Package psidev.psi.mi.jami.xml.model.extension.xml254

Class XmlParticipantEvidenceWrapper

java.lang.Object

psidev.psi.mi.jami.xml.model.extension.xml254.XmlParticipantEvidenceWrapper

All Implemented Interfaces:

FileSourceContext, Entity<ModelledFeature>, ModelledEntity, ModelledParticipant, NamedParticipant<ModelledInteraction,ModelledFeature>, Participant<ModelledInteraction,ModelledFeature>, ExtendedPsiXmlEntity<ModelledFeature>

Direct Known Subclasses:

XmlExperimentalParticipantPoolWrapper

public class XmlParticipantEvidenceWrapper
extends Object
implements ModelledParticipant, FileSourceContext, ExtendedPsiXmlEntity<ModelledFeature>, NamedParticipant<ModelledInteraction,ModelledFeature>

Wrapper for Xml participants Addeding new modelled feature to this participant will not add new feature evidences to the wrapped participant evidence as they are incompatibles.

Since:

11/10/13

Version:

$Id$

Author:

Marine Dumousseau (marine@ebi.ac.uk)

Field Summary

Fields inherited from interface psidev.psi.mi.jami.model.Participant

ACCEPTOR_ROLE, ACCEPTOR_ROLE_MI, BAIT_ROLE, BAIT_ROLE_MI, DONOR_ROLE, DONOR_ROLE_MI, ELECTRON_ACCEPTOR_ROLE, ELECTRON_ACCEPTOR_ROLE_MI, ELECTRON_DONOR_ROLE, ELECTRON_DONOR_ROLE_MI, ENZYME_REGULATOR_ROLE, ENZYME_REGULATOR_ROLE_MI, ENZYME_ROLE, ENZYME_ROLE_MI, ENZYME_TARGET_ROLE, ENZYME_TARGET_ROLE_MI, FLUORESCENCE_ACCEPTOR_ROLE, FLUORESCENCE_ACCEPTOR_ROLE_MI, FLUORESCENCE_DONOR_ROLE, FLUORESCENCE_DONOR_ROLE_MI, INHIBITED, INHIBITED_MI, INHIBITOR, INHIBITOR_MI, NEUTRAL, NEUTRAL_MI, PHOSPHATE_ACCEPTOR_ROLE, PHOSPHATE_ACCEPTOR_ROLE_MI, PHOSPHATE_DONOR_ROLE, PHOSPHATE_DONOR_ROLE_MI, PHOTON_ACCEPTOR_ROLE, PHOTON_ACCEPTOR_ROLE_MI, PHOTON_DONOR_ROLE, PHOTON_DONOR_ROLE_MI, PREDETERMINED, PREDETERMINED_MI, PREY, PREY_MI, PUTATIVE_SELF_ROLE, PUTATIVE_SELF_ROLE_MI, SELF_ROLE, SELF_ROLE_MI, SUPPRESSED_GENE_ROLE, SUPPRESSED_GENE_ROLE_MI, SUPPRESSOR_GENE_ROLE, SUPPRESSOR_GENE_ROLE_MI, UNSPECIFIED_ROLE, UNSPECIFIED_ROLE_MI

Constructor Summary

Constructors

Constructor	Description
XmlParticipantEvidenceWrapper(ExtendedPsiXmlParticipantEvidence part, XmlInteractionEvidenceComplexWrapper wrapper)	Constructor for XmlParticipantEvidenceWrapper.

Method Summary

Modifier and Type	Method	Description
boolean	addAllFeatures(Collection<? extends ModelledFeature> features)	This method will add all features and set the entity of the new features to this current entity
boolean	addFeature(ModelledFeature feature)	This method will add the feature and set the entity of the new feature to this current entity
Collection<Alias>	getAliases()	Collection of aliases which give more information about the participant.
Collection<Annotation>	getAnnotations()	Collection of annotations describing the participant.
CvTerm	getBiologicalEffect()	The biological effect of the participant in a causal interaction.
CvTerm	getBiologicalRole()	The biological role of the participant.
Collection<CausalRelationship>	getCausalRelationships()	The causal relationships of this entity on other entities usually part of an interaction.
EntityInteractorChangeListener	getChangeListener()	The entity change listener if set, null otherwise.
Collection<ModelledFeature>	getFeatures()	Properties for this entity.
String	getFullName()	The full name of the entity.
int	getId()	getId.
ModelledInteraction	getInteraction()	The interaction in which the participant is involved.
Interactor	getInteractor()	The molecule/complex of molecules which interacts.
String	getShortName()	The short name of the entity.
FileSourceLocator	getSourceLocator()	The locator of a position in a file.
Stoichiometry	getStoichiometry()	The stoichiometry for this participant.
ExtendedPsiXmlParticipantEvidence	getWrappedParticipant()	getWrappedParticipant.
Collection<Xref>	getXrefs()	Collection of cross references which give more information about the participant.
protected void	initialiseFeatures()	initialiseFeatures.
boolean	removeAllFeatures(Collection<? extends ModelledFeature> features)	This method will remove all the features and set the entity of the removed features to null.
boolean	removeFeature(ModelledFeature feature)	This method will remove the feature and set the entity of the removed feature to null.
void	setBiologicalEffect(CvTerm biologicalEffect)	Sets the biological effect of the participant in a causal interaction.
void	setBiologicalRole(CvTerm bioRole)	Sets the biological role.
void	setChangeListener(EntityInteractorChangeListener listener)	Sets the entity change listener
void	setFullName(String name)	Sets the full name of the entity
void	setId(int id)	setId.
void	setInteraction(ModelledInteraction interaction)	Sets the interaction.
void	setInteractionAndAddParticipant(ModelledInteraction interaction)	Sets the Interaction and add the new Participant to its list of Participants.
void	setInteractor(Interactor interactor)	Sets the interactor
void	setShortName(String name)	Sets the short name of an entity
void	setSourceLocator(FileSourceLocator locator)	Sets the source locator
void	setStoichiometry(Integer stoichiometry)	Sets the mean stoichiometry for this participant.
void	setStoichiometry(Stoichiometry stoichiometry)	Sets the stoichiometry for this participant.
String	toString()	toString

Methods inherited from class java.lang.Object

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

Constructor Detail

XmlParticipantEvidenceWrapper

public XmlParticipantEvidenceWrapper(ExtendedPsiXmlParticipantEvidence part,
                                     XmlInteractionEvidenceComplexWrapper wrapper)

Constructor for XmlParticipantEvidenceWrapper.

Parameters:

part - a ExtendedPsiXmlParticipantEvidence object.

wrapper - a XmlInteractionEvidenceComplexWrapper object.

Method Detail

getAliases

public Collection<Alias> getAliases()

Collection of aliases which give more information about the participant. The set of aliases cannot be null. If the participant does not have any aliases, the method should return an empty Collection. Ex: author assigned name, ...

Specified by:

getAliases in interface Participant<ModelledInteraction,ModelledFeature>

Returns:

the xrefs

getXrefs

public Collection<Xref> getXrefs()

Collection of cross references which give more information about the participant. The set of xrefs cannot be null. If the participant does not have any xrefs, the method should return an empty Collection. Ex: author identifiers, ...

Specified by:

getXrefs in interface Participant<ModelledInteraction,ModelledFeature>

Returns:

the xrefs

getInteractor

public Interactor getInteractor()

The molecule/complex of molecules which interacts. It cannot be null.

Specified by:

getInteractor in interface Entity<ModelledFeature>

Returns:

the interactor

setInteractor

public void setInteractor(Interactor interactor)

Sets the interactor

Specified by:

setInteractor in interface Entity<ModelledFeature>

Parameters:

interactor - : interactor

getCausalRelationships

public Collection<CausalRelationship> getCausalRelationships()

The causal relationships of this entity on other entities usually part of an interaction. The set of causal relationship cannot be null. If the entity does not have any causal relationship, the method should return an empty Collection. Ex: increasing, decreasing, disrupting, etc.

Specified by:

getCausalRelationships in interface Entity<ModelledFeature>

Returns:

the collection of causal relationships attached to this entity

getAnnotations

public Collection<Annotation> getAnnotations()

Collection of annotations describing the participant. The set cannot be null. If the participant does not have any annotations, the method should return an empty Collection.

Specified by:

getAnnotations in interface Participant<ModelledInteraction,ModelledFeature>

Returns:

the annotations

getStoichiometry

public Stoichiometry getStoichiometry()

The stoichiometry for this participant. If the stoichiometry for this participant is unknown, the method should return null.

Specified by:

getStoichiometry in interface Entity<ModelledFeature>

Returns:

the stoichiometry

setStoichiometry

public void setStoichiometry(Integer stoichiometry)

Sets the mean stoichiometry for this participant.

Specified by:

setStoichiometry in interface Entity<ModelledFeature>

Parameters:

stoichiometry - : mean stoichiometry value

setStoichiometry

public void setStoichiometry(Stoichiometry stoichiometry)

Sets the stoichiometry for this participant.

Specified by:

setStoichiometry in interface Entity<ModelledFeature>

Parameters:

stoichiometry - : the stoichiometry

getFeatures

public Collection<ModelledFeature> getFeatures()

Properties for this entity. The collection cannot be null. If the entity does not have any features, the method should return an empty collection.

Specified by:

getFeatures in interface Entity<ModelledFeature>

Returns:

the features

setChangeListener

public void setChangeListener(EntityInteractorChangeListener listener)

Sets the entity change listener

Specified by:

setChangeListener in interface Entity<ModelledFeature>

Parameters:

listener - : the entity change listener

addFeature

public boolean addFeature(ModelledFeature feature)

This method will add the feature and set the entity of the new feature to this current entity

Specified by:

addFeature in interface Entity<ModelledFeature>

Parameters:

feature - : feature to add

Returns:

true if feature is added to the list of features

removeFeature

public boolean removeFeature(ModelledFeature feature)

This method will remove the feature and set the entity of the removed feature to null.

Specified by:

removeFeature in interface Entity<ModelledFeature>

Parameters:

feature - : feature to remove

Returns:

true if feature is removed from the list of features

addAllFeatures

public boolean addAllFeatures(Collection<? extends ModelledFeature> features)

This method will add all features and set the entity of the new features to this current entity

Specified by:

addAllFeatures in interface Entity<ModelledFeature>

Parameters:

features - : features to add

Returns:

true if features are added to the list of features

removeAllFeatures

public boolean removeAllFeatures(Collection<? extends ModelledFeature> features)

This method will remove all the features and set the entity of the removed features to null.

Specified by:

removeAllFeatures in interface Entity<ModelledFeature>

Parameters:

features - : features to remove

Returns:

true if features are removed from the list of features

getChangeListener

public EntityInteractorChangeListener getChangeListener()

The entity change listener if set, null otherwise. The entity change listener listen to changes in entity (interactor changes)

Specified by:

getChangeListener in interface Entity<ModelledFeature>

Returns:

the participant change listener

getBiologicalRole

public CvTerm getBiologicalRole()

The biological role of the participant. It is a controlled vocabulary term and cannot be null. It the biological role of a participant is not known or not relevant, the method should return unspecified role (MI:0499) Ex: enzyme, enzyme target, ...

Specified by:

getBiologicalRole in interface Participant<ModelledInteraction,ModelledFeature>

Returns:

the biological role

setBiologicalRole

public void setBiologicalRole(CvTerm bioRole)

Sets the biological role. If the bioRole is null, should create a bioRole

Specified by:

setBiologicalRole in interface Participant<ModelledInteraction,ModelledFeature>

Parameters:

bioRole - : biological role unspecified role (MI:0499)

getBiologicalEffect

public CvTerm getBiologicalEffect()

The biological effect of the participant in a causal interaction. It is a controlled vocabulary term and can be null.

Specified by:

getBiologicalEffect in interface Participant<ModelledInteraction,ModelledFeature>

Returns:

the biological effect

setBiologicalEffect

public void setBiologicalEffect(CvTerm biologicalEffect)

Sets the biological effect of the participant in a causal interaction.

Specified by:

setBiologicalEffect in interface Participant<ModelledInteraction,ModelledFeature>

Parameters:

biologicalEffect - : biological effect

toString

public String toString()

toString

Specified by:

toString in interface FileSourceContext

Overrides:

toString in class Object

Returns:

the file source context as a String. If the source locator is not null, it should give the source locator properties

setInteractionAndAddParticipant

public void setInteractionAndAddParticipant(ModelledInteraction interaction)

Sets the Interaction and add the new Participant to its list of Participants. If the given interaction is null, it will remove the Participant from the previous interaction it was attached to

Specified by:

setInteractionAndAddParticipant in interface Participant<ModelledInteraction,ModelledFeature>

Parameters:

interaction - : interaction

getInteraction

public ModelledInteraction getInteraction()

The interaction in which the participant is involved. It can be null if the participant is not attached to any interactions. It can happen if the participant has been removed from an interaction and is now invalid.

Specified by:

getInteraction in interface Participant<ModelledInteraction,ModelledFeature>

Returns:

the interaction

setInteraction

public void setInteraction(ModelledInteraction interaction)

Sets the interaction.

Specified by:

setInteraction in interface Participant<ModelledInteraction,ModelledFeature>

Parameters:

interaction - : interaction

getWrappedParticipant

public ExtendedPsiXmlParticipantEvidence getWrappedParticipant()

getWrappedParticipant.

Returns:

a ExtendedPsiXmlParticipantEvidence object.

getSourceLocator

public FileSourceLocator getSourceLocator()

The locator of a position in a file. It can be null

Specified by:

getSourceLocator in interface FileSourceContext

Returns:

the file locator

setSourceLocator

public void setSourceLocator(FileSourceLocator locator)

Sets the source locator

Specified by:

setSourceLocator in interface FileSourceContext

Parameters:

locator - : the file locator

getId

public int getId()

getId.

Specified by:

getId in interface ExtendedPsiXmlEntity<ModelledFeature>

Returns:

a int.

setId

public void setId(int id)

setId.

Specified by:

setId in interface ExtendedPsiXmlEntity<ModelledFeature>

Parameters:

id - a int.

getShortName

public String getShortName()

The short name of the entity. It can be null or empty.

Specified by:

getShortName in interface NamedParticipant<ModelledInteraction,ModelledFeature>

Returns:

the short name

setShortName

public void setShortName(String name)

Sets the short name of an entity

Specified by:

setShortName in interface NamedParticipant<ModelledInteraction,ModelledFeature>

Parameters:

name - : short name

getFullName

public String getFullName()

The full name of the entity. It can be null

Specified by:

getFullName in interface NamedParticipant<ModelledInteraction,ModelledFeature>

Returns:

the full name

setFullName

public void setFullName(String name)

Sets the full name of the entity

Specified by:

setFullName in interface NamedParticipant<ModelledInteraction,ModelledFeature>

Parameters:

name - : full name

initialiseFeatures

protected void initialiseFeatures()

initialiseFeatures.