Package psidev.psi.mi.jami.xml.model.extension.xml253

Class XmlModelledInteractionComplexWrapper

java.lang.Object

psidev.psi.mi.jami.xml.model.extension.xml253.XmlModelledInteractionComplexWrapper

All Implemented Interfaces:

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

public class XmlModelledInteractionComplexWrapper
extends Object
implements Complex, FileSourceContext, ExtendedPsiXmlModelledInteraction

Wrapper for complexes that were loaded as abstract interactions

Since:

08/10/13

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
XmlModelledInteractionComplexWrapper(ExtendedPsiXmlModelledInteraction modelled)	Constructor for XmlModelledInteractionComplexWrapper.

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()	Collection of aliases for an interactor The Collection cannot be null and if the interactor does not have any aliases, the method should return an empty Collection.
Collection<Annotation>	getAnnotations()	Collection of annotations for an interactor.
Collection<Checksum>	getChecksums()	Set of checksums computed for this interactor.
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.
Entry	getEntry()	getEntry.
CvTerm	getEvidenceType()	The evidence type for this modelled interactions.
List<Experiment>	getExperiments()	getExperiments.
String	getFullName()	The full name of the interactor.
int	getId()	getId.
Collection<Xref>	getIdentifiers()	Set of identifiers for this interactor.
List<AbstractInferredInteraction>	getInferredInteractions()	getInferredInteractions.
Collection<InteractionEvidence>	getInteractionEvidences()	getInteractionEvidences.
CvTerm	getInteractionType()	getInteractionType.
List<CvTerm>	getInteractionTypes()	getInteractionTypes.
CvTerm	getInteractorType()	The molecule type of this interactor.
Collection<ModelledConfidence>	getModelledConfidences()	getModelledConfidences.
Collection<ModelledParameter>	getModelledParameters()	getModelledParameters.
Organism	getOrganism()	The original source organism for this interactor.
Collection<ModelledParticipant>	getParticipants()	getParticipants.
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.
String	getRigid()	The checksum computed from the rogids from all the proteins involved in the interaction.
String	getShortName()	The short name of the interactor.
Source	getSource()	getSource.
FileSourceLocator	getSourceLocator()	The locator of a position in a file.
String	getSystematicName()	The systematic name of a complex.
Date	getUpdatedDate()	getUpdatedDate.
Collection<Xref>	getXrefs()	Collection of other xrefs that give more information about the interactor.
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	setFullName(String name)	Sets the full name of the interactor
void	setId(int id)	setId.
void	setInteractionType(CvTerm term)	Sets the interaction 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	setIntraMolecular(boolean intra)	setIntraMolecular.
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	setRigid(String rigid)	Sets the rigid of this interaction.
void	setShortName(String name)	Sets the short name of an interactor
void	setSource(Source source)	Sets the source reporting the interaction.
void	setSourceLocator(FileSourceLocator locator)	Sets the source locator
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 java.lang.Object

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

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

getComparableParticipants

Constructor Detail

XmlModelledInteractionComplexWrapper

public XmlModelledInteractionComplexWrapper(ExtendedPsiXmlModelledInteraction modelled)

Constructor for XmlModelledInteractionComplexWrapper.

Parameters:

modelled - a ExtendedPsiXmlModelledInteraction object.

Method Detail

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

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

getParticipants

public Collection<ModelledParticipant> getParticipants()

getParticipants.

Specified by:

getParticipants in interface Interaction<ModelledParticipant>

Returns:

a Collection object.

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

isIntraMolecular

public boolean isIntraMolecular()

isIntraMolecular.

Specified by:

isIntraMolecular in interface PsiXmlInteraction<ModelledParticipant>

Returns:

a boolean.

setIntraMolecular

public void setIntraMolecular(boolean intra)

setIntraMolecular.

Specified by:

setIntraMolecular in interface PsiXmlInteraction<ModelledParticipant>

Parameters:

intra - a boolean.

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.

getAnnotations

public Collection<Annotation> getAnnotations()

Collection of annotations for an interactor. The set cannot be null and if the interactor does not have any annotations, the method should return an empty Collection. Ex: pharmacology, isoform-comment, etc.

Specified by:

getAnnotations in interface Interaction<ModelledParticipant>

Specified by:

getAnnotations in interface Interactor

Returns:

the annotations

getChecksums

public Collection<Checksum> getChecksums()

Set of checksums computed for this interactor. The Collection cannot be null so when an interactor does not have a checksum, the method should return an empty Collection Ex: rogid:u1FCes02jPb3CGRj1aDkzpbSiuI9606, standard Inchi key, ...

Specified by:

getChecksums in interface Interaction<ModelledParticipant>

Specified by:

getChecksums in interface Interactor

Returns:

the set of checksums

getXrefs

public Collection<Xref> getXrefs()

Collection of other xrefs that give more information about the interactor. Ex: GO references to gives function/process/location information

Specified by:

getXrefs in interface Interaction<ModelledParticipant>

Specified by:

getXrefs in interface Interactor

Returns:

other xrefs

getIdentifiers

public Collection<Xref> getIdentifiers()

Set of identifiers for this interactor. The identifiers can be from different databases, can be primary identifiers and secondary identifiers but they must be unambiguous. The Collection cannot be null, when an interactor does not have any identifiers, the method should return an empty Collection. Ex: uniprotkb secondary accession O00183, primary accessions, ...

Specified by:

getIdentifiers in interface Interaction<ModelledParticipant>

Specified by:

getIdentifiers in interface Interactor

Returns:

the alternative identifier

getShortName

public String getShortName()

The short name of the interactor. It cannot be null or empty. Ex: brca2

Specified by:

getShortName in interface Interaction<ModelledParticipant>

Specified by:

getShortName in interface Interactor

Returns:

the short name

setShortName

public void setShortName(String name)

Sets the short name of an interactor

Specified by:

setShortName in interface Interaction<ModelledParticipant>

Specified by:

setShortName in interface Interactor

Parameters:

name - : short name

getFullName

public String getFullName()

The full name of the interactor. It can be null Ex: Breast cancer type 2 susceptibility protein

Specified by:

getFullName in interface Interactor

Specified by:

getFullName in interface NamedInteraction<ModelledParticipant>

Returns:

the full name

setFullName

public void setFullName(String name)

Sets the full name of the interactor

Specified by:

setFullName in interface Interactor

Specified by:

setFullName in interface NamedInteraction<ModelledParticipant>

Parameters:

name - : full 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

getRigid

public String getRigid()

The checksum computed from the rogids from all the proteins involved in the interaction. It is only relevant for protein-protein interactions. This is a shortcut to the first rigid in the list of checksums

Specified by:

getRigid in interface Interaction<ModelledParticipant>

Returns:

the rigid

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

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

getAliases

public Collection<Alias> getAliases()

Collection of aliases for an interactor The Collection cannot be null and if the interactor does not have any aliases, the method should return an empty Collection. Ex: complex-synonym, author-assigned name, ...

Specified by:

getAliases in interface ExtendedPsiXmlInteraction<ModelledParticipant>

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>

Returns:

the aliases

getInteractionTypes

public List<CvTerm> getInteractionTypes()

getInteractionTypes.

Specified by:

getInteractionTypes in interface ExtendedPsiXmlInteraction<ModelledParticipant>

Returns:

a List object.

getEntry

public Entry getEntry()

getEntry.

Specified by:

getEntry in interface PsiXmlInteraction<ModelledParticipant>

Returns:

a Entry object.

setEntry

public void setEntry(Entry entry)

setEntry.

Specified by:

setEntry in interface PsiXmlInteraction<ModelledParticipant>

Parameters:

entry - a Entry object.

getInferredInteractions

public List<AbstractInferredInteraction> getInferredInteractions()

getInferredInteractions.

Specified by:

getInferredInteractions in interface ExtendedPsiXmlInteraction<ModelledParticipant>

Returns:

a List object.

getId

public int getId()

getId.

Specified by:

getId in interface PsiXmlInteraction<ModelledParticipant>

Returns:

a int.

setId

public void setId(int id)

setId.

Specified by:

setId in interface PsiXmlInteraction<ModelledParticipant>

Parameters:

id - a int.

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

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

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)

Sets the evidence type

Specified by:

setEvidenceType in interface ModelledInteraction

Parameters:

eco - : the evidence type

getExperiments

public List<Experiment> getExperiments()

getExperiments.

Specified by:

getExperiments in interface ExtendedPsiXmlModelledInteraction

Returns:

a List object.