Package psidev.psi.mi.jami.model

Interface Interactor

    • Field Detail

      • UNKNOWN_INTERACTOR

        static final String UNKNOWN_INTERACTOR
        Constant UNKNOWN_INTERACTOR="unknown participant"
        See Also:
        Constant Field Values

      • UNKNOWN_INTERACTOR_MI

        static final String UNKNOWN_INTERACTOR_MI
        Constant UNKNOWN_INTERACTOR_MI="MI:0329"
        See Also:
        Constant Field Values

    • Method Detail

      • getShortName

        String getShortName()
        The short name of the interactor. It cannot be null or empty. Ex: brca2
        Returns:
        the short name

      • setShortName

        void setShortName​(String name)
        Sets the short name of an interactor
        Parameters:
        name - : short name
        Throws:
        IllegalArgumentException - if name is null or empty

      • getFullName

        String getFullName()
        The full name of the interactor. It can be null Ex: Breast cancer type 2 susceptibility protein
        Returns:
        the full name

      • setFullName

        void setFullName​(String name)
        Sets the full name of the interactor
        Parameters:
        name - : full name

      • getIdentifiers

        <X extends Xref> Collection<X> getIdentifiers()
        Set of identifiers for this interactor. The identifiers can be from different databases, can be primary identifiers and secondary identifiers but they must be unambiguous. The Collection cannot be null, when an interactor does not have any identifiers, the method should return an empty Collection. Ex: uniprotkb secondary accession O00183, primary accessions, ...
        Type Parameters:
        X - a X object
        Returns:
        the alternative identifier

      • getPreferredIdentifier

        Xref getPreferredIdentifier()
        The identifier in the list of identifiers which is the preferred identifier. If no identifiers is preferred, it should return the first identifier of the list of identifiers, null if the list of identifiers is empty.
        Returns:
        the preferred identifier in the list of identifiers, null if the list of identifiers is empty

      • getPreferredName

        String getPreferredName()
        The preferred name is the name by which we want to refer the interactor on our web site.
        Returns:
        the preferred name

      • getChecksums

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

      • getXrefs

        <X extends Xref> Collection<X> getXrefs()
        Collection of other xrefs that give more information about the interactor. Ex: GO references to gives function/process/location information
        Type Parameters:
        X - a X object
        Returns:
        other xrefs

      • getAnnotations

        <A extends Annotation> Collection<A> getAnnotations()
        Collection of annotations for an interactor. The set cannot be null and if the interactor does not have any annotations, the method should return an empty Collection. Ex: pharmacology, isoform-comment, etc.
        Type Parameters:
        A - an A object
        Returns:
        the annotations

      • getAliases

        <A extends Alias> Collection<A> getAliases()
        Collection of aliases for an interactor The Collection cannot be null and if the interactor does not have any aliases, the method should return an empty Collection. Ex: complex-synonym, author-assigned name, ...
        Type Parameters:
        A - an A object
        Returns:
        the aliases

      • getOrganism

        Organism getOrganism()
        The original source organism for this interactor. It can be null in case of chemical compounds/synthetic peptides
        Returns:
        the organism

      • setOrganism

        void setOrganism​(Organism organism)
        Sets the source organism of this interactor
        Parameters:
        organism - : source organism

      • getInteractorType

        CvTerm getInteractorType()
        The molecule type of this interactor. It is a controlled vocabulary term and cannot be null. Ex: protein, gene, small molecule, ...
        Returns:
        interactor type

      • setInteractorType

        void setInteractorType​(CvTerm type)
        Sets the molecule type for this interactor If the given type is null, this method automatically sets the interactor type to 'unknown participant' (MI:0329)
        Parameters:
        type - : molecule type