Package psidev.psi.mi.jami.xml.model.extension.binary.xml30

Class XmlModelledBinaryInteractionWrapper

    • Method Detail

      • setCausalRegulatoryMechanism

        public void setCausalRegulatoryMechanism​(CvTerm causalRegulatoryMechanism)
        Sets the causal regulatory mechanism of this binary interaction
        Specified by:
        setCausalRegulatoryMechanism in interface BinaryInteraction<ModelledParticipant>
        Parameters:
        causalRegulatoryMechanism - : the complex regulatory mechanism CvTerm

      • getParticipants

        public Collection<ModelledParticipant> 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. The collection of participants for this binary interaction. It cannot be changed.
        Specified by:
        getParticipants in interface Interaction<ModelledParticipant>
        Returns:
        the particiants

      • addParticipant

        public boolean addParticipant​(ModelledParticipant part)
        This method will add the participant and set the interaction of the new participant to this current interaction Adds a new Participant and set the Interaction of this participant if added. If the participant B and A are null, it will first set the participantA. If the participantA is set, it will set the ParticipantB
        Specified by:
        addParticipant in interface Interaction<ModelledParticipant>
        Parameters:
        part - : participant to add
        Returns:
        true if participant is added to the list of participants

      • removeParticipant

        public boolean removeParticipant​(ModelledParticipant part)
        This method will remove the participant and set the interaction of the new participant to null Removes the Participant from this binary interaction
        Specified by:
        removeParticipant in interface Interaction<ModelledParticipant>
        Parameters:
        part - : participant to remove
        Returns:
        true if participant is removed from the list of participants

      • 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 Adds the participants and set the Interaction of this participant if added. If the participant B and A are null, it will first set the participantA. If the participantA is set, it will set the ParticipantB
        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

      • 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

      • getIdentifiers

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

      • getXrefs

        public Collection<Xref> 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, ...
        Specified by:
        getXrefs in interface Interaction<ModelledParticipant>
        Specified by:
        getXrefs in interface Interactor
        Returns:
        the xrefs

      • getChecksums

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

      • getAnnotations

        public Collection<Annotation> 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, ...
        Specified by:
        getAnnotations in interface Interaction<ModelledParticipant>
        Specified by:
        getAnnotations in interface Interactor
        Returns:
        the annotations

      • getInteractionType

        public CvTerm getInteractionType()
        The interaction type is a controlled vocabulary term. It can be null. Ex: direct interaction, association, ...
        Specified by:
        getInteractionType in interface Interaction<ModelledParticipant>
        Returns:
        the interaction type

      • 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

      • 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

      • getSource

        public Source getSource()
        The source which reported this modelled interaction. It can be an organization, institute, ... It can be null if the source is unknown or not relevant. Ex: IntAct, MINT, DIP, ...
        Specified by:
        getSource in interface ModelledInteraction
        Returns:
        the source

      • setSource

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

      • 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

      • getModelledConfidences

        public Collection<ModelledConfidence> getModelledConfidences()
        The confidences in this interaction. The Collection cannot be null. If the interaction does not have any confidences, the method should return an empty Collection. Ex: author based scores, statistical confidences, ...
        Specified by:
        getModelledConfidences in interface ModelledInteraction
        Returns:
        the confidences

      • getModelledParameters

        public Collection<ModelledParameter> getModelledParameters()
        Collection of numerical parameters for this interaction. The set cannot be null. If the interaction does not have any parameters, the method should return an empty Collection. Ex: IC50, ...
        Specified by:
        getModelledParameters in interface ModelledInteraction
        Returns:
        the parameters

      • getCooperativeEffects

        public Collection<CooperativeEffect> getCooperativeEffects()
        The collection of cooperative effects associated with this modelledInteraction. The collection cannot be null. If the ModelledInteraction does not have any cooperative effects, this method should return an empty collection.
        Specified by:
        getCooperativeEffects in interface ModelledInteraction
        Returns:
        the collection of cooperative effects for this modelled interaction

      • 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()
        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