Package psidev.psi.mi.jami.crosslink.extension

Class CsvInteractionEvidence

java.lang.Object

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

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

psidev.psi.mi.jami.crosslink.extension.CsvInteractionEvidence

All Implemented Interfaces:

CrosslinkCsvInteraction, FileSourceContext, Interaction<ParticipantEvidence>, InteractionEvidence

public class CsvInteractionEvidence
extends DefaultInteractionEvidence
implements FileSourceContext, CrosslinkCsvInteraction

CSV extension for InteractionEvidence

Since:

11/06/13

Version:

$Id$

Author:

Marine Dumousseau (marine@ebi.ac.uk)

Constructor Summary

Constructors

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

Method Summary

Modifier and Type	Method	Description
String	getNaryGroup()	getNaryGroup.
FileSourceLocator	getSourceLocator()	Getter for the field sourceLocator.
void	setNaryGroup(String bait)	setNaryGroup.
void	setSourceLocator(FileSourceLocator sourceLocator)	Sets the source locator
String	toString()

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

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

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

assignImexId, getAvailability, getConfidences, getExperiment, getImexId, getParameters, getVariableParameterValues, isInferred, isNegative, setAvailability, setExperiment, setExperimentAndAddInteractionEvidence, setInferred, setNegative

Constructor Detail

CsvInteractionEvidence

public CsvInteractionEvidence(Experiment experiment)

Constructor for CsvInteractionEvidence.

Parameters:

experiment - a Experiment object.

CsvInteractionEvidence

public CsvInteractionEvidence(Experiment experiment,
                              String shortName)

Constructor for CsvInteractionEvidence.

Parameters:

experiment - a Experiment object.

shortName - a String object.

CsvInteractionEvidence

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

Constructor for CsvInteractionEvidence.

Parameters:

experiment - a Experiment object.

shortName - a String object.

source - a Source object.

CsvInteractionEvidence

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

Constructor for CsvInteractionEvidence.

Parameters:

experiment - a Experiment object.

shortName - a String object.

type - a CvTerm object.

CsvInteractionEvidence

public CsvInteractionEvidence(Experiment experiment,
                              Xref imexId)

Constructor for CsvInteractionEvidence.

Parameters:

experiment - a Experiment object.

imexId - a Xref object.

CsvInteractionEvidence

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

Constructor for CsvInteractionEvidence.

Parameters:

experiment - a Experiment object.

shortName - a String object.

imexId - a Xref object.

CsvInteractionEvidence

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

Constructor for CsvInteractionEvidence.

Parameters:

experiment - a Experiment object.

shortName - a String object.

source - a Source object.

imexId - a Xref object.

CsvInteractionEvidence

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

Constructor for CsvInteractionEvidence.

Parameters:

experiment - a Experiment object.

shortName - a String object.

type - a CvTerm object.

imexId - a Xref object.

CsvInteractionEvidence

public CsvInteractionEvidence(Xref imexId)

Constructor for CsvInteractionEvidence.

Parameters:

imexId - a Xref object.

CsvInteractionEvidence

public CsvInteractionEvidence(String shortName,
                              Xref imexId)

Constructor for CsvInteractionEvidence.

Parameters:

shortName - a String object.

imexId - a Xref object.

CsvInteractionEvidence

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

Constructor for CsvInteractionEvidence.

Parameters:

shortName - a String object.

source - a Source object.

imexId - a Xref object.

CsvInteractionEvidence

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

Constructor for CsvInteractionEvidence.

Parameters:

shortName - a String object.

type - a CvTerm object.

imexId - a Xref object.

CsvInteractionEvidence

public CsvInteractionEvidence()

Constructor for CsvInteractionEvidence.

CsvInteractionEvidence

public CsvInteractionEvidence(String shortName)

Constructor for CsvInteractionEvidence.

Parameters:

shortName - a String object.

CsvInteractionEvidence

public CsvInteractionEvidence(String shortName,
                              CvTerm type)

Constructor for CsvInteractionEvidence.

Parameters:

shortName - a String object.

type - a CvTerm object.

Method Detail

getSourceLocator

public FileSourceLocator getSourceLocator()

Getter for the field sourceLocator.

Specified by:

getSourceLocator in interface FileSourceContext

Returns:

a FileSourceLocator object.

setSourceLocator

public void setSourceLocator(FileSourceLocator sourceLocator)

Sets the source locator

Specified by:

setSourceLocator in interface FileSourceContext

Parameters:

sourceLocator - : the file locator

toString

public String toString()

Specified by:

toString in interface FileSourceContext

Overrides:

toString in class DefaultInteractionEvidence

Returns:

the file source context as a String. If the source locator is not null, it should give the source locator properties

getNaryGroup

public String getNaryGroup()

getNaryGroup.

Specified by:

getNaryGroup in interface CrosslinkCsvInteraction

Returns:

a String object.

setNaryGroup

public void setNaryGroup(String bait)

setNaryGroup.

Specified by:

setNaryGroup in interface CrosslinkCsvInteraction

Parameters:

bait - : n-ary group name used for this interaction