Package psidev.psi.mi.jami.xml.model.extension.xml253

Class AbstractXmlParticipantPool<I extends Interaction,​F extends Feature,​P extends ParticipantCandidate>

    • Constructor Detail

      • AbstractXmlParticipantPool

        public AbstractXmlParticipantPool()

        Constructor for AbstractXmlParticipantPool.

    • Method Detail

      • initialiseComponentCandidatesSet

        protected void initialiseComponentCandidatesSet()

        initialiseComponentCandidatesSet.

      • initialiseComponentCandidatesSetWith

        protected void initialiseComponentCandidatesSetWith​(Collection<P> candidates)

        initialiseComponentCandidatesSetWith.

        Parameters:
        candidates - a Collection object.

      • setType

        public void setType​(CvTerm type)
        Sets the pool type for this participant pool If the given type is null, this method automatically sets the interactor type to 'molecule set' (MI:1304) Sets the component set type. Sets the type to molecule set (MI:1304) if the given type is null
        Specified by:
        setType in interface ParticipantPool<I extends Interaction,​F extends Feature,​P extends ParticipantCandidate>
        Parameters:
        type - : molecule type

      • toArray

        public <T> T[] toArray​(T[] ts)

        toArray.

        Specified by:
        toArray in interface Collection<I extends Interaction>
        Type Parameters:
        T - a T object.
        Parameters:
        ts - an array of T objects.
        Returns:
        an array of T objects.

      • add

        public boolean add​(P interactor)

        add.

        Specified by:
        add in interface Collection<I extends Interaction>
        Parameters:
        interactor - a P object.
        Returns:
        a boolean.

      • setJAXBType

        public void setJAXBType​(XmlCvTerm type)
        Sets the value of the molecule set type property.
        Parameters:
        type - allowed object is XmlCvTerm

      • getJAXBInteractorCandidates

        public Collection<P> getJAXBInteractorCandidates()

        getJAXBInteractorCandidates.

        Returns:
        a Collection object.

      • setInteractionAndAddParticipant

        public void setInteractionAndAddParticipant​(I interaction)
        Sets the Interaction and add the new Participant to its list of Participants. If the given interaction is null, it will remove the Participant from the previous interaction it was attached to
        Specified by:
        setInteractionAndAddParticipant in interface Participant<I extends Interaction,​F extends Feature>
        Parameters:
        interaction - : interaction

      • getInteraction

        public I getInteraction()
        The interaction in which the participant is involved. It can be null if the participant is not attached to any interactions. It can happen if the participant has been removed from an interaction and is now invalid.
        Specified by:
        getInteraction in interface Participant<I extends Interaction,​F extends Feature>
        Returns:
        the interaction

      • getBiologicalRole

        public CvTerm getBiologicalRole()
        The biological role of the participant. It is a controlled vocabulary term and cannot be null. It the biological role of a participant is not known or not relevant, the method should return unspecified role (MI:0499) Ex: enzyme, enzyme target, ...
        Specified by:
        getBiologicalRole in interface Participant<I extends Interaction,​F extends Feature>
        Returns:
        the biological role

      • setBiologicalRole

        public void setBiologicalRole​(CvTerm bioRole)
        Sets the biological role. If the bioRole is null, should create a bioRole
        Specified by:
        setBiologicalRole in interface Participant<I extends Interaction,​F extends Feature>
        Parameters:
        bioRole - : biological role unspecified role (MI:0499)

      • getBiologicalEffect

        public CvTerm getBiologicalEffect()
        The biological effect of the participant in a causal interaction. It is a controlled vocabulary term and can be null.
        Specified by:
        getBiologicalEffect in interface Participant<I extends Interaction,​F extends Feature>
        Returns:
        the biological effect

      • setBiologicalEffect

        public void setBiologicalEffect​(CvTerm biologicalEffect)
        Sets the biological effect of the participant in a causal interaction.
        Specified by:
        setBiologicalEffect in interface Participant<I extends Interaction,​F extends Feature>
        Parameters:
        biologicalEffect - : biological effect

      • getXrefs

        public Collection<Xref> getXrefs()
        Collection of cross references which give more information about the participant. The set of xrefs cannot be null. If the participant does not have any xrefs, the method should return an empty Collection. Ex: author identifiers, ...
        Specified by:
        getXrefs in interface Participant<I extends Interaction,​F extends Feature>
        Returns:
        the xrefs

      • getAnnotations

        public Collection<Annotation> getAnnotations()
        Collection of annotations describing the participant. The set cannot be null. If the participant does not have any annotations, the method should return an empty Collection.
        Specified by:
        getAnnotations in interface Participant<I extends Interaction,​F extends Feature>
        Returns:
        the annotations

      • getAliases

        public Collection<Alias> getAliases()
        Collection of aliases which give more information about the participant. The set of aliases cannot be null. If the participant does not have any aliases, the method should return an empty Collection. Ex: author assigned name, ...
        Specified by:
        getAliases in interface Participant<I extends Interaction,​F extends Feature>
        Returns:
        the xrefs

      • getCausalRelationships

        public Collection<CausalRelationship> getCausalRelationships()
        The causal relationships of this entity on other entities usually part of an interaction. The set of causal relationship cannot be null. If the entity does not have any causal relationship, the method should return an empty Collection. Ex: increasing, decreasing, disrupting, etc.
        Specified by:
        getCausalRelationships in interface Entity<I extends Interaction>
        Returns:
        the collection of causal relationships attached to this entity

      • getFeatures

        public Collection<F> getFeatures()
        Properties for this entity. The collection cannot be null. If the entity does not have any features, the method should return an empty collection.
        Specified by:
        getFeatures in interface Entity<I extends Interaction>
        Returns:
        the features

      • addFeature

        public boolean addFeature​(F feature)

        addFeature.

        Specified by:
        addFeature in interface Entity<I extends Interaction>
        Parameters:
        feature - a F object.
        Returns:
        a boolean.

      • removeFeature

        public boolean removeFeature​(F feature)

        removeFeature.

        Specified by:
        removeFeature in interface Entity<I extends Interaction>
        Parameters:
        feature - a F object.
        Returns:
        a boolean.

      • addAllFeatures

        public boolean addAllFeatures​(Collection<? extends F> features)
        This method will add all features and set the entity of the new features to this current entity
        Specified by:
        addAllFeatures in interface Entity<I extends Interaction>
        Parameters:
        features - : features to add
        Returns:
        true if features are added to the list of features

      • removeAllFeatures

        public boolean removeAllFeatures​(Collection<? extends F> features)
        This method will remove all the features and set the entity of the removed features to null.
        Specified by:
        removeAllFeatures in interface Entity<I extends Interaction>
        Parameters:
        features - : features to remove
        Returns:
        true if features are removed from the list of features

      • getStoichiometry

        public Stoichiometry getStoichiometry()
        The stoichiometry for this participant. If the stoichiometry for this participant is unknown, the method should return null.
        Specified by:
        getStoichiometry in interface Entity<I extends Interaction>
        Returns:
        the stoichiometry

      • setStoichiometry

        public void setStoichiometry​(Integer stoichiometry)
        Sets the mean stoichiometry for this participant.
        Specified by:
        setStoichiometry in interface Entity<I extends Interaction>
        Parameters:
        stoichiometry - : mean stoichiometry value

      • setStoichiometry

        public void setStoichiometry​(Stoichiometry stoichiometry)
        Sets the stoichiometry for this participant.
        Specified by:
        setStoichiometry in interface Entity<I extends Interaction>
        Parameters:
        stoichiometry - : the stoichiometry

      • initialiseDefaultDelegate

        protected abstract void initialiseDefaultDelegate()

        initialiseDefaultDelegate.