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

Class XmlPreAssembly

java.lang.Object

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

psidev.psi.mi.jami.model.impl.DefaultPreassemby

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

All Implemented Interfaces:

FileSourceContext, CooperativeEffect, Preassembly

public class XmlPreAssembly
extends DefaultPreassemby
implements FileSourceContext

Xml implementation of preassembly

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

Method Summary

Modifier and Type	Method	Description
void	addAffectedInteractionRef(int affectedInteraction, PsiXmlLocator locator)	addAffectedInteractionRef.
FileSourceLocator	getSourceLocator()	Getter for the field sourceLocator.
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

XmlPreAssembly

public XmlPreAssembly(CvTerm outcome)

Constructor for XmlPreAssembly.

Parameters:

outcome - a CvTerm object.

XmlPreAssembly

public XmlPreAssembly(CvTerm outcome,
                      CvTerm response)

Constructor for XmlPreAssembly.

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

addAffectedInteractionRef

public void addAffectedInteractionRef(int affectedInteraction,
                                      PsiXmlLocator locator)

addAffectedInteractionRef.

Parameters:

affectedInteraction - a int.

locator - a PsiXmlLocator object.