequence object trancribed from the DNASequence representing the extent of this annotation.
DADNASequence	getSequence() Returns the sequence covered by this feature (i.e. a new DADNASequence object representing this region of the genome, it might be a GAPSequence if no sequence info is available).
String	getSequenceAsString() Returns the string representation of the (genomic) sequence that this feature is annotated upon (at 'top level').
String	getSequenceAsString(Integer start, Integer stop) Returns the string representation of the (genomic) sequence that this feature is annotated upon (at 'top level'), for the specified range.
String	getStatus()
DADNASequence	getTargetSequence() Returns the (genomic) sequence that this feature is annotated upon (at 'top level').
MappingSet	getTopLevelMappings()
Coordinate	getTopLevelTargetCoordinates()
DADNASequence	getTopLevelTargetSequence()
Integer	getVersion()
protected void	inititializeTopLevel() This method is used to initialize the 'topLevelCS', the 'topLevelTargetCoordinates' and the 'topLevelTargetSequence' fields.
Boolean	isCurrent()
boolean	isInitialized()
Boolean	isObjectTypeMapped(ObjectType mappedType)
void	setCurrent(Boolean current)
void	setDescription(String description)
void	setDisplayName(String displayName)
void	setInitialized(boolean init)
void	setLength(Integer length)
void	setStatus(String status)

Methods inherited from class uk.ac.roslin.ensembl.datasourceaware.core.DACoreObject

getAssembly, getComparaDivision, getComparaFactory, getComparaFactory, getDaoFactory, getSpecies, getStableID, setCreationDate, setDBVersion, setModificationDate, setSpecies, setStableID, setVersion

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

getDBVersion, getHashID, 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, getSchemaVersion, getType, setId

Field Detail

mappings

protected MappingSet mappings

objectTypeMappings

protected HashMap<ObjectType,MappingSet> objectTypeMappings

mappedObjectTypes

protected Set<ObjectType> mappedObjectTypes

description

protected String description

displayXRef

protected DAXRef displayXRef

displayName

protected String displayName

status

protected DAFeature.Status status

current

protected Boolean current

thisSequence

protected DADNASequence thisSequence

length

protected Integer length

initialized

protected boolean initialized

Constructor Detail

DAFeature

public DAFeature()

DAFeature

public DAFeature(DAOCoreFactory factory)

Method Detail

getLoadedMappings

public MappingSet getLoadedMappings()

Specified by:

getLoadedMappings in interface MappableObject

getLoadedMappings

public MappingSet getLoadedMappings(ObjectType targetType)

Specified by:

getLoadedMappings in interface MappableObject

addMapping

public Boolean addMapping(Mapping mapping)

Specified by:

addMapping in interface MappableObject

addMappedObjectType

public void addMappedObjectType(ObjectType mappedType)

Specified by:

addMappedObjectType in interface Feature

isObjectTypeMapped

public Boolean isObjectTypeMapped(ObjectType mappedType)

Specified by:

isObjectTypeMapped in interface Feature

getTopLevelMappings

public MappingSet getTopLevelMappings()
                               throws DAOException

Throws:

DAOException

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

getAnnotationLevelMappings

public MappingSet getAnnotationLevelMappings()
                                      throws DAOException

Throws:

DAOException

getBuildLevelMappings

public MappingSet getBuildLevelMappings()
                                 throws DAOException

Throws:

DAOException

clearAllMappings

public void clearAllMappings()

Specified by:

clearAllMappings in interface MappableObject

getDescription

public String getDescription()

setDescription

public void setDescription(String description)

isInitialized

public boolean isInitialized()

setInitialized

public void setInitialized(boolean init)

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 Feature

setCurrent

public void setCurrent(Boolean current)

inititializeTopLevel

protected void inititializeTopLevel()
                             throws DAOException

This method is used to initialize the 'topLevelCS', the 'topLevelTargetCoordinates' and the 'topLevelTargetSequence' fields.

Throws:

DAOException

getSequence

public DADNASequence getSequence()

Returns the sequence covered by this feature (i.e. a new DADNASequence object representing this region of the genome, it might be a GAPSequence if no sequence info is available).

Returns:

DADNASequence

getTargetSequence

public DADNASequence getTargetSequence()

Returns the (genomic) sequence that this feature is annotated upon (at 'top level').

Returns:

DADNASequence

getFlankingTargetSequenceAsString

public String getFlankingTargetSequenceAsString(Integer start,
                                       Integer stop)
                                         throws RangeException

Retrieves the String representation of the target (genomic) sequence that this feature is annotated upon, for the given range. The range arguments are relative to the start of the annotation, and therefore can be used to get Flanking Sequences etc. The range arguments are transparently converted to coordinates on the target sequence. Arguments outwith the extent of the annotation (i.e greater than its length, or less than the start site of 1) will throw a (Runtime) RangeException.

Parameters:

start - Integer

stop - Integer

Returns:

String

Throws:

RangeException

getPaddedFlankingTargetSequenceAsString

public String getPaddedFlankingTargetSequenceAsString(Integer start,
                                             Integer stop)

Retrieves the String representation of the target (genomic) sequence that this feature is annotated upon, for the given range. The range arguments are relative to the start of the annotation, and therefore can be used to get Flanking Sequences etc. The range arguments are transparently converted to coordinates on the target sequence. Arguments outwith the extent of the target sequence (i.e greater than its length, or less than the start site of 1) will cause the returned sequence to be padded appropriately.

Parameters:

start - Integer

stop - Integer

Returns:

String

getSequenceAsString

public String getSequenceAsString()

Returns the string representation of the (genomic) sequence that this feature is annotated upon (at 'top level').

Returns:

String

getSequenceAsString

public String getSequenceAsString(Integer start,
                         Integer stop)
                           throws RangeException

Returns the string representation of the (genomic) sequence that this feature is annotated upon (at 'top level'), for the specified range. The range arguments are relative to the start of the annotation, i.e. on the correct strand, from '1' to 'length of annotation'. Arguments outwith the extent of the annotation (i.e greater than its length, or less than the start site of 1) will throw a (Runtime) RangeException. There is no Padding function available on Features.

Parameters:

start - Integer

stop - Integer

Returns:

String

Throws:

RangeException

convertChromosomePositionToFeature

public Integer convertChromosomePositionToFeature(Integer chromosomePosition)

Converts an Integer position on the TopLevel-annotated Target (typically the Chromosome) to the position on this feature. The TopLevel Target should only have a positive coordinate system. If the TopLevel Target coordinates are found to extend below 1, a range exception is thrown rather than try to handle this.

Parameters:

chromosomePosition - Integer

Returns:

Integer

convertToTargetPosition

public Integer convertToTargetPosition(Integer query)

Converts an Integer relative to the annotation start site to the position on the annotated TopLevel target (genomic) sequence. Whilst the TopLevel Target should only have a positive coordinate system (and if not a RangeException will be thrown here), the query Integer is allowed to be outwith the bounds of the Feature, and may possibly return a value outwith the bounds of the Chromosome.

Parameters:

query - Integer

Returns:

Integer

convertToTargetCoordinate

public Coordinate convertToTargetCoordinate(Integer start,
                                   Integer stop)

Converts a given range (relative to the annotation start site) to the Coordinates on the annotated target TopLevel (genomic) sequence. The TopLevel Target should only have a positive coordinate system (and if not a RangeException will be thrown here, originating in the call to 'convertToTargetPosition'). The returned Coordinate is given on the same strand as the feature.

Parameters:

start - Integer

stop - Integer

Returns:

Coordinate

getRNASequence

public RNASequence getRNASequence()

Returns an RNASequence object trancribed from the DNASequence representing the extent of this annotation. The TranscriptionEngine used is as specified by the genomic target (annotated) sequence.

Returns:

RNASequence

getRNASequenceAsString

public String getRNASequenceAsString()

Returns a string representation of the RNASequence object trancribed from the DNASequence representing the extent of this annotation. The TranscriptionEngine used is as specified by the genomic target (annotated) sequence.

Returns:

String

getRNASequenceAsString

public String getRNASequenceAsString(Integer start,
                            Integer stop)
                              throws RangeException

Returns a string representation for the given range of the RNASequence object trancribed from the DNASequence representing the extent of this annotation. The TranscriptionEngine used is as specified by the genomic target (annotated) sequence. Arguments outwith the extent of the annotation (i.e greater than its length, or less than the start site of 1) will throw a (Runtime) RangeException.

Parameters:

start -

stop -

Returns:

String

Throws:

RangeException

getLength

public Integer getLength()

Returns the length of this feature, as calculated from its mapped coordinates on the top level annotated sequence (typically the chromosome).

setLength

public void setLength(Integer length)

getTopLevelTargetCoordinates

public Coordinate getTopLevelTargetCoordinates()
                                        throws DAOException

Throws:

DAOException

getTopLevelTargetSequence

public DADNASequence getTopLevelTargetSequence()
                                        throws DAOException

Throws:

DAOException

getId

public Integer getId()

Specified by:

getId in interface IdentifiableObject

Overrides:

getId in class DAObject

getVersion

public Integer getVersion()

Specified by:

getVersion in interface StableID

Overrides:

getVersion in class DACoreObject

getModificationDate

public Date getModificationDate()

Specified by:

getModificationDate in interface StableID

Overrides:

getModificationDate in class DACoreObject

getCreationDate

public Date getCreationDate()

Specified by:

getCreationDate in interface StableID

Overrides:

getCreationDate in class DACoreObject