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

Class AbstractInteractorUpdater<T extends Interactor>

java.lang.Object

psidev.psi.mi.jami.enricher.impl.AbstractMIEnricher<T>

psidev.psi.mi.jami.enricher.impl.AbstractInteractorEnricher<T>

psidev.psi.mi.jami.enricher.impl.AbstractInteractorUpdater<T>

All Implemented Interfaces:

InteractorEnricher<T>, MIEnricher<T>

Direct Known Subclasses:

FullInteractorBaseUpdater, MinimalBioactiveEntityUpdater, MinimalGeneUpdater, MinimalInteractorBaseUpdater, MinimalProteinUpdater

public abstract class AbstractInteractorUpdater<T extends Interactor>
extends AbstractInteractorEnricher<T>

Abstract class for updater of interactors Minimal update: - enrich shortname of an interactor. If the shortname in the interactor to enrich id different from the shortname loaded from the fetched interactor, it will override the shortname of the interactor to enrich with the shortname of the fetched interactor - enrich fullname of an interactor. If the fullname in the interactor to enrich id different from the fullName loaded from the fetched interactor, it will override the fullname of the interactor to enrich with the fullname of the fetched interactor it will ignore the fullname loaded from the fetched interactor. - enrich identifiers (uniprot, ensembl, etc.) of an interactor. It will use DefaultXrefComparator to compare identifiers and add missing identifiers. It will remove identifiers that are not in the fectched interactor - enrich aliases (gene name, etc.) of an interactor. It will use DefaultAliasComparator to compare aliases and add missing aliases without removing any existing aliases. - enrich interactor type of an interactor if the cv term enricher is not null. If the interactor type in the interactor to enrich id different from the interactor type loaded from the fetched interactor (see DefaultCvTermComparator), it will override the interactor type of the interactor to enrich with the interactor type of the fetched interactor - enrich organism of an interactor if the organismEnricher is not null. If the organism in the interactor to enrich id different from the organism loaded from the fetched interactor (see DefaultOrganismComparator), it will override the organism of the interactor to enrich with the organism of the fetched interactor Full update: - enrich xrefs. It will use DefaultXrefComparator to compare xrefs and add missing xrefs without removing any existing xrefs. It will use DefaultXrefComparator to compare identifiers and add missing identifiers. It will remove xrefs that are not in the fectched interactor - enrich checksums, It will use DefaultChecksumComparator to compare checksums and add missing xrefs without removing any existing checksums. It will use DefaultXrefComparator to compare identifiers and add missing identifiers. It will remove checksum that are not in the fectched interactor - enrich annotations It will use DefaultAnnotationComparator to compare annotations and add missing xrefs without removing any existing annotations. It will use DefaultXrefComparator to compare identifiers and add missing identifiers. It will remove annotations that are not in the fectched interactor

Since:

01/10/13

Version:

$Id$

Author:

Marine Dumousseau (marine@ebi.ac.uk)

Constructor Summary

Constructors

Constructor	Description
AbstractInteractorUpdater(AbstractInteractorEnricher<T> interactorEnricher)	Constructor for AbstractInteractorUpdater.

Method Summary

Modifier and Type	Method	Description
protected boolean	canEnrichInteractor(T entityToEnrich, T fetchedEntity)	canEnrichInteractor.
T	find(T objectToEnrich)	find.
protected AbstractInteractorEnricher<T>	getInteractorEnricher()	Getter for the field interactorEnricher.
InteractorEnricherListener<T>	getListener()	Getter for the field listener.
protected boolean	isFullEnrichment()	isFullEnrichment.
protected void	onCompletedEnrichment(T objectToEnrich)	onCompletedEnrichment.
protected void	onEnrichedVersionNotFound(T objectToEnrich)	onEnrichedVersionNotFound.
protected void	onInteractorCheckFailure(T objectToEnrich, T fetchedObject)	onInteractorCheckFailure.
void	processAliases(T bioactiveEntityToEnrich, T fetched)	processAliases.
protected void	processAnnotations(T objectToEnrich, T fetchedObject)	processAnnotations.
protected void	processChecksums(T bioactiveEntityToEnrich, T fetched)	processChecksums.
void	processFullName(T bioactiveEntityToEnrich, T fetched)	processFullName.
protected void	processIdentifiers(T bioactiveEntityToEnrich, T fetched)	processIdentifiers.
void	processInteractorType(T entityToEnrich, T fetched)	processInteractorType.
void	processOrganism(T entityToEnrich, T fetched)	processOrganism.
protected void	processShortLabel(T bioactiveEntityToEnrich, T fetched)	processShortLabel.
protected void	processXrefs(T bioactiveEntityToEnrich, T fetched)	processXrefs.
void	setListener(InteractorEnricherListener<T> listener)	setListener.

Methods inherited from class psidev.psi.mi.jami.enricher.impl.AbstractInteractorEnricher

enrich, getCvTermEnricher, getInteractorFetcher, getOrganismEnricher, getRetryCount, processInteractorType, processOrganism, processOtherProperties, setCvTermEnricher, setOrganismEnricher, setRetryCount

Methods inherited from class psidev.psi.mi.jami.enricher.impl.AbstractMIEnricher

enrich, enrich

Methods inherited from class java.lang.Object

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

Methods inherited from interface psidev.psi.mi.jami.enricher.MIEnricher

enrich, enrich

Constructor Detail

AbstractInteractorUpdater

public AbstractInteractorUpdater(AbstractInteractorEnricher<T> interactorEnricher)

Constructor for AbstractInteractorUpdater.

Parameters:

interactorEnricher - a AbstractInteractorEnricher object.

Method Detail

processShortLabel

protected void processShortLabel(T bioactiveEntityToEnrich,
                                 T fetched)
                          throws EnricherException

processShortLabel.

Overrides:

processShortLabel in class AbstractInteractorEnricher<T extends Interactor>

Parameters:

bioactiveEntityToEnrich - a T object.

fetched - a T object.

Throws:

EnricherException - if any.

processAliases

public void processAliases(T bioactiveEntityToEnrich,
                           T fetched)
                    throws EnricherException

processAliases.

Overrides:

processAliases in class AbstractInteractorEnricher<T extends Interactor>

Parameters:

bioactiveEntityToEnrich - a T object.

fetched - a T object.

Throws:

EnricherException - if any.

processIdentifiers

protected void processIdentifiers(T bioactiveEntityToEnrich,
                                  T fetched)
                           throws EnricherException

processIdentifiers.

Overrides:

processIdentifiers in class AbstractInteractorEnricher<T extends Interactor>

Parameters:

bioactiveEntityToEnrich - a T object.

fetched - a T object.

Throws:

EnricherException - if any.

processFullName

public void processFullName(T bioactiveEntityToEnrich,
                            T fetched)
                     throws EnricherException

processFullName.

Overrides:

processFullName in class AbstractInteractorEnricher<T extends Interactor>

Parameters:

bioactiveEntityToEnrich - a T object.

fetched - a T object.

Throws:

EnricherException - if any.

processInteractorType

public void processInteractorType(T entityToEnrich,
                                  T fetched)
                           throws EnricherException

processInteractorType.

Overrides:

processInteractorType in class AbstractInteractorEnricher<T extends Interactor>

Parameters:

entityToEnrich - a T object.

fetched - a T object.

Throws:

EnricherException - if any.

processOrganism

public void processOrganism(T entityToEnrich,
                            T fetched)
                     throws EnricherException

processOrganism.

Overrides:

processOrganism in class AbstractInteractorEnricher<T extends Interactor>

Parameters:

entityToEnrich - a T object.

fetched - a T object.

Throws:

EnricherException - if any.

processChecksums

protected void processChecksums(T bioactiveEntityToEnrich,
                                T fetched)
                         throws EnricherException

processChecksums.

Overrides:

processChecksums in class AbstractInteractorEnricher<T extends Interactor>

Parameters:

bioactiveEntityToEnrich - a T object.

fetched - a T object.

Throws:

EnricherException - if any.

processAnnotations

protected void processAnnotations(T objectToEnrich,
                                  T fetchedObject)
                           throws EnricherException

processAnnotations.

Overrides:

processAnnotations in class AbstractInteractorEnricher<T extends Interactor>

Parameters:

objectToEnrich - a T object.

fetchedObject - a T object.

Throws:

EnricherException - if any.

processXrefs

protected void processXrefs(T bioactiveEntityToEnrich,
                            T fetched)
                     throws EnricherException

processXrefs.

Overrides:

processXrefs in class AbstractInteractorEnricher<T extends Interactor>

Parameters:

bioactiveEntityToEnrich - a T object.

fetched - a T object.

Throws:

EnricherException - if any.

getListener

public InteractorEnricherListener<T> getListener()

Getter for the field listener.

Specified by:

getListener in interface InteractorEnricher<T extends Interactor>

Overrides:

getListener in class AbstractInteractorEnricher<T extends Interactor>

Returns:

a InteractorEnricherListener object.

setListener

public void setListener(InteractorEnricherListener<T> listener)

setListener.

Specified by:

setListener in interface InteractorEnricher<T extends Interactor>

Overrides:

setListener in class AbstractInteractorEnricher<T extends Interactor>

Parameters:

listener - a InteractorEnricherListener object.

find

public T find(T objectToEnrich)
       throws EnricherException

find.

Specified by:

find in class AbstractInteractorEnricher<T extends Interactor>

Parameters:

objectToEnrich - a T object.

Returns:

a T object.

Throws:

EnricherException - if any.

onEnrichedVersionNotFound

protected void onEnrichedVersionNotFound(T objectToEnrich)
                                  throws EnricherException

onEnrichedVersionNotFound.

Overrides:

onEnrichedVersionNotFound in class AbstractInteractorEnricher<T extends Interactor>

Parameters:

objectToEnrich - a T object.

Throws:

EnricherException - if any.

isFullEnrichment

protected boolean isFullEnrichment()

isFullEnrichment.

Specified by:

isFullEnrichment in class AbstractInteractorEnricher<T extends Interactor>

Returns:

a boolean.

onCompletedEnrichment

protected void onCompletedEnrichment(T objectToEnrich)

onCompletedEnrichment.

Specified by:

onCompletedEnrichment in class AbstractInteractorEnricher<T extends Interactor>

Parameters:

objectToEnrich - a T object.

onInteractorCheckFailure

protected void onInteractorCheckFailure(T objectToEnrich,
                                        T fetchedObject)
                                 throws EnricherException

onInteractorCheckFailure.

Specified by:

onInteractorCheckFailure in class AbstractInteractorEnricher<T extends Interactor>

Parameters:

objectToEnrich - a T object.

fetchedObject - a T object.

Throws:

EnricherException - if any.

canEnrichInteractor

protected boolean canEnrichInteractor(T entityToEnrich,
                                      T fetchedEntity)
                               throws EnricherException

canEnrichInteractor.

Overrides:

canEnrichInteractor in class AbstractInteractorEnricher<T extends Interactor>

Parameters:

entityToEnrich - a T object.

fetchedEntity - a T object.

Returns:

a boolean.

Throws:

EnricherException - if any.

getInteractorEnricher

protected AbstractInteractorEnricher<T> getInteractorEnricher()

Getter for the field interactorEnricher.

Returns:

a AbstractInteractorEnricher object.