Package psidev.psi.mi.jami.xml.model.extension.xml254

Class XmlInteractionEvidenceComplexWrapper

    • Method Detail

      • addAllParticipants

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

      • removeAllParticipants

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

      • getInteractionEvidences

        public Collection<InteractionEvidence> getInteractionEvidences()
        Interaction evidences supporting this modelled interaction. The collection cannot be null. If the modelled interaction does not have experimental interactions attached to it, the method should return an empty set
        Specified by:
        getInteractionEvidences in interface ModelledInteraction
        Returns:
        the collection of experimental evidences

      • setSource

        public void setSource​(Source source)
        Sets the source reporting the interaction.
        Specified by:
        setSource in interface ModelledInteraction
        Parameters:
        source - : source for this interaction

      • getChecksums

        public Collection<Checksum> 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, ...
        Specified by:
        getChecksums in interface Interaction<ModelledParticipant>
        Specified by:
        getChecksums in interface Interactor
        Returns:
        the set of checksums

      • getIdentifiers

        public Collection<Xref> 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, ...
        Specified by:
        getIdentifiers in interface Interaction<ModelledParticipant>
        Specified by:
        getIdentifiers in interface Interactor
        Returns:
        the alternative identifier

      • getPreferredIdentifier

        public 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.
        Specified by:
        getPreferredIdentifier in interface Interactor
        Returns:
        the preferred identifier in the list of identifiers, null if the list of identifiers is empty

      • getPreferredName

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

      • getOrganism

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

      • setOrganism

        public void setOrganism​(Organism organism)
        Sets the source organism of this interactor
        Specified by:
        setOrganism in interface Interactor
        Parameters:
        organism - : source organism

      • getInteractorType

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

      • setInteractorType

        public 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)
        Specified by:
        setInteractorType in interface Interactor
        Parameters:
        type - : molecule type

      • getRigid

        public 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
        Specified by:
        getRigid in interface Interaction<ModelledParticipant>
        Returns:
        the rigid

      • setRigid

        public 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
        Specified by:
        setRigid in interface Interaction<ModelledParticipant>
        Parameters:
        rigid - : the rigid

      • initialiseModelledParameters

        protected void initialiseModelledParameters()

        initialiseModelledParameters.

      • initialiseModelledConfidences

        protected void initialiseModelledConfidences()

        initialiseModelledConfidences.

      • initialiseParticipants

        protected void initialiseParticipants()

        initialiseParticipants.

      • getComplexAc

        public 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
        Specified by:
        getComplexAc in interface Complex
        Returns:
        the complex accession

      • getComplexVersion

        public 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
        Specified by:
        getComplexVersion in interface Complex
        Returns:
        the complex version

      • assignComplexAc

        public 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
        Specified by:
        assignComplexAc in interface Complex
        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

      • assignComplexAc

        public void assignComplexAc​(String accession)
        Assign a complex accession to a complex. It will add the new complex-primary ref to the collection of xrefs
        Specified by:
        assignComplexAc in interface Complex
        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

      • getPhysicalProperties

        public String getPhysicalProperties()
        Description copied from interface: Complex
        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
        Specified by:
        getPhysicalProperties in interface Complex
        Returns:
        the properties

      • setPhysicalProperties

        public 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
        Specified by:
        setPhysicalProperties in interface Complex
        Parameters:
        properties - : complex properties

      • getRecommendedName

        public 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.
        Specified by:
        getRecommendedName in interface Complex
        Returns:
        the recommended name

      • setRecommendedName

        public 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
        Specified by:
        setRecommendedName in interface Complex
        Parameters:
        name - : the recommended name

      • getSystematicName

        public 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.
        Specified by:
        getSystematicName in interface Complex
        Returns:
        the systematic name

      • setSystematicName

        public 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
        Specified by:
        setSystematicName in interface Complex
        Parameters:
        name - : the systematic name

      • toString

        public String toString()

        toString

        Specified by:
        toString in interface FileSourceContext
        Overrides:
        toString in class Object
        Returns:
        the file source context as a String. If the source locator is not null, it should give the source locator properties

      • getEvidenceType

        public CvTerm getEvidenceType()
        The evidence type for this modelled interactions. Usually this Cv term is ECO (evidence code ontology) code. It can be null. Ex: ECO:0000021, physical interaction evidence
        Specified by:
        getEvidenceType in interface ModelledInteraction
        Returns:
        the evidence type