Package psidev.psi.mi.jami.model

Interface Publication

    • Method Detail

      • getPubmedId

        String getPubmedId()
        The pubmed identifier which identifies the publication. It is a shortcut for the first pubmed identifier in the collection of identifiers. It will be null if the collection of identifiers does not contain any pubmed identifiers.
        Returns:
        the pubmed identifier

      • setPubmedId

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

      • getDoi

        String getDoi()
        The doi number which identifies the publication. It is a shortcut for the first doi in the collection of identifiers. It will be null if the collection of identifiers does not contain any doi.
        Returns:
        the doi number

      • setDoi

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

      • getIdentifiers

        <X extends Xref> Collection<X> getIdentifiers()
        The publication identifiers. Usually a publication only has one pubmed id or DOI number, but it could also have a database internal identifier if the publication is not published yet. The Collection cannot be null. If the publication does not have any identifiers, the method should return an empty Collection Ex: pubmed:14681455
        Type Parameters:
        X - a X object
        Returns:
        the publication identifier

      • getImexId

        String getImexId()
        IMEx identifier of the publication if it has been registered in IMEx central as a publication curated following IMEx curation rules. It can be null if the publication is not registered in IMEx central or does not follow the IMEx curation rules. It is a shortcut to the first IMEx imex-primary reference in the list of xrefs. Ex: IM-123
        Returns:
        the IMEx identifier

      • assignImexId

        void assignImexId​(String identifier)
        Assign an IMEx id to a publication. It will add a Xref imex with qualifier imex-primary to the list of xrefs.
        Parameters:
        identifier - : the IMEx id from IMEx central
        Throws:
        IllegalArgumentException - if - the identifier is null or empty

      • getTitle

        String getTitle()
        The publication title. It can be null.
        Returns:
        the title

      • setTitle

        void setTitle​(String title)
        Set the publication title
        Parameters:
        title - : publication title

      • getJournal

        String getJournal()
        The journal where the publication has been published. It can be null if not published.
        Returns:
        the journal

      • setJournal

        void setJournal​(String journal)
        Set the journal where the publication has been published
        Parameters:
        journal - : the journal

      • getPublicationDate

        Date getPublicationDate()
        The date of publication. It can be null if not published
        Returns:
        the publication date

      • setPublicationDate

        void setPublicationDate​(Date date)
        Set the date of publication.
        Parameters:
        date - : publication date

      • getAuthors

        List<String> getAuthors()
        The List of authors with the same order as it appears in the publication. It cannot be null. If the publication does not have any authors, the collection should be empty.
        Returns:
        collection of authors

      • getXrefs

        <X extends Xref> Collection<X> getXrefs()
        Other cross references which give more information about the publication. It cannot be null. If the publication does not have any xrefs, the method should return an empty Collection. Ex: other primary references such as DOI : 10.1023/A:1005823620291
        Type Parameters:
        X - a X object
        Returns:
        the xrefs

      • getAnnotations

        <A extends Annotation> Collection<A> getAnnotations()
        Other publication annotations which can give more information about the curated publication. It cannot be null. If the publication does not have any other annotations, the method should return an empty Collection. Ex: topic = dataset value = Cyanobacteria - Interaction dataset based on Cyanobacteria proteins and related species
        Type Parameters:
        A - a A object
        Returns:
        the annotations

      • getExperiments

        <E extends Experiment> Collection<E> getExperiments()
        The curated experiments which have been described in the publication. It cannot be null. If no experiments have been curated in this publication, the method should return an empty collection.
        Type Parameters:
        E - a E object
        Returns:
        the collection of experiments

      • getCurationDepth

        CurationDepth getCurationDepth()
        The curation depth for this publication. If the curation depth is undefined, the method should not return null but CurationDepth.undefined. Ex: IMEx, MIMIx, undefined
        Returns:
        the curation depth

      • setCurationDepth

        void setCurationDepth​(CurationDepth curationDepth)
        Set the curation depth of the publication. If the curation depth is null, it should set the cuuration depth to CurationDepth.undefined
        Parameters:
        curationDepth - : the curation depth

      • getReleasedDate

        Date getReleasedDate()
        Publication released date by the interaction database or resource which curated the publication. It can be null if the publication is not released.
        Returns:
        the released date

      • setReleasedDate

        void setReleasedDate​(Date released)
        Set the released date of the curated publication
        Parameters:
        released - : the released date

      • getSource

        Source getSource()
        The source which curated this publication. It can be an organization, institute, ... It can be null if the source is unknown or not relevant. Ex: IntAct, MINT, DIP, ...
        Returns:
        the source

      • setSource

        void setSource​(Source source)
        Sets the source who curated the publication.
        Parameters:
        source - : source for this publication

      • addExperiment

        boolean addExperiment​(Experiment exp)
        This method will add the experiment and set the publication of the new experiment to this current publication
        Parameters:
        exp - : experiment to add
        Returns:
        true if experiment is added to the list of experiments

      • removeExperiment

        boolean removeExperiment​(Experiment exp)
        This method will remove the experiment and set the publication of the removed experiment to null.
        Parameters:
        exp - : experiment to remove
        Returns:
        true if experiment is removed from the list of experiments

      • addAllExperiments

        boolean addAllExperiments​(Collection<? extends Experiment> exp)
        This method will add all the experiments and set the publication of the new experiments to this current publication
        Parameters:
        exp - : experiments to add
        Returns:
        true if experiments are added to the list of experiments

      • removeAllExperiments

        boolean removeAllExperiments​(Collection<? extends Experiment> exp)
        This method will remove the experiments and set the publication of the removed experiments to null.
        Parameters:
        exp - : experiments to remove
        Returns:
        true if experiments are removed from the list of experiments