Package psidev.psi.mi.jami.model

Interface Complex

    • Method Detail

      • getComplexAc

        String getComplexAc()
        Complex accession if the complex has been curated under the Complex Portal curation rules. It can be null if the complex is not registered in the Complex Portal. This complex accession should be a shortcut to the complex-primary Xref in the collection of xrefs. Ex: CPX-123
        Returns:
        the complex accession

      • getComplexVersion

        String getComplexVersion()
        Complex version if the complex has been curated under the Complex Portal curation rules. It can be null if the complex is not registered in the Complex Portal. This complex version should be a shortcut to the complex-primary Xref version in the collection of xrefs. Ex: 1
        Returns:
        the complex version

      • assignComplexAc

        void assignComplexAc​(String accession)
        Assign a complex accession to a complex. It will add the new complex-primary ref to the collection of xrefs
        Parameters:
        accession - : the complex accession. If the version is added to the accession e.g. CPX-1234.2 the complex will be updated with the corresponding version, if not it is assumed version 1
        Throws:
        IllegalArgumentException - if - the accession is null or empty

      • assignComplexAc

        void assignComplexAc​(String accession,
                     String version)
        Assign a complex accession to a complex. It will add the new complex-primary ref to the collection of xrefs
        Parameters:
        accession - : the complex accession
        version - : the version of the complex if it is provided. If version is null it will create the complex with version 1
        Throws:
        IllegalArgumentException - if - the accession is null or empty

      • getPhysicalProperties

        String getPhysicalProperties()
        The physical properties for this complex. It is a shortcut which should point to the first complex-properties annotation in the collection of annotations. Example: Molecular mass = 154 kDa
        Returns:
        the properties

      • setPhysicalProperties

        void setPhysicalProperties​(String properties)
        Sets the physical properties of this complex. It will remove the old complex-properties annotation from the collection of annotations and replace it with the new complex-properties annotation. If the new complex-properties is null, all the existing complex-properties annotations will be removed from the collection of annotations
        Parameters:
        properties - : complex properties

      • getRecommendedName

        String getRecommendedName()
        The recommended name of a complex. It is a shortcut which should point to the first complex recommended name alias in the collection of aliases.
        Returns:
        the recommended name

      • setRecommendedName

        void setRecommendedName​(String name)
        Sets the recommended name of this complex. It will remove the old recommended name from the collection of aliases and replace it with the new recommended name. If the new recommended name is null, all the existing recommended names will be removed from the collection of aliases
        Parameters:
        name - : the recommended name

      • getSystematicName

        String getSystematicName()
        The systematic name of a complex. It is a shortcut which should point to the first complex systematic name alias in the collection of aliases.
        Returns:
        the systematic name

      • setSystematicName

        void setSystematicName​(String name)
        Sets the systematic name of this complex. It will remove the old systematic name from the collection of aliases and replace it with the new systematic name. If the new systematic name is null, all the existing systematic names will be removed from the collection of aliases
        Parameters:
        name - : the systematic name

      • getComparableParticipants

        default Collection<ModelledComparableParticipant> getComparableParticipants()
        Gets comparable participants for a complex. It will expand complex participant, pools. It will filter by proteins It will combine stoichiometry for same interactors Comparable participants are per interactor and are new instances.
        Returns:
        a collection of ModelledComparableParticipant objects.