Package psidev.psi.mi.jami.model

Interface CvTerm

    • Method Detail

      • getShortName

        String getShortName()
        Short name of a controlled vocabulary. It cannot be null or empty. Ex: electrophoresis, binding site, protein, ...
        Returns:
        the short name

      • setShortName

        void setShortName​(String name)
        Set the short name
        Parameters:
        name - : short name
        Throws:
        IllegalArgumentException - if name is null or empty

      • getFullName

        String getFullName()
        Full name of the controlled vocabulary as it appears in the ontology. It can be null. Ex: electrophoretic mobility-based method, binding-associated region, protein
        Returns:
        the full name

      • setFullName

        void setFullName​(String name)
        Set the full name
        Parameters:
        name - : full name

      • getIdentifiers

        <X extends Xref> Collection<X> getIdentifiers()
        The collection of identifiers which identifies this CvTerm. It is aimed at returning all existing identifiers from one to several external databases and including secondary identifiers or former identifiers. The collection cannot be null so if the term does not exist in any ontologies/databases, the method should return an empty collection. Ex: MI:0982 from the psi-mi ontology
        Type Parameters:
        X - a X object.
        Returns:
        the ontology identifier

      • getMIIdentifier

        String getMIIdentifier()
        The unique PSI-MI identifier which identifies the object in the PSI-MI ontology. It is a shortcut for the first psi-mi identifier in the collection of identifiers. It will be null if the collection of identifiers does not contain any PSI-MI Xref objects
        Returns:
        the unique PSI-MI identifier

      • getMODIdentifier

        String getMODIdentifier()
        The unique PSI-MOD identifier which identifies the object in the PSI-MOD ontology. It is a shortcut for the first psi-mod identifier in the collection of identifiers. It will be null if the collection of identifiers does not contain any PSI-MOD Xref objects
        Returns:
        the unique PSI-MOD identifier

      • getPARIdentifier

        String getPARIdentifier()
        The unique PSI-PAR identifier which identifies the object in the PSI-PAR ontology. It is a shortcut for the first psi-par identifier in the collection of identifiers. It will be null if the collection of identifiers does not contain any PSI-PAR Xref objects
        Returns:
        the unique PSI-PAR identifier

      • setMIIdentifier

        void setMIIdentifier​(String mi)
        Sets the PSI-MI identifier. It will remove the previous PSI-MI identifier from the collection of identifiers, and add the new one in the collection of identifiers with qualifier identity. If mi is null, it will remove all the psi-mi identifiers from the collection of identifiers.
        Parameters:
        mi - : mi identifier

      • setMODIdentifier

        void setMODIdentifier​(String mod)
        Sets the PSI-MOD identifier. It will remove the previous PSI-MOD identifier from the collection of xrefs, and add the new one in the collection of identifiers with qualifier identity. If mod is null, it will remove all the psi-mod identifiers from the collection of identifiers.
        Parameters:
        mod - : mod identifier

      • setPARIdentifier

        void setPARIdentifier​(String par)
        Sets the PSI-PAR identifier. It will remove the previous PSI-PAR identifier from the collection of xrefs, and add the new one in the collection of identifiers with qualifier identity. If par is null, it will remove all the psi-par identifiers from the collection of identifiers.
        Parameters:
        par - : par identifier

      • getXrefs

        <X extends Xref> Collection<X> getXrefs()
        Collection of cross references describing the CvTerm. This method should never return null. It can return an empty Collection if no xrefs are available for this Cvterm Ex: publication primary references
        Type Parameters:
        X - a X object.
        Returns:
        the set of Xrefs

      • getAnnotations

        <A extends Annotation> Collection<A> getAnnotations()
        Collection of annotations describing the CvTerm. This method should never return null. It can return an empty Collection if no annotations are available for this Cvterm. Ex: search url, validation regexp, etc
        Type Parameters:
        A - a A object.
        Returns:
        the set of annotations

      • getSynonyms

        <A extends Alias> Collection<A> getSynonyms()
        Collection of synonyms for this CvTerm This method should never return null. It can return an empty Collection if no synonyms are available for this Cvterm Ex: participant detection is a synonym of participant identification method (MI:0002)
        Type Parameters:
        A - a A object.
        Returns:
        the se of synonyms