Package psidev.psi.mi.jami.tab.extension

Class MitabFeatureEvidence

java.lang.Object

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

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

psidev.psi.mi.jami.tab.extension.MitabFeatureEvidence

All Implemented Interfaces:

FileSourceContext, Feature<ExperimentalEntity,FeatureEvidence>, FeatureEvidence, MitabFeature<ExperimentalEntity,FeatureEvidence>

public class MitabFeatureEvidence
extends DefaultFeatureEvidence
implements MitabFeature<ExperimentalEntity,FeatureEvidence>, FileSourceContext

Mitab 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
MitabFeatureEvidence()	Constructor for MitabFeatureEvidence.
MitabFeatureEvidence(String shortName, String fullName)	Constructor for MitabFeatureEvidence.
MitabFeatureEvidence(String shortName, String fullName, CvTerm type)	Constructor for MitabFeatureEvidence.
MitabFeatureEvidence(CvTerm type)	Constructor for MitabFeatureEvidence.
MitabFeatureEvidence(ParticipantEvidence participant)	Constructor for MitabFeatureEvidence.
MitabFeatureEvidence(ParticipantEvidence participant, String shortName, String fullName)	Constructor for MitabFeatureEvidence.
MitabFeatureEvidence(ParticipantEvidence participant, String shortName, String fullName, CvTerm type)	Constructor for MitabFeatureEvidence.
MitabFeatureEvidence(ParticipantEvidence participant, CvTerm type)	Constructor for MitabFeatureEvidence.

Method Summary

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

MitabFeatureEvidence

public MitabFeatureEvidence(ParticipantEvidence participant)

Constructor for MitabFeatureEvidence.

Parameters:

participant - a ParticipantEvidence object.

MitabFeatureEvidence

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

Constructor for MitabFeatureEvidence.

Parameters:

participant - a ParticipantEvidence object.

shortName - a String object.

fullName - a String object.

MitabFeatureEvidence

public MitabFeatureEvidence(ParticipantEvidence participant,
                            CvTerm type)

Constructor for MitabFeatureEvidence.

Parameters:

participant - a ParticipantEvidence object.

type - a CvTerm object.

MitabFeatureEvidence

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

Constructor for MitabFeatureEvidence.

Parameters:

participant - a ParticipantEvidence object.

shortName - a String object.

fullName - a String object.

type - a CvTerm object.

MitabFeatureEvidence

public MitabFeatureEvidence()

Constructor for MitabFeatureEvidence.

MitabFeatureEvidence

public MitabFeatureEvidence(String shortName,
                            String fullName)

Constructor for MitabFeatureEvidence.

Parameters:

shortName - a String object.

fullName - a String object.

MitabFeatureEvidence

public MitabFeatureEvidence(CvTerm type)

Constructor for MitabFeatureEvidence.

Parameters:

type - a CvTerm object.

MitabFeatureEvidence

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

Constructor for MitabFeatureEvidence.

Parameters:

shortName - a String object.

fullName - a String object.

type - a CvTerm object.

Method Detail

getText

public String getText()

Getter for the field text.

Specified by:

getText in interface MitabFeature<ExperimentalEntity,FeatureEvidence>

Returns:

a String object.

setText

public void setText(String text)

setText.

Specified by:

setText in interface MitabFeature<ExperimentalEntity,FeatureEvidence>

Parameters:

text - a String object.

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