Package psidev.psi.mi.jami.xml.model.reference

Class AbstractFeatureRef<E extends Entity,F extends Feature>

java.lang.Object

psidev.psi.mi.jami.xml.model.reference.AbstractXmlIdReference

psidev.psi.mi.jami.xml.model.reference.AbstractFeatureRef<E,F>

All Implemented Interfaces:

FileSourceContext, Feature<E,F>, ExtendedPsiXmlFeature<E,F>, XmlIdReference

public abstract class AbstractFeatureRef<E extends Entity,F extends Feature>
extends AbstractXmlIdReference
implements ExtendedPsiXmlFeature<E,F>

Abstract feature reference

Since:

11/10/13

Version:

$Id$

Author:

Marine Dumousseau (marine@ebi.ac.uk)

Field Summary

Fields inherited from class psidev.psi.mi.jami.xml.model.reference.AbstractXmlIdReference

ref

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
AbstractFeatureRef(int ref)	Constructor for AbstractFeatureRef.

Method Summary

Modifier and Type	Method	Description
Collection<Alias>	getAliases()	Collection of aliases for a feature.
Collection<Annotation>	getAnnotations()	getAnnotations.
protected ExtendedPsiXmlFeature<E,F>	getDelegate()	Getter for the field delegate.
String	getFullName()	getFullName.
int	getId()	getId.
Collection<Xref>	getIdentifiers()	getIdentifiers.
String	getInterpro()	getInterpro.
Collection<F>	getLinkedFeatures()	getLinkedFeatures.
E	getParticipant()	getParticipant.
Collection<Range>	getRanges()	getRanges.
CvTerm	getRole()	getRole.
String	getShortName()	getShortName.
CvTerm	getType()	getType.
Collection<Xref>	getXrefs()	getXrefs.
protected abstract void	initialiseFeatureDelegate()	initialiseFeatureDelegate.
protected void	setDelegate(ExtendedPsiXmlFeature<E,F> delegate)	Setter for the field delegate.
void	setFullName(String name)	Sets the full name that describes the molecule
void	setId(int id)	setId.
void	setInterpro(String interpro)	Sets the interpro identifier.
void	setParticipant(E participant)	setParticipant.
void	setParticipantAndAddFeature(E 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	setType(CvTerm type)	Sets the feature type.
String	toString()	toString

Methods inherited from class psidev.psi.mi.jami.xml.model.reference.AbstractXmlIdReference

getRef, registerForResolution

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.datasource.FileSourceContext

getSourceLocator, setSourceLocator

Methods inherited from interface psidev.psi.mi.jami.xml.model.reference.XmlIdReference

resolve

Constructor Detail

AbstractFeatureRef

public AbstractFeatureRef(int ref)

Constructor for AbstractFeatureRef.

Parameters:

ref - a int.

Method Detail

getShortName

public String getShortName()

getShortName.

Specified by:

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

Parameters:

name - : short name

getFullName

public String getFullName()

getFullName.

Specified by:

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

Parameters:

name - : full name

getInterpro

public String getInterpro()

getInterpro.

Specified by:

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

Parameters:

interpro - : the new interpro identifier

getIdentifiers

public Collection<Xref> getIdentifiers()

getIdentifiers.

Specified by:

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

Returns:

a Collection object.

getXrefs

public Collection<Xref> getXrefs()

getXrefs.

Specified by:

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

Returns:

a Collection object.

getAnnotations

public Collection<Annotation> getAnnotations()

getAnnotations.

Specified by:

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

Returns:

a Collection object.

getType

public CvTerm getType()

getType.

Specified by:

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

Parameters:

type - : feature type

getRanges

public Collection<Range> getRanges()

getRanges.

Specified by:

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

Returns:

a Collection object.

getRole

public CvTerm getRole()

getRole.

Specified by:

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

Parameters:

effect - : the feature role

getParticipant

public E getParticipant()

getParticipant.

Specified by:

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

Returns:

a E object.

setParticipant

public void setParticipant(E participant)

setParticipant.

Specified by:

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

Parameters:

participant - a E object.

setParticipantAndAddFeature

public void setParticipantAndAddFeature(E participant)

setParticipantAndAddFeature.

Specified by:

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

Parameters:

participant - a E object.

getLinkedFeatures

public Collection<F> getLinkedFeatures()

getLinkedFeatures.

Specified by:

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

Returns:

a Collection object.

setId

public void setId(int id)

setId.

Specified by:

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

Parameters:

id - a int.

getId

public int getId()

getId.

Specified by:

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

Returns:

a int.

getAliases

public Collection<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<E extends Entity,F extends Feature>

Returns:

the aliases

toString

public String toString()

toString

Specified by:

toString in interface FileSourceContext

Overrides:

toString in class AbstractXmlIdReference

Returns:

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

initialiseFeatureDelegate

protected abstract void initialiseFeatureDelegate()

initialiseFeatureDelegate.

getDelegate

protected ExtendedPsiXmlFeature<E,F> getDelegate()

Getter for the field delegate.

Returns:

a ExtendedPsiXmlFeature object.

setDelegate

protected void setDelegate(ExtendedPsiXmlFeature<E,F> delegate)

Setter for the field delegate.

Parameters:

delegate - a ExtendedPsiXmlFeature object.