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

Class AbstractXmlExperiment

java.lang.Object

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

All Implemented Interfaces:

com.sun.xml.bind.Locatable, FileSourceContext, Experiment, NamedExperiment, ExtendedPsiXmlExperiment

Direct Known Subclasses:

DefaultXmlExperiment, XmlExperiment

public abstract class AbstractXmlExperiment
extends Object
implements ExtendedPsiXmlExperiment, FileSourceContext, com.sun.xml.bind.Locatable

Xml im

Since:

25/07/13

Version:

$Id$

Author:

Marine Dumousseau (marine@ebi.ac.uk)

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
static class	AbstractXmlExperiment.JAXBAttributeWrapper
static class	AbstractXmlExperiment.JAXBConfidenceWrapper
static class	AbstractXmlExperiment.JAXBHostOrganismWrapper
static class	AbstractXmlExperiment.JAXBVariableParameterWrapper

Field Summary

Fields

Modifier and Type	Field	Description
protected Locator	locator

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
AbstractXmlExperiment()	Constructor for AbstractXmlExperiment.
AbstractXmlExperiment(Publication publication)	Constructor for AbstractXmlExperiment.
AbstractXmlExperiment(Publication publication, CvTerm interactionDetectionMethod)	Constructor for AbstractXmlExperiment.
AbstractXmlExperiment(Publication publication, CvTerm interactionDetectionMethod, Organism organism)	Constructor for AbstractXmlExperiment.

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
List<Alias>	getAliases()	Collection of aliases for an experiment.
Collection<Annotation>	getAnnotations()	getAnnotations.
Collection<Confidence>	getConfidences()	getConfidences.
NamesContainer	getExperimentNamesContainer()	Gets the value of the experimentNamesContainer property.
CvTerm	getFeatureDetectionMethod()	Gets the value of the featureDetectionMethod property.
String	getFullName()	The full name of the experiment.
Organism	getHostOrganism()	getHostOrganism.
List<Organism>	getHostOrganisms()	getHostOrganisms.
int	getId()	Gets the value of the id property.
CvTerm	getInteractionDetectionMethod()	Gets the value of the interactionDetectionMethod property.
Collection<InteractionEvidence>	getInteractionEvidences()	getInteractionEvidences.
CvTerm	getParticipantIdentificationMethod()	Gets the value of the participantIdentificationMethod property.
Publication	getPublication()	Getter for the field publication.
String	getShortName()	The short name of the experiment.
FileSourceLocator	getSourceLocator()	Getter for the field sourceLocator.
Collection<VariableParameter>	getVariableParameters()	Getter for the field variableParameters.
Collection<Xref>	getXrefs()	getXrefs.
protected void	initialiseAnnotationWrapper()	initialiseAnnotationWrapper.
protected void	initialiseConfidenceWrapper()	initialiseConfidenceWrapper.
protected abstract void	initialiseFullNameFromPublication(BibRef publication)	initialiseFullNameFromPublication.
protected void	initialiseInteractions()	initialiseInteractions.
protected void	initialiseVariableParameters()	initialiseVariableParameters.
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	setExperimentNamesContainer(NamesContainer value)	Sets the value of the experimentNamesContainer property.
void	setExperimentXrefContainer(ExperimentXrefContainer value)	Sets the value of the xref property.
void	setFeatureDetectionMethod(CvTerm value)	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 value)	setId.
void	setInteractionDetectionMethod(CvTerm value)	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	setJAXBAttributeWrapper(AbstractXmlExperiment.JAXBAttributeWrapper wrapper)	setJAXBAttributeWrapper.
void	setJAXBConfidenceWrapper(AbstractXmlExperiment.JAXBConfidenceWrapper wrapper)	setJAXBConfidenceWrapper.
void	setJAXBHostOrganismWrapper(AbstractXmlExperiment.JAXBHostOrganismWrapper wrapper)	setJAXBHostOrganismWrapper.
void	setJAXBId(int value)	setJAXBId.
void	setJAXBInteractionDetectionMethod(XmlCvTerm value)	Sets the value of the interactionDetectionMethod property.
void	setJAXBPublication(BibRef publication)	setJAXBPublication.
void	setJAXBVariableParameterValuesWrapper(AbstractXmlExperiment.JAXBVariableParameterWrapper jaxbVariableParameterList)	setJAXBVariableParameterValuesWrapper.
void	setParticipantIdentificationMethod(CvTerm value)	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
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

Field Detail

locator

protected Locator locator

Constructor Detail

AbstractXmlExperiment

public AbstractXmlExperiment()

Constructor for AbstractXmlExperiment.

AbstractXmlExperiment

public AbstractXmlExperiment(Publication publication)

Constructor for AbstractXmlExperiment.

Parameters:

publication - a Publication object.

AbstractXmlExperiment

public AbstractXmlExperiment(Publication publication,
                             CvTerm interactionDetectionMethod)

Constructor for AbstractXmlExperiment.

Parameters:

publication - a Publication object.

interactionDetectionMethod - a CvTerm object.

AbstractXmlExperiment

public AbstractXmlExperiment(Publication publication,
                             CvTerm interactionDetectionMethod,
                             Organism organism)

Constructor for AbstractXmlExperiment.

Parameters:

publication - a Publication object.

interactionDetectionMethod - a CvTerm object.

organism - a Organism object.

Method Detail

getPublication

public Publication getPublication()

Getter for the field publication.

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.

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

getInteractionDetectionMethod

public CvTerm getInteractionDetectionMethod()

Gets the value of the interactionDetectionMethod property.

Specified by:

getInteractionDetectionMethod in interface Experiment

Returns:

a CvTerm object.

setInteractionDetectionMethod

public void setInteractionDetectionMethod(CvTerm value)

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). Sets the value of the interactionDetectionMethod property.

Specified by:

setInteractionDetectionMethod in interface Experiment

Parameters:

value - : the detection method

getConfidences

public Collection<Confidence> getConfidences()

getConfidences.

Specified by:

getConfidences in interface Experiment

Returns:

a Collection object.

getAnnotations

public Collection<Annotation> getAnnotations()

getAnnotations.

Specified by:

getAnnotations in interface Experiment

Returns:

a Collection object.

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()

Getter for the field variableParameters.

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

getExperimentNamesContainer

public NamesContainer getExperimentNamesContainer()

Gets the value of the experimentNamesContainer property.

Returns:

a NamesContainer object.

setExperimentNamesContainer

public void setExperimentNamesContainer(NamesContainer value)

Sets the value of the experimentNamesContainer property.

Parameters:

value - allowed object is NamesContainer

setJAXBPublication

public void setJAXBPublication(BibRef publication)

setJAXBPublication.

Parameters:

publication - a BibRef object.

initialiseFullNameFromPublication

protected abstract void initialiseFullNameFromPublication(BibRef publication)

initialiseFullNameFromPublication.

Parameters:

publication - a BibRef object.

setExperimentXrefContainer

public void setExperimentXrefContainer(ExperimentXrefContainer value)

Sets the value of the xref property.

Parameters:

value - allowed object is XrefContainer

setJAXBHostOrganismWrapper

public void setJAXBHostOrganismWrapper(AbstractXmlExperiment.JAXBHostOrganismWrapper wrapper)

setJAXBHostOrganismWrapper.

Parameters:

wrapper - a AbstractXmlExperiment.JAXBHostOrganismWrapper object.

setJAXBInteractionDetectionMethod

public void setJAXBInteractionDetectionMethod(XmlCvTerm value)

Sets the value of the interactionDetectionMethod property.

Parameters:

value - allowed object is XmlCvTerm

getParticipantIdentificationMethod

public CvTerm getParticipantIdentificationMethod()

Gets the value of the participantIdentificationMethod property.

Specified by:

getParticipantIdentificationMethod in interface ExtendedPsiXmlExperiment

Returns:

a CvTerm object.

setParticipantIdentificationMethod

public void setParticipantIdentificationMethod(CvTerm value)

setParticipantIdentificationMethod.

Sets the value of the participantIdentificationMethod property.

Specified by:

setParticipantIdentificationMethod in interface ExtendedPsiXmlExperiment

Parameters:

value - a CvTerm object.

getFeatureDetectionMethod

public CvTerm getFeatureDetectionMethod()

Gets the value of the featureDetectionMethod property.

Specified by:

getFeatureDetectionMethod in interface ExtendedPsiXmlExperiment

Returns:

a CvTerm object.

setFeatureDetectionMethod

public void setFeatureDetectionMethod(CvTerm value)

setFeatureDetectionMethod.

Sets the value of the featureDetectionMethod property.

Specified by:

setFeatureDetectionMethod in interface ExtendedPsiXmlExperiment

Parameters:

value - a CvTerm object.

setJAXBConfidenceWrapper

public void setJAXBConfidenceWrapper(AbstractXmlExperiment.JAXBConfidenceWrapper wrapper)

setJAXBConfidenceWrapper.

Parameters:

wrapper - a AbstractXmlExperiment.JAXBConfidenceWrapper object.

setJAXBVariableParameterValuesWrapper

public void setJAXBVariableParameterValuesWrapper(AbstractXmlExperiment.JAXBVariableParameterWrapper jaxbVariableParameterList)

setJAXBVariableParameterValuesWrapper.

Parameters:

jaxbVariableParameterList - a AbstractXmlExperiment.JAXBVariableParameterWrapper object.

setJAXBAttributeWrapper

public void setJAXBAttributeWrapper(AbstractXmlExperiment.JAXBAttributeWrapper wrapper)

setJAXBAttributeWrapper.

Parameters:

wrapper - a AbstractXmlExperiment.JAXBAttributeWrapper object.

getId

public int getId()

Gets the value of the id property.

Specified by:

getId in interface ExtendedPsiXmlExperiment

Returns:

a int.

setId

public void setId(int value)

setId.

Sets the value of the id property.

Specified by:

setId in interface ExtendedPsiXmlExperiment

Parameters:

value - a int.

setJAXBId

public void setJAXBId(int value)

setJAXBId.

Parameters:

value - a int.

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

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 List<Alias> 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

Returns:

the aliases

getHostOrganisms

public List<Organism> getHostOrganisms()

getHostOrganisms.

Specified by:

getHostOrganisms in interface ExtendedPsiXmlExperiment

Returns:

a List object.

initialiseAnnotationWrapper

protected void initialiseAnnotationWrapper()

initialiseAnnotationWrapper.

initialiseInteractions

protected void initialiseInteractions()

initialiseInteractions.

initialiseConfidenceWrapper

protected void initialiseConfidenceWrapper()

initialiseConfidenceWrapper.

initialiseVariableParameters

protected void initialiseVariableParameters()

initialiseVariableParameters.