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

Class XmlModelledBinaryInteractionWrapper

java.lang.Object

psidev.psi.mi.jami.xml.model.extension.binary.XmlModelledBinaryInteractionWrapper

All Implemented Interfaces:

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

public class XmlModelledBinaryInteractionWrapper
extends Object
implements ModelledBinaryInteraction, FileSourceContext, ExtendedPsiXmlModelledInteraction

Wrapper for Xml binary interactions

Since:

16/10/13

Version:

$Id$

Author:

Marine Dumousseau (marine@ebi.ac.uk)

Field Summary

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

ECO, ECO_MI

Constructor Summary

Constructors

Constructor	Description
XmlModelledBinaryInteractionWrapper(ExtendedPsiXmlModelledInteraction interaction)	Constructor for XmlModelledBinaryInteractionWrapper.
XmlModelledBinaryInteractionWrapper(ExtendedPsiXmlModelledInteraction interaction, CvTerm complexExpansion)	Constructor for XmlModelledBinaryInteractionWrapper.

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)	This method will add the participant and set the interaction of the new participant to this current interaction
Collection<Alias>	getAliases()	getAliases.
Collection<Annotation>	getAnnotations()	The Collection of annotations describing the interaction.
CvTerm	getCausalRegulatoryMechanism()	getCausalRegulatoryMechanism.
Collection<Checksum>	getChecksums()	Set of checksums computed for this interaction..
CvTerm	getComplexExpansion()	getComplexExpansion.
Collection<CooperativeEffect>	getCooperativeEffects()	The collection of cooperative effects associated with this modelledInteraction.
Date	getCreatedDate()	The creation date.
Entry	getEntry()	getEntry.
CvTerm	getEvidenceType()	The evidence type for this modelled interactions.
List<Experiment>	getExperiments()	getExperiments.
String	getFullName()	The full name of the interaction.
int	getId()	getId.
Collection<Xref>	getIdentifiers()	The identifiers for an interaction.
List<AbstractInferredInteraction>	getInferredInteractions()	getInferredInteractions.
Collection<InteractionEvidence>	getInteractionEvidences()	Interaction evidences supporting this modelled interaction.
CvTerm	getInteractionType()	The interaction type is a controlled vocabulary term.
List<CvTerm>	getInteractionTypes()	getInteractionTypes.
Collection<ModelledConfidence>	getModelledConfidences()	The confidences in this interaction.
Collection<ModelledParameter>	getModelledParameters()	Collection of numerical parameters for this interaction.
ModelledParticipant	getParticipantA()	getParticipantA.
ModelledParticipant	getParticipantB()	getParticipantB.
Collection<ModelledParticipant>	getParticipants()	The collection of participants involved in this interaction.
String	getRigid()	The checksum computed from the rogids from all the proteins involved in the interaction.
String	getShortName()	The short name of the interaction.
Source	getSource()	The source which reported this modelled interaction.
FileSourceLocator	getSourceLocator()	The locator of a position in a file.
Date	getUpdatedDate()	The last update date.
Collection<Xref>	getXrefs()	The external cross references for an interaction.
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)	This method will remove the participant and set the interaction of the new participant to null
void	setCausalRegulatoryMechanism(CvTerm causalRegulatoryMechanism)	Sets the causal regulatory mechanism of this binary interaction
void	setComplexExpansion(CvTerm expansion)	Sets the complex expansion of this binary interaction
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 interaction
void	setId(int id)	setId.
void	setInteractionType(CvTerm term)	Sets the interaction type.
void	setIntraMolecular(boolean intra)	setIntraMolecular.
void	setParticipantA(ModelledParticipant participantA)	setParticipantA.
void	setParticipantB(ModelledParticipant participantB)	setParticipantB.
void	setRigid(String rigid)	Sets the rigid of this interaction.
void	setShortName(String name)	Sets the short name of the interaction
void	setSource(Source source)	Sets the source reporting the interaction.
void	setSourceLocator(FileSourceLocator locator)	Sets the source locator
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

Constructor Detail

XmlModelledBinaryInteractionWrapper

public XmlModelledBinaryInteractionWrapper(ExtendedPsiXmlModelledInteraction interaction)

Constructor for XmlModelledBinaryInteractionWrapper.

Parameters:

interaction - a ExtendedPsiXmlModelledInteraction object.

XmlModelledBinaryInteractionWrapper

public XmlModelledBinaryInteractionWrapper(ExtendedPsiXmlModelledInteraction interaction,
                                           CvTerm complexExpansion)

Constructor for XmlModelledBinaryInteractionWrapper.

Parameters:

interaction - a ExtendedPsiXmlModelledInteraction object.

complexExpansion - a CvTerm object.

Method Detail

getParticipantA

public ModelledParticipant getParticipantA()

getParticipantA.

Specified by:

getParticipantA in interface BinaryInteraction<ModelledParticipant>

Returns:

a ModelledParticipant object.

getParticipantB

public ModelledParticipant getParticipantB()

getParticipantB.

Specified by:

getParticipantB in interface BinaryInteraction<ModelledParticipant>

Returns:

a ModelledParticipant object.

setParticipantA

public void setParticipantA(ModelledParticipant participantA)

setParticipantA.

Specified by:

setParticipantA in interface BinaryInteraction<ModelledParticipant>

Parameters:

participantA - a ModelledParticipant object.

setParticipantB

public void setParticipantB(ModelledParticipant participantB)

setParticipantB.

Specified by:

setParticipantB in interface BinaryInteraction<ModelledParticipant>

Parameters:

participantB - a ModelledParticipant object.

getComplexExpansion

public CvTerm getComplexExpansion()

getComplexExpansion.

Specified by:

getComplexExpansion in interface BinaryInteraction<ModelledParticipant>

Returns:

a CvTerm object.

setComplexExpansion

public void setComplexExpansion(CvTerm expansion)

Sets the complex expansion of this binary interaction

Specified by:

setComplexExpansion in interface BinaryInteraction<ModelledParticipant>

Parameters:

expansion - : the complex expansion

getCausalRegulatoryMechanism

public CvTerm getCausalRegulatoryMechanism()

getCausalRegulatoryMechanism.

Specified by:

getCausalRegulatoryMechanism in interface BinaryInteraction<ModelledParticipant>

Returns:

a CvTerm object.

setCausalRegulatoryMechanism

public void setCausalRegulatoryMechanism(CvTerm causalRegulatoryMechanism)

Sets the causal regulatory mechanism of this binary interaction

Specified by:

setCausalRegulatoryMechanism in interface BinaryInteraction<ModelledParticipant>

Parameters:

causalRegulatoryMechanism - : the complex regulatory mechanism CvTerm

getParticipants

public Collection<ModelledParticipant> getParticipants()

The collection of participants involved in this interaction. The collection cannot be null. If the interaction does not involve any participants, the method should return an empty set. The collection of participants for this binary interaction. It cannot be changed.

Specified by:

getParticipants in interface Interaction<ModelledParticipant>

Returns:

the particiants

addParticipant

public boolean addParticipant(ModelledParticipant part)

This method will add the participant and set the interaction of the new participant to this current interaction 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<ModelledParticipant>

Parameters:

part - : participant to add

Returns:

true if participant is added to the list of participants

removeParticipant

public boolean removeParticipant(ModelledParticipant part)

This method will remove the participant and set the interaction of the new participant to null Removes the Participant from this binary interaction

Specified by:

removeParticipant in interface Interaction<ModelledParticipant>

Parameters:

part - : participant to remove

Returns:

true if participant is removed from the list of participants

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 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<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

getFullName

public String getFullName()

The full name of the interaction. It can be null

Specified by:

getFullName in interface NamedInteraction<ModelledParticipant>

Returns:

the full name

setFullName

public void setFullName(String name)

Sets the full name of the interaction

Specified by:

setFullName in interface NamedInteraction<ModelledParticipant>

Parameters:

name - : full name

getAliases

public Collection<Alias> getAliases()

getAliases.

Specified by:

getAliases in interface ExtendedPsiXmlInteraction<ModelledParticipant>

Specified by:

getAliases in interface ExtendedPsiXmlModelledInteraction

Specified by:

getAliases in interface NamedInteraction<ModelledParticipant>

Specified by:

getAliases in interface PsiXmlInteraction<ModelledParticipant>

Returns:

a Collection object.

getInteractionTypes

public List<CvTerm> getInteractionTypes()

getInteractionTypes.

Specified by:

getInteractionTypes in interface ExtendedPsiXmlInteraction<ModelledParticipant>

Returns:

a List object.

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.

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

getShortName

public String getShortName()

The short name of the interaction. It can be null. Ex: foxc1-flna, ...

Specified by:

getShortName in interface Interaction<ModelledParticipant>

Returns:

short name of the interaction

setShortName

public void setShortName(String name)

Sets the short name of the interaction

Specified by:

setShortName in interface Interaction<ModelledParticipant>

Parameters:

name - : short name

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

getIdentifiers

public Collection<Xref> getIdentifiers()

The identifiers for an interaction. The Collection cannot be null. If the interaction does not have any identifiers (IMEx is not among the identifiers), the method should return an emtpy Collection. Ex: original interaction database accession, ...

Specified by:

getIdentifiers in interface Interaction<ModelledParticipant>

Returns:

the xrefs

getXrefs

public Collection<Xref> getXrefs()

The external cross references for an interaction. The Collection cannot be null. If the interaction does not have any xrefs, the method should return an emtpy Collection. Ex: GO process xrefs, GO component xrefs, database accession that can identify the interaction, ...

Specified by:

getXrefs in interface Interaction<ModelledParticipant>

Returns:

the xrefs

getChecksums

public Collection<Checksum> getChecksums()

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

Specified by:

getChecksums in interface Interaction<ModelledParticipant>

Returns:

the set of checksums

getAnnotations

public Collection<Annotation> getAnnotations()

The Collection of annotations describing the interaction. The Collection cannot be null. If the interaction does not have any annotations, the method should return an empty Collection. Ex: figure-legend annotations, comments, cautions, ...

Specified by:

getAnnotations in interface Interaction<ModelledParticipant>

Returns:

the annotations

getUpdatedDate

public Date getUpdatedDate()

The last update date. It can be null if not relevant or not known.

Specified by:

getUpdatedDate in interface Interaction<ModelledParticipant>

Returns:

the last update date

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()

The creation date. It can be null if not relevant or not known.

Specified by:

getCreatedDate in interface Interaction<ModelledParticipant>

Returns:

the last update date

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()

The interaction type is a controlled vocabulary term. It can be null. Ex: direct interaction, association, ...

Specified by:

getInteractionType in interface Interaction<ModelledParticipant>

Returns:

the interaction type

setInteractionType

public void setInteractionType(CvTerm term)

Sets the interaction type.

Specified by:

setInteractionType in interface Interaction<ModelledParticipant>

Parameters:

term - : interaction type

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

getInteractionEvidences

public Collection<InteractionEvidence> getInteractionEvidences()

Interaction evidences supporting this modelled interaction. The collection cannot be null. If the modelled interaction does not have experimental interactions attached to it, the method should return an empty set

Specified by:

getInteractionEvidences in interface ModelledInteraction

Returns:

the collection of experimental evidences

getSource

public Source getSource()

The source which reported this modelled interaction. It can be an organization, institute, ... It can be null if the source is unknown or not relevant. Ex: IntAct, MINT, DIP, ...

Specified by:

getSource in interface ModelledInteraction

Returns:

the source

setSource

public void setSource(Source source)

Sets the source reporting the interaction.

Specified by:

setSource in interface ModelledInteraction

Parameters:

source - : source for this interaction

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

getModelledConfidences

public Collection<ModelledConfidence> getModelledConfidences()

The confidences in this interaction. The Collection cannot be null. If the interaction does not have any confidences, the method should return an empty Collection. Ex: author based scores, statistical confidences, ...

Specified by:

getModelledConfidences in interface ModelledInteraction

Returns:

the confidences

getModelledParameters

public Collection<ModelledParameter> getModelledParameters()

Collection of numerical parameters for this interaction. The set cannot be null. If the interaction does not have any parameters, the method should return an empty Collection. Ex: IC50, ...

Specified by:

getModelledParameters in interface ModelledInteraction

Returns:

the parameters

getCooperativeEffects

public Collection<CooperativeEffect> getCooperativeEffects()

The collection of cooperative effects associated with this modelledInteraction. The collection cannot be null. If the ModelledInteraction does not have any cooperative effects, this method should return an empty collection.

Specified by:

getCooperativeEffects in interface ModelledInteraction

Returns:

the collection of cooperative effects for this modelled interaction

getExperiments

public List<Experiment> getExperiments()

getExperiments.

Specified by:

getExperiments in interface ExtendedPsiXmlModelledInteraction

Returns:

a List object.