Package psidev.psi.mi.jami.model

Interface Feature<P extends Entity,​F extends Feature>

    • Method Detail

      • getShortName

        String getShortName()
        The short name of a feature. It can be null Ex: region, SH3 domains
        Returns:
        the short name

      • setShortName

        void setShortName​(String name)
        Sets the short name of the feature
        Parameters:
        name - : short name

      • getFullName

        String getFullName()
        The full name that describes the feature. It can be null. Ex: SWIB/MDM2 domain (IPR003121)
        Returns:
        the full name

      • setFullName

        void setFullName​(String name)
        Sets the full name that describes the molecule
        Parameters:
        name - : full name

      • getInterpro

        String getInterpro()
        The interpro identifier if it exists, null otherwise. It is a shortcut to the first interpro identifier in the list of identifiers.
        Returns:
        the interpro identifier if it exists.

      • setInterpro

        void setInterpro​(String interpro)
        Sets the interpro identifier. It will remove the old interpro identifier and add a new interpro identity Xref in the list of identifiers. If interpro is null, it will remove all existing interpro Xref in the list of identifiers.
        Parameters:
        interpro - : the new interpro identifier

      • getIdentifiers

        <X extends Xref> Collection<X> getIdentifiers()
        Collection of External identifiers which describes this feature. The Collection cannot be null and if the feature is not described in an external databases, the method should return an empty Collection. Ex: interpro:IPR003121
        Type Parameters:
        X - a X object
        Returns:
        the identifier

      • getXrefs

        <X extends Xref> Collection<X> getXrefs()
        Collection of cross references which give more information about the feature. The set cannot be null. If the feature does not have any other xrefs, the method should return an empty Collection. Ex: GO xrefs to give information about process or function
        Type Parameters:
        X - a X object
        Returns:
        the xrefs

      • getAnnotations

        <A extends Annotation> Collection<A> getAnnotations()
        Collection of annotations which describe the feature The set cannot be null. If the feature does not have any annotations, the method should return an empty Collection. Ex: observed ptm, cautions, comments, ...
        Type Parameters:
        A - an A object
        Returns:
        the annotations

      • getType

        CvTerm getType()
        The type for this feature. It is a controlled vocabulary term and can be null. Ex: fluorophore, tag, mutation, ...
        Returns:
        The feature type

      • setType

        void setType​(CvTerm type)
        Sets the feature type.
        Parameters:
        type - : feature type

      • getRanges

        <R extends Range> Collection<R> getRanges()
        The ranges which locate the feature in the interactor sequence/structure. The collection cannot be null. If the feature does not have any ranges, the method should return an empty collection
        Type Parameters:
        R - a R object.
        Returns:
        a collection of ranges

      • getRole

        CvTerm getRole()
        The effect of this feature on the interaction where the feature has been reported or the interaction dependency between the interaction reporting this feature and this feature. It can be null if the feature does not have any effects on the interaction or it is not relevant Ex: increasing interaction, decreasing interaction, disrupting interaction, etc. Ex: resulting-ptm,prerequisite-ptm ...
        Returns:
        the effect of this feature on the interaction

      • setRole

        void setRole​(CvTerm role)
        Sets the interaction effect/role for this feature.
        Parameters:
        role - : the feature role

      • getParticipant

        P getParticipant()
        The participant to which the feature is attached. It can be any entity (participant, participant pool, participant candidate, etc.) It can be null if the feature is not attached to any participants.
        Returns:
        the participant

      • setParticipant

        void setParticipant​(P participant)
        Sets the participant.
        Parameters:
        participant - : participant

      • setParticipantAndAddFeature

        void setParticipantAndAddFeature​(P participant)
        Sets the participant and add this feature to its list of features. If participant is null, it will remove this feature from the previous participant attached to this feature
        Parameters:
        participant - : participant

      • getLinkedFeatures

        <T extends F> Collection<T> getLinkedFeatures()
        The other features that can bind to this feature. The collection cannot be null. If the feature does not bind with any other features, the method should return an empty collection
        Type Parameters:
        T - a T object.
        Returns:
        the binding features

      • getAliases

        <A extends Alias> Collection<A> getAliases()
        Collection of aliases for a feature. The Collection cannot be null and if the experiment does not have any aliases, the method should return an empty Collection.
        Type Parameters:
        A - a A object.
        Returns:
        the aliases