Package psidev.psi.mi.jami.binary.impl

Class AbstractBinaryInteractionWrapper<I extends Interaction<T>,T extends Participant>

java.lang.Object

psidev.psi.mi.jami.binary.impl.AbstractBinaryInteractionWrapper<I,T>

All Implemented Interfaces:

BinaryInteraction<T>, Interaction<T>

Direct Known Subclasses:

BinaryInteractionEvidenceWrapper, BinaryInteractionWrapper, ModelledBinaryInteractionWrapper

public class AbstractBinaryInteractionWrapper<I extends Interaction<T>,T extends Participant>
extends Object
implements BinaryInteraction<T>

Abstract class for binary interactions that wrap an Interaction.

Since:

05/06/13

Version:

$Id$

Author:

Marine Dumousseau (marine@ebi.ac.uk)

Constructor Summary

Constructors

Constructor	Description
AbstractBinaryInteractionWrapper(I interaction)	Constructor for AbstractBinaryInteractionWrapper.
AbstractBinaryInteractionWrapper(I interaction, CvTerm complexExpansion)	Constructor for AbstractBinaryInteractionWrapper.

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)	Adds a new Participant and set the Interaction of this participant if added.
Collection<Annotation>	getAnnotations()	Getter for the field annotations.
CvTerm	getCausalRegulatoryMechanism()	Getter for the field causalRegulatoryMechanism
Collection<Checksum>	getChecksums()	getChecksums
CvTerm	getComplexExpansion()	Getter for the field complexExpansion.
Date	getCreatedDate()	getCreatedDate
Collection<Xref>	getIdentifiers()	getIdentifiers
CvTerm	getInteractionType()	getInteractionType
T	getParticipantA()	Getter for the field participantA.
T	getParticipantB()	Getter for the field participantB.
Collection<T>	getParticipants()	The collection of participants for this binary interaction.
String	getRigid()	getRigid
String	getShortName()	getShortName
Date	getUpdatedDate()	getUpdatedDate
protected I	getWrappedInteraction()	Getter for the field wrappedInteraction.
Collection<Xref>	getXrefs()	getXrefs
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)	Removes the Participant from this binary interaction
void	setCausalRegulatoryMechanism(CvTerm causalRegulatoryMechanism)	Setter for the field causalRegulatoryMechanism.
void	setComplexExpansion(CvTerm expansion)	Sets the complex expansion of this binary interaction
void	setCreatedDate(Date created)	Sets the created date
void	setInteractionType(CvTerm term)	Sets the interaction type.
void	setParticipantA(T participantA)	Setter for the field participantA.
void	setParticipantB(T participantB)	Setter for the field participantB.
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

AbstractBinaryInteractionWrapper

public AbstractBinaryInteractionWrapper(I interaction)

Constructor for AbstractBinaryInteractionWrapper.

Parameters:

interaction - : the interaction to wrap

AbstractBinaryInteractionWrapper

public AbstractBinaryInteractionWrapper(I interaction,
                                        CvTerm complexExpansion)

Constructor for AbstractBinaryInteractionWrapper.

Parameters:

interaction - : the interaction to wrap

complexExpansion - : the complex expansion method

Method Detail

getParticipantA

public T getParticipantA()

Getter for the field participantA.

Specified by:

getParticipantA in interface BinaryInteraction<I extends Interaction<T>>

Returns:

a T object.

getParticipantB

public T getParticipantB()

Getter for the field participantB.

Specified by:

getParticipantB in interface BinaryInteraction<I extends Interaction<T>>

Returns:

a T object.

setParticipantA

public void setParticipantA(T participantA)

Setter for the field participantA.

Specified by:

setParticipantA in interface BinaryInteraction<I extends Interaction<T>>

Parameters:

participantA - a T object.

setParticipantB

public void setParticipantB(T participantB)

Setter for the field participantB.

Specified by:

setParticipantB in interface BinaryInteraction<I extends Interaction<T>>

Parameters:

participantB - a T object.

getComplexExpansion

public CvTerm getComplexExpansion()

Getter for the field complexExpansion.

Specified by:

getComplexExpansion in interface BinaryInteraction<I extends Interaction<T>>

Returns:

a CvTerm object.

setComplexExpansion

public void setComplexExpansion(CvTerm expansion)

Sets the complex expansion of this binary interaction

Specified by:

setComplexExpansion in interface BinaryInteraction<I extends Interaction<T>>

Parameters:

expansion - : the complex expansion

getCausalRegulatoryMechanism

public CvTerm getCausalRegulatoryMechanism()

Getter for the field causalRegulatoryMechanism

Specified by:

getCausalRegulatoryMechanism in interface BinaryInteraction<I extends Interaction<T>>

Returns:

a CvTerm object.

setCausalRegulatoryMechanism

public void setCausalRegulatoryMechanism(CvTerm causalRegulatoryMechanism)

Setter for the field causalRegulatoryMechanism.

Specified by:

setCausalRegulatoryMechanism in interface BinaryInteraction<I extends Interaction<T>>

Parameters:

causalRegulatoryMechanism - a CvTerm object.

getShortName

public String getShortName()

getShortName

Specified by:

getShortName in interface Interaction<I extends Interaction<T>>

Returns:

a String object.

setShortName

public void setShortName(String name)

Sets the short name of the interaction

Specified by:

setShortName in interface Interaction<I extends Interaction<T>>

Parameters:

name - : short name

getRigid

public String getRigid()

getRigid

Specified by:

getRigid in interface Interaction<I extends Interaction<T>>

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<I extends Interaction<T>>

Parameters:

rigid - : the rigid

getIdentifiers

public Collection<Xref> getIdentifiers()

getIdentifiers

Specified by:

getIdentifiers in interface Interaction<I extends Interaction<T>>

Returns:

a Collection object.

getXrefs

public Collection<Xref> getXrefs()

getXrefs

Specified by:

getXrefs in interface Interaction<I extends Interaction<T>>

Returns:

a Collection object.

getChecksums

public Collection<Checksum> getChecksums()

getChecksums

Specified by:

getChecksums in interface Interaction<I extends Interaction<T>>

Returns:

a Collection object.

getAnnotations

public Collection<Annotation> getAnnotations()

Getter for the field annotations.

Specified by:

getAnnotations in interface Interaction<I extends Interaction<T>>

Returns:

a Collection object.

getUpdatedDate

public Date getUpdatedDate()

getUpdatedDate

Specified by:

getUpdatedDate in interface Interaction<I extends Interaction<T>>

Returns:

a Date object.

setUpdatedDate

public void setUpdatedDate(Date updated)

Sets the last update date

Specified by:

setUpdatedDate in interface Interaction<I extends Interaction<T>>

Parameters:

updated - : last update date

getCreatedDate

public Date getCreatedDate()

getCreatedDate

Specified by:

getCreatedDate in interface Interaction<I extends Interaction<T>>

Returns:

a Date object.

setCreatedDate

public void setCreatedDate(Date created)

Sets the created date

Specified by:

setCreatedDate in interface Interaction<I extends Interaction<T>>

Parameters:

created - : created date

getInteractionType

public CvTerm getInteractionType()

getInteractionType

Specified by:

getInteractionType in interface Interaction<I extends Interaction<T>>

Returns:

a CvTerm object.

setInteractionType

public void setInteractionType(CvTerm term)

Sets the interaction type.

Specified by:

setInteractionType in interface Interaction<I extends Interaction<T>>

Parameters:

term - : interaction type

getParticipants

public Collection<T> getParticipants()

The collection of participants for this binary interaction. It cannot be changed.

Specified by:

getParticipants in interface Interaction<I extends Interaction<T>>

Returns:

The collection of participants

addParticipant

public boolean addParticipant(T part)

Adds a new Participant and set the Interaction of this participant if added. If the participant B and A are null, it will first set the participantA. If the participantA is set, it will set the ParticipantB

Specified by:

addParticipant in interface Interaction<I extends Interaction<T>>

Parameters:

part - : participant to add

Returns:

true if the participant has been added, false otherwise

Throws:

IllegalArgumentException - if this Binary interaction already contains two participants

removeParticipant

public boolean removeParticipant(T part)

Removes the Participant from this binary interaction

Specified by:

removeParticipant in interface Interaction<I extends Interaction<T>>

Parameters:

part - : participant to remove

Returns:

true if the participant has been removed, false otherwise

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 Adds the participants and set the Interaction of this participant if added. If the participant B and A are null, it will first set the participantA. If the participantA is set, it will set the ParticipantB

Specified by:

addAllParticipants in interface Interaction<I extends Interaction<T>>

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<I extends Interaction<T>>

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

getWrappedInteraction

protected I getWrappedInteraction()

Getter for the field wrappedInteraction.

Returns:

a I object.