Package psidev.psi.mi.jami.model.impl

Class DefaultNamedInteractionEvidence

java.lang.Object

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

psidev.psi.mi.jami.model.impl.DefaultInteractionEvidence

psidev.psi.mi.jami.model.impl.DefaultNamedInteractionEvidence

All Implemented Interfaces:

Interaction<ParticipantEvidence>, InteractionEvidence, NamedInteraction<ParticipantEvidence>

public class DefaultNamedInteractionEvidence
extends DefaultInteractionEvidence
implements NamedInteraction<ParticipantEvidence>

Default implementation for Named InteractionEvidence

Since:

13/11/13

Version:

$Id$

Author:

Marine Dumousseau (marine@ebi.ac.uk)

Constructor Summary

Constructors

Constructor	Description
DefaultNamedInteractionEvidence()	Constructor for DefaultNamedInteractionEvidence.
DefaultNamedInteractionEvidence(String shortName)	Constructor for DefaultNamedInteractionEvidence.
DefaultNamedInteractionEvidence(String shortName, CvTerm type)	Constructor for DefaultNamedInteractionEvidence.
DefaultNamedInteractionEvidence(String shortName, CvTerm type, Xref imexId)	Constructor for DefaultNamedInteractionEvidence.
DefaultNamedInteractionEvidence(String shortName, Source source, Xref imexId)	Constructor for DefaultNamedInteractionEvidence.
DefaultNamedInteractionEvidence(String shortName, Xref imexId)	Constructor for DefaultNamedInteractionEvidence.
DefaultNamedInteractionEvidence(Experiment experiment)	Constructor for DefaultNamedInteractionEvidence.
DefaultNamedInteractionEvidence(Experiment experiment, String shortName)	Constructor for DefaultNamedInteractionEvidence.
DefaultNamedInteractionEvidence(Experiment experiment, String shortName, CvTerm type)	Constructor for DefaultNamedInteractionEvidence.
DefaultNamedInteractionEvidence(Experiment experiment, String shortName, CvTerm type, Xref imexId)	Constructor for DefaultNamedInteractionEvidence.
DefaultNamedInteractionEvidence(Experiment experiment, String shortName, Source source)	Constructor for DefaultNamedInteractionEvidence.
DefaultNamedInteractionEvidence(Experiment experiment, String shortName, Source source, Xref imexId)	Constructor for DefaultNamedInteractionEvidence.
DefaultNamedInteractionEvidence(Experiment experiment, String shortName, Xref imexId)	Constructor for DefaultNamedInteractionEvidence.
DefaultNamedInteractionEvidence(Experiment experiment, Xref imexId)	Constructor for DefaultNamedInteractionEvidence.
DefaultNamedInteractionEvidence(Xref imexId)	Constructor for DefaultNamedInteractionEvidence.

Method Summary

Modifier and Type	Method	Description
Collection<Alias>	getAliases()	Getter for the field aliases.
String	getFullName()	Getter for the field fullName.
protected void	initialiseAliases()	initialiseAliases
protected void	initialiseAliasesWith(Collection<Alias> aliases)	initialiseAliasesWith
void	setFullName(String fullName)	Sets the full name of the interaction

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

assignImexId, clearPropertiesLinkedToXrefs, getAvailability, getConfidences, getExperiment, getImexId, getParameters, getVariableParameterValues, initialiseExperimentalConfidences, initialiseExperimentalConfidencesWith, initialiseExperimentalParameters, initialiseExperimentalParametersWith, initialiseVariableParameterValueSets, initialiseVariableParameterValueSetsWith, initialiseXrefs, isInferred, isNegative, processAddedXrefEvent, processRemovedXrefEvent, setAvailability, setExperiment, setExperimentAndAddInteractionEvidence, setInferred, setNegative, toString

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

addAllParticipants, addParticipant, clearPropertiesLinkedToChecksums, getAnnotations, getChecksums, getCreatedDate, getIdentifiers, getInteractionType, getParticipants, getRigid, getShortName, getUpdatedDate, getXrefs, initialiseAnnotations, initialiseAnnotationsWith, initialiseChecksums, initialiseChecksumWith, initialiseIdentifiers, initialiseIdentifiersWith, initialiseParticipants, initialiseParticipantsWith, initialiseXrefsWith, processAddedChecksumEvent, processRemovedChecksumEvent, removeAllParticipants, removeParticipant, 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.model.Interaction

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

Constructor Detail

DefaultNamedInteractionEvidence

public DefaultNamedInteractionEvidence(Experiment experiment)

Constructor for DefaultNamedInteractionEvidence.

Parameters:

experiment - a Experiment object.

DefaultNamedInteractionEvidence

public DefaultNamedInteractionEvidence(Experiment experiment,
                                       String shortName)

Constructor for DefaultNamedInteractionEvidence.

Parameters:

experiment - a Experiment object.

shortName - a String object.

DefaultNamedInteractionEvidence

public DefaultNamedInteractionEvidence(Experiment experiment,
                                       String shortName,
                                       Source source)

Constructor for DefaultNamedInteractionEvidence.

Parameters:

experiment - a Experiment object.

shortName - a String object.

source - a Source object.

DefaultNamedInteractionEvidence

public DefaultNamedInteractionEvidence(Experiment experiment,
                                       String shortName,
                                       CvTerm type)

Constructor for DefaultNamedInteractionEvidence.

Parameters:

experiment - a Experiment object.

shortName - a String object.

type - a CvTerm object.

DefaultNamedInteractionEvidence

public DefaultNamedInteractionEvidence(Experiment experiment,
                                       Xref imexId)

Constructor for DefaultNamedInteractionEvidence.

Parameters:

experiment - a Experiment object.

imexId - a Xref object.

DefaultNamedInteractionEvidence

public DefaultNamedInteractionEvidence(Experiment experiment,
                                       String shortName,
                                       Xref imexId)

Constructor for DefaultNamedInteractionEvidence.

Parameters:

experiment - a Experiment object.

shortName - a String object.

imexId - a Xref object.

DefaultNamedInteractionEvidence

public DefaultNamedInteractionEvidence(Experiment experiment,
                                       String shortName,
                                       Source source,
                                       Xref imexId)

Constructor for DefaultNamedInteractionEvidence.

Parameters:

experiment - a Experiment object.

shortName - a String object.

source - a Source object.

imexId - a Xref object.

DefaultNamedInteractionEvidence

public DefaultNamedInteractionEvidence(Experiment experiment,
                                       String shortName,
                                       CvTerm type,
                                       Xref imexId)

Constructor for DefaultNamedInteractionEvidence.

Parameters:

experiment - a Experiment object.

shortName - a String object.

type - a CvTerm object.

imexId - a Xref object.

DefaultNamedInteractionEvidence

public DefaultNamedInteractionEvidence(Xref imexId)

Constructor for DefaultNamedInteractionEvidence.

Parameters:

imexId - a Xref object.

DefaultNamedInteractionEvidence

public DefaultNamedInteractionEvidence(String shortName,
                                       Xref imexId)

Constructor for DefaultNamedInteractionEvidence.

Parameters:

shortName - a String object.

imexId - a Xref object.

DefaultNamedInteractionEvidence

public DefaultNamedInteractionEvidence(String shortName,
                                       Source source,
                                       Xref imexId)

Constructor for DefaultNamedInteractionEvidence.

Parameters:

shortName - a String object.

source - a Source object.

imexId - a Xref object.

DefaultNamedInteractionEvidence

public DefaultNamedInteractionEvidence(String shortName,
                                       CvTerm type,
                                       Xref imexId)

Constructor for DefaultNamedInteractionEvidence.

Parameters:

shortName - a String object.

type - a CvTerm object.

imexId - a Xref object.

DefaultNamedInteractionEvidence

public DefaultNamedInteractionEvidence()

Constructor for DefaultNamedInteractionEvidence.

DefaultNamedInteractionEvidence

public DefaultNamedInteractionEvidence(String shortName)

Constructor for DefaultNamedInteractionEvidence.

Parameters:

shortName - a String object.

DefaultNamedInteractionEvidence

public DefaultNamedInteractionEvidence(String shortName,
                                       CvTerm type)

Constructor for DefaultNamedInteractionEvidence.

Parameters:

shortName - a String object.

type - a CvTerm object.

Method Detail

initialiseAliases

protected void initialiseAliases()

initialiseAliases

initialiseAliasesWith

protected void initialiseAliasesWith(Collection<Alias> aliases)

initialiseAliasesWith

Parameters:

aliases - a Collection object.

getFullName

public String getFullName()

Getter for the field fullName.

Specified by:

getFullName in interface NamedInteraction<ParticipantEvidence>

Returns:

a String object.

setFullName

public void setFullName(String fullName)

Sets the full name of the interaction

Specified by:

setFullName in interface NamedInteraction<ParticipantEvidence>

Parameters:

fullName - : full name

getAliases

public Collection<Alias> getAliases()

Getter for the field aliases.

Specified by:

getAliases in interface NamedInteraction<ParticipantEvidence>

Returns:

a Collection object.