Package psidev.psi.mi.jami.model.impl

Class AbstractInteraction<T extends Participant>

java.lang.Object

psidev.psi.mi.jami.model.impl.AbstractInteraction<T>

All Implemented Interfaces:

Interaction<T>

Direct Known Subclasses:

AbstractBinaryInteraction, DefaultInteraction, DefaultInteractionEvidence, DefaultModelledInteraction

public abstract class AbstractInteraction<T extends Participant>
extends Object
implements Interaction<T>

Abstract class for interactions

Since:

09/07/13

Version:

$Id$

Author:

Marine Dumousseau (marine@ebi.ac.uk)

Constructor Summary

Constructors

Constructor	Description
AbstractInteraction()	Constructor for AbstractInteraction.
AbstractInteraction(String shortName)	Constructor for AbstractInteraction.
AbstractInteraction(String shortName, CvTerm type)	Constructor for AbstractInteraction.

Method Summary

Modifier and Type	Method	Description
boolean	addAllParticipants(Collection<? extends T> participants)	This method will add all the participant and set the interaction of the new participant to this current interaction
boolean	addParticipant(T part)	addParticipant
protected void	clearPropertiesLinkedToChecksums()	clearPropertiesLinkedToChecksums
Collection<Annotation>	getAnnotations()	Getter for the field annotations.
Collection<Checksum>	getChecksums()	Getter for the field checksums.
Date	getCreatedDate()	Getter for the field createdDate.
Collection<Xref>	getIdentifiers()	Getter for the field identifiers.
CvTerm	getInteractionType()	Getter for the field interactionType.
Collection<T>	getParticipants()	Getter for the field participants.
String	getRigid()	Getter for the field rigid.
String	getShortName()	Getter for the field shortName.
Date	getUpdatedDate()	Getter for the field updatedDate.
Collection<Xref>	getXrefs()	Getter for the field xrefs.
protected void	initialiseAnnotations()	initialiseAnnotations
protected void	initialiseAnnotationsWith(Collection<Annotation> annotations)	initialiseAnnotationsWith
protected void	initialiseChecksums()	initialiseChecksums
protected void	initialiseChecksumWith(Collection<Checksum> checksums)	initialiseChecksumWith
protected void	initialiseIdentifiers()	initialiseIdentifiers
protected void	initialiseIdentifiersWith(Collection<Xref> identifiers)	initialiseIdentifiersWith
protected void	initialiseParticipants()	initialiseParticipants
protected void	initialiseParticipantsWith(Collection<T> participants)	initialiseParticipantsWith
protected void	initialiseXrefs()	initialiseXrefs
protected void	initialiseXrefsWith(Collection<Xref> xrefs)	initialiseXrefsWith
protected void	processAddedChecksumEvent(Checksum added)	processAddedChecksumEvent
protected void	processRemovedChecksumEvent(Checksum removed)	processRemovedChecksumEvent
boolean	removeAllParticipants(Collection<? extends T> participants)	This method will remove the participant and set the interaction of the removed participant to null.
boolean	removeParticipant(T part)	removeParticipant
void	setCreatedDate(Date created)	Sets the created date
void	setInteractionType(CvTerm term)	Sets the interaction type.
void	setRigid(String rigid)	Sets the rigid of this interaction.
void	setShortName(String name)	Sets the short name of the interaction
void	setUpdatedDate(Date updated)	Sets the last update date
String	toString()

Methods inherited from class java.lang.Object

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

Constructor Detail

AbstractInteraction

public AbstractInteraction()

Constructor for AbstractInteraction.

AbstractInteraction

public AbstractInteraction(String shortName)

Constructor for AbstractInteraction.

Parameters:

shortName - a String object.

AbstractInteraction

public AbstractInteraction(String shortName,
                           CvTerm type)

Constructor for AbstractInteraction.

Parameters:

shortName - a String object.

type - a CvTerm object.

Method Detail

initialiseAnnotations

protected void initialiseAnnotations()

initialiseAnnotations

initialiseXrefs

protected void initialiseXrefs()

initialiseXrefs

initialiseIdentifiers

protected void initialiseIdentifiers()

initialiseIdentifiers

initialiseParticipants

protected void initialiseParticipants()

initialiseParticipants

initialiseParticipantsWith

protected void initialiseParticipantsWith(Collection<T> participants)

initialiseParticipantsWith

Parameters:

participants - a Collection object.

initialiseChecksums

protected void initialiseChecksums()

initialiseChecksums

initialiseXrefsWith

protected void initialiseXrefsWith(Collection<Xref> xrefs)

initialiseXrefsWith

Parameters:

xrefs - a Collection object.

initialiseIdentifiersWith

protected void initialiseIdentifiersWith(Collection<Xref> identifiers)

initialiseIdentifiersWith

Parameters:

identifiers - a Collection object.

initialiseChecksumWith

protected void initialiseChecksumWith(Collection<Checksum> checksums)

initialiseChecksumWith

Parameters:

checksums - a Collection object.

initialiseAnnotationsWith

protected void initialiseAnnotationsWith(Collection<Annotation> annotations)

initialiseAnnotationsWith

Parameters:

annotations - a Collection object.

getShortName

public String getShortName()

Getter for the field shortName.

Specified by:

getShortName in interface Interaction<T extends Participant>

Returns:

a String object.

setShortName

public void setShortName(String name)

Sets the short name of the interaction

Specified by:

setShortName in interface Interaction<T extends Participant>

Parameters:

name - : short name

getRigid

public String getRigid()

Getter for the field rigid.

Specified by:

getRigid in interface Interaction<T extends Participant>

Returns:

a String object.

setRigid

public void setRigid(String rigid)

Sets the rigid of this interaction. It will remove the previous rigid from the list of checksum and add the new one. If rigid is null, it will remove all the rigid in the list of checksum

Specified by:

setRigid in interface Interaction<T extends Participant>

Parameters:

rigid - : the rigid

getIdentifiers

public Collection<Xref> getIdentifiers()

Getter for the field identifiers.

Specified by:

getIdentifiers in interface Interaction<T extends Participant>

Returns:

a Collection object.

getXrefs

public Collection<Xref> getXrefs()

Getter for the field xrefs.

Specified by:

getXrefs in interface Interaction<T extends Participant>

Returns:

a Collection object.

getChecksums

public Collection<Checksum> getChecksums()

Getter for the field checksums.

Specified by:

getChecksums in interface Interaction<T extends Participant>

Returns:

a Collection object.

getAnnotations

public Collection<Annotation> getAnnotations()

Getter for the field annotations.

Specified by:

getAnnotations in interface Interaction<T extends Participant>

Returns:

a Collection object.

getUpdatedDate

public Date getUpdatedDate()

Getter for the field updatedDate.

Specified by:

getUpdatedDate in interface Interaction<T extends Participant>

Returns:

a Date object.

setUpdatedDate

public void setUpdatedDate(Date updated)

Sets the last update date

Specified by:

setUpdatedDate in interface Interaction<T extends Participant>

Parameters:

updated - : last update date

getCreatedDate

public Date getCreatedDate()

Getter for the field createdDate.

Specified by:

getCreatedDate in interface Interaction<T extends Participant>

Returns:

a Date object.

setCreatedDate

public void setCreatedDate(Date created)

Sets the created date

Specified by:

setCreatedDate in interface Interaction<T extends Participant>

Parameters:

created - : created date

getInteractionType

public CvTerm getInteractionType()

Getter for the field interactionType.

Specified by:

getInteractionType in interface Interaction<T extends Participant>

Returns:

a CvTerm object.

setInteractionType

public void setInteractionType(CvTerm term)

Sets the interaction type.

Specified by:

setInteractionType in interface Interaction<T extends Participant>

Parameters:

term - : interaction type

getParticipants

public Collection<T> getParticipants()

Getter for the field participants.

Specified by:

getParticipants in interface Interaction<T extends Participant>

Returns:

a Collection object.

addParticipant

public boolean addParticipant(T part)

addParticipant

Specified by:

addParticipant in interface Interaction<T extends Participant>

Parameters:

part - a T object.

Returns:

a boolean.

removeParticipant

public boolean removeParticipant(T part)

removeParticipant

Specified by:

removeParticipant in interface Interaction<T extends Participant>

Parameters:

part - a T object.

Returns:

a boolean.

addAllParticipants

public boolean addAllParticipants(Collection<? extends T> participants)

This method will add all the participant and set the interaction of the new participant to this current interaction

Specified by:

addAllParticipants in interface Interaction<T extends Participant>

Parameters:

participants - : participants to add

Returns:

true if participant are added to the list of participants

removeAllParticipants

public boolean removeAllParticipants(Collection<? extends T> participants)

This method will remove the participant and set the interaction of the removed participant to null.

Specified by:

removeAllParticipants in interface Interaction<T extends Participant>

Parameters:

participants - : participants to remove

Returns:

true if participant are removed from the list of participants

toString

public String toString()

Overrides:

toString in class Object

processAddedChecksumEvent

protected void processAddedChecksumEvent(Checksum added)

processAddedChecksumEvent

Parameters:

added - a Checksum object.

processRemovedChecksumEvent

protected void processRemovedChecksumEvent(Checksum removed)

processRemovedChecksumEvent

Parameters:

removed - a Checksum object.

clearPropertiesLinkedToChecksums

protected void clearPropertiesLinkedToChecksums()

clearPropertiesLinkedToChecksums