Package psidev.psi.mi.jami.xml.model.extension.xml300

Class XmlFeatureEvidence

java.lang.Object

psidev.psi.mi.jami.xml.model.extension.xml300.AbstractXmlFeature<ExperimentalEntity,FeatureEvidence>

psidev.psi.mi.jami.xml.model.extension.xml300.XmlFeatureEvidence

All Implemented Interfaces:

com.sun.xml.bind.Locatable, FileSourceContext, Feature<ExperimentalEntity,FeatureEvidence>, FeatureEvidence, ExtendedPsiXmlFeature<ExperimentalEntity,FeatureEvidence>, ExtendedPsiXmlFeatureEvidence

public class XmlFeatureEvidence
extends AbstractXmlFeature<ExperimentalEntity,FeatureEvidence>
implements ExtendedPsiXmlFeatureEvidence

Xml implementation of a Feature

Since:

24/07/13

Version:

$Id$

Author:

Marine Dumousseau (marine@ebi.ac.uk)

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
static class	XmlFeatureEvidence.JAXBExperimentRefWrapper
static class	XmlFeatureEvidence.JAXBParameterWrapper

Nested classes/interfaces inherited from class psidev.psi.mi.jami.xml.model.extension.xml300.AbstractXmlFeature

AbstractXmlFeature.JAXBAttributeWrapper, AbstractXmlFeature.JAXBRangeWrapper

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
XmlFeatureEvidence()	Constructor for XmlFeatureEvidence.
XmlFeatureEvidence(String shortName, String fullName)	Constructor for XmlFeatureEvidence.
XmlFeatureEvidence(String shortName, String fullName, String interpro)	Constructor for XmlFeatureEvidence.
XmlFeatureEvidence(String shortName, String fullName, CvTerm type)	Constructor for XmlFeatureEvidence.
XmlFeatureEvidence(String shortName, String fullName, CvTerm type, String interpro)	Constructor for XmlFeatureEvidence.
XmlFeatureEvidence(CvTerm type)	Constructor for XmlFeatureEvidence.
XmlFeatureEvidence(CvTerm type, String interpro)	Constructor for XmlFeatureEvidence.

Method Summary

Modifier and Type	Method	Description
Collection<CvTerm>	getDetectionMethods()	getDetectionMethods.
List<Experiment>	getExperiments()	getExperiments.
List<CvTerm>	getJAXBFeatureDetectionMethods()	getJAXBFeatureDetectionMethods.
Collection<Parameter>	getParameters()	Numerical parameters associated with this feature.
FileSourceLocator	getSourceLocator()	Getter for the field sourceLocator.
protected void	initialiseDetectionMethods()	initialiseDetectionMethods.
void	setJAXBAttributeWrapper(AbstractXmlFeature.JAXBAttributeWrapper jaxbAttributeWrapper)	setJAXBAttributeWrapper.
void	setJAXBExperimentRefWrapper(XmlFeatureEvidence.JAXBExperimentRefWrapper wrapper)	setJAXBExperimentRefWrapper.
void	setJAXBFeatureRole(XmlCvTerm role)	setJAXBFeatureRole.
void	setJAXBId(int id)	setJAXBId.
void	setJAXBNames(NamesContainer value)	Sets the value of the names property.
void	setJAXBParameterWrapper(XmlFeatureEvidence.JAXBParameterWrapper wrapper)	setJAXBParameterWrapper.
void	setJAXBRangeWrapper(AbstractXmlFeature.JAXBRangeWrapper jaxbRangeWrapper)	setJAXBRangeWrapper.
void	setJAXBType(XmlCvTerm type)	setJAXBType.
void	setJAXBXref(FeatureXrefContainer value)	Sets the value of the xref property.
protected void	setOriginalParticipant(XmlParticipantEvidence p)	Setter for the field originalParticipant.

Methods inherited from class psidev.psi.mi.jami.xml.model.extension.xml300.AbstractXmlFeature

getAliases, getAnnotations, getFullName, getId, getIdentifiers, getInterpro, getJAXBAttributeWrapper, getJAXBRangeWrapper, getLinkedFeatures, getParticipant, getRanges, getRole, getShortName, getType, getXrefs, initialiseAnnotationWrapper, initialiseLinkedFeatures, initialiseRangeWrapper, initialiseRole, setFullName, setId, setInterpro, setParticipant, setParticipantAndAddFeature, setRole, setShortName, setSourceLocator, setType, sourceLocation, 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.xml.model.extension.ExtendedPsiXmlFeature

getId, setId

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

XmlFeatureEvidence

public XmlFeatureEvidence()

Constructor for XmlFeatureEvidence.

XmlFeatureEvidence

public XmlFeatureEvidence(String shortName,
                          String fullName)

Constructor for XmlFeatureEvidence.

Parameters:

shortName - a String object.

fullName - a String object.

XmlFeatureEvidence

public XmlFeatureEvidence(CvTerm type)

Constructor for XmlFeatureEvidence.

Parameters:

type - a CvTerm object.

XmlFeatureEvidence

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

Constructor for XmlFeatureEvidence.

Parameters:

shortName - a String object.

fullName - a String object.

type - a CvTerm object.

XmlFeatureEvidence

public XmlFeatureEvidence(String shortName,
                          String fullName,
                          String interpro)

Constructor for XmlFeatureEvidence.

Parameters:

shortName - a String object.

fullName - a String object.

interpro - a String object.

XmlFeatureEvidence

public XmlFeatureEvidence(CvTerm type,
                          String interpro)

Constructor for XmlFeatureEvidence.

Parameters:

type - a CvTerm object.

interpro - a String object.

XmlFeatureEvidence

public XmlFeatureEvidence(String shortName,
                          String fullName,
                          CvTerm type,
                          String interpro)

Constructor for XmlFeatureEvidence.

Parameters:

shortName - a String object.

fullName - a String object.

type - a CvTerm object.

interpro - a String object.

Method Detail

getDetectionMethods

public Collection<CvTerm> getDetectionMethods()

getDetectionMethods.

Specified by:

getDetectionMethods in interface FeatureEvidence

Returns:

a Collection object.

getExperiments

public List<Experiment> getExperiments()

getExperiments.

Specified by:

getExperiments in interface ExtendedPsiXmlFeatureEvidence

Returns:

a List object.

setJAXBNames

public void setJAXBNames(NamesContainer value)

Sets the value of the names property.

Overrides:

setJAXBNames in class AbstractXmlFeature<ExperimentalEntity,FeatureEvidence>

Parameters:

value - allowed object is NamesContainer

setJAXBXref

public void setJAXBXref(FeatureXrefContainer value)

Sets the value of the xref property.

Overrides:

setJAXBXref in class AbstractXmlFeature<ExperimentalEntity,FeatureEvidence>

Parameters:

value - allowed object is FeatureXrefContainer

setJAXBType

public void setJAXBType(XmlCvTerm type)

setJAXBType.

Overrides:

setJAXBType in class AbstractXmlFeature<ExperimentalEntity,FeatureEvidence>

Parameters:

type - a XmlCvTerm object.

setJAXBFeatureRole

public void setJAXBFeatureRole(XmlCvTerm role)

setJAXBFeatureRole.

Overrides:

setJAXBFeatureRole in class AbstractXmlFeature<ExperimentalEntity,FeatureEvidence>

Parameters:

role - a XmlCvTerm object.

setJAXBAttributeWrapper

public void setJAXBAttributeWrapper(AbstractXmlFeature.JAXBAttributeWrapper jaxbAttributeWrapper)

setJAXBAttributeWrapper.

Overrides:

setJAXBAttributeWrapper in class AbstractXmlFeature<ExperimentalEntity,FeatureEvidence>

Parameters:

jaxbAttributeWrapper - a AbstractXmlFeature.JAXBAttributeWrapper object.

setJAXBRangeWrapper

public void setJAXBRangeWrapper(AbstractXmlFeature.JAXBRangeWrapper jaxbRangeWrapper)

setJAXBRangeWrapper.

Overrides:

setJAXBRangeWrapper in class AbstractXmlFeature<ExperimentalEntity,FeatureEvidence>

Parameters:

jaxbRangeWrapper - a AbstractXmlFeature.JAXBRangeWrapper object.

setJAXBId

public void setJAXBId(int id)

setJAXBId.

Parameters:

id - a int.

getJAXBFeatureDetectionMethods

public List<CvTerm> getJAXBFeatureDetectionMethods()

getJAXBFeatureDetectionMethods.

Returns:

a List object.

setJAXBExperimentRefWrapper

public void setJAXBExperimentRefWrapper(XmlFeatureEvidence.JAXBExperimentRefWrapper wrapper)

setJAXBExperimentRefWrapper.

Parameters:

wrapper - a XmlFeatureEvidence.JAXBExperimentRefWrapper object.

setJAXBParameterWrapper

public void setJAXBParameterWrapper(XmlFeatureEvidence.JAXBParameterWrapper wrapper)

setJAXBParameterWrapper.

Parameters:

wrapper - a XmlFeatureEvidence.JAXBParameterWrapper object.

getSourceLocator

public FileSourceLocator getSourceLocator()

Getter for the field sourceLocator.

Specified by:

getSourceLocator in interface FileSourceContext

Overrides:

getSourceLocator in class AbstractXmlFeature<ExperimentalEntity,FeatureEvidence>

Returns:

a FileSourceLocator object.

getParameters

public Collection<Parameter> getParameters()

Numerical parameters associated with this feature. The Collection cannot be null. If the feature does not have any parameters, the method should return an empty Collection.

Specified by:

getParameters in interface FeatureEvidence

Returns:

the parameters

initialiseDetectionMethods

protected void initialiseDetectionMethods()

initialiseDetectionMethods.

setOriginalParticipant

protected void setOriginalParticipant(XmlParticipantEvidence p)

Setter for the field originalParticipant.

Parameters:

p - a XmlParticipantEvidence object.