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

Class CsvFeatureEvidence

java.lang.Object

psidev.psi.mi.jami.model.impl.AbstractFeature<ExperimentalEntity,FeatureEvidence>

psidev.psi.mi.jami.model.impl.DefaultFeatureEvidence

psidev.psi.mi.jami.crosslink.extension.CsvFeatureEvidence

All Implemented Interfaces:

FileSourceContext, Feature<ExperimentalEntity,FeatureEvidence>, FeatureEvidence

public class CsvFeatureEvidence
extends DefaultFeatureEvidence
implements FileSourceContext

CrossLink CSV extension for FeatureEvidence

Since:

09/07/13

Version:

$Id$

Author:

Marine Dumousseau (marine@ebi.ac.uk)

Nested Class Summary

Nested classes/interfaces inherited from class psidev.psi.mi.jami.model.impl.AbstractFeature

AbstractFeature.FeatureIdentifierList

Field Summary

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

ALLOSTERIC_PTM, ALLOSTERIC_PTM_MI, BINDING_SITE, BINDING_SITE_MI, BIOLOGICAL_FEATURE, BIOLOGICAL_FEATURE_MI, DECREASING_PTM, DECREASING_PTM_MI, DIRECT_BINDING, DIRECT_BINDING_MI, DISRUPTING_PTM, DISRUPTING_PTM_MI, EXPERIMENTAL_FEATURE, EXPERIMENTAL_FEATURE_MI, INCREASING_PTM, INCREASING_PTM_MI, MUTATION, MUTATION_MI, OBSERVED_PTM, OBSERVED_PTM_MI, PREREQUISITE_PTM, PREREQUISITE_PTM_MI, RESULTING_CLEAVAGE, RESULTING_CLEAVAGE_MI, RESULTING_PTM, RESULTING_PTM_MI, SUFFICIENT_BINDING, SUFFICIENT_BINDING_MI, VARIANT, VARIANT_MI

Constructor Summary

Constructors

Constructor	Description
CsvFeatureEvidence()	Constructor for CsvFeatureEvidence.
CsvFeatureEvidence(String shortName, String fullName)	Constructor for CsvFeatureEvidence.
CsvFeatureEvidence(String shortName, String fullName, CvTerm type)	Constructor for CsvFeatureEvidence.
CsvFeatureEvidence(CvTerm type)	Constructor for CsvFeatureEvidence.
CsvFeatureEvidence(ParticipantEvidence participant)	Constructor for CsvFeatureEvidence.
CsvFeatureEvidence(ParticipantEvidence participant, String shortName, String fullName)	Constructor for CsvFeatureEvidence.
CsvFeatureEvidence(ParticipantEvidence participant, String shortName, String fullName, CvTerm type)	Constructor for CsvFeatureEvidence.
CsvFeatureEvidence(ParticipantEvidence participant, CvTerm type)	Constructor for CsvFeatureEvidence.

Method Summary

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

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

getDetectionMethods, getParameters, initialiseDetectionMethods, initialiseDetectionMethodsWith, initialiseParameters, initialiseParametersWith

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

clearPropertiesLinkedToIdentifiers, getAliases, getAnnotations, getFullName, getIdentifiers, getInterpro, getLinkedFeatures, getParticipant, getRanges, getRole, getShortName, getType, getXrefs, initialiseAliases, initialiseAliasesWith, initialiseAnnotations, initialiseAnnotationsWith, initialiseIdentifiers, initialiseIdentifiersWith, initialiseLinkedFeatures, initialiseLinkedFeaturesWith, initialiseRanges, initialiseRangesWith, initialiseXrefs, initialiseXrefsWith, processAddedIdentifierEvent, processRemovedIdentifierEvent, setFullName, setInterpro, setParticipant, setParticipantAndAddFeature, setRole, setShortName, setType

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.Feature

getAliases, getAnnotations, getFullName, getIdentifiers, getInterpro, getLinkedFeatures, getParticipant, getRanges, getRole, getShortName, getType, getXrefs, setFullName, setInterpro, setParticipant, setParticipantAndAddFeature, setRole, setShortName, setType

Constructor Detail

CsvFeatureEvidence

public CsvFeatureEvidence(ParticipantEvidence participant)

Constructor for CsvFeatureEvidence.

Parameters:

participant - a ParticipantEvidence object.

CsvFeatureEvidence

public CsvFeatureEvidence(ParticipantEvidence participant,
                          String shortName,
                          String fullName)

Constructor for CsvFeatureEvidence.

Parameters:

participant - a ParticipantEvidence object.

shortName - a String object.

fullName - a String object.

CsvFeatureEvidence

public CsvFeatureEvidence(ParticipantEvidence participant,
                          CvTerm type)

Constructor for CsvFeatureEvidence.

Parameters:

participant - a ParticipantEvidence object.

type - a CvTerm object.

CsvFeatureEvidence

public CsvFeatureEvidence(ParticipantEvidence participant,
                          String shortName,
                          String fullName,
                          CvTerm type)

Constructor for CsvFeatureEvidence.

Parameters:

participant - a ParticipantEvidence object.

shortName - a String object.

fullName - a String object.

type - a CvTerm object.

CsvFeatureEvidence

public CsvFeatureEvidence()

Constructor for CsvFeatureEvidence.

CsvFeatureEvidence

public CsvFeatureEvidence(String shortName,
                          String fullName)

Constructor for CsvFeatureEvidence.

Parameters:

shortName - a String object.

fullName - a String object.

CsvFeatureEvidence

public CsvFeatureEvidence(CvTerm type)

Constructor for CsvFeatureEvidence.

Parameters:

type - a CvTerm object.

CsvFeatureEvidence

public CsvFeatureEvidence(String shortName,
                          String fullName,
                          CvTerm type)

Constructor for CsvFeatureEvidence.

Parameters:

shortName - a String object.

fullName - 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 AbstractFeature<ExperimentalEntity,FeatureEvidence>

Returns:

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