Package psidev.psi.mi.jami.enricher.impl.minimal

Class MinimalFeatureEnricher<F extends Feature>

java.lang.Object

psidev.psi.mi.jami.enricher.impl.minimal.MinimalFeatureEnricher<F>

All Implemented Interfaces:

EventListener, FeatureEnricher<F>, EnricherListener<Protein>, InteractorEnricherListener<Protein>, ProteinEnricherListener, MIEnricher<F>, ProteinListeningFeatureEnricher<F>, AliasesChangeListener<Protein>, AnnotationsChangeListener<Protein>, ChecksumsChangeListener<Protein>, IdentifiersChangeListener<Protein>, InteractorChangeListener<Protein>, PolymerChangeListener<Protein>, ProteinChangeListener, XrefsChangeListener<Protein>

Direct Known Subclasses:

FullFeatureEnricher, MinimalFeatureEvidenceEnricher, MinimalFeatureUpdater

public class MinimalFeatureEnricher<F extends Feature>
extends Object
implements ProteinListeningFeatureEnricher<F>

Provides minimal enrichment of feature. - enrich shortName if not set - enrich fullName if not set - enrich feature type with CvTerm enricher if not null. It will not override any existing feature type - enrich identifiers. Only add missing identifiers (using DefaultXrefComparator) - Ignore all other properties of a feature

Since:

13/08/13

Author:

Gabriel Aldam (galdam@ebi.ac.uk)

Constructor Summary

Constructors

Constructor	Description
MinimalFeatureEnricher()	Constructor for MinimalFeatureEnricher.

Method Summary

Modifier and Type	Method	Description
void	enrich(F featureToEnrich)	Enrichment of a single feature.
void	enrich(F objectToEnrich, F objectSource)	enrich.
void	enrich(Collection<F> objects)	enrich.
CvTermEnricher	getCvTermEnricher()	Gets the subEnricher for CvTerms.
FeatureEnricherListener<F>	getFeatureEnricherListener()	Retrieves the listener of feature changes.
void	onAddedAlias(Protein o, Alias added)	Listen to the event where an alias has been added to the object aliases.
void	onAddedAnnotation(Protein o, Annotation added)	Listen to the event where an annotation has been added to the object annotations.
void	onAddedChecksum(Protein interactor, Checksum added)	Listen to the event where a checksum has been added to the interactor checksums.
void	onAddedIdentifier(Protein o, Xref added)	Listen to the event where an identifier has been added to the protein identifiers.
void	onAddedXref(Protein o, Xref added)	Listen to the event where a xref has been added to the protein xrefs.
void	onEnrichmentComplete(Protein object, EnrichmentStatus status, String message)	onEnrichmentComplete.
void	onEnrichmentError(Protein object, String message, Exception e)	onEnrichmentError.
void	onFullNameUpdate(Protein interactor, String oldFullName)	Listens for the event where the fullName has been changed.
void	onInteractorTypeUpdate(Protein interactor, CvTerm old)	Listen to the event where the interactor type has been initialised.
protected void	onInvalidRange(F feature, Range range, Collection<String> errorMessages)	onInvalidRange.
void	onOrganismUpdate(Protein interactor, Organism o)	Listen to the event where the organism of a interactor has been initialised.
protected void	onOutOfDateRange(F feature, Range range, Collection<String> errorMessages, String oldSequence)	onOutOfDateRange.
void	onRemovedAlias(Protein o, Alias removed)	Listen to the event where an alias has been removed from the object aliases.
void	onRemovedAnnotation(Protein o, Annotation removed)	Listen to the event where an annotation has been removed from the object annotations.
void	onRemovedChecksum(Protein interactor, Checksum removed)	Listen to the event where a checksum has been removed from the interactor checksums.
void	onRemovedIdentifier(Protein o, Xref removed)	Listen to the event where an identifier has been removed from the protein identifiers.
void	onRemovedXref(Protein o, Xref removed)	Listen to the event where a xref has been removed from the interactor xrefs.
void	onSequenceUpdate(Protein protein, String oldSequence)	Listen to the event where the sequence of a protein has been changed.
void	onShortNameUpdate(Protein interactor, String oldShortName)	Listens for the event where the shortName has been changed.
protected void	processFeatureType(F featureToEnrich)	processFeatureType.
protected void	processFeatureType(F featureToEnrich, F objectSource)	processFeatureType.
protected void	processFullName(F objectToEnrich, F objectSource)	processFullName.
protected void	processIdentifiers(F objectToEnrich, F objectSource)	processIdentifiers.
void	processMinimalUpdates(F featureToEnrich)	processMinimalUpdates.
void	processMinimalUpdates(F objectToEnrich, F objectSource)	processMinimalUpdates.
protected void	processOtherProperties(F featureToEnrich)	processOtherProperties.
protected void	processOtherProperties(F featureToEnrich, F objectSource)	processOtherProperties.
protected void	processRanges(F featureToEnrich)	processRanges.
protected void	processRanges(F objectToEnrich, F objectSource)	processRanges.
protected void	processRangeStatus(CvTerm status)	processRangeStatus.
protected void	processShortLabel(F objectToEnrich, F objectSource)	processShortLabel.
void	setCvTermEnricher(CvTermEnricher cvTermEnricher)	setCvTermEnricher.
void	setFeatureEnricherListener(FeatureEnricherListener<F> featureEnricherListener)	setFeatureEnricherListener.
void	setFeaturesWithRangesToUpdate(Collection<F> features)	setFeaturesWithRangesToUpdate.
protected boolean	updateRangePositions()	updateRangePositions.

Methods inherited from class java.lang.Object

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

Constructor Detail

MinimalFeatureEnricher

public MinimalFeatureEnricher()

Constructor for MinimalFeatureEnricher.

Method Detail

enrich

public void enrich(F featureToEnrich)
            throws EnricherException

Enrichment of a single feature.

Specified by:

enrich in interface MIEnricher<F extends Feature>

Parameters:

featureToEnrich - The feature which is to be enriched.

Throws:

EnricherException - Thrown if problems are encountered in the fetcher

processMinimalUpdates

public void processMinimalUpdates(F featureToEnrich)
                           throws EnricherException

processMinimalUpdates.

Parameters:

featureToEnrich - a F object.

Throws:

EnricherException - if any.

processRanges

protected void processRanges(F featureToEnrich)
                      throws EnricherException

processRanges.

Parameters:

featureToEnrich - a F object.

Throws:

EnricherException - if any.

processRangeStatus

protected void processRangeStatus(CvTerm status)
                           throws EnricherException

processRangeStatus.

Parameters:

status - a CvTerm object.

Throws:

EnricherException - if any.

enrich

public void enrich(Collection<F> objects)
            throws EnricherException

enrich.

Specified by:

enrich in interface MIEnricher<F extends Feature>

Parameters:

objects - a Collection object.

Throws:

EnricherException - if any.

enrich

public void enrich(F objectToEnrich,
                   F objectSource)
            throws EnricherException

enrich.

Specified by:

enrich in interface MIEnricher<F extends Feature>

Parameters:

objectToEnrich - a F object.

objectSource - a F object.

Throws:

EnricherException - if any.

processMinimalUpdates

public void processMinimalUpdates(F objectToEnrich,
                                  F objectSource)
                           throws EnricherException

processMinimalUpdates.

Parameters:

objectToEnrich - a F object.

objectSource - a F object.

Throws:

EnricherException - if any.

processRanges

protected void processRanges(F objectToEnrich,
                             F objectSource)
                      throws EnricherException

processRanges.

Parameters:

objectToEnrich - a F object.

objectSource - a F object.

Throws:

EnricherException - if any.

processIdentifiers

protected void processIdentifiers(F objectToEnrich,
                                  F objectSource)
                           throws EnricherException

processIdentifiers.

Parameters:

objectToEnrich - a F object.

objectSource - a F object.

Throws:

EnricherException - if any.

processFullName

protected void processFullName(F objectToEnrich,
                               F objectSource)
                        throws EnricherException

processFullName.

Parameters:

objectToEnrich - a F object.

objectSource - a F object.

Throws:

EnricherException - if any.

processShortLabel

protected void processShortLabel(F objectToEnrich,
                                 F objectSource)
                          throws EnricherException

processShortLabel.

Parameters:

objectToEnrich - a F object.

objectSource - a F object.

Throws:

EnricherException - if any.

processOtherProperties

protected void processOtherProperties(F featureToEnrich)
                               throws EnricherException

processOtherProperties.

Parameters:

featureToEnrich - a F object.

Throws:

EnricherException - if any.

processOtherProperties

protected void processOtherProperties(F featureToEnrich,
                                      F objectSource)
                               throws EnricherException

processOtherProperties.

Parameters:

featureToEnrich - a F object.

objectSource - a F object.

Throws:

EnricherException - if any.

setFeaturesWithRangesToUpdate

public void setFeaturesWithRangesToUpdate(Collection<F> features)

setFeaturesWithRangesToUpdate.

Specified by:

setFeaturesWithRangesToUpdate in interface FeatureEnricher<F extends Feature>

Parameters:

features - a Collection object.

setFeatureEnricherListener

public void setFeatureEnricherListener(FeatureEnricherListener<F> featureEnricherListener)

setFeatureEnricherListener.

Sets the listener of feature changes. Can be null.

Specified by:

setFeatureEnricherListener in interface FeatureEnricher<F extends Feature>

Parameters:

featureEnricherListener - a FeatureEnricherListener object.

getFeatureEnricherListener

public FeatureEnricherListener<F> getFeatureEnricherListener()

Retrieves the listener of feature changes. May be null if changes are not being listened to.

Specified by:

getFeatureEnricherListener in interface FeatureEnricher<F extends Feature>

Returns:

The current listener of feature changes.

setCvTermEnricher

public void setCvTermEnricher(CvTermEnricher cvTermEnricher)

setCvTermEnricher.

Sets the subEnricher for CvTerms. Can be null.

Specified by:

setCvTermEnricher in interface FeatureEnricher<F extends Feature>

Parameters:

cvTermEnricher - a CvTermEnricher object.

getCvTermEnricher

public CvTermEnricher getCvTermEnricher()

Gets the subEnricher for CvTerms. Can be null.

Specified by:

getCvTermEnricher in interface FeatureEnricher<F extends Feature>

Returns:

The CvTerm enricher which is being used.

onSequenceUpdate

public void onSequenceUpdate(Protein protein,
                             String oldSequence)

Listen to the event where the sequence of a protein has been changed. If oldSequence is null, it means that the sequence has been initialised. If the sequence of the protein is null, it means that the sequence of the protein has been reset

Specified by:

onSequenceUpdate in interface PolymerChangeListener<F extends Feature>

Parameters:

protein - : updated polymer

oldSequence - : old sequence

onShortNameUpdate

public void onShortNameUpdate(Protein interactor,
                              String oldShortName)

Listens for the event where the shortName has been changed.

Specified by:

onShortNameUpdate in interface InteractorChangeListener<F extends Feature>

Parameters:

interactor - The interactor which has changed.

oldShortName - The old shortName.

onFullNameUpdate

public void onFullNameUpdate(Protein interactor,
                             String oldFullName)

Listens for the event where the fullName has been changed.

Specified by:

onFullNameUpdate in interface InteractorChangeListener<F extends Feature>

Parameters:

interactor - The interactor which has changed.

oldFullName - The old fullName.

onOrganismUpdate

public void onOrganismUpdate(Protein interactor,
                             Organism o)

Listen to the event where the organism of a interactor has been initialised. This event happens when a interactor does not have any organisms

Specified by:

onOrganismUpdate in interface InteractorChangeListener<F extends Feature>

Parameters:

interactor - The interactor which has changed.

o - a Organism object.

onInteractorTypeUpdate

public void onInteractorTypeUpdate(Protein interactor,
                                   CvTerm old)

Listen to the event where the interactor type has been initialised. This event happens when a interactor does not have any interactor types

Specified by:

onInteractorTypeUpdate in interface InteractorChangeListener<F extends Feature>

Parameters:

interactor - The interactor which has changed.

old - a CvTerm object.

onAddedAlias

public void onAddedAlias(Protein o,
                         Alias added)

Listen to the event where an alias has been added to the object aliases.

Specified by:

onAddedAlias in interface AliasesChangeListener<F extends Feature>

Parameters:

o - The object which has changed.

added - The added alias.

onRemovedAlias

public void onRemovedAlias(Protein o,
                           Alias removed)

Listen to the event where an alias has been removed from the object aliases.

Specified by:

onRemovedAlias in interface AliasesChangeListener<F extends Feature>

Parameters:

o - The object which has changed.

removed - The removed alias.

onAddedAnnotation

public void onAddedAnnotation(Protein o,
                              Annotation added)

Listen to the event where an annotation has been added to the object annotations.

Specified by:

onAddedAnnotation in interface AnnotationsChangeListener<F extends Feature>

Parameters:

o - : the parent of this annotation

added - : the added annotation

onRemovedAnnotation

public void onRemovedAnnotation(Protein o,
                                Annotation removed)

Listen to the event where an annotation has been removed from the object annotations.

Specified by:

onRemovedAnnotation in interface AnnotationsChangeListener<F extends Feature>

Parameters:

o - : the parent of this annotation

removed - : the removed annotation

onAddedChecksum

public void onAddedChecksum(Protein interactor,
                            Checksum added)

Listen to the event where a checksum has been added to the interactor checksums.

Specified by:

onAddedChecksum in interface ChecksumsChangeListener<F extends Feature>

Parameters:

interactor - The interactor which has changed.

added - The added checksum.

onRemovedChecksum

public void onRemovedChecksum(Protein interactor,
                              Checksum removed)

Listen to the event where a checksum has been removed from the interactor checksums.

Specified by:

onRemovedChecksum in interface ChecksumsChangeListener<F extends Feature>

Parameters:

interactor - The interactor which has changed.

removed - The removed checksum.

onAddedIdentifier

public void onAddedIdentifier(Protein o,
                              Xref added)

Listen to the event where an identifier has been added to the protein identifiers.

Specified by:

onAddedIdentifier in interface IdentifiersChangeListener<F extends Feature>

Parameters:

o - The object which has changed.

added - The added identifier

onRemovedIdentifier

public void onRemovedIdentifier(Protein o,
                                Xref removed)

Listen to the event where an identifier has been removed from the protein identifiers.

Specified by:

onRemovedIdentifier in interface IdentifiersChangeListener<F extends Feature>

Parameters:

o - The object which has changed.

removed - The removed identifier.

onAddedXref

public void onAddedXref(Protein o,
                        Xref added)

Listen to the event where a xref has been added to the protein xrefs.

Specified by:

onAddedXref in interface XrefsChangeListener<F extends Feature>

Parameters:

o - The object which has changed.

added - The added Xref.

onRemovedXref

public void onRemovedXref(Protein o,
                          Xref removed)

Listen to the event where a xref has been removed from the interactor xrefs.

Specified by:

onRemovedXref in interface XrefsChangeListener<F extends Feature>

Parameters:

o - The object which has changed.

removed - The removed Xref.

processFeatureType

protected void processFeatureType(F featureToEnrich)
                           throws EnricherException

processFeatureType.

Parameters:

featureToEnrich - a F object.

Throws:

EnricherException - if any.

processFeatureType

protected void processFeatureType(F featureToEnrich,
                                  F objectSource)
                           throws EnricherException

processFeatureType.

Parameters:

featureToEnrich - a F object.

objectSource - a F object.

Throws:

EnricherException - if any.

onInvalidRange

protected void onInvalidRange(F feature,
                              Range range,
                              Collection<String> errorMessages)

onInvalidRange.

Parameters:

feature - a F object.

range - a Range object.

errorMessages - a Collection object.

onOutOfDateRange

protected void onOutOfDateRange(F feature,
                                Range range,
                                Collection<String> errorMessages,
                                String oldSequence)

onOutOfDateRange.

Parameters:

feature - a F object.

range - a Range object.

errorMessages - a Collection object.

oldSequence - a String object.

updateRangePositions

protected boolean updateRangePositions()

updateRangePositions.

Returns:

a boolean.

onEnrichmentComplete

public void onEnrichmentComplete(Protein object,
                                 EnrichmentStatus status,
                                 String message)

onEnrichmentComplete.

Specified by:

onEnrichmentComplete in interface EnricherListener<F extends Feature>

Parameters:

object - a T object.

status - a EnrichmentStatus object.

message - a String object.

onEnrichmentError

public void onEnrichmentError(Protein object,
                              String message,
                              Exception e)

onEnrichmentError.

Specified by:

onEnrichmentError in interface EnricherListener<F extends Feature>

Parameters:

object - a T object.

message - a String object.

e - a Exception object.