Class AbstractExperimentRef
- java.lang.Object
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- psidev.psi.mi.jami.xml.model.reference.AbstractXmlIdReference
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- psidev.psi.mi.jami.xml.model.reference.xml300.AbstractExperimentRef
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- 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)
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Field Summary
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Fields inherited from class psidev.psi.mi.jami.xml.model.reference.AbstractXmlIdReference
ref
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Fields inherited from interface psidev.psi.mi.jami.model.Experiment
INFERRED_BY_CURATOR, INFERRED_BY_CURATOR_MI, UNSPECIFIED_METHOD, UNSPECIFIED_METHOD_MI
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Constructor Summary
Constructors Constructor Description AbstractExperimentRef(int ref)
Constructor for AbstractExperimentRef.
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Method Summary
All Methods Instance Methods Concrete Methods 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 experimentboolean
addAllVariableParameters(Collection<? extends VariableParameter> variableParameters)
This method will add all variableParameters and set the experiment of the new variableParameters to this current experimentboolean
addInteractionEvidence(InteractionEvidence evidence)
This method will add the interaction evidence and set the experiment of the new interaction evidence to this current experimentboolean
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 fielddelegate
.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 nullboolean
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 experimentvoid
setHostOrganism(Organism organism)
Sets the host organism of an experimentvoid
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 experimentvoid
setShortName(String name)
Sets the short name of an experimentString
toString()
toString-
Methods inherited from class psidev.psi.mi.jami.xml.model.reference.AbstractXmlIdReference
getRef, registerForResolution
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Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait
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Methods inherited from interface psidev.psi.mi.jami.datasource.FileSourceContext
getSourceLocator, setSourceLocator
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Methods inherited from interface psidev.psi.mi.jami.xml.model.reference.XmlIdReference
resolve
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Method Detail
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getPublication
public Publication getPublication()
getPublication.
- Specified by:
getPublication
in interfaceExperiment
- Returns:
- a
Publication
object.
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setPublication
public void setPublication(Publication publication)
Set the publication where the experiment has been described.- Specified by:
setPublication
in interfaceExperiment
- Parameters:
publication
- : the publication
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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 interfaceExperiment
- Parameters:
publication
- : the publication
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getXrefs
public Collection<Xref> getXrefs()
getXrefs.
- Specified by:
getXrefs
in interfaceExperiment
- Returns:
- a
Collection
object.
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getAnnotations
public Collection<Annotation> getAnnotations()
getAnnotations.
- Specified by:
getAnnotations
in interfaceExperiment
- Returns:
- a
Collection
object.
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getConfidences
public Collection<Confidence> getConfidences()
getConfidences.
- Specified by:
getConfidences
in interfaceExperiment
- Returns:
- a
Collection
object.
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getInteractionDetectionMethod
public CvTerm getInteractionDetectionMethod()
getInteractionDetectionMethod.
- Specified by:
getInteractionDetectionMethod
in interfaceExperiment
- Returns:
- a
CvTerm
object.
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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 interfaceExperiment
- Parameters:
term
- : the detection method
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getHostOrganism
public Organism getHostOrganism()
getHostOrganism.
- Specified by:
getHostOrganism
in interfaceExperiment
- Returns:
- a
Organism
object.
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setHostOrganism
public void setHostOrganism(Organism organism)
Sets the host organism of an experiment- Specified by:
setHostOrganism
in interfaceExperiment
- Parameters:
organism
- : host organism
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getInteractionEvidences
public Collection<InteractionEvidence> getInteractionEvidences()
getInteractionEvidences.
- Specified by:
getInteractionEvidences
in interfaceExperiment
- Returns:
- a
Collection
object.
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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 interfaceExperiment
- Parameters:
evidence
- : evidence to add- Returns:
- true if interaction evidence is added to the list of interactions
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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 interfaceExperiment
- Parameters:
evidence
- : evidence to remove- Returns:
- true if interaction evidence is removed from the list of interactions
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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 interfaceExperiment
- Parameters:
evidences
- : evidences to add- Returns:
- true if interaction evidences are added to the list of interaction evidences
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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 interfaceExperiment
- Parameters:
evidences
- : evidences to remove- Returns:
- true if interaction evidences are removed from the list of interactions
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getVariableParameters
public Collection<VariableParameter> getVariableParameters()
getVariableParameters.
- Specified by:
getVariableParameters
in interfaceExperiment
- Returns:
- a
Collection
object.
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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 interfaceExperiment
- Parameters:
variableParameter
- : parameter to add- Returns:
- true if variableParameter is added to the list of variableParameters
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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 interfaceExperiment
- Parameters:
variableParameter
- : parameter to remove- Returns:
- true if variableParameter is removed from the list of variableParameters
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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 interfaceExperiment
- Parameters:
variableParameters
- : parameters to add- Returns:
- true if variableParameters are added to the list of variableParameters
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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 interfaceExperiment
- Parameters:
variableParameters
- : parameters to remove- Returns:
- true if variableParameters are removed from the list of variableParameters
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setFeatureDetectionMethod
public void setFeatureDetectionMethod(CvTerm method)
setFeatureDetectionMethod.
- Specified by:
setFeatureDetectionMethod
in interfaceExtendedPsiXmlExperiment
- Parameters:
method
- aCvTerm
object.
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getFeatureDetectionMethod
public CvTerm getFeatureDetectionMethod()
getFeatureDetectionMethod.
- Specified by:
getFeatureDetectionMethod
in interfaceExtendedPsiXmlExperiment
- Returns:
- a
CvTerm
object.
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setParticipantIdentificationMethod
public void setParticipantIdentificationMethod(CvTerm method)
setParticipantIdentificationMethod.
- Specified by:
setParticipantIdentificationMethod
in interfaceExtendedPsiXmlExperiment
- Parameters:
method
- aCvTerm
object.
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getParticipantIdentificationMethod
public CvTerm getParticipantIdentificationMethod()
getParticipantIdentificationMethod.
- Specified by:
getParticipantIdentificationMethod
in interfaceExtendedPsiXmlExperiment
- Returns:
- a
CvTerm
object.
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getHostOrganisms
public List<Organism> getHostOrganisms()
getHostOrganisms.
- Specified by:
getHostOrganisms
in interfaceExtendedPsiXmlExperiment
- Returns:
- a
List
object.
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setId
public void setId(int id)
setId.
- Specified by:
setId
in interfaceExtendedPsiXmlExperiment
- Parameters:
id
- a int.
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getId
public int getId()
getId.
- Specified by:
getId
in interfaceExtendedPsiXmlExperiment
- Returns:
- a int.
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getShortName
public String getShortName()
The short name of the experiment. It can be null or empty. Ex: author-2013-1- Specified by:
getShortName
in interfaceNamedExperiment
- Returns:
- the short name
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setShortName
public void setShortName(String name)
Sets the short name of an experiment- Specified by:
setShortName
in interfaceNamedExperiment
- Parameters:
name
- : short name
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getFullName
public String getFullName()
The full name of the experiment. It can be null Ex: publication title, experiment description- Specified by:
getFullName
in interfaceNamedExperiment
- Returns:
- the full name
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setFullName
public void setFullName(String name)
Sets the full name of the experiment- Specified by:
setFullName
in interfaceNamedExperiment
- Parameters:
name
- : full name
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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 interfaceNamedExperiment
- Type Parameters:
A
- an A object- Returns:
- the aliases
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toString
public String toString()
toString
- Specified by:
toString
in interfaceFileSourceContext
- Overrides:
toString
in classAbstractXmlIdReference
- Returns:
- the file source context as a String. If the source locator is not null, it should give the source locator properties
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initialiseExperimentDelegate
protected void initialiseExperimentDelegate()
initialiseExperimentDelegate.
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getDelegate
protected ExtendedPsiXmlExperiment getDelegate()
Getter for the field
delegate
.- Returns:
- a
ExtendedPsiXmlExperiment
object.
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