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

Class DefaultFeatureEvidence

java.lang.Object

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

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

All Implemented Interfaces:

Feature<ExperimentalEntity,FeatureEvidence>, FeatureEvidence

Direct Known Subclasses:

CsvFeatureEvidence, MitabFeatureEvidence

public class DefaultFeatureEvidence
extends AbstractFeature<ExperimentalEntity,FeatureEvidence>
implements FeatureEvidence

Default implementation for FeatureEvidence Notes: The equals and hashcode methods have NOT been overridden because the FeatureEvidence object is a complex object. To compare FeatureEvidence objects, you can use some comparators provided by default: - DefaultFeatureEvidenceComparator - UnambiguousFeatureEvidenceComparator

Since:

04/02/13

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

Method Summary

Modifier and Type	Method	Description
Collection<CvTerm>	getDetectionMethods()	Getter for the field detectionMethods.
Collection<Parameter>	getParameters()	Getter for the field parameters.
protected void	initialiseDetectionMethods()	initialiseDetectionMethods
protected void	initialiseDetectionMethodsWith(Collection<CvTerm> methods)	initialiseDetectionMethodsWith
protected void	initialiseParameters()	initialiseParameters
protected void	initialiseParametersWith(Collection<Parameter> parameters)	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, toString

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

DefaultFeatureEvidence

public DefaultFeatureEvidence(ParticipantEvidence participant)

Constructor for DefaultFeatureEvidence.

Parameters:

participant - a ParticipantEvidence object.

DefaultFeatureEvidence

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

Constructor for DefaultFeatureEvidence.

Parameters:

participant - a ParticipantEvidence object.

shortName - a String object.

fullName - a String object.

DefaultFeatureEvidence

public DefaultFeatureEvidence(ParticipantEvidence participant,
                              CvTerm type)

Constructor for DefaultFeatureEvidence.

Parameters:

participant - a ParticipantEvidence object.

type - a CvTerm object.

DefaultFeatureEvidence

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

Constructor for DefaultFeatureEvidence.

Parameters:

participant - a ParticipantEvidence object.

shortName - a String object.

fullName - a String object.

type - a CvTerm object.

DefaultFeatureEvidence

public DefaultFeatureEvidence()

Constructor for DefaultFeatureEvidence.

DefaultFeatureEvidence

public DefaultFeatureEvidence(String shortName,
                              String fullName)

Constructor for DefaultFeatureEvidence.

Parameters:

shortName - a String object.

fullName - a String object.

DefaultFeatureEvidence

public DefaultFeatureEvidence(CvTerm type)

Constructor for DefaultFeatureEvidence.

Parameters:

type - a CvTerm object.

DefaultFeatureEvidence

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

Constructor for DefaultFeatureEvidence.

Parameters:

shortName - a String object.

fullName - a String object.

type - a CvTerm object.

Method Detail

initialiseParameters

protected void initialiseParameters()

initialiseParameters

initialiseDetectionMethods

protected void initialiseDetectionMethods()

initialiseDetectionMethods

initialiseDetectionMethodsWith

protected void initialiseDetectionMethodsWith(Collection<CvTerm> methods)

initialiseDetectionMethodsWith

Parameters:

methods - a Collection object.

initialiseParametersWith

protected void initialiseParametersWith(Collection<Parameter> parameters)

initialiseParametersWith

Parameters:

parameters - a Collection object.

getDetectionMethods

public Collection<CvTerm> getDetectionMethods()

Getter for the field detectionMethods.

Specified by:

getDetectionMethods in interface FeatureEvidence

Returns:

a Collection object.

getParameters

public Collection<Parameter> getParameters()

Getter for the field parameters.

Specified by:

getParameters in interface FeatureEvidence

Returns:

a Collection object.