Package psidev.psi.mi.jami.model

Interface InteractionEvidence

    • Method Detail

      • getImexId

        String getImexId()
        IMEx identifier if the interaction has been curated following IMEx curation rules. It can be null if the interaction is not registered in IMEx central or does not follow the IMEx curation rules. This imex id should be a shortcut to the imex-primary Xref in the collection of xrefs. Ex: IM-123-2
        Returns:
        the IMEx identifier

      • assignImexId

        void assignImexId​(String identifier)
        Assign an IMEx id to an interaction. It will add the new imex-primary ref to the collection of xrefs
        Parameters:
        identifier - : the IMEx id from IMEx central
        Throws:
        IllegalArgumentException - if - the identifier is null or empty

      • getExperiment

        Experiment getExperiment()
        The experiment which determined the interaction. It can be null if the interaction evidence is detached from experiment.
        Returns:
        the experiment

      • setExperiment

        void setExperiment​(Experiment experiment)
        Sets the experiment for this interaction.
        Parameters:
        experiment - : experiment

      • setExperimentAndAddInteractionEvidence

        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
        Parameters:
        experiment - : experiment

      • getVariableParameterValues

        <V extends VariableParameterValueSet> Collection<V> getVariableParameterValues()
        The collection of variableParameterValueSet this interaction has been observed with. Each variableParameterValueSet contains a set of variableParameterValues which have been used together. This collection cannot be null. If the interactionEvidence does not have any variableParameterValueSet, this method should return an empty set.
        Type Parameters:
        V - a V object
        Returns:
        the collection of variableParameterValueSet

      • getAvailability

        String getAvailability()
        The availability for this interaction. By default it is null because freely available. Ex: copyrights, ...
        Returns:
        the availability

      • setAvailability

        void setAvailability​(String availability)
        Sets the availability.
        Parameters:
        availability - : availability

      • getParameters

        <P extends Parameter> Collection<P> getParameters()
        Collection of numerical parameters for this interaction. The set cannot be null. If the interaction does not have any parameters, the method should return an empty Collection. Ex: IC50, ...
        Type Parameters:
        P - an P object
        Returns:
        the parameters

      • isInferred

        boolean isInferred()
        Boolean value to know if the interaction is inferred from multiple experiments which on their own would not support the interaction. By default is false.
        Returns:
        true if the interaction is inferred from multiple experiments which on their own would not support the interaction

      • setInferred

        void setInferred​(boolean inferred)
        Sets the inferred boolean value
        Parameters:
        inferred - : inferred boolean value

      • getConfidences

        <C extends Confidence> Collection<C> getConfidences()
        The confidences in this interaction. The Collection cannot be null. If the interaction does not have any confidences, the method should return an empty Collection. Ex: author based scores, statistical confidences, ...
        Type Parameters:
        C - a C object
        Returns:
        the confidences

      • isNegative

        boolean isNegative()
        Boolean value to know if an interaction is negative. It is false by default (positive interaction by default)
        Returns:
        true if the interaction is negative

      • setNegative

        void setNegative​(boolean negative)
        Sets the negative boolean value.
        Parameters:
        negative - : negative value