Package psidev.psi.mi.jami.xml.model.extension.binary.xml30

Class XmlModelledBinaryInteraction

java.lang.Object

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

psidev.psi.mi.jami.binary.impl.AbstractBinaryInteraction<P>

psidev.psi.mi.jami.xml.model.extension.binary.AbstractXmlBinaryInteraction<ModelledParticipant>

psidev.psi.mi.jami.xml.model.extension.binary.xml30.XmlModelledBinaryInteraction

All Implemented Interfaces:

BinaryInteraction<ModelledParticipant>, ModelledBinaryInteraction, FileSourceContext, Complex, Interaction<ModelledParticipant>, Interactor, ModelledInteraction, NamedInteraction<ModelledParticipant>, PsiXmlInteraction<ModelledParticipant>, ExtendedPsiXmlModelledInteraction

public class XmlModelledBinaryInteraction
extends AbstractXmlBinaryInteraction<ModelledParticipant>
implements ModelledBinaryInteraction, ExtendedPsiXmlModelledInteraction

Xml implementation of ModelledInteraction

Since:

16/10/13

Version:

$Id$

Author:

Marine Dumousseau (marine@ebi.ac.uk)

Field Summary

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
XmlModelledBinaryInteraction()	Constructor for XmlModelledBinaryInteraction.
XmlModelledBinaryInteraction(String shortName)	Constructor for XmlModelledBinaryInteraction.
XmlModelledBinaryInteraction(String shortName, CvTerm type)	Constructor for XmlModelledBinaryInteraction.
XmlModelledBinaryInteraction(String shortName, CvTerm type, CvTerm complexExpansion)	Constructor for XmlModelledBinaryInteraction.
XmlModelledBinaryInteraction(String shortName, CvTerm type, ModelledParticipant participantA, ModelledParticipant participantB)	Constructor for XmlModelledBinaryInteraction.
XmlModelledBinaryInteraction(String shortName, CvTerm type, ModelledParticipant participantA, ModelledParticipant participantB, CvTerm complexExpansion)	Constructor for XmlModelledBinaryInteraction.
XmlModelledBinaryInteraction(String shortName, ModelledParticipant participantA, ModelledParticipant participantB)	Constructor for XmlModelledBinaryInteraction.
XmlModelledBinaryInteraction(String shortName, ModelledParticipant participantA, ModelledParticipant participantB, CvTerm complexExpansion)	Constructor for XmlModelledBinaryInteraction.
XmlModelledBinaryInteraction(CvTerm complexExpansion)	Constructor for XmlModelledBinaryInteraction.
XmlModelledBinaryInteraction(ModelledParticipant participantA, ModelledParticipant participantB)	Constructor for XmlModelledBinaryInteraction.
XmlModelledBinaryInteraction(ModelledParticipant participantA, ModelledParticipant participantB, CvTerm complexExpansion)	Constructor for XmlModelledBinaryInteraction.

Method Summary

Modifier and Type	Method	Description
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()	Getter for the field annotations.
List<BindingFeatures>	getBindingFeatures()	getBindingFeatures.
List<ExtendedPsiXmlCausalRelationship>	getCausalRelationships()	getCausalRelationships.
Collection<Checksum>	getChecksums()	Getter for the field checksums.
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()	Getter for the field cooperativeEffects.
CvTerm	getEvidenceType()	Getter for the field evidenceType.
Collection<Xref>	getIdentifiers()	Getter for the field identifiers.
Collection<InteractionEvidence>	getInteractionEvidences()	Getter for the field interactionEvidences.
CvTerm	getInteractorType()	The molecule type of this interactor.
Collection<ModelledConfidence>	getModelledConfidences()	Getter for the field modelledConfidences.
Collection<ModelledParameter>	getModelledParameters()	Getter for the field modelledParameters.
Organism	getOrganism()	The original source organism for this interactor.
String	getPhysicalProperties()	The physical properties for this complex.
Xref	getPreferredIdentifier()	The identifier in the list of identifiers which is the preferred identifier.
String	getPreferredName()	The preferred name is the name by which we want to refer the interactor on our web site.
String	getRecommendedName()	The recommended name of a complex.
Source	getSource()	Getter for the field source.
String	getSystematicName()	The systematic name of a complex.
Collection<Xref>	getXrefs()	Getter for the field xrefs.
protected void	initialiseCooperativeEffects()	initialiseCooperativeEffects.
protected void	initialiseInteractionEvidences()	initialiseInteractionEvidences.
protected void	initialiseModelledConfidences()	initialiseModelledConfidences.
protected void	initialiseModelledParameters()	initialiseModelledParameters.
void	setEvidenceType(CvTerm evidenceType)	Sets the evidence type
void	setInteractorType(CvTerm type)	Sets the molecule type for this interactor If the given type is null, this method automatically sets the interactor type to 'unknown participant' (MI:0329)
void	setOrganism(Organism organism)	Sets the source organism of this interactor
void	setPhysicalProperties(String properties)	Sets the physical properties of this complex.
void	setRecommendedName(String name)	Sets the recommended name of this complex.
void	setSource(Source source)	Sets the source reporting the interaction.
void	setSystematicName(String name)	Sets the systematic name of this complex.

Methods inherited from class psidev.psi.mi.jami.xml.model.extension.binary.AbstractXmlBinaryInteraction

getEntry, getFullName, getId, getSourceLocator, isIntraMolecular, setEntry, setFullName, setId, setIntraMolecular, setSourceLocator, toString

Methods inherited from class psidev.psi.mi.jami.binary.impl.AbstractBinaryInteraction

addAllParticipants, addParticipant, getCausalRegulatoryMechanism, getComplexExpansion, getParticipantA, getParticipantB, getParticipants, removeAllParticipants, removeParticipant, setCausalRegulatoryMechanism, setComplexExpansion, setParticipantA, setParticipantB

Methods inherited from class psidev.psi.mi.jami.model.impl.AbstractInteraction

clearPropertiesLinkedToChecksums, getCreatedDate, getInteractionType, getRigid, getShortName, getUpdatedDate, initialiseAnnotations, initialiseAnnotationsWith, initialiseChecksums, initialiseChecksumWith, initialiseIdentifiers, initialiseIdentifiersWith, initialiseParticipants, initialiseParticipantsWith, initialiseXrefs, initialiseXrefsWith, processAddedChecksumEvent, processRemovedChecksumEvent, setCreatedDate, setInteractionType, setRigid, setShortName, setUpdatedDate

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.binary.BinaryInteraction

getCausalRegulatoryMechanism, getComplexExpansion, getParticipantA, getParticipantB, setCausalRegulatoryMechanism, setComplexExpansion, setParticipantA, setParticipantB

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

getComparableParticipants

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

getSourceLocator, setSourceLocator, toString

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

addAllParticipants, addParticipant, getCreatedDate, getInteractionType, getParticipants, getRigid, getShortName, getUpdatedDate, removeAllParticipants, removeParticipant, setCreatedDate, setInteractionType, setRigid, setShortName, setUpdatedDate

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

getFullName, getShortName, setFullName, 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

getEntry, getId, isIntraMolecular, setEntry, setId, setIntraMolecular

Constructor Detail

XmlModelledBinaryInteraction

public XmlModelledBinaryInteraction()

Constructor for XmlModelledBinaryInteraction.

XmlModelledBinaryInteraction

public XmlModelledBinaryInteraction(String shortName,
                                    CvTerm type)

Constructor for XmlModelledBinaryInteraction.

Parameters:

shortName - a String object.

type - a CvTerm object.

XmlModelledBinaryInteraction

public XmlModelledBinaryInteraction(String shortName)

Constructor for XmlModelledBinaryInteraction.

Parameters:

shortName - a String object.

XmlModelledBinaryInteraction

public XmlModelledBinaryInteraction(ModelledParticipant participantA,
                                    ModelledParticipant participantB)

Constructor for XmlModelledBinaryInteraction.

Parameters:

participantA - a ModelledParticipant object.

participantB - a ModelledParticipant object.

XmlModelledBinaryInteraction

public XmlModelledBinaryInteraction(String shortName,
                                    ModelledParticipant participantA,
                                    ModelledParticipant participantB)

Constructor for XmlModelledBinaryInteraction.

Parameters:

shortName - a String object.

participantA - a ModelledParticipant object.

participantB - a ModelledParticipant object.

XmlModelledBinaryInteraction

public XmlModelledBinaryInteraction(String shortName,
                                    CvTerm type,
                                    ModelledParticipant participantA,
                                    ModelledParticipant participantB)

Constructor for XmlModelledBinaryInteraction.

Parameters:

shortName - a String object.

type - a CvTerm object.

participantA - a ModelledParticipant object.

participantB - a ModelledParticipant object.

XmlModelledBinaryInteraction

public XmlModelledBinaryInteraction(CvTerm complexExpansion)

Constructor for XmlModelledBinaryInteraction.

Parameters:

complexExpansion - a CvTerm object.

XmlModelledBinaryInteraction

public XmlModelledBinaryInteraction(String shortName,
                                    CvTerm type,
                                    CvTerm complexExpansion)

Constructor for XmlModelledBinaryInteraction.

Parameters:

shortName - a String object.

type - a CvTerm object.

complexExpansion - a CvTerm object.

XmlModelledBinaryInteraction

public XmlModelledBinaryInteraction(ModelledParticipant participantA,
                                    ModelledParticipant participantB,
                                    CvTerm complexExpansion)

Constructor for XmlModelledBinaryInteraction.

Parameters:

participantA - a ModelledParticipant object.

participantB - a ModelledParticipant object.

complexExpansion - a CvTerm object.

XmlModelledBinaryInteraction

public XmlModelledBinaryInteraction(String shortName,
                                    ModelledParticipant participantA,
                                    ModelledParticipant participantB,
                                    CvTerm complexExpansion)

Constructor for XmlModelledBinaryInteraction.

Parameters:

shortName - a String object.

participantA - a ModelledParticipant object.

participantB - a ModelledParticipant object.

complexExpansion - a CvTerm object.

XmlModelledBinaryInteraction

public XmlModelledBinaryInteraction(String shortName,
                                    CvTerm type,
                                    ModelledParticipant participantA,
                                    ModelledParticipant participantB,
                                    CvTerm complexExpansion)

Constructor for XmlModelledBinaryInteraction.

Parameters:

shortName - a String object.

type - a CvTerm object.

participantA - a ModelledParticipant object.

participantB - a ModelledParticipant object.

complexExpansion - a CvTerm object.

Method Detail

initialiseInteractionEvidences

protected void initialiseInteractionEvidences()

initialiseInteractionEvidences.

initialiseCooperativeEffects

protected void initialiseCooperativeEffects()

initialiseCooperativeEffects.

initialiseModelledConfidences

protected void initialiseModelledConfidences()

initialiseModelledConfidences.

initialiseModelledParameters

protected void initialiseModelledParameters()

initialiseModelledParameters.

getInteractionEvidences

public Collection<InteractionEvidence> getInteractionEvidences()

Getter for the field interactionEvidences.

Specified by:

getInteractionEvidences in interface ModelledInteraction

Returns:

a Collection object.

getSource

public Source getSource()

Getter for the field source.

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()

Getter for the field modelledConfidences.

Specified by:

getModelledConfidences in interface ModelledInteraction

Returns:

a Collection object.

getModelledParameters

public Collection<ModelledParameter> getModelledParameters()

Getter for the field modelledParameters.

Specified by:

getModelledParameters in interface ModelledInteraction

Returns:

a Collection object.

getCooperativeEffects

public Collection<CooperativeEffect> getCooperativeEffects()

Getter for the field cooperativeEffects.

Specified by:

getCooperativeEffects in interface ModelledInteraction

Returns:

a Collection object.

getEvidenceType

public CvTerm getEvidenceType()

Getter for the field evidenceType.

Specified by:

getEvidenceType in interface ModelledInteraction

Returns:

a CvTerm object.

setEvidenceType

public void setEvidenceType(CvTerm evidenceType)

Sets the evidence type

Specified by:

setEvidenceType in interface ModelledInteraction

Parameters:

evidenceType - : the evidence type

getBindingFeatures

public List<BindingFeatures> getBindingFeatures()

getBindingFeatures.

Specified by:

getBindingFeatures in interface ExtendedPsiXmlModelledInteraction

Returns:

a List object.

getCausalRelationships

public List<ExtendedPsiXmlCausalRelationship> getCausalRelationships()

getCausalRelationships.

Specified by:

getCausalRelationships in interface ExtendedPsiXmlModelledInteraction

Returns:

a List object.

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()

Description copied from interface: Complex

The physical properties for this complex. It is a shortcut which should point to the first complex-properties annotation in the collection of annotations. Example: Molecular mass = 154 kDa

Specified by:

getPhysicalProperties in interface Complex

Returns:

the properties

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

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

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

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

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

getPreferredIdentifier

public Xref getPreferredIdentifier()

The identifier in the list of identifiers which is the preferred identifier. If no identifiers is preferred, it should return the first identifier of the list of identifiers, null if the list of identifiers is empty.

Specified by:

getPreferredIdentifier in interface Interactor

Returns:

the preferred identifier in the list of identifiers, null if the list of identifiers is empty

getPreferredName

public String getPreferredName()

The preferred name is the name by which we want to refer the interactor on our web site.

Specified by:

getPreferredName in interface Interactor

Returns:

the preferred name

getOrganism

public Organism getOrganism()

The original source organism for this interactor. It can be null in case of chemical compounds/synthetic peptides

Specified by:

getOrganism in interface Interactor

Returns:

the organism

setOrganism

public void setOrganism(Organism organism)

Sets the source organism of this interactor

Specified by:

setOrganism in interface Interactor

Parameters:

organism - : source organism

getInteractorType

public CvTerm getInteractorType()

The molecule type of this interactor. It is a controlled vocabulary term and cannot be null. Ex: protein, gene, small molecule, ...

Specified by:

getInteractorType in interface Interactor

Returns:

interactor type

setInteractorType

public void setInteractorType(CvTerm type)

Sets the molecule type for this interactor If the given type is null, this method automatically sets the interactor type to 'unknown participant' (MI:0329)

Specified by:

setInteractorType in interface Interactor

Parameters:

type - : molecule type

getAliases

public Collection<Alias> getAliases()

getAliases.

Specified by:

getAliases in interface ExtendedPsiXmlModelledInteraction

Specified by:

getAliases in interface Interactor

Specified by:

getAliases in interface NamedInteraction<ModelledParticipant>

Specified by:

getAliases in interface PsiXmlInteraction<ModelledParticipant>

Overrides:

getAliases in class AbstractXmlBinaryInteraction<ModelledParticipant>

Returns:

a Collection object.

getXrefs

public Collection<Xref> getXrefs()

Getter for the field xrefs.

Specified by:

getXrefs in interface Interaction<ModelledParticipant>

Specified by:

getXrefs in interface Interactor

Overrides:

getXrefs in class AbstractInteraction<ModelledParticipant>

Returns:

a Collection object.

getIdentifiers

public Collection<Xref> getIdentifiers()

Getter for the field identifiers.

Specified by:

getIdentifiers in interface Interaction<ModelledParticipant>

Specified by:

getIdentifiers in interface Interactor

Overrides:

getIdentifiers in class AbstractInteraction<ModelledParticipant>

Returns:

a Collection object.

getAnnotations

public Collection<Annotation> getAnnotations()

Getter for the field annotations.

Specified by:

getAnnotations in interface Interaction<ModelledParticipant>

Specified by:

getAnnotations in interface Interactor

Overrides:

getAnnotations in class AbstractInteraction<ModelledParticipant>

Returns:

a Collection object.

getChecksums

public Collection<Checksum> getChecksums()

Getter for the field checksums.

Specified by:

getChecksums in interface Interaction<ModelledParticipant>

Specified by:

getChecksums in interface Interactor

Overrides:

getChecksums in class AbstractInteraction<ModelledParticipant>

Returns:

a Collection object.