Package psidev.psi.mi.jami.xml.model.extension.xml254

Class AbstractXmlFeature<P extends Entity,F extends Feature>

java.lang.Object

psidev.psi.mi.jami.xml.model.extension.xml254.AbstractXmlFeature<P,F>

All Implemented Interfaces:

com.sun.xml.bind.Locatable, FileSourceContext, Feature<P,F>, ExtendedPsiXmlFeature<P,F>

Direct Known Subclasses:

XmlFeature, XmlFeatureEvidence, XmlModelledFeature

public abstract class AbstractXmlFeature<P extends Entity,F extends Feature>
extends Object
implements Feature<P,F>, FileSourceContext, com.sun.xml.bind.Locatable, ExtendedPsiXmlFeature<P,F>

Abstract class for Xml features

Since:

25/07/13

Version:

$Id$

Author:

Marine Dumousseau (marine@ebi.ac.uk)

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
static class	AbstractXmlFeature.JAXBAttributeWrapper
static class	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
AbstractXmlFeature()	Constructor for AbstractXmlFeature.
AbstractXmlFeature(String shortName, String fullName)	Constructor for AbstractXmlFeature.
AbstractXmlFeature(String shortName, String fullName, String interpro)	Constructor for AbstractXmlFeature.
AbstractXmlFeature(String shortName, String fullName, CvTerm type)	Constructor for AbstractXmlFeature.
AbstractXmlFeature(String shortName, String fullName, CvTerm type, String interpro)	Constructor for AbstractXmlFeature.
AbstractXmlFeature(CvTerm type)	Constructor for AbstractXmlFeature.
AbstractXmlFeature(CvTerm type, String interpro)	Constructor for AbstractXmlFeature.

Method Summary

Modifier and Type	Method	Description
List<Alias>	getAliases()	Collection of aliases for a feature.
Collection<Annotation>	getAnnotations()	getAnnotations.
String	getFullName()	getFullName.
int	getId()	Gets the value of the id property.
Collection<Xref>	getIdentifiers()	getIdentifiers.
String	getInterpro()	getInterpro.
protected AbstractXmlFeature.JAXBAttributeWrapper	getJAXBAttributeWrapper()	getJAXBAttributeWrapper.
protected AbstractXmlFeature.JAXBRangeWrapper	getJAXBRangeWrapper()	getJAXBRangeWrapper.
Collection<F>	getLinkedFeatures()	Getter for the field linkedFeatures.
P	getParticipant()	Getter for the field participant.
Collection<Range>	getRanges()	getRanges.
CvTerm	getRole()	Getter for the field role.
String	getShortName()	getShortName.
FileSourceLocator	getSourceLocator()	Getter for the field sourceLocator.
CvTerm	getType()	Getter for the field type.
Collection<Xref>	getXrefs()	getXrefs.
protected void	initialiseAnnotationWrapper()	initialiseAnnotationWrapper.
protected void	initialiseLinkedFeatures()	initialiseLinkedFeatures.
protected void	initialiseRangeWrapper()	initialiseRangeWrapper.
protected void	initialiseRole()	initialiseRole.
void	setFullName(String name)	Sets the full name that describes the molecule
void	setId(int value)	setId.
void	setInterpro(String interpro)	Sets the interpro identifier.
void	setJAXBAttributeWrapper(AbstractXmlFeature.JAXBAttributeWrapper jaxbAttributeWrapper)	setJAXBAttributeWrapper.
void	setJAXBFeatureRole(XmlCvTerm role)	setJAXBFeatureRole.
void	setJAXBNames(NamesContainer value)	Sets the value of the names property.
void	setJAXBRangeWrapper(AbstractXmlFeature.JAXBRangeWrapper jaxbRangeWrapper)	setJAXBRangeWrapper.
void	setJAXBType(XmlCvTerm type)	setJAXBType.
void	setJAXBXref(FeatureXrefContainer value)	Sets the value of the xref property.
void	setParticipant(P participant)	Setter for the field participant.
void	setParticipantAndAddFeature(P participant)	setParticipantAndAddFeature.
void	setRole(CvTerm effect)	Sets the interaction effect/role for this feature.
void	setShortName(String name)	Sets the short name of the feature
void	setSourceLocator(FileSourceLocator sourceLocator)	Sets the source locator
void	setType(CvTerm type)	Sets the feature type.
Locator	sourceLocation()
String	toString()	toString

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Constructor Detail

AbstractXmlFeature

public AbstractXmlFeature()

Constructor for AbstractXmlFeature.

AbstractXmlFeature

public AbstractXmlFeature(String shortName,
                          String fullName)

Constructor for AbstractXmlFeature.

Parameters:

shortName - a String object.

fullName - a String object.

AbstractXmlFeature

public AbstractXmlFeature(CvTerm type)

Constructor for AbstractXmlFeature.

Parameters:

type - a CvTerm object.

AbstractXmlFeature

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

Constructor for AbstractXmlFeature.

Parameters:

shortName - a String object.

fullName - a String object.

type - a CvTerm object.

AbstractXmlFeature

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

Constructor for AbstractXmlFeature.

Parameters:

shortName - a String object.

fullName - a String object.

interpro - a String object.

AbstractXmlFeature

public AbstractXmlFeature(CvTerm type,
                          String interpro)

Constructor for AbstractXmlFeature.

Parameters:

type - a CvTerm object.

interpro - a String object.

AbstractXmlFeature

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

Constructor for AbstractXmlFeature.

Parameters:

shortName - a String object.

fullName - a String object.

type - a CvTerm object.

interpro - a String object.

Method Detail

initialiseAnnotationWrapper

protected void initialiseAnnotationWrapper()

initialiseAnnotationWrapper.

initialiseRangeWrapper

protected void initialiseRangeWrapper()

initialiseRangeWrapper.

initialiseLinkedFeatures

protected void initialiseLinkedFeatures()

initialiseLinkedFeatures.

setJAXBNames

public void setJAXBNames(NamesContainer value)

Sets the value of the names property.

Parameters:

value - allowed object is NamesContainer

getShortName

public String getShortName()

getShortName.

Specified by:

getShortName in interface Feature<P extends Entity,F extends Feature>

Returns:

a String object.

setShortName

public void setShortName(String name)

Sets the short name of the feature

Specified by:

setShortName in interface Feature<P extends Entity,F extends Feature>

Parameters:

name - : short name

getFullName

public String getFullName()

getFullName.

Specified by:

getFullName in interface Feature<P extends Entity,F extends Feature>

Returns:

a String object.

setFullName

public void setFullName(String name)

Sets the full name that describes the molecule

Specified by:

setFullName in interface Feature<P extends Entity,F extends Feature>

Parameters:

name - : full name

getAliases

public List<Alias> getAliases()

Collection of aliases for a feature. The Collection cannot be null and if the experiment does not have any aliases, the method should return an empty Collection.

Specified by:

getAliases in interface Feature<P extends Entity,F extends Feature>

Returns:

the aliases

setJAXBXref

public void setJAXBXref(FeatureXrefContainer value)

Sets the value of the xref property.

Parameters:

value - allowed object is FeatureXrefContainer

getInterpro

public String getInterpro()

getInterpro.

Specified by:

getInterpro in interface Feature<P extends Entity,F extends Feature>

Returns:

a String object.

setInterpro

public void setInterpro(String interpro)

Sets the interpro identifier. It will remove the old interpro identifier and add a new interpro identity Xref in the list of identifiers. If interpro is null, it will remove all existing interpro Xref in the list of identifiers.

Specified by:

setInterpro in interface Feature<P extends Entity,F extends Feature>

Parameters:

interpro - : the new interpro identifier

getIdentifiers

public Collection<Xref> getIdentifiers()

getIdentifiers.

Specified by:

getIdentifiers in interface Feature<P extends Entity,F extends Feature>

Returns:

a Collection object.

getXrefs

public Collection<Xref> getXrefs()

getXrefs.

Specified by:

getXrefs in interface Feature<P extends Entity,F extends Feature>

Returns:

a Collection object.

getAnnotations

public Collection<Annotation> getAnnotations()

getAnnotations.

Specified by:

getAnnotations in interface Feature<P extends Entity,F extends Feature>

Returns:

a Collection object.

getType

public CvTerm getType()

Getter for the field type.

Specified by:

getType in interface Feature<P extends Entity,F extends Feature>

Returns:

a CvTerm object.

setType

public void setType(CvTerm type)

Sets the feature type.

Specified by:

setType in interface Feature<P extends Entity,F extends Feature>

Parameters:

type - : feature type

setJAXBType

public void setJAXBType(XmlCvTerm type)

setJAXBType.

Parameters:

type - a XmlCvTerm object.

getRanges

public Collection<Range> getRanges()

getRanges.

Specified by:

getRanges in interface Feature<P extends Entity,F extends Feature>

Returns:

a Collection object.

getRole

public CvTerm getRole()

Getter for the field role.

Specified by:

getRole in interface Feature<P extends Entity,F extends Feature>

Returns:

a CvTerm object.

setRole

public void setRole(CvTerm effect)

Sets the interaction effect/role for this feature.

Specified by:

setRole in interface Feature<P extends Entity,F extends Feature>

Parameters:

effect - : the feature role

getParticipant

public P getParticipant()

Getter for the field participant.

Specified by:

getParticipant in interface Feature<P extends Entity,F extends Feature>

Returns:

a P object.

setParticipant

public void setParticipant(P participant)

Setter for the field participant.

Specified by:

setParticipant in interface Feature<P extends Entity,F extends Feature>

Parameters:

participant - a P object.

setParticipantAndAddFeature

public void setParticipantAndAddFeature(P participant)

setParticipantAndAddFeature.

Specified by:

setParticipantAndAddFeature in interface Feature<P extends Entity,F extends Feature>

Parameters:

participant - a P object.

getLinkedFeatures

public Collection<F> getLinkedFeatures()

Getter for the field linkedFeatures.

Specified by:

getLinkedFeatures in interface Feature<P extends Entity,F extends Feature>

Returns:

a Collection object.

toString

public String toString()

toString

Specified by:

toString in interface FileSourceContext

Overrides:

toString in class Object

Returns:

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

sourceLocation

public Locator sourceLocation()

Specified by:

sourceLocation in interface com.sun.xml.bind.Locatable

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

getId

public int getId()

Gets the value of the id property.

Specified by:

getId in interface ExtendedPsiXmlFeature<P extends Entity,F extends Feature>

Returns:

a int.

setId

public void setId(int value)

setId.

Sets the value of the id property. Adds this object in the mapOfReferencedObjects of this entry

Specified by:

setId in interface ExtendedPsiXmlFeature<P extends Entity,F extends Feature>

Parameters:

value - a int.

setJAXBAttributeWrapper

public void setJAXBAttributeWrapper(AbstractXmlFeature.JAXBAttributeWrapper jaxbAttributeWrapper)

setJAXBAttributeWrapper.

Parameters:

jaxbAttributeWrapper - a AbstractXmlFeature.JAXBAttributeWrapper object.

setJAXBRangeWrapper

public void setJAXBRangeWrapper(AbstractXmlFeature.JAXBRangeWrapper jaxbRangeWrapper)

setJAXBRangeWrapper.

Parameters:

jaxbRangeWrapper - a AbstractXmlFeature.JAXBRangeWrapper object.

setJAXBFeatureRole

public void setJAXBFeatureRole(XmlCvTerm role)

setJAXBFeatureRole.

Parameters:

role - a XmlCvTerm object.

getJAXBRangeWrapper

protected AbstractXmlFeature.JAXBRangeWrapper getJAXBRangeWrapper()

getJAXBRangeWrapper.

Returns:

a AbstractXmlFeature.JAXBRangeWrapper object.

getJAXBAttributeWrapper

protected AbstractXmlFeature.JAXBAttributeWrapper getJAXBAttributeWrapper()

getJAXBAttributeWrapper.

Returns:

a AbstractXmlFeature.JAXBAttributeWrapper object.

initialiseRole

protected void initialiseRole()

initialiseRole.