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

Class AbstractFeature<P extends Entity,F extends Feature>

java.lang.Object

psidev.psi.mi.jami.model.impl.AbstractFeature<P,F>

All Implemented Interfaces:

Feature<P,F>

Direct Known Subclasses:

DefaultFeature, DefaultFeatureEvidence, DefaultModelledFeature

public abstract class AbstractFeature<P extends Entity,F extends Feature>
extends Object
implements Feature<P,F>

Abstract class for Feature

Since:

09/07/13

Version:

$Id$

Author:

Marine Dumousseau (marine@ebi.ac.uk)

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
protected class	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
AbstractFeature()	Constructor for AbstractFeature.
AbstractFeature(String shortName, String fullName)	Constructor for AbstractFeature.
AbstractFeature(String shortName, String fullName, String interpro)	Constructor for AbstractFeature.
AbstractFeature(String shortName, String fullName, CvTerm type)	Constructor for AbstractFeature.
AbstractFeature(String shortName, String fullName, CvTerm type, String interpro)	Constructor for AbstractFeature.
AbstractFeature(CvTerm type)	Constructor for AbstractFeature.
AbstractFeature(CvTerm type, String interpro)	Constructor for AbstractFeature.

Method Summary

Modifier and Type	Method	Description
protected void	clearPropertiesLinkedToIdentifiers()	clearPropertiesLinkedToIdentifiers
Collection<Alias>	getAliases()	Getter for the field aliases.
Collection<Annotation>	getAnnotations()	Getter for the field annotations.
String	getFullName()	Getter for the field fullName.
Collection<Xref>	getIdentifiers()	Getter for the field identifiers.
String	getInterpro()	Getter for the field interpro.
Collection<F>	getLinkedFeatures()	Getter for the field linkedFeatures.
P	getParticipant()	Getter for the field participant.
Collection<Range>	getRanges()	Getter for the field ranges.
CvTerm	getRole()	Getter for the field role.
String	getShortName()	Getter for the field shortName.
CvTerm	getType()	Getter for the field type.
Collection<Xref>	getXrefs()	Getter for the field xrefs.
protected void	initialiseAliases()	initialiseAliases
protected void	initialiseAliasesWith(Collection<Alias> aliases)	initialiseAliasesWith
protected void	initialiseAnnotations()	initialiseAnnotations
protected void	initialiseAnnotationsWith(Collection<Annotation> annotations)	initialiseAnnotationsWith
protected void	initialiseIdentifiers()	initialiseIdentifiers
protected void	initialiseIdentifiersWith(Collection<Xref> identifiers)	initialiseIdentifiersWith
protected void	initialiseLinkedFeatures()	initialiseLinkedFeatures
protected void	initialiseLinkedFeaturesWith(Collection<F> features)	initialiseLinkedFeaturesWith
protected void	initialiseRanges()	initialiseRanges
protected void	initialiseRangesWith(Collection<Range> ranges)	initialiseRangesWith
protected void	initialiseXrefs()	initialiseXrefs
protected void	initialiseXrefsWith(Collection<Xref> xrefs)	initialiseXrefsWith
protected void	processAddedIdentifierEvent(Xref added)	processAddedIdentifierEvent
protected void	processRemovedIdentifierEvent(Xref removed)	processRemovedIdentifierEvent
void	setFullName(String name)	Sets the full name that describes the molecule
void	setInterpro(String interpro)	Sets the interpro identifier.
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	setType(CvTerm type)	Sets the feature type.
String	toString()

Methods inherited from class java.lang.Object

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

Constructor Detail

AbstractFeature

public AbstractFeature()

Constructor for AbstractFeature.

AbstractFeature

public AbstractFeature(String shortName,
                       String fullName)

Constructor for AbstractFeature.

Parameters:

shortName - a String object.

fullName - a String object.

AbstractFeature

public AbstractFeature(CvTerm type)

Constructor for AbstractFeature.

Parameters:

type - a CvTerm object.

AbstractFeature

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

Constructor for AbstractFeature.

Parameters:

shortName - a String object.

fullName - a String object.

type - a CvTerm object.

AbstractFeature

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

Constructor for AbstractFeature.

Parameters:

shortName - a String object.

fullName - a String object.

interpro - a String object.

AbstractFeature

public AbstractFeature(CvTerm type,
                       String interpro)

Constructor for AbstractFeature.

Parameters:

type - a CvTerm object.

interpro - a String object.

AbstractFeature

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

Constructor for AbstractFeature.

Parameters:

shortName - a String object.

fullName - a String object.

type - a CvTerm object.

interpro - a String object.

Method Detail

initialiseIdentifiers

protected void initialiseIdentifiers()

initialiseIdentifiers

initialiseAnnotations

protected void initialiseAnnotations()

initialiseAnnotations

initialiseXrefs

protected void initialiseXrefs()

initialiseXrefs

initialiseRanges

protected void initialiseRanges()

initialiseRanges

initialiseIdentifiersWith

protected void initialiseIdentifiersWith(Collection<Xref> identifiers)

initialiseIdentifiersWith

Parameters:

identifiers - a Collection object.

initialiseAnnotationsWith

protected void initialiseAnnotationsWith(Collection<Annotation> annotations)

initialiseAnnotationsWith

Parameters:

annotations - a Collection object.

initialiseXrefsWith

protected void initialiseXrefsWith(Collection<Xref> xrefs)

initialiseXrefsWith

Parameters:

xrefs - a Collection object.

initialiseRangesWith

protected void initialiseRangesWith(Collection<Range> ranges)

initialiseRangesWith

Parameters:

ranges - a Collection object.

initialiseLinkedFeatures

protected void initialiseLinkedFeatures()

initialiseLinkedFeatures

initialiseLinkedFeaturesWith

protected void initialiseLinkedFeaturesWith(Collection<F> features)

initialiseLinkedFeaturesWith

Parameters:

features - a Collection object.

initialiseAliases

protected void initialiseAliases()

initialiseAliases

initialiseAliasesWith

protected void initialiseAliasesWith(Collection<Alias> aliases)

initialiseAliasesWith

Parameters:

aliases - a Collection object.

getShortName

public String getShortName()

Getter for the field shortName.

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()

Getter for the field fullName.

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

getInterpro

public String getInterpro()

Getter for the field interpro.

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()

Getter for the field identifiers.

Specified by:

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

Returns:

a Collection object.

getXrefs

public Collection<Xref> getXrefs()

Getter for the field xrefs.

Specified by:

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

Returns:

a Collection object.

getAnnotations

public Collection<Annotation> getAnnotations()

Getter for the field annotations.

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

getRanges

public Collection<Range> getRanges()

Getter for the field ranges.

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.

getAliases

public Collection<Alias> getAliases()

Getter for the field aliases.

Specified by:

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

Returns:

a Collection object.

processAddedIdentifierEvent

protected void processAddedIdentifierEvent(Xref added)

processAddedIdentifierEvent

Parameters:

added - a Xref object.

processRemovedIdentifierEvent

protected void processRemovedIdentifierEvent(Xref removed)

processRemovedIdentifierEvent

Parameters:

removed - a Xref object.

clearPropertiesLinkedToIdentifiers

protected void clearPropertiesLinkedToIdentifiers()

clearPropertiesLinkedToIdentifiers

toString

public String toString()

Overrides:

toString in class Object