Package psidev.psi.mi.jami.model

Interface Interaction<T extends Participant>

    • Method Detail

      • getShortName

        String getShortName()
        The short name of the interaction. It can be null. Ex: foxc1-flna, ...
        Returns:
        short name of the interaction

      • setShortName

        void setShortName​(String name)
        Sets the short name of the interaction
        Parameters:
        name - : short name

      • getRigid

        String getRigid()
        The checksum computed from the rogids from all the proteins involved in the interaction. It is only relevant for protein-protein interactions. This is a shortcut to the first rigid in the list of checksums
        Returns:
        the rigid

      • setRigid

        void setRigid​(String rigid)
        Sets the rigid of this interaction. It will remove the previous rigid from the list of checksum and add the new one. If rigid is null, it will remove all the rigid in the list of checksum
        Parameters:
        rigid - : the rigid

      • getIdentifiers

        <X extends Xref> Collection<X> getIdentifiers()
        The identifiers for an interaction. The Collection cannot be null. If the interaction does not have any identifiers (IMEx is not among the identifiers), the method should return an emtpy Collection. Ex: original interaction database accession, ...
        Type Parameters:
        X - a X object.
        Returns:
        the xrefs

      • getXrefs

        <X extends Xref> Collection<X> getXrefs()
        The external cross references for an interaction. The Collection cannot be null. If the interaction does not have any xrefs, the method should return an emtpy Collection. Ex: GO process xrefs, GO component xrefs, database accession that can identify the interaction, ...
        Type Parameters:
        X - a X object.
        Returns:
        the xrefs

      • getChecksums

        <C extends Checksum> Collection<C> getChecksums()
        Set of checksums computed for this interaction.. The Collection cannot be null so when an interaction does not have a checksum, the method should return an empty Collection Ex: rigid:u1FCes02jPb3CGRj1aDkzpbSiuI9606, ...
        Type Parameters:
        C - a C object.
        Returns:
        the set of checksums

      • getAnnotations

        <A extends Annotation> Collection<A> getAnnotations()
        The Collection of annotations describing the interaction. The Collection cannot be null. If the interaction does not have any annotations, the method should return an empty Collection. Ex: figure-legend annotations, comments, cautions, ...
        Type Parameters:
        A - a A object.
        Returns:
        the annotations

      • getUpdatedDate

        Date getUpdatedDate()
        The last update date. It can be null if not relevant or not known.
        Returns:
        the last update date

      • setUpdatedDate

        void setUpdatedDate​(Date updated)
        Sets the last update date
        Parameters:
        updated - : last update date

      • getCreatedDate

        Date getCreatedDate()
        The creation date. It can be null if not relevant or not known.
        Returns:
        the last update date

      • setCreatedDate

        void setCreatedDate​(Date created)
        Sets the created date
        Parameters:
        created - : created date

      • getInteractionType

        CvTerm getInteractionType()
        The interaction type is a controlled vocabulary term. It can be null. Ex: direct interaction, association, ...
        Returns:
        the interaction type

      • setInteractionType

        void setInteractionType​(CvTerm term)
        Sets the interaction type.
        Parameters:
        term - : interaction type

      • getParticipants

        <T2 extends T> Collection<T2> getParticipants()
        The collection of participants involved in this interaction. The collection cannot be null. If the interaction does not involve any participants, the method should return an empty set.
        Type Parameters:
        T2 - a T2 object.
        Returns:
        the particiants

      • addParticipant

        boolean addParticipant​(T part)
        This method will add the participant and set the interaction of the new participant to this current interaction
        Parameters:
        part - : participant to add
        Returns:
        true if participant is added to the list of participants

      • removeParticipant

        boolean removeParticipant​(T part)
        This method will remove the participant and set the interaction of the new participant to null
        Parameters:
        part - : participant to remove
        Returns:
        true if participant is removed from the list of participants

      • addAllParticipants

        boolean addAllParticipants​(Collection<? extends T> participants)
        This method will add all the participant and set the interaction of the new participant to this current interaction
        Parameters:
        participants - : participants to add
        Returns:
        true if participant are added to the list of participants

      • removeAllParticipants

        boolean removeAllParticipants​(Collection<? extends T> participants)
        This method will remove the participant and set the interaction of the removed participant to null.
        Parameters:
        participants - : participants to remove
        Returns:
        true if participant are removed from the list of participants