uk.ac.roslin.ensembl.datasourceaware.core

Class DATranscript

java.lang.Object

uk.ac.roslin.ensembl.datasourceaware.DAObject

uk.ac.roslin.ensembl.datasourceaware.core.DACoreObject

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

uk.ac.roslin.ensembl.datasourceaware.core.DAAnalyzedFeature

uk.ac.roslin.ensembl.datasourceaware.core.DATranscript

All Implemented Interfaces:

Serializable, Analyzed, CoreObject, Feature, Transcript, VegaFeature, WithDisplayXRef, IdentifiableObject, MappableObject, StableID, XRefed

public class DATranscript
extends DAAnalyzedFeature
implements Transcript, VegaFeature, XRefed

See Also:

Serialized Form

Nested Class Summary

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

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 HashMap<ExternalDBType,Set<DAXRef>>	typedXRefs
protected Set<DAXRef>	xrefs

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

current, description, displayName, displayXRef, initialized, length, mappedObjectTypes, mappings, objectTypeMappings, status, 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
DATranscript()
DATranscript(DAOCoreFactory daoFactory)

Method Summary

Methods

Modifier and Type	Method and Description
void	addExon(Exon exon) Method used by the ExonDAO to add an Exon to the 'exonHash', hashed on the 'Rank' integer held by the Exon.
protected void	addTranslation(DATranslation trl) Package method to add a Translation to the 'translationHash', hashed on the internal database ID of the Translation, and to set the canonicalTranlation/ID where applicable.
void	addTranslations(Collection<DATranslation> trls) Method used by the TranslationDAO to add Translations to the 'translationHash', hashed on the internal database ID of the Translation.
protected void	addTypedXRefs(ExternalDBType type, Collection<? extends XRef> xrefs)
Integer	convertChromosomeToPrimaryTranscriptPosition(Integer chromosomePosition) Returns the mapped relative primaryTranscript position for a given Chromosome (or other Toplevel genomic) position.
Integer	convertChromosomeToProcessedTranscriptPosition(Integer chromosomePosition) Converts an Integer position on the TopLevel-annotated Target (typically the Chromosome) to the position on the processed (spliced) Transcript.
Integer	convertPrimaryToProcessedTranscriptPosition(Integer primaryTranscriptPosition) Returns the mapped position on the Processed transcript equivalent to the given position on the Primary (unprocessed) transcript
Integer	convertPrimaryTranscriptPositionToChromosome(Integer primaryTranscriptPosition) Returns the mapped Chromosomal position for a given primaryTranscript position.
Integer	convertProcessedToPrimaryTranscriptPosition(Integer processedTranscriptPosition) Returns the mapped position on the Primary transcript equivalent to the given position on the processed transcript
Integer	convertProcessedTranscriptPositionToChromosome(Integer processedTranscriptPosition) Converts an Integer position on the processed (spliced) transcript to the position on the TopLevel-annotated Target (typically the Chromosome).
TreeSet<String>	getAllSynonyms()
Set<DAXRef>	getAllXRefs()
String	getBiotype()
DATranslation	getCanonicalTranslation() Returns the canonical Translation for this Transcript (if there is one).
Integer	getCanonicalTranslationID() Returns the internal database ID for the Translation object marked as 'Canonical'.
String	getCcdsID() Returns any curated CCDS for this transcript.
Set<DAXRef>	getCCDSXRefs()
String	getDisplayName()
DAXRef	getDisplayXRef() Triggers lazyload if Transcript is not initialized.
Collection<DAExon>	getExons() Returns a Collection of Exons for this Transcript.
DAGene	getGene() Gets the Gene associated with this transcript, using the stableID for the gene set on Transcript initialization.
Integer	getGeneID()
DADNASequence	getPrimaryTranscript() Returns a DADNASequence object representing the unprocessed primary Transcript.
Integer	getPrimaryTranscriptLength() Returns the length of the unprocessed (primary) version of this Transcript.
RNASequence	getPrimaryTranscriptRNASequence() Preferred method to explicitly get the RNASequence object representing the PrimaryTranscript.
String	getPrimaryTranscriptRNASequenceAsString() Preferred method to explicitly get a String representing the RNA sequence of the PrimaryTranscript.
String	getPrimaryTranscriptRNASequenceAsString(Integer start, Integer stop) Preferred method to explicitly get a String representing the RNA sequence of the PrimaryTranscript, for the given range.
DADNASequence	getProcessedTranscript() Returns a DADNASequence object representing the processed (spliced exons) version of this Transcript.
Integer	getProcessedTranscriptLength() Returns the length of the processed (spliced exons) version of this Transcript.
RNASequence	getProcessedTranscriptRNASequence() Returns an RNASequence object representing the Processed (RNA spliced) Transcript.
String	getProcessedTranscriptRNASequenceAsString() Returns a String representing the RNA sequence of the Processed (RNA spliced) Transcript.
String	getProcessedTranscriptRNASequenceAsString(Integer start, Integer stop) Returns a String representing the RNA sequence of the Processed (RNA spliced) Transcript, for the given range.
RNASequence	getRNASequence() Deprecated.
String	getRNASequenceAsString() Deprecated.
String	getRNASequenceAsString(Integer start, Integer stop) Deprecated.
TreeSet<String>	getSynonyms(XRef xref)
Collection<? extends Translation>	getTranslations() Returns all of the Translation objects associated with this Transcript (typically there will only be one, the canonical translation, there may also be no translation for a transcript).
ObjectType	getType()
String	getVegaID() Returns any curated VegaID for the Transcript, forcing lazy load if not set, and defaulting to an empty string if absent (e.g. for all the invertebrate species in EnsemblGenomes).
Set<DAXRef>	getVegaXRefs()
protected Set<DAXRef>	getXRefs(ExternalDBType type) Beware: this method does not trigger lazyloading of typed XRefs.
boolean	isCanonical() Returns true if this Transcript has been annotated by Ensembl as 'Canonical', according to the following rules: A 'Canonical' Transcript is the longest CCDS model in a gene.
boolean	isTranslated() Returns whether this Transcript has (at least one, canonical) Translation.
void	setBiotype(String biotype)
void	setCanonical(boolean canonical)
void	setCanonicalTranslationID(Integer canonicalTranslationID)
void	setDisplayXRef(DAXRef xref)
void	setGene(DAGene gene)
void	setGeneID(Integer geneID)

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

getAnalysis, getAnalysisID, setAnalysisID

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

addMappedObjectType, addMapping, clearAllMappings, convertChromosomePositionToFeature, convertToTargetCoordinate, convertToTargetPosition, getAnnotationLevelMappings, getBuildLevelMappings, getChromosomeMapping, getChromosomeMapping, getChromosomeMappings, getCreationDate, getDescription, getFlankingTargetSequenceAsString, getId, getLength, getLoadedMappings, getLoadedMappings, getModificationDate, getPaddedFlankingTargetSequenceAsString, getSequence, getSequenceAsString, getSequenceAsString, getStatus, getTargetSequence, getTopLevelMappings, getTopLevelTargetCoordinates, getTopLevelTargetSequence, getVersion, inititializeTopLevel, isCurrent, isInitialized, isObjectTypeMapped, setCurrent, setDescription, setDisplayName, setInitialized, setLength, setStatus

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.core.Feature

addMappedObjectType, getChromosomeMapping, getChromosomeMapping, getChromosomeMappings, isCurrent, isObjectTypeMapped

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

addMapping, clearAllMappings, getLoadedMappings, getLoadedMappings

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

getDBVersion, getHashID, getId, getSchemaVersion, setId

Methods inherited from interface uk.ac.roslin.ensembl.model.core.Analyzed

getAnalysis, getAnalysisID, setAnalysisID

Field Detail

xrefs

protected Set<DAXRef> xrefs

typedXRefs

protected HashMap<ExternalDBType,Set<DAXRef>> typedXRefs

Constructor Detail

DATranscript

public DATranscript()

DATranscript

public DATranscript(DAOCoreFactory daoFactory)

Parameters:

daoFactory -

Method Detail

getType

public ObjectType getType()

Specified by:

getType in interface IdentifiableObject

getTranslations

public Collection<? extends Translation> getTranslations()

Returns all of the Translation objects associated with this Transcript (typically there will only be one, the canonical translation, there may also be no translation for a transcript). If the 'translationHash' object has not yet been instantiated, a lazy load by the TranslationDAO object returned by the DAOFactory is triggered.

Specified by:

getTranslations in interface Transcript

Returns:

Collection of Translation objects.

getCanonicalTranslation

public DATranslation getCanonicalTranslation()

Returns the canonical Translation for this Transcript (if there is one). If not set, a lazy load using 'getTranslations()' is triggered.

Specified by:

getCanonicalTranslation in interface Transcript

getBiotype

public String getBiotype()

setBiotype

public void setBiotype(String biotype)

getGene

public DAGene getGene()

Gets the Gene associated with this transcript, using the stableID for the gene set on Transcript initialization.

Specified by:

getGene in interface Transcript

setGene

public void setGene(DAGene gene)

getGeneID

public Integer getGeneID()

setGeneID

public void setGeneID(Integer geneID)

isCanonical

public boolean isCanonical()

Returns true if this Transcript has been annotated by Ensembl as 'Canonical', according to the following rules: A 'Canonical' Transcript is the longest CCDS model in a gene. If none is available then the longest coding Ensembl-Havana merged transcript is chosen. If no merged transcript is present, the longest coding transcript is used, regardless of their source; this can be either an Ensembl or a Havana transcript. Finally, if there are no coding transcripts in the gene, the longest non-coding transcript is selected.

setCanonical

public void setCanonical(boolean canonical)

getDisplayName

public String getDisplayName()

Overrides:

getDisplayName in class DAFeature

getExons

public Collection<DAExon> getExons()

Returns a Collection of Exons for this Transcript. These are returned in (Ranked) order from the exonHash of this Transcript, which will be initialized by lazy loading. The ordered exons are used to make the 'processedTranscript' object for this Transcript (the full length transcript being considered the 'pimaryTranscript'

Specified by:

getExons in interface Transcript

addExon

public void addExon(Exon exon)

Method used by the ExonDAO to add an Exon to the 'exonHash', hashed on the 'Rank' integer held by the Exon.

Parameters:

exon -

getCanonicalTranslationID

public Integer getCanonicalTranslationID()

Returns the internal database ID for the Translation object marked as 'Canonical'. (Prior to Ensembl57 there was a single translation object for each transcript, considered as canonical.)

setCanonicalTranslationID

public void setCanonicalTranslationID(Integer canonicalTranslationID)

addTranslation

protected void addTranslation(DATranslation trl)

Package method to add a Translation to the 'translationHash', hashed on the internal database ID of the Translation, and to set the canonicalTranlation/ID where applicable.

Parameters:

trl -

addTranslations

public void addTranslations(Collection<DATranslation> trls)

Method used by the TranslationDAO to add Translations to the 'translationHash', hashed on the internal database ID of the Translation.

Parameters:

trls - Collection<DATranslation>

isTranslated

public boolean isTranslated()

Returns whether this Transcript has (at least one, canonical) Translation.

Specified by:

isTranslated in interface Transcript

convertChromosomeToPrimaryTranscriptPosition

public Integer convertChromosomeToPrimaryTranscriptPosition(Integer chromosomePosition)

Returns the mapped relative primaryTranscript position for a given Chromosome (or other Toplevel genomic) position. Wraps the DAFeature 'convertChromosomePositionToFeature' method. 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 -

convertPrimaryTranscriptPositionToChromosome

public Integer convertPrimaryTranscriptPositionToChromosome(Integer primaryTranscriptPosition)

Returns the mapped Chromosomal position for a given primaryTranscript position. Wraps the DAFeature 'convertToTargetPosition' method. 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:

primaryTranscriptPosition -

convertProcessedTranscriptPositionToChromosome

public Integer convertProcessedTranscriptPositionToChromosome(Integer processedTranscriptPosition)
                                                       throws DAOException

Converts an Integer position on the processed (spliced) transcript to the position on the TopLevel-annotated Target (typically the Chromosome). The TopLevel Target should only have a positive coordinate system. However negative values will be returned here if appropriate.

Parameters:

processedTranscriptPosition - Integer

Returns:

Integer

Throws:

DAOException

convertChromosomeToProcessedTranscriptPosition

public Integer convertChromosomeToProcessedTranscriptPosition(Integer chromosomePosition)
                                                       throws DAOException

Converts an Integer position on the TopLevel-annotated Target (typically the Chromosome) to the position on the processed (spliced) Transcript. The TopLevel Target should only have a positive coordinate system. If the TopLevel Target position is less than 1, a range exception is thrown rather than try to handle this. Although the chromosomePosition parameter may not be less than 1, the method does cope with negative coordinate transcript/exon mappings on the chromosome.

Parameters:

chromosomePosition - Integer

Returns:

Integer

Throws:

DAOException

convertProcessedToPrimaryTranscriptPosition

public Integer convertProcessedToPrimaryTranscriptPosition(Integer processedTranscriptPosition)
                                                    throws DAOException

Returns the mapped position on the Primary transcript equivalent to the given position on the processed transcript

Parameters:

processedTranscriptPosition -

Throws:

DAOException

convertPrimaryToProcessedTranscriptPosition

public Integer convertPrimaryToProcessedTranscriptPosition(Integer primaryTranscriptPosition)
                                                    throws DAOException

Returns the mapped position on the Processed transcript equivalent to the given position on the Primary (unprocessed) transcript

Parameters:

primaryTranscriptPosition -

Throws:

DAOException

getProcessedTranscript

public DADNASequence getProcessedTranscript()
                                     throws DAOException

Returns a DADNASequence object representing the processed (spliced exons) version of this Transcript.

Throws:

DAOException

getProcessedTranscriptLength

public Integer getProcessedTranscriptLength()
                                     throws DAOException

Returns the length of the processed (spliced exons) version of this Transcript.

Throws:

DAOException

getPrimaryTranscriptLength

public Integer getPrimaryTranscriptLength()

Returns the length of the unprocessed (primary) version of this Transcript. (Wraps the DAFeature method 'getLength()').

Throws:

DAOException

getPrimaryTranscript

public DADNASequence getPrimaryTranscript()

Returns a DADNASequence object representing the unprocessed primary Transcript. (Wraps the DAFeature 'getSequence()' method.)

getRNASequence

@Deprecated
public RNASequence getRNASequence()

Deprecated.

Use of this deprecated method is equivalent to the preferred method 'getPrimaryTranscripRNASequence'.

Overrides:

getRNASequence in class DAFeature

Returns:

RNASequence

getPrimaryTranscriptRNASequence

public RNASequence getPrimaryTranscriptRNASequence()

Preferred method to explicitly get the RNASequence object representing the PrimaryTranscript. Wraps DAFeature getRNASequence().

getRNASequenceAsString

@Deprecated
public String getRNASequenceAsString()

Deprecated.

Use of this deprecated method is equivalent to the preferred method 'getPrimaryTranscripRNASequenceAsString'.

Overrides:

getRNASequenceAsString in class DAFeature

Returns:

String

getPrimaryTranscriptRNASequenceAsString

public String getPrimaryTranscriptRNASequenceAsString()

Preferred method to explicitly get a String representing the RNA sequence of the PrimaryTranscript. Wraps DAFeature getRNASequenceAsString().

getRNASequenceAsString

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

Deprecated.

Use of this deprecated method is equivalent to the preferred method 'getPrimaryTranscripRNASequenceAsString(int,int)'.

Overrides:

getRNASequenceAsString in class DAFeature

Returns:

String

Throws:

RangeException

getPrimaryTranscriptRNASequenceAsString

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

Preferred method to explicitly get a String representing the RNA sequence of the PrimaryTranscript, for the given range. Wraps DAFeature getRNASequenceAsString(int,int).

Throws:

RangeException

getProcessedTranscriptRNASequence

public RNASequence getProcessedTranscriptRNASequence()
                                              throws DAOException

Returns an RNASequence object representing the Processed (RNA spliced) Transcript.

Throws:

DAOException

getProcessedTranscriptRNASequenceAsString

public String getProcessedTranscriptRNASequenceAsString()
                                                 throws DAOException

Returns a String representing the RNA sequence of the Processed (RNA spliced) Transcript.

Throws:

DAOException

getProcessedTranscriptRNASequenceAsString

public String getProcessedTranscriptRNASequenceAsString(Integer start,
                                               Integer stop)
                                                 throws RangeException,
                                                        DAOException

Returns a String representing the RNA sequence of the Processed (RNA spliced) Transcript, for the given range.

Throws:

RangeException

DAOException

getXRefs

protected Set<DAXRef> getXRefs(ExternalDBType type)

Beware: this method does not trigger lazyloading of typed XRefs.

Parameters:

type -

getDisplayXRef

public DAXRef getDisplayXRef()

Triggers lazyload if Transcript is not initialized.

Specified by:

getDisplayXRef in interface WithDisplayXRef

setDisplayXRef

public void setDisplayXRef(DAXRef xref)

getVegaID

public String getVegaID()

Returns any curated VegaID for the Transcript, forcing lazy load if not set, and defaulting to an empty string if absent (e.g. for all the invertebrate species in EnsemblGenomes).

Specified by:

getVegaID in interface VegaFeature

getVegaXRefs

public Set<DAXRef> getVegaXRefs()

Specified by:

getVegaXRefs in interface VegaFeature

getCCDSXRefs

public Set<DAXRef> getCCDSXRefs()

Specified by:

getCCDSXRefs in interface Transcript

getAllXRefs

public Set<DAXRef> getAllXRefs()

Specified by:

getAllXRefs in interface XRefed

getAllSynonyms

public TreeSet<String> getAllSynonyms()

Specified by:

getAllSynonyms in interface XRefed

getSynonyms

public TreeSet<String> getSynonyms(XRef xref)

Specified by:

getSynonyms in interface XRefed

addTypedXRefs

protected void addTypedXRefs(ExternalDBType type,
                 Collection<? extends XRef> xrefs)

getCcdsID

public String getCcdsID()

Returns any curated CCDS for this transcript. The Consensus CDS (CCDS) project is a collaborative effort to identify a core set of human and mouse protein coding regions that are consistently annotated and of high quality. The long term goal is to support convergence towards a standard set of gene annotations.

Specified by:

getCcdsID in interface Transcript