Package psidev.psi.mi.jami.xml.model.reference.xml300

Class AbstractComplexRef

java.lang.Object

psidev.psi.mi.jami.xml.model.reference.AbstractXmlIdReference

psidev.psi.mi.jami.xml.model.reference.xml300.AbstractInteractorRef

psidev.psi.mi.jami.xml.model.reference.xml300.AbstractComplexRef

All Implemented Interfaces:

FileSourceContext, Complex, Interaction<ModelledParticipant>, Interactor, ModelledInteraction, NamedInteraction<ModelledParticipant>, ExtendedPsiXmlInteraction<ModelledParticipant>, ExtendedPsiXmlInteractor, PsiXmlInteraction<ModelledParticipant>, XmlIdReference

public abstract class AbstractComplexRef
extends AbstractInteractorRef
implements Complex, ExtendedPsiXmlInteraction<ModelledParticipant>

Abstract class for references to a complex

Since:

11/10/13

Version:

$Id$

Author:

Marine Dumousseau (marine@ebi.ac.uk)

Field Summary

Fields inherited from class psidev.psi.mi.jami.xml.model.reference.AbstractXmlIdReference

ref

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

COMPLEX, COMPLEX_MI

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

UNKNOWN_INTERACTOR, UNKNOWN_INTERACTOR_MI

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

ECO, ECO_MI

Constructor Summary

Constructors

Constructor	Description
AbstractComplexRef(int ref)	Constructor for AbstractComplexRef.

Method Summary

Modifier and Type	Method	Description
boolean	addAllParticipants(Collection<? extends ModelledParticipant> participants)	This method will add all the participant and set the interaction of the new participant to this current interaction
boolean	addParticipant(ModelledParticipant part)	addParticipant.
void	assignComplexAc(String accession)	Assign a complex accession to a complex.
void	assignComplexAc(String accession, String version)	Assign a complex accession to a complex.
Collection<Alias>	getAliases()	getAliases.
Collection<Annotation>	getAnnotations()	getAnnotations.
Collection<Checksum>	getChecksums()	getChecksums.
String	getComplexAc()	Complex accession if the complex has been curated under the Complex Portal curation rules.
String	getComplexVersion()	Complex version if the complex has been curated under the Complex Portal curation rules.
Collection<CooperativeEffect>	getCooperativeEffects()	getCooperativeEffects.
Date	getCreatedDate()	getCreatedDate.
protected DefaultXmlComplex	getDelegate()	Getter for the field delegate.
Entry	getEntry()	getEntry.
CvTerm	getEvidenceType()	The evidence type for this modelled interactions.
Collection<Xref>	getIdentifiers()	getIdentifiers.
List<AbstractInferredInteraction>	getInferredInteractions()	getInferredInteractions.
Collection<InteractionEvidence>	getInteractionEvidences()	getInteractionEvidences.
CvTerm	getInteractionType()	getInteractionType.
List<CvTerm>	getInteractionTypes()	getInteractionTypes.
Collection<ModelledConfidence>	getModelledConfidences()	getModelledConfidences.
Collection<ModelledParameter>	getModelledParameters()	getModelledParameters.
Collection<ModelledParticipant>	getParticipants()	getParticipants.
String	getPhysicalProperties()	getPhysicalProperties.
String	getRecommendedName()	The recommended name of a complex.
String	getRigid()	getRigid.
Source	getSource()	getSource.
String	getSystematicName()	The systematic name of a complex.
Date	getUpdatedDate()	getUpdatedDate.
Collection<Xref>	getXrefs()	getXrefs.
protected void	initialiseInteractorDelegate()	initialiseInteractorDelegate.
boolean	isIntraMolecular()	isIntraMolecular.
boolean	removeAllParticipants(Collection<? extends ModelledParticipant> participants)	This method will remove the participant and set the interaction of the removed participant to null.
boolean	removeParticipant(ModelledParticipant part)	removeParticipant.
void	setCreatedDate(Date created)	Sets the created date
void	setEntry(Entry entry)	setEntry.
void	setEvidenceType(CvTerm eco)	Sets the evidence type
void	setInteractionType(CvTerm term)	Sets the interaction type.
void	setIntraMolecular(boolean intra)	setIntraMolecular.
void	setPhysicalProperties(String properties)	Sets the physical properties of this complex.
void	setRecommendedName(String name)	Sets the recommended name of this complex.
void	setRigid(String rigid)	Sets the rigid of this interaction.
void	setSource(Source source)	Sets the source reporting the interaction.
void	setSystematicName(String name)	Sets the systematic name of this complex.
void	setUpdatedDate(Date updated)	Sets the last update date
String	toString()	toString

Methods inherited from class psidev.psi.mi.jami.xml.model.reference.xml300.AbstractInteractorRef

getFullName, getId, getInteractorType, getOrganism, getPreferredIdentifier, getPreferredName, getShortName, setDelegate, setFullName, setId, setInteractorType, setOrganism, setShortName

Methods inherited from class psidev.psi.mi.jami.xml.model.reference.AbstractXmlIdReference

getRef, registerForResolution

Methods inherited from class java.lang.Object

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

Methods inherited from interface psidev.psi.mi.jami.model.Complex

getComparableParticipants

Methods inherited from interface psidev.psi.mi.jami.datasource.FileSourceContext

getSourceLocator, setSourceLocator

Methods inherited from interface psidev.psi.mi.jami.model.Interaction

getShortName, setShortName

Methods inherited from interface psidev.psi.mi.jami.model.Interactor

getFullName, getInteractorType, getOrganism, getPreferredIdentifier, getPreferredName, getShortName, setFullName, setInteractorType, setOrganism, setShortName

Methods inherited from interface psidev.psi.mi.jami.model.NamedInteraction

getFullName, setFullName

Methods inherited from interface psidev.psi.mi.jami.xml.model.extension.PsiXmlInteraction

getId, setId

Methods inherited from interface psidev.psi.mi.jami.xml.model.reference.XmlIdReference

resolve

Constructor Detail

AbstractComplexRef

public AbstractComplexRef(int ref)

Constructor for AbstractComplexRef.

Parameters:

ref - a int.

Method Detail

getEvidenceType

public CvTerm getEvidenceType()

The evidence type for this modelled interactions. Usually this Cv term is ECO (evidence code ontology) code. It can be null. Ex: ECO:0000021, physical interaction evidence

Specified by:

getEvidenceType in interface ModelledInteraction

Returns:

the evidence type

setEvidenceType

public void setEvidenceType(CvTerm eco)

Description copied from interface: ModelledInteraction

Sets the evidence type

Specified by:

setEvidenceType in interface ModelledInteraction

Parameters:

eco - : the evidence type

getComplexAc

public String getComplexAc()

Complex accession if the complex has been curated under the Complex Portal curation rules. It can be null if the complex is not registered in the Complex Portal. This complex accession should be a shortcut to the complex-primary Xref in the collection of xrefs. Ex: CPX-123

Specified by:

getComplexAc in interface Complex

Returns:

the complex accession

getComplexVersion

public String getComplexVersion()

Complex version if the complex has been curated under the Complex Portal curation rules. It can be null if the complex is not registered in the Complex Portal. This complex version should be a shortcut to the complex-primary Xref version in the collection of xrefs. Ex: 1

Specified by:

getComplexVersion in interface Complex

Returns:

the complex version

assignComplexAc

public void assignComplexAc(String accession,
                            String version)

Assign a complex accession to a complex. It will add the new complex-primary ref to the collection of xrefs

Specified by:

assignComplexAc in interface Complex

Parameters:

accession - : the complex accession

version - : the version of the complex if it is provided. If version is null it will create the complex with version 1

assignComplexAc

public void assignComplexAc(String accession)

Assign a complex accession to a complex. It will add the new complex-primary ref to the collection of xrefs

Specified by:

assignComplexAc in interface Complex

Parameters:

accession - : the complex accession. If the version is added to the accession e.g. CPX-1234.2 the complex will be updated with the corresponding version, if not it is assumed version 1

getPhysicalProperties

public String getPhysicalProperties()

getPhysicalProperties.

Specified by:

getPhysicalProperties in interface Complex

Returns:

a String object.

setPhysicalProperties

public void setPhysicalProperties(String properties)

Sets the physical properties of this complex. It will remove the old complex-properties annotation from the collection of annotations and replace it with the new complex-properties annotation. If the new complex-properties is null, all the existing complex-properties annotations will be removed from the collection of annotations

Specified by:

setPhysicalProperties in interface Complex

Parameters:

properties - : complex properties

getInteractionEvidences

public Collection<InteractionEvidence> getInteractionEvidences()

getInteractionEvidences.

Specified by:

getInteractionEvidences in interface ModelledInteraction

Returns:

a Collection object.

getSource

public Source getSource()

getSource.

Specified by:

getSource in interface ModelledInteraction

Returns:

a Source object.

setSource

public void setSource(Source source)

Sets the source reporting the interaction.

Specified by:

setSource in interface ModelledInteraction

Parameters:

source - : source for this interaction

getModelledConfidences

public Collection<ModelledConfidence> getModelledConfidences()

getModelledConfidences.

Specified by:

getModelledConfidences in interface ModelledInteraction

Returns:

a Collection object.

getModelledParameters

public Collection<ModelledParameter> getModelledParameters()

getModelledParameters.

Specified by:

getModelledParameters in interface ModelledInteraction

Returns:

a Collection object.

getCooperativeEffects

public Collection<CooperativeEffect> getCooperativeEffects()

getCooperativeEffects.

Specified by:

getCooperativeEffects in interface ModelledInteraction

Returns:

a Collection object.

getRigid

public String getRigid()

getRigid.

Specified by:

getRigid in interface Interaction<ModelledParticipant>

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<ModelledParticipant>

Parameters:

rigid - : the rigid

getUpdatedDate

public Date getUpdatedDate()

getUpdatedDate.

Specified by:

getUpdatedDate in interface Interaction<ModelledParticipant>

Returns:

a Date object.

setUpdatedDate

public void setUpdatedDate(Date updated)

Sets the last update date

Specified by:

setUpdatedDate in interface Interaction<ModelledParticipant>

Parameters:

updated - : last update date

getCreatedDate

public Date getCreatedDate()

getCreatedDate.

Specified by:

getCreatedDate in interface Interaction<ModelledParticipant>

Returns:

a Date object.

setCreatedDate

public void setCreatedDate(Date created)

Sets the created date

Specified by:

setCreatedDate in interface Interaction<ModelledParticipant>

Parameters:

created - : created date

getInteractionType

public CvTerm getInteractionType()

getInteractionType.

Specified by:

getInteractionType in interface Interaction<ModelledParticipant>

Returns:

a CvTerm object.

setInteractionType

public void setInteractionType(CvTerm term)

Sets the interaction type.

Specified by:

setInteractionType in interface Interaction<ModelledParticipant>

Parameters:

term - : interaction type

getParticipants

public Collection<ModelledParticipant> getParticipants()

getParticipants.

Specified by:

getParticipants in interface Interaction<ModelledParticipant>

Returns:

a Collection object.

addParticipant

public boolean addParticipant(ModelledParticipant part)

addParticipant.

Specified by:

addParticipant in interface Interaction<ModelledParticipant>

Parameters:

part - a ModelledParticipant object.

Returns:

a boolean.

removeParticipant

public boolean removeParticipant(ModelledParticipant part)

removeParticipant.

Specified by:

removeParticipant in interface Interaction<ModelledParticipant>

Parameters:

part - a ModelledParticipant object.

Returns:

a boolean.

addAllParticipants

public boolean addAllParticipants(Collection<? extends ModelledParticipant> 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<ModelledParticipant>

Parameters:

participants - : participants to add

Returns:

true if participant are added to the list of participants

removeAllParticipants

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

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

Specified by:

removeAllParticipants in interface Interaction<ModelledParticipant>

Parameters:

participants - : participants to remove

Returns:

true if participant are removed from the list of participants

getAnnotations

public Collection<Annotation> getAnnotations()

getAnnotations.

Specified by:

getAnnotations in interface Interaction<ModelledParticipant>

Specified by:

getAnnotations in interface Interactor

Overrides:

getAnnotations in class AbstractInteractorRef

Returns:

a Collection object.

getChecksums

public Collection<Checksum> getChecksums()

getChecksums.

Specified by:

getChecksums in interface Interaction<ModelledParticipant>

Specified by:

getChecksums in interface Interactor

Overrides:

getChecksums in class AbstractInteractorRef

Returns:

a Collection object.

getXrefs

public Collection<Xref> getXrefs()

getXrefs.

Specified by:

getXrefs in interface Interaction<ModelledParticipant>

Specified by:

getXrefs in interface Interactor

Overrides:

getXrefs in class AbstractInteractorRef

Returns:

a Collection object.

getAliases

public Collection<Alias> getAliases()

getAliases.

Specified by:

getAliases in interface ExtendedPsiXmlInteraction<ModelledParticipant>

Specified by:

getAliases in interface Interactor

Specified by:

getAliases in interface NamedInteraction<ModelledParticipant>

Specified by:

getAliases in interface PsiXmlInteraction<ModelledParticipant>

Overrides:

getAliases in class AbstractInteractorRef

Returns:

a Collection object.

getIdentifiers

public Collection<Xref> getIdentifiers()

getIdentifiers.

Specified by:

getIdentifiers in interface Interaction<ModelledParticipant>

Specified by:

getIdentifiers in interface Interactor

Overrides:

getIdentifiers in class AbstractInteractorRef

Returns:

a Collection object.

setIntraMolecular

public void setIntraMolecular(boolean intra)

setIntraMolecular.

Specified by:

setIntraMolecular in interface PsiXmlInteraction<ModelledParticipant>

Parameters:

intra - a boolean.

isIntraMolecular

public boolean isIntraMolecular()

isIntraMolecular.

Specified by:

isIntraMolecular in interface PsiXmlInteraction<ModelledParticipant>

Returns:

a boolean.

getInferredInteractions

public List<AbstractInferredInteraction> getInferredInteractions()

getInferredInteractions.

Specified by:

getInferredInteractions in interface ExtendedPsiXmlInteraction<ModelledParticipant>

Returns:

a List object.

setEntry

public void setEntry(Entry entry)

setEntry.

Specified by:

setEntry in interface PsiXmlInteraction<ModelledParticipant>

Parameters:

entry - a Entry object.

getEntry

public Entry getEntry()

getEntry.

Specified by:

getEntry in interface PsiXmlInteraction<ModelledParticipant>

Returns:

a Entry object.

getInteractionTypes

public List<CvTerm> getInteractionTypes()

getInteractionTypes.

Specified by:

getInteractionTypes in interface ExtendedPsiXmlInteraction<ModelledParticipant>

Returns:

a List object.

setSystematicName

public void setSystematicName(String name)

Sets the systematic name of this complex. It will remove the old systematic name from the collection of aliases and replace it with the new systematic name. If the new systematic name is null, all the existing systematic names will be removed from the collection of aliases

Specified by:

setSystematicName in interface Complex

Parameters:

name - : the systematic name

getSystematicName

public String getSystematicName()

The systematic name of a complex. It is a shortcut which should point to the first complex systematic name alias in the collection of aliases.

Specified by:

getSystematicName in interface Complex

Returns:

the systematic name

setRecommendedName

public void setRecommendedName(String name)

Sets the recommended name of this complex. It will remove the old recommended name from the collection of aliases and replace it with the new recommended name. If the new recommended name is null, all the existing recommended names will be removed from the collection of aliases

Specified by:

setRecommendedName in interface Complex

Parameters:

name - : the recommended name

getRecommendedName

public String getRecommendedName()

The recommended name of a complex. It is a shortcut which should point to the first complex recommended name alias in the collection of aliases.

Specified by:

getRecommendedName in interface Complex

Returns:

the recommended name

toString

public String toString()

toString

Specified by:

toString in interface FileSourceContext

Overrides:

toString in class AbstractInteractorRef

Returns:

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

initialiseInteractorDelegate

protected void initialiseInteractorDelegate()

initialiseInteractorDelegate.

Overrides:

initialiseInteractorDelegate in class AbstractInteractorRef

getDelegate

protected DefaultXmlComplex getDelegate()

Getter for the field delegate.

Overrides:

getDelegate in class AbstractInteractorRef

Returns:

a ExtendedPsiXmlInteractor object.