Package psidev.psi.mi.jami.model

Interface Experiment

    • Field Detail

      • UNSPECIFIED_METHOD

        static final String UNSPECIFIED_METHOD
        Constant UNSPECIFIED_METHOD="unspecified method"
        See Also:
        Constant Field Values

      • UNSPECIFIED_METHOD_MI

        static final String UNSPECIFIED_METHOD_MI
        Constant UNSPECIFIED_METHOD_MI="MI:0686"
        See Also:
        Constant Field Values

      • INFERRED_BY_CURATOR

        static final String INFERRED_BY_CURATOR
        Constant INFERRED_BY_CURATOR="inferred by curator"
        See Also:
        Constant Field Values

      • INFERRED_BY_CURATOR_MI

        static final String INFERRED_BY_CURATOR_MI
        Constant INFERRED_BY_CURATOR_MI="MI:0364"
        See Also:
        Constant Field Values

    • Method Detail

      • getPublication

        Publication getPublication()
        The publication where the experiment has been described. It can be null if the experiment is not attached to any publications. This can happen when an experiment has been removed from a publication and is not valid anymore.
        Returns:
        the publication

      • setPublication

        void setPublication​(Publication publication)
        Set the publication where the experiment has been described.
        Parameters:
        publication - : the publication

      • setPublicationAndAddExperiment

        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
        Parameters:
        publication - : the publication

      • getXrefs

        <X extends Xref> Collection<X> getXrefs()
        Collection of cross references for an experiment which can give more information about the experiment. It cannot be null and if the experiment does not have any xrefs, the method should return an empty Collection. Ex: PRIDE experiment/project xrefs
        Type Parameters:
        X - a X object.
        Returns:
        the xrefs

      • getAnnotations

        <A extends Annotation> Collection<A> getAnnotations()
        Collection of annotations for an experiment. It cannot be null. If the experiment does not have any annotations, the method should return an empty Collection. Ex: data-processing, comments, cautions, confidence-mapping annotations
        Type Parameters:
        A - a A object.
        Returns:
        the annotations

      • getConfidences

        <C extends Confidence> Collection<C> getConfidences()
        Collection of confidences for a specific experiment. It can happen that an authors give different confidences to the same experiment depending on the environment. It cannot be null. If the experiment does not have any confidences, the method should return an empty Collection.
        Type Parameters:
        C - a C object.
        Returns:
        the confidences for this experiment

      • getInteractionDetectionMethod

        CvTerm getInteractionDetectionMethod()
        The experimental method to determine the interaction. It is a controlled vocabulary term and cannot not be null. Ex: pull down, coip, ...
        Returns:
        the interaction detection method

      • setInteractionDetectionMethod

        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).
        Parameters:
        term - : the detection method

      • getHostOrganism

        Organism getHostOrganism()
        The host organism where the interaction took place in this experiment. It can be null. Ex: in vitro, human-hela cells
        Returns:
        the host organism

      • setHostOrganism

        void setHostOrganism​(Organism organism)
        Sets the host organism of an experiment
        Parameters:
        organism - : host organism

      • getInteractionEvidences

        <I extends InteractionEvidence> Collection<I> getInteractionEvidences()
        The interactions determined in this experiment. The collection cannot be null. If the experiment did not show any interactions, the method should return an empty collection
        Type Parameters:
        I - a I object.
        Returns:
        the interactions

      • addInteractionEvidence

        boolean addInteractionEvidence​(InteractionEvidence evidence)
        This method will add the interaction evidence and set the experiment of the new interaction evidence to this current experiment
        Parameters:
        evidence - : evidence to add
        Returns:
        true if interaction evidence is added to the list of interactions

      • removeInteractionEvidence

        boolean removeInteractionEvidence​(InteractionEvidence evidence)
        This method will remove the interaction evidence and set the experiment of the new interaction evidence to null
        Parameters:
        evidence - : evidence to remove
        Returns:
        true if interaction evidence is removed from the list of interactions

      • addAllInteractionEvidences

        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
        Parameters:
        evidences - : evidences to add
        Returns:
        true if interaction evidences are added to the list of interaction evidences

      • removeAllInteractionEvidences

        boolean removeAllInteractionEvidences​(Collection<? extends InteractionEvidence> evidences)
        This method will remove the interaction evidences and set the experiment of the removed interaction evidences to null.
        Parameters:
        evidences - : evidences to remove
        Returns:
        true if interaction evidences are removed from the list of interactions

      • getVariableParameters

        <V extends VariableParameter> Collection<V> getVariableParameters()
        The collection of variableParameters and their values used in this experiment. The collection cannot be null. If the experiment does not have any variableParameters, this method should return an empty collection.
        Type Parameters:
        V - a V object.
        Returns:
        the collection of variableParameters and their values used in this experiment

      • addVariableParameter

        boolean addVariableParameter​(VariableParameter variableParameter)
        This method will add the variableParameter and set the experiment of the new variableParameter to this current experiment
        Parameters:
        variableParameter - : parameter to add
        Returns:
        true if variableParameter is added to the list of variableParameters

      • removeVariableParameter

        boolean removeVariableParameter​(VariableParameter variableParameter)
        This method will remove the variableParameter and set the experiment of the removed variableParameter to null.
        Parameters:
        variableParameter - : parameter to remove
        Returns:
        true if variableParameter is removed from the list of variableParameters

      • addAllVariableParameters

        boolean addAllVariableParameters​(Collection<? extends VariableParameter> variableParameters)
        This method will add all variableParameters and set the experiment of the new variableParameters to this current experiment
        Parameters:
        variableParameters - : parameters to add
        Returns:
        true if variableParameters are added to the list of variableParameters

      • removeAllVariableParameters

        boolean removeAllVariableParameters​(Collection<? extends VariableParameter> variableParameters)
        This method will remove all the variableParameters and set the experiment of the removed variableParameters to null.
        Parameters:
        variableParameters - : parameters to remove
        Returns:
        true if variableParameters are removed from the list of variableParameters