Package psidev.psi.mi.jami.xml.model.reference.xml254

Class AbstractExperimentRef

java.lang.Object

psidev.psi.mi.jami.xml.model.reference.AbstractXmlIdReference

psidev.psi.mi.jami.xml.model.reference.xml254.AbstractExperimentRef

All Implemented Interfaces:

FileSourceContext, Experiment, NamedExperiment, ExtendedPsiXmlExperiment, XmlIdReference

public abstract class AbstractExperimentRef
extends AbstractXmlIdReference
implements ExtendedPsiXmlExperiment

Abstract class for an ModelledInteractionRef

Since:

11/10/13

Version:

$Id$

Author:

Marine Dumousseau (marine@ebi.ac.uk)

Field Summary

Fields inherited from class psidev.psi.mi.jami.xml.model.reference.AbstractXmlIdReference

ref

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

INFERRED_BY_CURATOR, INFERRED_BY_CURATOR_MI, UNSPECIFIED_METHOD, UNSPECIFIED_METHOD_MI

Constructor Summary

Constructors

Constructor	Description
AbstractExperimentRef(int ref)	Constructor for AbstractExperimentRef.

Method Summary

Modifier and Type	Method	Description
boolean	addAllInteractionEvidences(Collection<? extends InteractionEvidence> evidences)	This method will add all the interaction evidences and set the experiment of the new interaction evidences to this current experiment
boolean	addAllVariableParameters(Collection<? extends VariableParameter> variableParameters)	This method will add all variableParameters and set the experiment of the new variableParameters to this current experiment
boolean	addInteractionEvidence(InteractionEvidence evidence)	This method will add the interaction evidence and set the experiment of the new interaction evidence to this current experiment
boolean	addVariableParameter(VariableParameter variableParameter)	This method will add the variableParameter and set the experiment of the new variableParameter to this current experiment
<A extends Alias> Collection<A>	getAliases()	Collection of aliases for an experiment.
Collection<Annotation>	getAnnotations()	getAnnotations.
Collection<Confidence>	getConfidences()	getConfidences.
protected ExtendedPsiXmlExperiment	getDelegate()	Getter for the field delegate.
CvTerm	getFeatureDetectionMethod()	getFeatureDetectionMethod.
String	getFullName()	The full name of the experiment.
Organism	getHostOrganism()	getHostOrganism.
List<Organism>	getHostOrganisms()	getHostOrganisms.
int	getId()	getId.
CvTerm	getInteractionDetectionMethod()	getInteractionDetectionMethod.
Collection<InteractionEvidence>	getInteractionEvidences()	getInteractionEvidences.
CvTerm	getParticipantIdentificationMethod()	getParticipantIdentificationMethod.
Publication	getPublication()	getPublication.
String	getShortName()	The short name of the experiment.
Collection<VariableParameter>	getVariableParameters()	getVariableParameters.
Collection<Xref>	getXrefs()	getXrefs.
protected void	initialiseExperimentDelegate()	initialiseExperimentDelegate.
boolean	removeAllInteractionEvidences(Collection<? extends InteractionEvidence> evidences)	This method will remove the interaction evidences and set the experiment of the removed interaction evidences to null.
boolean	removeAllVariableParameters(Collection<? extends VariableParameter> variableParameters)	This method will remove all the variableParameters and set the experiment of the removed variableParameters to null.
boolean	removeInteractionEvidence(InteractionEvidence evidence)	This method will remove the interaction evidence and set the experiment of the new interaction evidence to null
boolean	removeVariableParameter(VariableParameter variableParameter)	This method will remove the variableParameter and set the experiment of the removed variableParameter to null.
void	setFeatureDetectionMethod(CvTerm method)	setFeatureDetectionMethod.
void	setFullName(String name)	Sets the full name of the experiment
void	setHostOrganism(Organism organism)	Sets the host organism of an experiment
void	setId(int id)	setId.
void	setInteractionDetectionMethod(CvTerm term)	Set the interaction detection method for this experiment If term is null, this method will set the interaction detection method to 'unspecified method' (MI:0686).
void	setParticipantIdentificationMethod(CvTerm method)	setParticipantIdentificationMethod.
void	setPublication(Publication publication)	Set the publication where the experiment has been described.
void	setPublicationAndAddExperiment(Publication publication)	Set the publication where the experiment has been described and add the experiment to the list of experiments for this publication If publication is null, it will remove this experiment from the previous publication attached to this experiment
void	setShortName(String name)	Sets the short name of an experiment
String	toString()	toString

Methods inherited from class psidev.psi.mi.jami.xml.model.reference.AbstractXmlIdReference

getRef, registerForResolution

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.datasource.FileSourceContext

getSourceLocator, setSourceLocator

Methods inherited from interface psidev.psi.mi.jami.xml.model.reference.XmlIdReference

resolve

Constructor Detail

AbstractExperimentRef

public AbstractExperimentRef(int ref)

Constructor for AbstractExperimentRef.

Parameters:

ref - a int.

Method Detail

getPublication

public Publication getPublication()

getPublication.

Specified by:

getPublication in interface Experiment

Returns:

a Publication object.

setPublication

public void setPublication(Publication publication)

Set the publication where the experiment has been described.

Specified by:

setPublication in interface Experiment

Parameters:

publication - : the publication

setPublicationAndAddExperiment

public void setPublicationAndAddExperiment(Publication publication)

Set the publication where the experiment has been described and add the experiment to the list of experiments for this publication If publication is null, it will remove this experiment from the previous publication attached to this experiment

Specified by:

setPublicationAndAddExperiment in interface Experiment

Parameters:

publication - : the publication

getXrefs

public Collection<Xref> getXrefs()

getXrefs.

Specified by:

getXrefs in interface Experiment

Returns:

a Collection object.

getAnnotations

public Collection<Annotation> getAnnotations()

getAnnotations.

Specified by:

getAnnotations in interface Experiment

Returns:

a Collection object.

getConfidences

public Collection<Confidence> getConfidences()

getConfidences.

Specified by:

getConfidences in interface Experiment

Returns:

a Collection object.

getInteractionDetectionMethod

public CvTerm getInteractionDetectionMethod()

getInteractionDetectionMethod.

Specified by:

getInteractionDetectionMethod in interface Experiment

Returns:

a CvTerm object.

setInteractionDetectionMethod

public void setInteractionDetectionMethod(CvTerm term)

Set the interaction detection method for this experiment If term is null, this method will set the interaction detection method to 'unspecified method' (MI:0686).

Specified by:

setInteractionDetectionMethod in interface Experiment

Parameters:

term - : the detection method

getHostOrganism

public Organism getHostOrganism()

getHostOrganism.

Specified by:

getHostOrganism in interface Experiment

Returns:

a Organism object.

setHostOrganism

public void setHostOrganism(Organism organism)

Sets the host organism of an experiment

Specified by:

setHostOrganism in interface Experiment

Parameters:

organism - : host organism

getInteractionEvidences

public Collection<InteractionEvidence> getInteractionEvidences()

getInteractionEvidences.

Specified by:

getInteractionEvidences in interface Experiment

Returns:

a Collection object.

addInteractionEvidence

public boolean addInteractionEvidence(InteractionEvidence evidence)

This method will add the interaction evidence and set the experiment of the new interaction evidence to this current experiment

Specified by:

addInteractionEvidence in interface Experiment

Parameters:

evidence - : evidence to add

Returns:

true if interaction evidence is added to the list of interactions

removeInteractionEvidence

public boolean removeInteractionEvidence(InteractionEvidence evidence)

This method will remove the interaction evidence and set the experiment of the new interaction evidence to null

Specified by:

removeInteractionEvidence in interface Experiment

Parameters:

evidence - : evidence to remove

Returns:

true if interaction evidence is removed from the list of interactions

addAllInteractionEvidences

public boolean addAllInteractionEvidences(Collection<? extends InteractionEvidence> evidences)

This method will add all the interaction evidences and set the experiment of the new interaction evidences to this current experiment

Specified by:

addAllInteractionEvidences in interface Experiment

Parameters:

evidences - : evidences to add

Returns:

true if interaction evidences are added to the list of interaction evidences

removeAllInteractionEvidences

public boolean removeAllInteractionEvidences(Collection<? extends InteractionEvidence> evidences)

This method will remove the interaction evidences and set the experiment of the removed interaction evidences to null.

Specified by:

removeAllInteractionEvidences in interface Experiment

Parameters:

evidences - : evidences to remove

Returns:

true if interaction evidences are removed from the list of interactions

getVariableParameters

public Collection<VariableParameter> getVariableParameters()

getVariableParameters.

Specified by:

getVariableParameters in interface Experiment

Returns:

a Collection object.

addVariableParameter

public boolean addVariableParameter(VariableParameter variableParameter)

This method will add the variableParameter and set the experiment of the new variableParameter to this current experiment

Specified by:

addVariableParameter in interface Experiment

Parameters:

variableParameter - : parameter to add

Returns:

true if variableParameter is added to the list of variableParameters

removeVariableParameter

public boolean removeVariableParameter(VariableParameter variableParameter)

This method will remove the variableParameter and set the experiment of the removed variableParameter to null.

Specified by:

removeVariableParameter in interface Experiment

Parameters:

variableParameter - : parameter to remove

Returns:

true if variableParameter is removed from the list of variableParameters

addAllVariableParameters

public boolean addAllVariableParameters(Collection<? extends VariableParameter> variableParameters)

This method will add all variableParameters and set the experiment of the new variableParameters to this current experiment

Specified by:

addAllVariableParameters in interface Experiment

Parameters:

variableParameters - : parameters to add

Returns:

true if variableParameters are added to the list of variableParameters

removeAllVariableParameters

public boolean removeAllVariableParameters(Collection<? extends VariableParameter> variableParameters)

This method will remove all the variableParameters and set the experiment of the removed variableParameters to null.

Specified by:

removeAllVariableParameters in interface Experiment

Parameters:

variableParameters - : parameters to remove

Returns:

true if variableParameters are removed from the list of variableParameters

setFeatureDetectionMethod

public void setFeatureDetectionMethod(CvTerm method)

setFeatureDetectionMethod.

Specified by:

setFeatureDetectionMethod in interface ExtendedPsiXmlExperiment

Parameters:

method - a CvTerm object.

getFeatureDetectionMethod

public CvTerm getFeatureDetectionMethod()

getFeatureDetectionMethod.

Specified by:

getFeatureDetectionMethod in interface ExtendedPsiXmlExperiment

Returns:

a CvTerm object.

setParticipantIdentificationMethod

public void setParticipantIdentificationMethod(CvTerm method)

setParticipantIdentificationMethod.

Specified by:

setParticipantIdentificationMethod in interface ExtendedPsiXmlExperiment

Parameters:

method - a CvTerm object.

getParticipantIdentificationMethod

public CvTerm getParticipantIdentificationMethod()

getParticipantIdentificationMethod.

Specified by:

getParticipantIdentificationMethod in interface ExtendedPsiXmlExperiment

Returns:

a CvTerm object.

getHostOrganisms

public List<Organism> getHostOrganisms()

getHostOrganisms.

Specified by:

getHostOrganisms in interface ExtendedPsiXmlExperiment

Returns:

a List object.

setId

public void setId(int id)

setId.

Specified by:

setId in interface ExtendedPsiXmlExperiment

Parameters:

id - a int.

getId

public int getId()

getId.

Specified by:

getId in interface ExtendedPsiXmlExperiment

Returns:

a int.

getShortName

public String getShortName()

The short name of the experiment. It can be null or empty. Ex: author-2013-1

Specified by:

getShortName in interface NamedExperiment

Returns:

the short name

setShortName

public void setShortName(String name)

Sets the short name of an experiment

Specified by:

setShortName in interface NamedExperiment

Parameters:

name - : short name

getFullName

public String getFullName()

The full name of the experiment. It can be null Ex: publication title, experiment description

Specified by:

getFullName in interface NamedExperiment

Returns:

the full name

setFullName

public void setFullName(String name)

Sets the full name of the experiment

Specified by:

setFullName in interface NamedExperiment

Parameters:

name - : full name

getAliases

public <A extends Alias> Collection<A> getAliases()

Collection of aliases for an experiment. 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 NamedExperiment

Type Parameters:

A - an A object

Returns:

the aliases

toString

public String toString()

toString

Specified by:

toString in interface FileSourceContext

Overrides:

toString in class AbstractXmlIdReference

Returns:

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

initialiseExperimentDelegate

protected void initialiseExperimentDelegate()

initialiseExperimentDelegate.

getDelegate

protected ExtendedPsiXmlExperiment getDelegate()

Getter for the field delegate.

Returns:

a ExtendedPsiXmlExperiment object.