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

Class XmlFeatureEvidenceWrapper

java.lang.Object

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

All Implemented Interfaces:

FileSourceContext, Feature<ModelledEntity,ModelledFeature>, ModelledFeature, ExtendedPsiXmlFeature<ModelledEntity,ModelledFeature>

public class XmlFeatureEvidenceWrapper
extends Object
implements ModelledFeature, ExtendedPsiXmlFeature<ModelledEntity,ModelledFeature>, FileSourceContext

Xml wrapper for feature evidences. The new linked features added to this wrapper are NOT added to the wrapped feature evidence because they are incompatibles.

Since:

11/10/13

Version:

$Id$

Author:

Marine Dumousseau (marine@ebi.ac.uk)

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
XmlFeatureEvidenceWrapper(ExtendedPsiXmlFeatureEvidence part, ModelledEntity wrapper)	Constructor for XmlFeatureEvidenceWrapper.

Method Summary

Modifier and Type	Method	Description
Collection<Alias>	getAliases()	Collection of aliases for a feature.
Collection<Annotation>	getAnnotations()	Collection of annotations which describe the feature The set cannot be null.
String	getFullName()	The full name that describes the feature.
int	getId()	getId.
Collection<Xref>	getIdentifiers()	Collection of External identifiers which describes this feature.
String	getInterpro()	The interpro identifier if it exists, null otherwise.
Collection<ModelledFeature>	getLinkedFeatures()	The other features that can bind to this feature.
ModelledEntity	getParticipant()	The participant to which the feature is attached.
Collection<Range>	getRanges()	The ranges which locate the feature in the interactor sequence/structure.
CvTerm	getRole()	The effect of this feature on the interaction where the feature has been reported or the interaction dependency between the interaction reporting this feature and this feature.
String	getShortName()	The short name of a feature.
FileSourceLocator	getSourceLocator()	The locator of a position in a file.
CvTerm	getType()	The type for this feature.
ExtendedPsiXmlFeatureEvidence	getWrappedFeature()	getWrappedFeature.
Collection<Xref>	getXrefs()	Collection of cross references which give more information about the feature.
protected void	initialiseLinkedFeatures()	initialiseLinkedFeatures.
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(ModelledEntity participant)	Sets the participant.
void	setParticipantAndAddFeature(ModelledEntity participant)	Sets the participant and add this feature to its list of features.
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 locator)	Sets the source locator
void	setType(CvTerm type)	Sets the feature type.
String	toString()	toString

Methods inherited from class java.lang.Object

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

Constructor Detail

XmlFeatureEvidenceWrapper

public XmlFeatureEvidenceWrapper(ExtendedPsiXmlFeatureEvidence part,
                                 ModelledEntity wrapper)

Constructor for XmlFeatureEvidenceWrapper.

Parameters:

part - a ExtendedPsiXmlFeatureEvidence object.

wrapper - a ModelledEntity object.

Method Detail

getShortName

public String getShortName()

The short name of a feature. It can be null Ex: region, SH3 domains

Specified by:

getShortName in interface Feature<ModelledEntity,ModelledFeature>

Returns:

the short name

setShortName

public void setShortName(String name)

Sets the short name of the feature

Specified by:

setShortName in interface Feature<ModelledEntity,ModelledFeature>

Parameters:

name - : short name

getFullName

public String getFullName()

The full name that describes the feature. It can be null. Ex: SWIB/MDM2 domain (IPR003121)

Specified by:

getFullName in interface Feature<ModelledEntity,ModelledFeature>

Returns:

the full name

setFullName

public void setFullName(String name)

Sets the full name that describes the molecule

Specified by:

setFullName in interface Feature<ModelledEntity,ModelledFeature>

Parameters:

name - : full name

getInterpro

public String getInterpro()

The interpro identifier if it exists, null otherwise. It is a shortcut to the first interpro identifier in the list of identifiers.

Specified by:

getInterpro in interface Feature<ModelledEntity,ModelledFeature>

Returns:

the interpro identifier if it exists.

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<ModelledEntity,ModelledFeature>

Parameters:

interpro - : the new interpro identifier

getIdentifiers

public Collection<Xref> getIdentifiers()

Collection of External identifiers which describes this feature. The Collection cannot be null and if the feature is not described in an external databases, the method should return an empty Collection. Ex: interpro:IPR003121

Specified by:

getIdentifiers in interface Feature<ModelledEntity,ModelledFeature>

Returns:

the identifier

getXrefs

public Collection<Xref> getXrefs()

Collection of cross references which give more information about the feature. The set cannot be null. If the feature does not have any other xrefs, the method should return an empty Collection. Ex: GO xrefs to give information about process or function

Specified by:

getXrefs in interface Feature<ModelledEntity,ModelledFeature>

Returns:

the xrefs

getAnnotations

public Collection<Annotation> getAnnotations()

Collection of annotations which describe the feature The set cannot be null. If the feature does not have any annotations, the method should return an empty Collection. Ex: observed ptm, cautions, comments, ...

Specified by:

getAnnotations in interface Feature<ModelledEntity,ModelledFeature>

Returns:

the annotations

getType

public CvTerm getType()

The type for this feature. It is a controlled vocabulary term and can be null. Ex: fluorophore, tag, mutation, ...

Specified by:

getType in interface Feature<ModelledEntity,ModelledFeature>

Returns:

The feature type

setType

public void setType(CvTerm type)

Sets the feature type.

Specified by:

setType in interface Feature<ModelledEntity,ModelledFeature>

Parameters:

type - : feature type

getRanges

public Collection<Range> getRanges()

The ranges which locate the feature in the interactor sequence/structure. The collection cannot be null. If the feature does not have any ranges, the method should return an empty collection

Specified by:

getRanges in interface Feature<ModelledEntity,ModelledFeature>

Returns:

a collection of ranges

getRole

public CvTerm getRole()

The effect of this feature on the interaction where the feature has been reported or the interaction dependency between the interaction reporting this feature and this feature. It can be null if the feature does not have any effects on the interaction or it is not relevant Ex: increasing interaction, decreasing interaction, disrupting interaction, etc. Ex: resulting-ptm,prerequisite-ptm ...

Specified by:

getRole in interface Feature<ModelledEntity,ModelledFeature>

Returns:

the effect of this feature on the interaction

setRole

public void setRole(CvTerm effect)

Sets the interaction effect/role for this feature.

Specified by:

setRole in interface Feature<ModelledEntity,ModelledFeature>

Parameters:

effect - : the feature role

getParticipant

public ModelledEntity getParticipant()

The participant to which the feature is attached. It can be any entity (participant, participant pool, participant candidate, etc.) It can be null if the feature is not attached to any participants.

Specified by:

getParticipant in interface Feature<ModelledEntity,ModelledFeature>

Returns:

the participant

setParticipant

public void setParticipant(ModelledEntity participant)

Sets the participant.

Specified by:

setParticipant in interface Feature<ModelledEntity,ModelledFeature>

Parameters:

participant - : participant

setParticipantAndAddFeature

public void setParticipantAndAddFeature(ModelledEntity participant)

Sets the participant and add this feature to its list of features. If participant is null, it will remove this feature from the previous participant attached to this feature

Specified by:

setParticipantAndAddFeature in interface Feature<ModelledEntity,ModelledFeature>

Parameters:

participant - : participant

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<ModelledEntity,ModelledFeature>

Returns:

the aliases

getLinkedFeatures

public Collection<ModelledFeature> getLinkedFeatures()

The other features that can bind to this feature. The collection cannot be null. If the feature does not bind with any other features, the method should return an empty collection

Specified by:

getLinkedFeatures in interface Feature<ModelledEntity,ModelledFeature>

Returns:

the binding features

getSourceLocator

public FileSourceLocator getSourceLocator()

The locator of a position in a file. It can be null

Specified by:

getSourceLocator in interface FileSourceContext

Returns:

the file locator

setSourceLocator

public void setSourceLocator(FileSourceLocator locator)

Sets the source locator

Specified by:

setSourceLocator in interface FileSourceContext

Parameters:

locator - : the file locator

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

getWrappedFeature

public ExtendedPsiXmlFeatureEvidence getWrappedFeature()

getWrappedFeature.

Returns:

a ExtendedPsiXmlFeatureEvidence object.

initialiseLinkedFeatures

protected void initialiseLinkedFeatures()

initialiseLinkedFeatures.

getId

public int getId()

getId.

Specified by:

getId in interface ExtendedPsiXmlFeature<ModelledEntity,ModelledFeature>

Returns:

a int.

setId

public void setId(int id)

setId.

Specified by:

setId in interface ExtendedPsiXmlFeature<ModelledEntity,ModelledFeature>

Parameters:

id - a int.