Class DefaultBinaryInteractionEvidence

    • Method Detail

      • initialiseExperimentalConfidences

        protected void initialiseExperimentalConfidences()

        initialiseExperimentalConfidences

      • initialiseExperimentalConfidencesWith

        protected void initialiseExperimentalConfidencesWith​(Collection<Confidence> confidences)

        initialiseExperimentalConfidencesWith

        Parameters:
        confidences - a Collection object.
      • initialiseVariableParameterValueSets

        protected void initialiseVariableParameterValueSets()

        initialiseVariableParameterValueSets

      • initialiseVariableParameterValueSetsWith

        protected void initialiseVariableParameterValueSetsWith​(Collection<VariableParameterValueSet> variableValues)

        initialiseVariableParameterValueSetsWith

        Parameters:
        variableValues - a Collection object.
      • initialiseExperimentalParameters

        protected void initialiseExperimentalParameters()

        initialiseExperimentalParameters

      • initialiseExperimentalParametersWith

        protected void initialiseExperimentalParametersWith​(Collection<Parameter> parameters)

        initialiseExperimentalParametersWith

        Parameters:
        parameters - a Collection object.
      • assignImexId

        public void assignImexId​(String identifier)
        Assign an IMEx id to an interaction. It will add the new imex-primary ref to the collection of xrefs
        Specified by:
        assignImexId in interface InteractionEvidence
        Parameters:
        identifier - : the IMEx id from IMEx central
      • setExperiment

        public void setExperiment​(Experiment experiment)
        Sets the experiment for this interaction.
        Specified by:
        setExperiment in interface InteractionEvidence
        Parameters:
        experiment - : experiment
      • setExperimentAndAddInteractionEvidence

        public void setExperimentAndAddInteractionEvidence​(Experiment experiment)
        Sets the experiment for this interaction and add the interaction to the list of interaction evidences If the given experiment is null, it will remove this interaction evidence from the previous experiment attached to this interaction
        Specified by:
        setExperimentAndAddInteractionEvidence in interface InteractionEvidence
        Parameters:
        experiment - : experiment
      • setAvailability

        public void setAvailability​(String availability)
        Sets the availability.
        Specified by:
        setAvailability in interface InteractionEvidence
        Parameters:
        availability - : availability
      • setNegative

        public void setNegative​(boolean negative)
        Sets the negative boolean value.
        Specified by:
        setNegative in interface InteractionEvidence
        Parameters:
        negative - : negative value
      • setInferred

        public void setInferred​(boolean inferred)
        Sets the inferred boolean value
        Specified by:
        setInferred in interface InteractionEvidence
        Parameters:
        inferred - : inferred boolean value
      • processAddedXrefEvent

        protected void processAddedXrefEvent​(Xref added)

        processAddedXrefEvent

        Parameters:
        added - a Xref object.
      • processRemovedXrefEvent

        protected void processRemovedXrefEvent​(Xref removed)

        processRemovedXrefEvent

        Parameters:
        removed - a Xref object.
      • clearPropertiesLinkedToXrefs

        protected void clearPropertiesLinkedToXrefs()

        clearPropertiesLinkedToXrefs