Uses of Interface
psidev.psi.mi.jami.model.Confidence
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Uses of Confidence in psidev.psi.mi.jami.binary.impl
Methods in psidev.psi.mi.jami.binary.impl that return types with arguments of type Confidence Modifier and Type Method Description Collection<Confidence>
BinaryInteractionEvidenceWrapper. getConfidences()
getConfidencesCollection<Confidence>
DefaultBinaryInteractionEvidence. getConfidences()
Getter for the fieldconfidences
.Method parameters in psidev.psi.mi.jami.binary.impl with type arguments of type Confidence Modifier and Type Method Description protected void
DefaultBinaryInteractionEvidence. initialiseExperimentalConfidencesWith(Collection<Confidence> confidences)
initialiseExperimentalConfidencesWith -
Uses of Confidence in psidev.psi.mi.jami.enricher.listener.impl
Methods in psidev.psi.mi.jami.enricher.listener.impl with parameters of type Confidence Modifier and Type Method Description void
ExperimentEnricherListenerManager. onAddedConfidence(Experiment experiment, Confidence added)
Listen to the event where a confidence has been added to the object confidences.void
InteractionEvidenceEnricherListenerManager. onAddedConfidence(InteractionEvidence o, Confidence added)
Listen to the event where a confidence has been added to the object confidences.void
ModelledInteractionEnricherListenerManager. onAddedConfidence(I o, Confidence added)
Listen to the event where a confidence has been added to the object confidences.void
ParticipantEvidenceEnricherListenerManager. onAddedConfidence(P o, Confidence added)
Listen to the event where a confidence has been added to the object confidences.void
ExperimentEnricherListenerManager. onRemovedConfidence(Experiment experiment, Confidence removed)
Listen to the event where a confidence has been removed from the object confidences.void
InteractionEvidenceEnricherListenerManager. onRemovedConfidence(InteractionEvidence o, Confidence removed)
Listen to the event where a confidence has been removed from the object confidences.void
ModelledInteractionEnricherListenerManager. onRemovedConfidence(I o, Confidence removed)
Listen to the event where a confidence has been removed from the object confidences.void
ParticipantEvidenceEnricherListenerManager. onRemovedConfidence(P o, Confidence removed)
Listen to the event where a confidence has been removed from the object confidences. -
Uses of Confidence in psidev.psi.mi.jami.enricher.listener.impl.writer
Methods in psidev.psi.mi.jami.enricher.listener.impl.writer with parameters of type Confidence Modifier and Type Method Description void
ExperimentEnricherStatisticsWriter. onAddedConfidence(Experiment o, Confidence added)
Listen to the event where a confidence has been added to the object confidences.void
InteractionEvidenceEnricherStatisticsWriter. onAddedConfidence(InteractionEvidence o, Confidence added)
Listen to the event where a confidence has been added to the object confidences.void
ModelledInteractionEnricherStatisticsWriter. onAddedConfidence(I o, Confidence added)
Listen to the event where a confidence has been added to the object confidences.void
ParticipantEvidenceEnricherStatisticsWriter. onAddedConfidence(P o, Confidence added)
Listen to the event where a confidence has been added to the object confidences.void
ExperimentEnricherStatisticsWriter. onRemovedConfidence(Experiment o, Confidence removed)
Listen to the event where a confidence has been removed from the object confidences.void
InteractionEvidenceEnricherStatisticsWriter. onRemovedConfidence(InteractionEvidence o, Confidence removed)
Listen to the event where a confidence has been removed from the object confidences.void
ModelledInteractionEnricherStatisticsWriter. onRemovedConfidence(I o, Confidence removed)
Listen to the event where a confidence has been removed from the object confidences.void
ParticipantEvidenceEnricherStatisticsWriter. onRemovedConfidence(P o, Confidence removed)
Listen to the event where a confidence has been removed from the object confidences. -
Uses of Confidence in psidev.psi.mi.jami.enricher.util
Methods in psidev.psi.mi.jami.enricher.util with type parameters of type Confidence Modifier and Type Method Description static <T,C extends Confidence>
voidEnricherUtils. mergeConfidences(T termToEnrich, Collection<C> toEnrichConfidences, Collection<C> fetchedConfidences, boolean remove, ConfidencesChangeListener<T> confListener)
mergeConfidences. -
Uses of Confidence in psidev.psi.mi.jami.json.elements
Methods in psidev.psi.mi.jami.json.elements that return types with arguments of type Confidence Modifier and Type Method Description JsonElementWriter<Confidence>
SimpleJsonInteractionEvidenceWriter. getConfidenceWriter()
Getter for the fieldconfidenceWriter
.JsonElementWriter<Confidence>
SimpleJsonModelledInteractionWriter. getConfidenceWriter()
Getter for the fieldconfidenceWriter
.JsonElementWriter<Confidence>
SimpleJsonParticipantEvidenceWriter. getConfidenceWriter()
Getter for the fieldconfidenceWriter
.Methods in psidev.psi.mi.jami.json.elements with parameters of type Confidence Modifier and Type Method Description void
SimpleJsonConfidenceWriter. write(Confidence object)
write.Method parameters in psidev.psi.mi.jami.json.elements with type arguments of type Confidence Modifier and Type Method Description void
SimpleJsonInteractionEvidenceWriter. setConfidenceWriter(JsonElementWriter<Confidence> confidenceWriter)
Setter for the fieldconfidenceWriter
.void
SimpleJsonModelledInteractionWriter. setConfidenceWriter(JsonElementWriter<Confidence> confidenceWriter)
Setter for the fieldconfidenceWriter
.void
SimpleJsonParticipantEvidenceWriter. setConfidenceWriter(JsonElementWriter<Confidence> confidenceWriter)
Setter for the fieldconfidenceWriter
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Uses of Confidence in psidev.psi.mi.jami.listener
Methods in psidev.psi.mi.jami.listener with parameters of type Confidence Modifier and Type Method Description void
ConfidencesChangeListener. onAddedConfidence(T o, Confidence added)
Listen to the event where a confidence has been added to the object confidences.void
ConfidencesChangeListener. onRemovedConfidence(T o, Confidence removed)
Listen to the event where a confidence has been removed from the object confidences. -
Uses of Confidence in psidev.psi.mi.jami.listener.impl
Methods in psidev.psi.mi.jami.listener.impl with parameters of type Confidence Modifier and Type Method Description void
ComplexChangeLogger. onAddedConfidence(Complex o, Confidence added)
Listen to the event where a confidence has been added to the object confidences.void
ExperimentChangeLogger. onAddedConfidence(Experiment experiment, Confidence added)
Listen to the event where a confidence has been added to the object confidences.void
InteractionEvidenceChangeLogger. onAddedConfidence(InteractionEvidence o, Confidence added)
Listen to the event where a confidence has been added to the object confidences.void
ModelledInteractionChangeLogger. onAddedConfidence(I o, Confidence added)
Listen to the event where a confidence has been added to the object confidences.void
ParticipantEvidenceChangeLogger. onAddedConfidence(T o, Confidence added)
Listen to the event where a confidence has been added to the object confidences.void
ComplexChangeLogger. onRemovedConfidence(Complex o, Confidence removed)
Listen to the event where a confidence has been removed from the object confidences.void
ExperimentChangeLogger. onRemovedConfidence(Experiment experiment, Confidence removed)
Listen to the event where a confidence has been removed from the object confidences.void
InteractionEvidenceChangeLogger. onRemovedConfidence(InteractionEvidence o, Confidence removed)
Listen to the event where a confidence has been removed from the object confidences.void
ModelledInteractionChangeLogger. onRemovedConfidence(I o, Confidence removed)
Listen to the event where a confidence has been removed from the object confidences.void
ParticipantEvidenceChangeLogger. onRemovedConfidence(T o, Confidence removed)
Listen to the event where a confidence has been removed from the object confidences. -
Uses of Confidence in psidev.psi.mi.jami.model
Subinterfaces of Confidence in psidev.psi.mi.jami.model Modifier and Type Interface Description interface
ModelledConfidence
A modelled confidence is a confidence for a modelled interaction.Methods in psidev.psi.mi.jami.model with type parameters of type Confidence Modifier and Type Method Description <C extends Confidence>
Collection<C>Experiment. getConfidences()
Collection of confidences for a specific experiment.<C extends Confidence>
Collection<C>InteractionEvidence. getConfidences()
The confidences in this interaction.<C extends Confidence>
Collection<C>ParticipantEvidence. getConfidences()
The confidences for this participant. -
Uses of Confidence in psidev.psi.mi.jami.model.impl
Classes in psidev.psi.mi.jami.model.impl that implement Confidence Modifier and Type Class Description class
DefaultConfidence
Default implementation for Confidence Notes: The equals and hashcode methods have been overridden to be consistent with UnambiguousConfidenceComparatorclass
DefaultModelledConfidence
Default implementation for ModelledInteraction Notes: The equals and hashcode methods have been overridden to be consistent with UnambiguousConfidenceComparatorMethods in psidev.psi.mi.jami.model.impl that return types with arguments of type Confidence Modifier and Type Method Description Collection<Confidence>
DefaultExperiment. getConfidences()
Getter for the fieldconfidences
.Collection<Confidence>
DefaultExperimentalParticipantPool. getConfidences()
Getter for the fieldconfidences
.Collection<Confidence>
DefaultInteractionEvidence. getConfidences()
Getter for the fieldconfidences
.Collection<Confidence>
DefaultParticipantEvidence. getConfidences()
Getter for the fieldconfidences
.Method parameters in psidev.psi.mi.jami.model.impl with type arguments of type Confidence Modifier and Type Method Description protected void
DefaultExperiment. initialiseConfidencesWith(Collection<Confidence> confs)
initialiseConfidencesWithprotected void
DefaultExperimentalParticipantPool. initialiseConfidencesWith(Collection<Confidence> confidences)
initialiseConfidencesWithprotected void
DefaultParticipantEvidence. initialiseConfidencesWith(Collection<Confidence> confidences)
initialiseConfidencesWithprotected void
DefaultInteractionEvidence. initialiseExperimentalConfidencesWith(Collection<Confidence> confidences)
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Uses of Confidence in psidev.psi.mi.jami.tab.extension
Classes in psidev.psi.mi.jami.tab.extension that implement Confidence Modifier and Type Class Description class
MitabConfidence
A MitabConfidence is a confidence with some text -
Uses of Confidence in psidev.psi.mi.jami.tab.io.writer.feeder
Methods in psidev.psi.mi.jami.tab.io.writer.feeder with parameters of type Confidence Modifier and Type Method Description void
AbstractMitabColumnFeeder. writeConfidence(Confidence conf)
This method will write a confidence with a text if text is not nullvoid
DefaultMitabColumnFeeder. writeConfidence(Confidence conf)
This method will write a confidence with a text if text is not nullvoid
MitabColumnFeeder. writeConfidence(Confidence conf)
This method will write a confidence with a text if text is not null -
Uses of Confidence in psidev.psi.mi.jami.tab.io.writer.feeder.extended
Methods in psidev.psi.mi.jami.tab.io.writer.feeder.extended with parameters of type Confidence Modifier and Type Method Description void
ExtendedMitabInteractionEvidenceFeeder. writeConfidence(Confidence conf)
This method will write a confidence with a text if text is not nullvoid
ExtendedMitabModelledInteractionFeeder. writeConfidence(Confidence conf)
This method will write a confidence with a text if text is not null -
Uses of Confidence in psidev.psi.mi.jami.utils
Methods in psidev.psi.mi.jami.utils that return Confidence Modifier and Type Method Description static Confidence
ConfidenceUtils. createAuthorBasedConfidence(String value)
createAuthorBasedConfidencestatic Confidence
ConfidenceUtils. createConfidence(String typeName, String value)
createConfidencestatic Confidence
ConfidenceUtils. createConfidence(String typeName, String typeMi, String value)
createConfidenceMethods in psidev.psi.mi.jami.utils that return types with arguments of type Confidence Modifier and Type Method Description static Collection<Confidence>
ConfidenceUtils. collectAllConfidencesHavingType(Collection<? extends Confidence> confs, String typeId, String typeName)
Collect all confidences having a specific typeMethods in psidev.psi.mi.jami.utils with parameters of type Confidence Modifier and Type Method Description static boolean
ConfidenceUtils. doesConfidenceHaveType(Confidence conf, String typeId, String typeName)
Check the type of a confidenceMethod parameters in psidev.psi.mi.jami.utils with type arguments of type Confidence Modifier and Type Method Description static Collection<Confidence>
ConfidenceUtils. collectAllConfidencesHavingType(Collection<? extends Confidence> confs, String typeId, String typeName)
Collect all confidences having a specific type -
Uses of Confidence in psidev.psi.mi.jami.utils.comparator.confidence
Methods in psidev.psi.mi.jami.utils.comparator.confidence with parameters of type Confidence Modifier and Type Method Description static boolean
DefaultConfidenceComparator. areEquals(Confidence confidence1, Confidence confidence2)
Use DefaultConfidenceComparator to know if two confidences are equals.static boolean
UnambiguousConfidenceComparator. areEquals(Confidence conf1, Confidence conf2)
Use UnambiguousConfidenceComparator to know if two confidences are equals.int
ConfidenceComparator. compare(Confidence confidence1, Confidence confidence2)
It will compares the confidence types first, then the units and finally the value.int
UnambiguousConfidenceComparator. compare(Confidence confidence1, Confidence confidence2)
It will compares the confidence types first, then the units and finally the value.static int
UnambiguousConfidenceComparator. hashCode(Confidence conf)
hashCode -
Uses of Confidence in psidev.psi.mi.jami.xml.io.writer.elements
Methods in psidev.psi.mi.jami.xml.io.writer.elements that return types with arguments of type Confidence Modifier and Type Method Description static PsiXmlElementWriter<Confidence>[]
PsiXmlElementWriterFactory. createConfidenceWriters(XMLStreamWriter streamWriter, boolean extended, PsiXmlObjectCache objectIndex, PsiXmlVersion version, PsiXmlVariableNameWriter<CvTerm> confidenceTypeWriter, PsiXmlPublicationWriter publicationWriter)
createConfidenceWriters. -
Uses of Confidence in psidev.psi.mi.jami.xml.io.writer.elements.impl
Methods in psidev.psi.mi.jami.xml.io.writer.elements.impl with parameters of type Confidence Modifier and Type Method Description void
XmlConfidenceWriter. write(Confidence object)
write.protected void
XmlConfidenceWriter. writeOtherProperties(Confidence object)
writeOtherProperties. -
Uses of Confidence in psidev.psi.mi.jami.xml.io.writer.elements.impl.abstracts
Methods in psidev.psi.mi.jami.xml.io.writer.elements.impl.abstracts that return types with arguments of type Confidence Modifier and Type Method Description PsiXmlElementWriter<Confidence>
AbstractXmlExperimentWriter. getConfidenceWriter()
Getter for the fieldconfidenceWriter
.PsiXmlElementWriter<Confidence>
AbstractXmlInteractionEvidenceWriter. getConfidenceWriter()
Getter for the fieldconfidenceWriter
.PsiXmlElementWriter<Confidence>
AbstractXmlModelledInteractionWriter. getConfidenceWriter()
Getter for the fieldconfidenceWriter
.PsiXmlElementWriter<Confidence>
AbstractXmlParticipantEvidenceWriter. getConfidenceWriter()
Getter for the fieldconfidenceWriter
.Method parameters in psidev.psi.mi.jami.xml.io.writer.elements.impl.abstracts with type arguments of type Confidence Modifier and Type Method Description void
AbstractXmlExperimentWriter. setConfidenceWriter(PsiXmlElementWriter<Confidence> confidenceWriter)
Setter for the fieldconfidenceWriter
.void
AbstractXmlInteractionEvidenceWriter. setConfidenceWriter(PsiXmlElementWriter<Confidence> confidenceWriter)
Setter for the fieldconfidenceWriter
.void
AbstractXmlModelledInteractionWriter. setConfidenceWriter(PsiXmlElementWriter<Confidence> confidenceWriter)
Setter for the fieldconfidenceWriter
.void
AbstractXmlParticipantEvidenceWriter. setConfidenceWriter(PsiXmlElementWriter<Confidence> confidenceWriter)
Setter for the fieldconfidenceWriter
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Uses of Confidence in psidev.psi.mi.jami.xml.io.writer.elements.impl.extended.xml25.xml253
Methods in psidev.psi.mi.jami.xml.io.writer.elements.impl.extended.xml25.xml253 with parameters of type Confidence Modifier and Type Method Description void
XmlConfidenceWriter. write(Confidence object)
write. -
Uses of Confidence in psidev.psi.mi.jami.xml.io.writer.elements.impl.extended.xml25.xml254
Methods in psidev.psi.mi.jami.xml.io.writer.elements.impl.extended.xml25.xml254 with parameters of type Confidence Modifier and Type Method Description void
XmlConfidenceWriter. write(Confidence object)
write. -
Uses of Confidence in psidev.psi.mi.jami.xml.io.writer.elements.impl.extended.xml30
Methods in psidev.psi.mi.jami.xml.io.writer.elements.impl.extended.xml30 with parameters of type Confidence Modifier and Type Method Description void
XmlConfidenceWriter. write(Confidence object)
write. -
Uses of Confidence in psidev.psi.mi.jami.xml.io.writer.elements.impl.xml30
Methods in psidev.psi.mi.jami.xml.io.writer.elements.impl.xml30 with parameters of type Confidence Modifier and Type Method Description void
XmlModelledConfidenceWriter. write(Confidence object)
write.protected void
XmlModelledConfidenceWriter. writeOtherProperties(Confidence object)
writeOtherProperties. -
Uses of Confidence in psidev.psi.mi.jami.xml.model.extension.binary
Methods in psidev.psi.mi.jami.xml.model.extension.binary that return types with arguments of type Confidence Modifier and Type Method Description Collection<Confidence>
AbstractXmlBinaryInteractionEvidence. getConfidences()
Getter for the fieldconfidences
.Collection<Confidence>
XmlBinaryInteractionEvidenceWrapper. getConfidences()
The confidences in this interaction. -
Uses of Confidence in psidev.psi.mi.jami.xml.model.extension.xml253
Classes in psidev.psi.mi.jami.xml.model.extension.xml253 that implement Confidence Modifier and Type Class Description class
AbstractXmlConfidence
abstract Xml implementation of confidenceclass
XmlConfidence
Xml implementation of confidenceclass
XmlConfidenceWrapper
A wrapper for confidencesclass
XmlModelledConfidence
Xml implementation of ModelledConfidenceMethods in psidev.psi.mi.jami.xml.model.extension.xml253 that return types with arguments of type Confidence Modifier and Type Method Description Collection<Confidence>
AbstractXmlExperiment. getConfidences()
getConfidences.Collection<Confidence>
AbstractXmlInteractionEvidence. getConfidences()
getConfidences.Collection<Confidence>
XmlExperimentalParticipantPool. getConfidences()
The confidences for this participant.Collection<Confidence>
XmlParticipantEvidence. getConfidences()
getConfidences.List<Confidence>
AbstractXmlExperiment.JAXBConfidenceWrapper. getJAXBConfidences()
List<Confidence>
AbstractXmlInteractionEvidence.JAXBConfidenceWrapper. getJAXBConfidences()
List<Confidence>
XmlParticipantEvidence.JAXBConfidenceWrapper. getJAXBConfidences()
Constructors in psidev.psi.mi.jami.xml.model.extension.xml253 with parameters of type Confidence Constructor Description XmlConfidenceWrapper(Confidence conf)
Constructor for XmlConfidenceWrapper. -
Uses of Confidence in psidev.psi.mi.jami.xml.model.extension.xml254
Classes in psidev.psi.mi.jami.xml.model.extension.xml254 that implement Confidence Modifier and Type Class Description class
AbstractXmlConfidence
abstract Xml implementation of confidenceclass
XmlConfidence
Xml implementation of confidenceclass
XmlConfidenceWrapper
A wrapper for confidencesclass
XmlModelledConfidence
Xml implementation of ModelledConfidenceMethods in psidev.psi.mi.jami.xml.model.extension.xml254 that return types with arguments of type Confidence Modifier and Type Method Description Collection<Confidence>
AbstractXmlExperiment. getConfidences()
getConfidences.Collection<Confidence>
AbstractXmlInteractionEvidence. getConfidences()
getConfidences.Collection<Confidence>
XmlExperimentalParticipantPool. getConfidences()
The confidences for this participant.Collection<Confidence>
XmlParticipantEvidence. getConfidences()
getConfidences.List<Confidence>
AbstractXmlExperiment.JAXBConfidenceWrapper. getJAXBConfidences()
List<Confidence>
AbstractXmlInteractionEvidence.JAXBConfidenceWrapper. getJAXBConfidences()
List<Confidence>
XmlParticipantEvidence.JAXBConfidenceWrapper. getJAXBConfidences()
Constructors in psidev.psi.mi.jami.xml.model.extension.xml254 with parameters of type Confidence Constructor Description XmlConfidenceWrapper(Confidence conf)
Constructor for XmlConfidenceWrapper. -
Uses of Confidence in psidev.psi.mi.jami.xml.model.extension.xml300
Classes in psidev.psi.mi.jami.xml.model.extension.xml300 that implement Confidence Modifier and Type Class Description class
AbstractXmlConfidence
abstract Xml implementation of confidenceclass
XmlConfidence
Xml implementation of confidenceclass
XmlConfidenceWrapper
A wrapper for confidencesclass
XmlModelledConfidence
Xml 3.0 implementation of ModelledConfidenceMethods in psidev.psi.mi.jami.xml.model.extension.xml300 that return types with arguments of type Confidence Modifier and Type Method Description Collection<Confidence>
AbstractXmlExperiment. getConfidences()
getConfidences.Collection<Confidence>
AbstractXmlInteractionEvidence. getConfidences()
getConfidences.Collection<Confidence>
XmlExperimentalParticipantPool. getConfidences()
The confidences for this participant.Collection<Confidence>
XmlParticipantEvidence. getConfidences()
getConfidences.List<Confidence>
AbstractXmlExperiment.JAXBConfidenceWrapper. getJAXBConfidences()
List<Confidence>
AbstractXmlInteractionEvidence.JAXBConfidenceWrapper. getJAXBConfidences()
List<Confidence>
XmlParticipantEvidence.JAXBConfidenceWrapper. getJAXBConfidences()
Constructors in psidev.psi.mi.jami.xml.model.extension.xml300 with parameters of type Confidence Constructor Description XmlConfidenceWrapper(Confidence conf)
Constructor for XmlConfidenceWrapper. -
Uses of Confidence in psidev.psi.mi.jami.xml.model.reference.xml253
Methods in psidev.psi.mi.jami.xml.model.reference.xml253 that return types with arguments of type Confidence Modifier and Type Method Description Collection<Confidence>
AbstractExperimentRef. getConfidences()
getConfidences. -
Uses of Confidence in psidev.psi.mi.jami.xml.model.reference.xml254
Methods in psidev.psi.mi.jami.xml.model.reference.xml254 that return types with arguments of type Confidence Modifier and Type Method Description Collection<Confidence>
AbstractExperimentRef. getConfidences()
getConfidences. -
Uses of Confidence in psidev.psi.mi.jami.xml.model.reference.xml300
Methods in psidev.psi.mi.jami.xml.model.reference.xml300 that return types with arguments of type Confidence Modifier and Type Method Description Collection<Confidence>
AbstractExperimentRef. getConfidences()
getConfidences.
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