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

Class XmlBinaryInteractionEvidenceWrapper

java.lang.Object

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

All Implemented Interfaces:

BinaryInteraction<ParticipantEvidence>, BinaryInteractionEvidence, FileSourceContext, Interaction<ParticipantEvidence>, InteractionEvidence, NamedInteraction<ParticipantEvidence>, ExtendedPsiXmlInteraction<ParticipantEvidence>, ExtendedPsiXmlInteractionEvidence, PsiXmlInteraction<ParticipantEvidence>

Direct Known Subclasses:

XmlBinaryInteractionEvidenceWrapper

public class XmlBinaryInteractionEvidenceWrapper
extends Object
implements BinaryInteractionEvidence, FileSourceContext, ExtendedPsiXmlInteractionEvidence

Xml implementation of BinaryInteractionWrapper with a source locator

Since:

16/10/13

Version:

$Id$

Author:

Marine Dumousseau (marine@ebi.ac.uk)

Constructor Summary

Constructors

Constructor	Description
XmlBinaryInteractionEvidenceWrapper(ExtendedPsiXmlInteractionEvidence interaction)	Constructor for XmlBinaryInteractionEvidenceWrapper.
XmlBinaryInteractionEvidenceWrapper(ExtendedPsiXmlInteractionEvidence interaction, CvTerm complexExpansion)	Constructor for XmlBinaryInteractionEvidenceWrapper.

Method Summary

Modifier and Type	Method	Description
boolean	addAllParticipants(Collection<? extends ParticipantEvidence> participants)	This method will add all the participant and set the interaction of the new participant to this current interaction
boolean	addParticipant(ParticipantEvidence part)	This method will add the participant and set the interaction of the new participant to this current interaction
void	assignImexId(String identifier)	Assign an IMEx id to an interaction.
Collection<Alias>	getAliases()	getAliases.
Collection<Annotation>	getAnnotations()	The Collection of annotations describing the interaction.
String	getAvailability()	The availability for this interaction.
CvTerm	getCausalRegulatoryMechanism()	getCausalRegulatoryMechanism.
Collection<Checksum>	getChecksums()	Set of checksums computed for this interaction..
CvTerm	getComplexExpansion()	getComplexExpansion.
Collection<Confidence>	getConfidences()	The confidences in this interaction.
Date	getCreatedDate()	The creation date.
Entry	getEntry()	getEntry.
Experiment	getExperiment()	The experiment which determined the interaction.
List<Experiment>	getExperiments()	getExperiments.
String	getFullName()	The full name of the interaction.
int	getId()	getId.
Collection<Xref>	getIdentifiers()	The identifiers for an interaction.
String	getImexId()	IMEx identifier if the interaction has been curated following IMEx curation rules.
List<AbstractInferredInteraction>	getInferredInteractions()	getInferredInteractions.
CvTerm	getInteractionType()	The interaction type is a controlled vocabulary term.
List<CvTerm>	getInteractionTypes()	getInteractionTypes.
List<ExtendedPsiXmlExperiment>	getOriginalExperiments()	getOriginalExperiments.
Collection<Parameter>	getParameters()	Collection of numerical parameters for this interaction.
ParticipantEvidence	getParticipantA()	getParticipantA.
ParticipantEvidence	getParticipantB()	getParticipantB.
Collection<ParticipantEvidence>	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.
FileSourceLocator	getSourceLocator()	The locator of a position in a file.
Date	getUpdatedDate()	The last update date.
Collection<VariableParameterValueSet>	getVariableParameterValues()	The collection of variableParameterValueSet this interaction has been observed with.
protected ExtendedPsiXmlInteractionEvidence	getWrappedInteraction()	Getter for the field wrappedInteraction.
AbstractAvailability	getXmlAvailability()	getXmlAvailability.
Collection<Xref>	getXrefs()	The external cross references for an interaction.
boolean	isInferred()	Boolean value to know if the interaction is inferred from multiple experiments which on their own would not support the interaction.
boolean	isIntraMolecular()	isIntraMolecular.
boolean	isModelled()	isModelled.
boolean	isNegative()	Boolean value to know if an interaction is negative.
boolean	removeAllParticipants(Collection<? extends ParticipantEvidence> participants)	This method will remove the participant and set the interaction of the removed participant to null.
boolean	removeParticipant(ParticipantEvidence part)	This method will remove the participant and set the interaction of the new participant to null
void	setAvailability(String availability)	Sets the availability.
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	setExperiment(Experiment experiment)	Sets the experiment for this interaction.
void	setExperimentAndAddInteractionEvidence(Experiment experiment)	Sets the experiment for this interaction and add the interaction to the list of interaction evidences If the given experiment is null, it will remove this interaction evidence from the previous experiment attached to this interaction
void	setFullName(String name)	Sets the full name of the interaction
void	setId(int id)	setId.
void	setInferred(boolean inferred)	Sets the inferred boolean value
void	setInteractionType(CvTerm term)	Sets the interaction type.
void	setIntraMolecular(boolean intra)	setIntraMolecular.
void	setModelled(boolean modelled)	setModelled.
void	setNegative(boolean negative)	Sets the negative boolean value.
void	setParticipantA(ParticipantEvidence participantA)	setParticipantA.
void	setParticipantB(ParticipantEvidence participantB)	setParticipantB.
void	setRigid(String rigid)	Sets the rigid of this interaction.
void	setShortName(String name)	Sets the short name of the interaction
void	setSourceLocator(FileSourceLocator locator)	Sets the source locator
void	setUpdatedDate(Date updated)	Sets the last update date
void	setXmlAvailability(AbstractAvailability availability)	setXmlAvailability.
String	toString()	toString

Methods inherited from class java.lang.Object

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

Constructor Detail

XmlBinaryInteractionEvidenceWrapper

public XmlBinaryInteractionEvidenceWrapper(ExtendedPsiXmlInteractionEvidence interaction)

Constructor for XmlBinaryInteractionEvidenceWrapper.

Parameters:

interaction - a ExtendedPsiXmlInteractionEvidence object.

XmlBinaryInteractionEvidenceWrapper

public XmlBinaryInteractionEvidenceWrapper(ExtendedPsiXmlInteractionEvidence interaction,
                                           CvTerm complexExpansion)

Constructor for XmlBinaryInteractionEvidenceWrapper.

Parameters:

interaction - a ExtendedPsiXmlInteractionEvidence object.

complexExpansion - a CvTerm object.

Method Detail

getParticipantA

public ParticipantEvidence getParticipantA()

getParticipantA.

Specified by:

getParticipantA in interface BinaryInteraction<ParticipantEvidence>

Returns:

a ParticipantEvidence object.

getParticipantB

public ParticipantEvidence getParticipantB()

getParticipantB.

Specified by:

getParticipantB in interface BinaryInteraction<ParticipantEvidence>

Returns:

a ParticipantEvidence object.

setParticipantA

public void setParticipantA(ParticipantEvidence participantA)

setParticipantA.

Specified by:

setParticipantA in interface BinaryInteraction<ParticipantEvidence>

Parameters:

participantA - a ParticipantEvidence object.

setParticipantB

public void setParticipantB(ParticipantEvidence participantB)

setParticipantB.

Specified by:

setParticipantB in interface BinaryInteraction<ParticipantEvidence>

Parameters:

participantB - a ParticipantEvidence object.

getComplexExpansion

public CvTerm getComplexExpansion()

getComplexExpansion.

Specified by:

getComplexExpansion in interface BinaryInteraction<ParticipantEvidence>

Returns:

a CvTerm object.

setComplexExpansion

public void setComplexExpansion(CvTerm expansion)

Sets the complex expansion of this binary interaction

Specified by:

setComplexExpansion in interface BinaryInteraction<ParticipantEvidence>

Parameters:

expansion - : the complex expansion

getCausalRegulatoryMechanism

public CvTerm getCausalRegulatoryMechanism()

getCausalRegulatoryMechanism.

Specified by:

getCausalRegulatoryMechanism in interface BinaryInteraction<ParticipantEvidence>

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<ParticipantEvidence>

Parameters:

causalRegulatoryMechanism - : the complex regulatory mechanism CvTerm

getParticipants

public Collection<ParticipantEvidence> 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<ParticipantEvidence>

Returns:

the particiants

addParticipant

public boolean addParticipant(ParticipantEvidence 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<ParticipantEvidence>

Parameters:

part - : participant to add

Returns:

true if participant is added to the list of participants

removeParticipant

public boolean removeParticipant(ParticipantEvidence 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<ParticipantEvidence>

Parameters:

part - : participant to remove

Returns:

true if participant is removed from the list of participants

addAllParticipants

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

Parameters:

participants - : participants to add

Returns:

true if participant are added to the list of participants

removeAllParticipants

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

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

Specified by:

removeAllParticipants in interface Interaction<ParticipantEvidence>

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<ParticipantEvidence>

Returns:

the full name

setFullName

public void setFullName(String name)

Sets the full name of the interaction

Specified by:

setFullName in interface NamedInteraction<ParticipantEvidence>

Parameters:

name - : full name

getAliases

public Collection<Alias> getAliases()

getAliases.

Specified by:

getAliases in interface ExtendedPsiXmlInteraction<ParticipantEvidence>

Specified by:

getAliases in interface ExtendedPsiXmlInteractionEvidence

Specified by:

getAliases in interface NamedInteraction<ParticipantEvidence>

Specified by:

getAliases in interface PsiXmlInteraction<ParticipantEvidence>

Returns:

a Collection object.

getInteractionTypes

public List<CvTerm> getInteractionTypes()

getInteractionTypes.

Specified by:

getInteractionTypes in interface ExtendedPsiXmlInteraction<ParticipantEvidence>

Returns:

a List object.

getEntry

public Entry getEntry()

getEntry.

Specified by:

getEntry in interface PsiXmlInteraction<ParticipantEvidence>

Returns:

a Entry object.

setEntry

public void setEntry(Entry entry)

setEntry.

Specified by:

setEntry in interface PsiXmlInteraction<ParticipantEvidence>

Parameters:

entry - a Entry object.

getInferredInteractions

public List<AbstractInferredInteraction> getInferredInteractions()

getInferredInteractions.

Specified by:

getInferredInteractions in interface ExtendedPsiXmlInteraction<ParticipantEvidence>

Returns:

a List object.

getId

public int getId()

getId.

Specified by:

getId in interface PsiXmlInteraction<ParticipantEvidence>

Returns:

a int.

setId

public void setId(int id)

setId.

Specified by:

setId in interface PsiXmlInteraction<ParticipantEvidence>

Parameters:

id - a int.

isIntraMolecular

public boolean isIntraMolecular()

isIntraMolecular.

Specified by:

isIntraMolecular in interface PsiXmlInteraction<ParticipantEvidence>

Returns:

a boolean.

setIntraMolecular

public void setIntraMolecular(boolean intra)

setIntraMolecular.

Specified by:

setIntraMolecular in interface PsiXmlInteraction<ParticipantEvidence>

Parameters:

intra - a boolean.

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<ParticipantEvidence>

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<ParticipantEvidence>

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<ParticipantEvidence>

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<ParticipantEvidence>

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<ParticipantEvidence>

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<ParticipantEvidence>

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<ParticipantEvidence>

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<ParticipantEvidence>

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<ParticipantEvidence>

Returns:

the last update date

setUpdatedDate

public void setUpdatedDate(Date updated)

Sets the last update date

Specified by:

setUpdatedDate in interface Interaction<ParticipantEvidence>

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<ParticipantEvidence>

Returns:

the last update date

setCreatedDate

public void setCreatedDate(Date created)

Sets the created date

Specified by:

setCreatedDate in interface Interaction<ParticipantEvidence>

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<ParticipantEvidence>

Returns:

the interaction type

setInteractionType

public void setInteractionType(CvTerm term)

Sets the interaction type.

Specified by:

setInteractionType in interface Interaction<ParticipantEvidence>

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

getXmlAvailability

public AbstractAvailability getXmlAvailability()

getXmlAvailability.

Specified by:

getXmlAvailability in interface ExtendedPsiXmlInteractionEvidence

Returns:

a AbstractAvailability object.

setXmlAvailability

public void setXmlAvailability(AbstractAvailability availability)

setXmlAvailability.

Specified by:

setXmlAvailability in interface ExtendedPsiXmlInteractionEvidence

Parameters:

availability - a AbstractAvailability object.

isModelled

public boolean isModelled()

isModelled.

Specified by:

isModelled in interface ExtendedPsiXmlInteractionEvidence

Returns:

a boolean.

setModelled

public void setModelled(boolean modelled)

setModelled.

Specified by:

setModelled in interface ExtendedPsiXmlInteractionEvidence

Parameters:

modelled - a boolean.

getExperiments

public List<Experiment> getExperiments()

getExperiments.

Specified by:

getExperiments in interface ExtendedPsiXmlInteractionEvidence

Returns:

a List object.

getOriginalExperiments

public List<ExtendedPsiXmlExperiment> getOriginalExperiments()

getOriginalExperiments.

Specified by:

getOriginalExperiments in interface ExtendedPsiXmlInteractionEvidence

Returns:

a List object.

getImexId

public String getImexId()

IMEx identifier if the interaction has been curated following IMEx curation rules. It can be null if the interaction is not registered in IMEx central or does not follow the IMEx curation rules. This imex id should be a shortcut to the imex-primary Xref in the collection of xrefs. Ex: IM-123-2

Specified by:

getImexId in interface InteractionEvidence

Returns:

the IMEx identifier

assignImexId

public void assignImexId(String identifier)

Assign an IMEx id to an interaction. It will add the new imex-primary ref to the collection of xrefs

Specified by:

assignImexId in interface InteractionEvidence

Parameters:

identifier - : the IMEx id from IMEx central

getExperiment

public Experiment getExperiment()

The experiment which determined the interaction. It can be null if the interaction evidence is detached from experiment.

Specified by:

getExperiment in interface InteractionEvidence

Returns:

the experiment

setExperiment

public void setExperiment(Experiment experiment)

Sets the experiment for this interaction.

Specified by:

setExperiment in interface InteractionEvidence

Parameters:

experiment - : experiment

setExperimentAndAddInteractionEvidence

public void setExperimentAndAddInteractionEvidence(Experiment experiment)

Sets the experiment for this interaction and add the interaction to the list of interaction evidences If the given experiment is null, it will remove this interaction evidence from the previous experiment attached to this interaction

Specified by:

setExperimentAndAddInteractionEvidence in interface InteractionEvidence

Parameters:

experiment - : experiment

getVariableParameterValues

public Collection<VariableParameterValueSet> getVariableParameterValues()

The collection of variableParameterValueSet this interaction has been observed with. Each variableParameterValueSet contains a set of variableParameterValues which have been used together. This collection cannot be null. If the interactionEvidence does not have any variableParameterValueSet, this method should return an empty set.

Specified by:

getVariableParameterValues in interface InteractionEvidence

Returns:

the collection of variableParameterValueSet

getAvailability

public String getAvailability()

The availability for this interaction. By default it is null because freely available. Ex: copyrights, ...

Specified by:

getAvailability in interface InteractionEvidence

Returns:

the availability

setAvailability

public void setAvailability(String availability)

Sets the availability.

Specified by:

setAvailability in interface InteractionEvidence

Parameters:

availability - : availability

getParameters

public Collection<Parameter> getParameters()

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:

getParameters in interface InteractionEvidence

Returns:

the parameters

isInferred

public boolean isInferred()

Boolean value to know if the interaction is inferred from multiple experiments which on their own would not support the interaction. By default is false.

Specified by:

isInferred in interface InteractionEvidence

Returns:

true if the interaction is inferred from multiple experiments which on their own would not support the interaction

setInferred

public void setInferred(boolean inferred)

Sets the inferred boolean value

Specified by:

setInferred in interface InteractionEvidence

Parameters:

inferred - : inferred boolean value

getConfidences

public Collection<Confidence> getConfidences()

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:

getConfidences in interface InteractionEvidence

Returns:

the confidences

isNegative

public boolean isNegative()

Boolean value to know if an interaction is negative. It is false by default (positive interaction by default)

Specified by:

isNegative in interface InteractionEvidence

Returns:

true if the interaction is negative

setNegative

public void setNegative(boolean negative)

Sets the negative boolean value.

Specified by:

setNegative in interface InteractionEvidence

Parameters:

negative - : negative value

getWrappedInteraction

protected ExtendedPsiXmlInteractionEvidence getWrappedInteraction()

Getter for the field wrappedInteraction.

Returns:

a ExtendedPsiXmlInteractionEvidence object.