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

Class AbstractXmlCooperativeEffect

java.lang.Object

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

All Implemented Interfaces:

com.sun.xml.bind.Locatable, FileSourceContext, CooperativeEffect

Direct Known Subclasses:

XmlAllostery, XmlPreAssembly

public abstract class AbstractXmlCooperativeEffect
extends Object
implements CooperativeEffect, FileSourceContext, com.sun.xml.bind.Locatable

Abstract class for XML 3.0 cooperative effects

Since:

29/05/14

Version:

$Id$

Author:

Marine Dumousseau (marine@ebi.ac.uk)

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
static class	AbstractXmlCooperativeEffect.JAXBAffectedInteractionRefWrapper
static class	AbstractXmlCooperativeEffect.JAXBAttributeWrapper
static class	AbstractXmlCooperativeEffect.JAXBCooperativityEvidenceWrapper

Field Summary

Fields inherited from interface psidev.psi.mi.jami.model.CooperativeEffect

AFFECTED_INTERACTION, AFFECTED_INTERACTION_ID, ALLOSTERIC_DYNAMIC_CHANGE, ALLOSTERIC_DYNAMIC_CHANGE_ID, ALLOSTERIC_EFFECTOR, ALLOSTERIC_EFFECTOR_ID, ALLOSTERIC_K_RESPONSE, ALLOSTERIC_K_RESPONSE_ID, ALLOSTERIC_MOLECULE, ALLOSTERIC_MOLECULE_ID, ALLOSTERIC_PTM, ALLOSTERIC_PTM_ID, ALLOSTERIC_STRUCTURE_CHANE, ALLOSTERIC_STRUCTURE_CHANE_ID, ALLOSTERIC_V_RESPONSE, ALLOSTERIC_V_RESPONSE_ID, ALLOSTERY, ALLOSTERY_ID, ALTERED_PHYSICO_COMPATIBILITY, ALTERED_PHYSICO_COMPATIBILITY_ID, BINDING_HIDING, BINDING_HIDING_ID, COMPOSITE_BINDING, COMPOSITE_BINDING_ID, COOPERATIVE_EFFECT_VALUE, COOPERATIVE_EFFECT_VALUE_ID, EFFECT_OUTCOME, EFFECT_OUTCOME_MI, HETEROTROPIC_ALLOSTERY, HETEROTROPIC_ALLOSTERY_ID, HOMOTROPIC_ALLOSTERY, HOMOTROPIC_ALLOSTERY_ID, NEGATIVE_EFFECT, NEGATIVE_EFFECT_ID, PARTICIPANT_REF, PARTICIPANT_REF_ID, POSITIVE_EFFECT, POSITIVE_EFFECT_ID, PRE_ORGANIZATION, PRE_ORGANIZATION_ID, PREASSEMBLY, PREASSEMBLY_ID

Constructor Summary

Constructors

Constructor	Description
AbstractXmlCooperativeEffect()	Constructor for AbstractXmlCooperativeEffect.
AbstractXmlCooperativeEffect(CvTerm outcome)	Constructor for AbstractXmlCooperativeEffect.
AbstractXmlCooperativeEffect(CvTerm outcome, CvTerm response)	Constructor for AbstractXmlCooperativeEffect.

Method Summary

Modifier and Type	Method	Description
void	addAffectedInteractionRef(int affectedInteraction, PsiXmlLocator locator)	addAffectedInteractionRef.
Collection<ModelledInteraction>	getAffectedInteractions()	getAffectedInteractions.
Collection<Annotation>	getAnnotations()	getAnnotations.
Collection<CooperativityEvidence>	getCooperativityEvidences()	getCooperativityEvidences.
CvTerm	getOutCome()	getOutCome.
CvTerm	getResponse()	Getter for the field response.
FileSourceLocator	getSourceLocator()	Getter for the field sourceLocator.
protected void	initialiseAffectedInteractions()	initialiseAffectedInteractions.
protected void	initialiseAnnotations()	initialiseAnnotations.
protected void	initialiseCooperativityEvidences()	initialiseCooperativityEvidences.
void	setJAXBAffectedInteractionWrapper(AbstractXmlCooperativeEffect.JAXBAffectedInteractionRefWrapper wrapper)	setJAXBAffectedInteractionWrapper.
void	setJAXBAttributeWrapper(AbstractXmlCooperativeEffect.JAXBAttributeWrapper wrapper)	setJAXBAttributeWrapper.
void	setJAXBCooperativityEvidenceWrapper(AbstractXmlCooperativeEffect.JAXBCooperativityEvidenceWrapper wrapper)	setJAXBCooperativityEvidenceWrapper.
void	setJAXBOutCome(XmlCvTerm outcome)	setJAXBOutCome.
void	setJAXBResponse(XmlCvTerm response)	setJAXBResponse.
void	setOutCome(CvTerm effect)	Sets the cooperative effect outcome
void	setResponse(CvTerm response)	Sets the response.
void	setSourceLocation(PsiXmlLocator sourceLocator)	setSourceLocation.
void	setSourceLocator(FileSourceLocator sourceLocator)	Sets the source locator
Locator	sourceLocation()
String	toString()	toString

Methods inherited from class java.lang.Object

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

Constructor Detail

AbstractXmlCooperativeEffect

public AbstractXmlCooperativeEffect()

Constructor for AbstractXmlCooperativeEffect.

AbstractXmlCooperativeEffect

public AbstractXmlCooperativeEffect(CvTerm outcome)

Constructor for AbstractXmlCooperativeEffect.

Parameters:

outcome - a CvTerm object.

AbstractXmlCooperativeEffect

public AbstractXmlCooperativeEffect(CvTerm outcome,
                                    CvTerm response)

Constructor for AbstractXmlCooperativeEffect.

Parameters:

outcome - a CvTerm object.

response - a CvTerm object.

Method Detail

initialiseCooperativityEvidences

protected void initialiseCooperativityEvidences()

initialiseCooperativityEvidences.

initialiseAffectedInteractions

protected void initialiseAffectedInteractions()

initialiseAffectedInteractions.

initialiseAnnotations

protected void initialiseAnnotations()

initialiseAnnotations.

getCooperativityEvidences

public Collection<CooperativityEvidence> getCooperativityEvidences()

getCooperativityEvidences.

Specified by:

getCooperativityEvidences in interface CooperativeEffect

Returns:

a Collection object.

getAffectedInteractions

public Collection<ModelledInteraction> getAffectedInteractions()

getAffectedInteractions.

Specified by:

getAffectedInteractions in interface CooperativeEffect

Returns:

a Collection object.

addAffectedInteractionRef

public void addAffectedInteractionRef(int affectedInteraction,
                                      PsiXmlLocator locator)

addAffectedInteractionRef.

Parameters:

affectedInteraction - a int.

locator - a PsiXmlLocator object.

getAnnotations

public Collection<Annotation> getAnnotations()

getAnnotations.

Specified by:

getAnnotations in interface CooperativeEffect

Returns:

a Collection object.

getOutCome

public CvTerm getOutCome()

getOutCome.

Specified by:

getOutCome in interface CooperativeEffect

Returns:

a CvTerm object.

setOutCome

public void setOutCome(CvTerm effect)

Sets the cooperative effect outcome

Specified by:

setOutCome in interface CooperativeEffect

Parameters:

effect - : cooperative effect outcome

getResponse

public CvTerm getResponse()

Getter for the field response.

Specified by:

getResponse in interface CooperativeEffect

Returns:

a CvTerm object.

setResponse

public void setResponse(CvTerm response)

Sets the response.

Specified by:

setResponse in interface CooperativeEffect

Parameters:

response - : the allosteric or pre-assembly response

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

setSourceLocation

public void setSourceLocation(PsiXmlLocator sourceLocator)

setSourceLocation.

Parameters:

sourceLocator - a PsiXmlLocator object.

setJAXBCooperativityEvidenceWrapper

public void setJAXBCooperativityEvidenceWrapper(AbstractXmlCooperativeEffect.JAXBCooperativityEvidenceWrapper wrapper)

setJAXBCooperativityEvidenceWrapper.

Parameters:

wrapper - a AbstractXmlCooperativeEffect.JAXBCooperativityEvidenceWrapper object.

setJAXBAffectedInteractionWrapper

public void setJAXBAffectedInteractionWrapper(AbstractXmlCooperativeEffect.JAXBAffectedInteractionRefWrapper wrapper)

setJAXBAffectedInteractionWrapper.

Parameters:

wrapper - a AbstractXmlCooperativeEffect.JAXBAffectedInteractionRefWrapper object.

setJAXBOutCome

public void setJAXBOutCome(XmlCvTerm outcome)

setJAXBOutCome.

Parameters:

outcome - a XmlCvTerm object.

setJAXBResponse

public void setJAXBResponse(XmlCvTerm response)

setJAXBResponse.

Parameters:

response - a XmlCvTerm object.

setJAXBAttributeWrapper

public void setJAXBAttributeWrapper(AbstractXmlCooperativeEffect.JAXBAttributeWrapper wrapper)

setJAXBAttributeWrapper.

Parameters:

wrapper - a AbstractXmlCooperativeEffect.JAXBAttributeWrapper object.