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

Class FullModelledInteractionEnricher<I extends ModelledInteraction>

java.lang.Object

psidev.psi.mi.jami.enricher.impl.minimal.MinimalInteractionEnricher<I>

psidev.psi.mi.jami.enricher.impl.minimal.MinimalModelledInteractionEnricher<I>

psidev.psi.mi.jami.enricher.impl.full.FullModelledInteractionEnricher<I>

All Implemented Interfaces:

InteractionEnricher<I>, MIEnricher<I>, ModelledInteractionEnricher<I>

Direct Known Subclasses:

FullComplexEnricher, FullModelledInteractionUpdater

public class FullModelledInteractionEnricher<I extends ModelledInteraction>
extends MinimalModelledInteractionEnricher<I>

Full enricher for ModelledInteraction

Since:

01/10/13

Version:

$Id$

Author:

Marine Dumousseau (marine@ebi.ac.uk)

Constructor Summary

Constructors

Modifier	Constructor	Description
	FullModelledInteractionEnricher()	Constructor for FullModelledInteractionEnricher.
protected	FullModelledInteractionEnricher(FullInteractionEnricher<I> interactionEnricher)	Constructor for FullModelledInteractionEnricher.

Method Summary

Modifier and Type	Method	Description
CvTermEnricher<CvTerm>	getCvTermEnricher()	Sets the sub enricher for CvTerms.
InteractionEvidenceEnricher	getEvidenceEnricher()	Getter for the field evidenceEnricher.
protected FullInteractionEnricher<I>	getInteractionEnricher()	Getter for the field interactionEnricher.
InteractionEnricherListener<I>	getInteractionEnricherListener()	The listener for changes made to interactions.
ParticipantEnricher	getParticipantEnricher()	The current sub enricher for participants.
protected void	mergeCooperativeEffects(I interactionToEnrich, I objectSource, boolean remove)	mergeCooperativeEffects.
protected void	mergeInteractionEvidences(I interactionToEnrich, I objectSource, boolean remove)	mergeInteractionEvidences.
protected void	processConfidences(I objectToEnrich, I objectSource)	processConfidences.
protected void	processCooperativeEffects(I objectToEnrich, I objectSource)	processCooperativeEffects.
protected void	processEvidenceType(I interactionToEnrich)	processEvidenceType.
protected void	processEvidenceType(I objectToEnrich, I objectSource)	processEvidenceType.
protected void	processInteractionEvidences(I objectToEnrich)	processInteractionEvidences.
protected void	processInteractionEvidences(I objectToEnrich, I objectSource)	processInteractionEvidences.
protected void	processOtherProperties(I interactionToEnrich)	Strategy for the Interaction enrichment.
protected void	processOtherProperties(I objectToEnrich, I objectSource)	processOtherProperties.
protected void	processParameters(I objectToEnrich, I objectSource)	processParameters.
void	setCvTermEnricher(CvTermEnricher cvTermEnricher)	setCvTermEnricher.
void	setEvidenceEnricher(InteractionEvidenceEnricher evidenceEnricher)	Setter for the field evidenceEnricher.
void	setInteractionEnricherListener(InteractionEnricherListener<I> listener)	setInteractionEnricherListener.
void	setParticipantEnricher(ParticipantEnricher participantEnricher)	setParticipantEnricher.

Methods inherited from class psidev.psi.mi.jami.enricher.impl.minimal.MinimalModelledInteractionEnricher

getSourceEnricher, processSource, processSource, setSourceEnricher

Methods inherited from class psidev.psi.mi.jami.enricher.impl.minimal.MinimalInteractionEnricher

enrich, enrich, enrich, processCreatedDate, processIdentifiers, processInteractionType, processInteractionType, processMinimalUpdates, processParticipants, processParticipants, processShortName, processUpdateDate

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, enrich

Constructor Detail

FullModelledInteractionEnricher

public FullModelledInteractionEnricher()

Constructor for FullModelledInteractionEnricher.

FullModelledInteractionEnricher

protected FullModelledInteractionEnricher(FullInteractionEnricher<I> interactionEnricher)

Constructor for FullModelledInteractionEnricher.

Parameters:

interactionEnricher - a FullInteractionEnricher object.

Method Detail

processOtherProperties

protected void processOtherProperties(I interactionToEnrich)
                               throws EnricherException

Strategy for the Interaction enrichment. This method can be overwritten to change how the interaction is enriched.

Overrides:

processOtherProperties in class MinimalModelledInteractionEnricher<I extends ModelledInteraction>

Parameters:

interactionToEnrich - The interaction to be enriched.

Throws:

EnricherException - if any.

processEvidenceType

protected void processEvidenceType(I interactionToEnrich)
                            throws EnricherException

processEvidenceType.

Parameters:

interactionToEnrich - a I object.

Throws:

EnricherException - if any.

processOtherProperties

protected void processOtherProperties(I objectToEnrich,
                                      I objectSource)
                               throws EnricherException

processOtherProperties.

Overrides:

processOtherProperties in class MinimalModelledInteractionEnricher<I extends ModelledInteraction>

Parameters:

objectToEnrich - a I object.

objectSource - a I object.

Throws:

EnricherException - if any.

processEvidenceType

protected void processEvidenceType(I objectToEnrich,
                                   I objectSource)
                            throws EnricherException

processEvidenceType.

Parameters:

objectToEnrich - a I object.

objectSource - a I object.

Throws:

EnricherException - if any.

getCvTermEnricher

public CvTermEnricher<CvTerm> getCvTermEnricher()

Sets the sub enricher for CvTerms.

Specified by:

getCvTermEnricher in interface InteractionEnricher<I extends ModelledInteraction>

Overrides:

getCvTermEnricher in class MinimalInteractionEnricher<I extends ModelledInteraction>

Returns:

The enricher for CvTerms. Can be null.

getParticipantEnricher

public ParticipantEnricher getParticipantEnricher()

The current sub enricher for participants.

Specified by:

getParticipantEnricher in interface InteractionEnricher<I extends ModelledInteraction>

Overrides:

getParticipantEnricher in class MinimalInteractionEnricher<I extends ModelledInteraction>

Returns:

The enricher for participants. Can be null.

getInteractionEnricherListener

public InteractionEnricherListener<I> getInteractionEnricherListener()

The listener for changes made to interactions.

Specified by:

getInteractionEnricherListener in interface InteractionEnricher<I extends ModelledInteraction>

Overrides:

getInteractionEnricherListener in class MinimalInteractionEnricher<I extends ModelledInteraction>

Returns:

The listener for interaction changes. Can be null.

setCvTermEnricher

public void setCvTermEnricher(CvTermEnricher cvTermEnricher)

setCvTermEnricher.

The current sub enricher for CvTerms.

Specified by:

setCvTermEnricher in interface InteractionEnricher<I extends ModelledInteraction>

Overrides:

setCvTermEnricher in class MinimalInteractionEnricher<I extends ModelledInteraction>

Parameters:

cvTermEnricher - a CvTermEnricher object.

setParticipantEnricher

public void setParticipantEnricher(ParticipantEnricher participantEnricher)

setParticipantEnricher.

Sets the sub enricher for participants.

Specified by:

setParticipantEnricher in interface InteractionEnricher<I extends ModelledInteraction>

Overrides:

setParticipantEnricher in class MinimalInteractionEnricher<I extends ModelledInteraction>

Parameters:

participantEnricher - a ParticipantEnricher object.

setInteractionEnricherListener

public void setInteractionEnricherListener(InteractionEnricherListener<I> listener)

setInteractionEnricherListener.

Sets the listener to be used when interactions are changed.

Specified by:

setInteractionEnricherListener in interface InteractionEnricher<I extends ModelledInteraction>

Overrides:

setInteractionEnricherListener in class MinimalInteractionEnricher<I extends ModelledInteraction>

Parameters:

listener - a InteractionEnricherListener object.

processConfidences

protected void processConfidences(I objectToEnrich,
                                  I objectSource)

processConfidences.

Parameters:

objectToEnrich - a I object.

objectSource - a I object.

processParameters

protected void processParameters(I objectToEnrich,
                                 I objectSource)

processParameters.

Parameters:

objectToEnrich - a I object.

objectSource - a I object.

processCooperativeEffects

protected void processCooperativeEffects(I objectToEnrich,
                                         I objectSource)

processCooperativeEffects.

Parameters:

objectToEnrich - a I object.

objectSource - a I object.

mergeCooperativeEffects

protected void mergeCooperativeEffects(I interactionToEnrich,
                                       I objectSource,
                                       boolean remove)

mergeCooperativeEffects.

Parameters:

interactionToEnrich - a I object.

objectSource - a I object.

remove - a boolean.

processInteractionEvidences

protected void processInteractionEvidences(I objectToEnrich)
                                    throws EnricherException

processInteractionEvidences.

Parameters:

objectToEnrich - a I object.

Throws:

EnricherException - if any.

processInteractionEvidences

protected void processInteractionEvidences(I objectToEnrich,
                                           I objectSource)
                                    throws EnricherException

processInteractionEvidences.

Parameters:

objectToEnrich - a I object.

objectSource - a I object.

Throws:

EnricherException - if any.

mergeInteractionEvidences

protected void mergeInteractionEvidences(I interactionToEnrich,
                                         I objectSource,
                                         boolean remove)
                                  throws EnricherException

mergeInteractionEvidences.

Parameters:

interactionToEnrich - a I object.

objectSource - a I object.

remove - a boolean.

Throws:

EnricherException - if any.

getEvidenceEnricher

public InteractionEvidenceEnricher getEvidenceEnricher()

Getter for the field evidenceEnricher.

Returns:

a InteractionEvidenceEnricher object.

setEvidenceEnricher

public void setEvidenceEnricher(InteractionEvidenceEnricher evidenceEnricher)

Setter for the field evidenceEnricher.

Parameters:

evidenceEnricher - a InteractionEvidenceEnricher object.

getInteractionEnricher

protected FullInteractionEnricher<I> getInteractionEnricher()

Getter for the field interactionEnricher.

Returns:

a FullInteractionEnricher object.