Package psidev.psi.mi.jami.xml.model.extension.xml253

Class XmlAllostery<T extends AllostericEffector>

java.lang.Object

psidev.psi.mi.jami.model.impl.DefaultCooperativeEffect

psidev.psi.mi.jami.xml.model.extension.xml253.XmlAllostery<T>

All Implemented Interfaces:

FileSourceContext, Allostery<T>, CooperativeEffect

public class XmlAllostery<T extends AllostericEffector>
extends DefaultCooperativeEffect
implements FileSourceContext, Allostery<T>

XML implementation of Allostery

Since:

15/11/13

Version:

$Id$

Author:

Marine Dumousseau (marine@ebi.ac.uk)

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
XmlAllostery(CvTerm outcome)	Constructor for XmlAllostery.
XmlAllostery(CvTerm outcome, CvTerm response)	Constructor for XmlAllostery.

Method Summary

Modifier and Type	Method	Description
void	addAffectedInteractionRef(int affectedInteraction, PsiXmlLocator locator)	addAffectedInteractionRef.
T	getAllostericEffector()	Getter for the field allostericEffector.
CvTerm	getAllostericMechanism()	Getter for the field allostericMechanism.
ModelledEntity	getAllostericMolecule()	Getter for the field allostericMolecule.
CvTerm	getAllosteryType()	Getter for the field allosteryType.
FileSourceLocator	getSourceLocator()	Getter for the field sourceLocator.
void	setAllostericEffector(T effector)	Setter for the field allostericEffector.
void	setAllostericEffectorRef(int ref, PsiXmlLocator locator)	setAllostericEffectorRef.
void	setAllostericMechanism(CvTerm mechanism)	Sets the allosteric mechanism.
void	setAllostericMolecule(ModelledEntity participant)	Sets the allosteric molecule.
void	setAllostericMoleculeRef(int ref, PsiXmlLocator locator)	setAllostericMoleculeRef.
void	setAllostericPTMRef(int ref, PsiXmlLocator locator)	setAllostericPTMRef.
void	setAllosteryType(CvTerm type)	Sets the allostery type.
void	setSourceLocator(FileSourceLocator locator)	Sets the source locator
void	setSourceLocator(PsiXmlLocator locator)	Setter for the field sourceLocator.
String	toString()

Methods inherited from class psidev.psi.mi.jami.model.impl.DefaultCooperativeEffect

getAffectedInteractions, getAnnotations, getCooperativityEvidences, getOutCome, getResponse, initialiseAffectedInteractions, initialiseAffectedInteractionsWith, initialiseAnnotations, initialiseAnnotationsWith, initialiseCooperativityEvidences, initialiseCooperativityEvidencesWith, setOutCome, setResponse

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.model.CooperativeEffect

getAffectedInteractions, getAnnotations, getCooperativityEvidences, getOutCome, getResponse, setOutCome, setResponse

Constructor Detail

XmlAllostery

public XmlAllostery(CvTerm outcome)

Constructor for XmlAllostery.

Parameters:

outcome - a CvTerm object.

XmlAllostery

public XmlAllostery(CvTerm outcome,
                    CvTerm response)

Constructor for XmlAllostery.

Parameters:

outcome - a CvTerm object.

response - a CvTerm object.

Method Detail

getSourceLocator

public FileSourceLocator getSourceLocator()

Getter for the field sourceLocator.

Specified by:

getSourceLocator in interface FileSourceContext

Returns:

a FileSourceLocator object.

setSourceLocator

public void setSourceLocator(FileSourceLocator locator)

Sets the source locator

Specified by:

setSourceLocator in interface FileSourceContext

Parameters:

locator - : the file locator

setSourceLocator

public void setSourceLocator(PsiXmlLocator locator)

Setter for the field sourceLocator.

Parameters:

locator - a PsiXmlLocator object.

toString

public String toString()

Specified by:

toString in interface FileSourceContext

Overrides:

toString in class DefaultCooperativeEffect

Returns:

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

getAllostericMechanism

public CvTerm getAllostericMechanism()

Getter for the field allostericMechanism.

Specified by:

getAllostericMechanism in interface Allostery<T extends AllostericEffector>

Returns:

a CvTerm object.

setAllostericMechanism

public void setAllostericMechanism(CvTerm mechanism)

Sets the allosteric mechanism.

Specified by:

setAllostericMechanism in interface Allostery<T extends AllostericEffector>

Parameters:

mechanism - : allosteric mechanism

getAllosteryType

public CvTerm getAllosteryType()

Getter for the field allosteryType.

Specified by:

getAllosteryType in interface Allostery<T extends AllostericEffector>

Returns:

a CvTerm object.

setAllosteryType

public void setAllosteryType(CvTerm type)

Sets the allostery type.

Specified by:

setAllosteryType in interface Allostery<T extends AllostericEffector>

Parameters:

type - : allostery type

getAllostericMolecule

public ModelledEntity getAllostericMolecule()

Getter for the field allostericMolecule.

Specified by:

getAllostericMolecule in interface Allostery<T extends AllostericEffector>

Returns:

a ModelledEntity object.

setAllostericMolecule

public void setAllostericMolecule(ModelledEntity participant)

Sets the allosteric molecule.

Specified by:

setAllostericMolecule in interface Allostery<T extends AllostericEffector>

Parameters:

participant - : allosteric molecule (can refer to any participating entity)

getAllostericEffector

public T getAllostericEffector()

Getter for the field allostericEffector.

Specified by:

getAllostericEffector in interface Allostery<T extends AllostericEffector>

Returns:

a T object.

setAllostericEffector

public void setAllostericEffector(T effector)

Setter for the field allostericEffector.

Specified by:

setAllostericEffector in interface Allostery<T extends AllostericEffector>

Parameters:

effector - a T object.

addAffectedInteractionRef

public void addAffectedInteractionRef(int affectedInteraction,
                                      PsiXmlLocator locator)

addAffectedInteractionRef.

Parameters:

affectedInteraction - a int.

locator - a PsiXmlLocator object.

setAllostericMoleculeRef

public void setAllostericMoleculeRef(int ref,
                                     PsiXmlLocator locator)

setAllostericMoleculeRef.

Parameters:

ref - a int.

locator - a PsiXmlLocator object.

setAllostericPTMRef

public void setAllostericPTMRef(int ref,
                                PsiXmlLocator locator)

setAllostericPTMRef.

Parameters:

ref - a int.

locator - a PsiXmlLocator object.

setAllostericEffectorRef

public void setAllostericEffectorRef(int ref,
                                     PsiXmlLocator locator)

setAllostericEffectorRef.

Parameters:

ref - a int.

locator - a PsiXmlLocator object.