Package psidev.psi.mi.jami.tab.io.writer.feeder

Interface MitabColumnFeeder<T extends BinaryInteraction,​P extends Participant>

    • Method Detail

      • writeUniqueIdentifier

        void writeUniqueIdentifier​(P participant)
                    throws IOException
        This method will write the unique identifier of a participant
        Parameters:
        participant - a P object.
        Throws:
        IOException - if any.

      • writeAlternativeIdentifiers

        void writeAlternativeIdentifiers​(P participant)
                          throws IOException
        This method writes all the remaining identifiers (ignore the first identifier) of the participant
        Parameters:
        participant - a P object.
        Throws:
        IOException - if any.

      • writeAliases

        void writeAliases​(P participant)
           throws IOException
        This method writes all the aliases of the participant
        Parameters:
        participant - a P object.
        Throws:
        IOException - if any.

      • writeInteractionDetectionMethod

        void writeInteractionDetectionMethod​(T interaction)
                              throws IOException
        Writes the interaction detection method of the experiment.
        Parameters:
        interaction - a T object.
        Throws:
        IOException - if any.

      • writeFirstAuthor

        void writeFirstAuthor​(T interaction)
               throws IOException
        Writes the first author of a publication in an experiment
        Parameters:
        interaction - a T object.
        Throws:
        IOException - if any.

      • writePublicationIdentifiers

        void writePublicationIdentifiers​(T interaction)
                          throws IOException
        Writes the publication identifiers of a publication in an experiment. This method will write the first publication identifier (pubmed before doi) and also the IMEx id
        Parameters:
        interaction - a T object.
        Throws:
        IOException - if any.

      • writeInteractorOrganism

        void writeInteractorOrganism​(P participant)
                      throws IOException
        Writes the organism of a participant. Empty column if the organism is not provided
        Parameters:
        participant - a P object.
        Throws:
        IOException - if any.

      • writeInteractionType

        void writeInteractionType​(T interaction)
                   throws IOException
        Writes the interaction type of an interaction
        Parameters:
        interaction - a T object.
        Throws:
        IOException - if any.

      • writeSource

        void writeSource​(T interaction)
          throws IOException
        Writes the interaction source from the modelled interaction
        Parameters:
        interaction - a T object.
        Throws:
        IOException - if any.

      • writeInteractionIdentifiers

        void writeInteractionIdentifiers​(T interaction)
                          throws IOException
        Writes the interaction identifiers of an interaction. This method will write the first interaction identifier and also the IMEx id
        Parameters:
        interaction - a T object.
        Throws:
        IOException - if any.

      • writeInteractionConfidences

        void writeInteractionConfidences​(T interaction)
                          throws IOException
        Writes the confidences of an interaction evidence
        Parameters:
        interaction - a T object.
        Throws:
        IOException - if any.

      • writeConfidence

        void writeConfidence​(Confidence conf)
              throws IOException
        This method will write a confidence with a text if text is not null
        Parameters:
        conf - a Confidence object.
        Throws:
        IOException - if any.

      • writeOrganism

        void writeOrganism​(Organism organism)
            throws IOException
        Write an organism. Will duplicate taxid if needs to provide both common name and scientific name
        Parameters:
        organism - a Organism object.
        Throws:
        IOException - if any.

      • writeCvTerm

        void writeCvTerm​(CvTerm cv)
          throws IOException
        Write the CvTerm. If it is null, it writes an empty column (-)
        Parameters:
        cv - a CvTerm object.
        Throws:
        IOException - if any.

      • writeAlias

        void writeAlias​(Alias alias)
         throws IOException
        This methods write the dbsource, alias name and alias type of an alias
        Parameters:
        alias - a Alias object.
        Throws:
        IOException - if any.

      • writeAlias

        void writeAlias​(P participant,
                Alias alias)
         throws IOException
        This methods write the dbsource, alias name and alias type of an alias. It can use the modelled participant to find dbsource
        Parameters:
        alias - a Alias object.
        participant - a P object.
        Throws:
        IOException - if any.

      • writeIdentifier

        void writeIdentifier​(Xref identifier)
              throws IOException
        This methods write the database, id and version of an identifier
        Parameters:
        identifier - a Xref object.
        Throws:
        IOException - if any.

      • escapeAndWriteString

        void escapeAndWriteString​(String stringToEscape)
                   throws IOException
        This method replaces line breaks and tab characters with a space. It escapes the StringToEscape with doble quote if it finds a special MITAB character
        Parameters:
        stringToEscape - a String object.
        Throws:
        IOException - if any.

      • writeComplexExpansion

        void writeComplexExpansion​(T binary)
                    throws IOException
        Writes the complex expansion of a binary interaction
        Parameters:
        binary - a T object.
        Throws:
        IOException - if any.

      • writeBiologicalRole

        void writeBiologicalRole​(P participant)
                  throws IOException
        Writes the biological role of a participant
        Parameters:
        participant - a P object.
        Throws:
        IOException - if any.

      • writeExperimentalRole

        void writeExperimentalRole​(P participant)
                    throws IOException
        Writes the experimentsl role of a participant evidence
        Parameters:
        participant - a P object.
        Throws:
        IOException - if any.

      • writeInteractorType

        void writeInteractorType​(P participant)
                  throws IOException
        Writes the interactor type of a participant
        Parameters:
        participant - a P object.
        Throws:
        IOException - if any.

      • writeParticipantXrefs

        void writeParticipantXrefs​(P participant)
                    throws IOException
        Write Xref of participant and interactor
        Parameters:
        participant - a P object.
        Throws:
        IOException - if any.

      • writeInteractionXrefs

        void writeInteractionXrefs​(T interaction)
                    throws IOException
        Write interaction Xref r
        Parameters:
        interaction - a T object.
        Throws:
        IOException - if any.

      • writeParticipantAnnotations

        void writeParticipantAnnotations​(P participant)
                          throws IOException
        Writes participant annotations
        Parameters:
        participant - a P object.
        Throws:
        IOException - if any.

      • writeInteractionAnnotations

        void writeInteractionAnnotations​(T interaction)
                          throws IOException
        Writes interaction annotations
        Parameters:
        interaction - a T object.
        Throws:
        IOException - if any.

      • writeHostOrganism

        void writeHostOrganism​(T interaction)
                throws IOException
        Writes experiment host organism
        Parameters:
        interaction - a T object.
        Throws:
        IOException - if any.

      • writeInteractionParameters

        void writeInteractionParameters​(T interaction)
                         throws IOException
        Writes interaction parameters
        Parameters:
        interaction - a T object.
        Throws:
        IOException - if any.

      • writeDate

        void writeDate​(Date date)
        throws IOException
        Writes created date of an interaction
        Parameters:
        date - a Date object.
        Throws:
        IOException - if any.

      • writeParticipantChecksums

        void writeParticipantChecksums​(P participant)
                        throws IOException
        Writes participant checksum
        Parameters:
        participant - a P object.
        Throws:
        IOException - if any.

      • writeInteractionChecksums

        void writeInteractionChecksums​(T interaction)
                        throws IOException
        Writes interaction checksum
        Parameters:
        interaction - a T object.
        Throws:
        IOException - if any.

      • writeNegativeProperty

        void writeNegativeProperty​(T interaction)
                    throws IOException
        Writes interaction negative property if true
        Parameters:
        interaction - a T object.
        Throws:
        IOException - if any.

      • writeXref

        void writeXref​(Xref xref)
        throws IOException
        This methods write the database, id, version and qualifier of an xref
        Parameters:
        xref - a Xref object.
        Throws:
        IOException - if any.

      • writeParticipantFeatures

        void writeParticipantFeatures​(P participant)
                       throws IOException
        Writes participant features
        Parameters:
        participant - a P object.
        Throws:
        IOException - if any.

      • writeParticipantStoichiometry

        void writeParticipantStoichiometry​(P participant)
                            throws IOException
        Writes participant stoichiometry
        Parameters:
        participant - a P object.
        Throws:
        IOException - if any.

      • writeParticipantIdentificationMethod

        void writeParticipantIdentificationMethod​(P participant)
                                   throws IOException
        Writes participant identification method(s)
        Parameters:
        participant - a P object.
        Throws:
        IOException - if any.

      • writeParticipantBiologicalEffect

        void writeParticipantBiologicalEffect​(P participant)
                               throws IOException
        Writes participant biological effect
        Parameters:
        participant - a P object.
        Throws:
        IOException - if any.

      • writeInteractionCausalRegulatoryMechanism

        void writeInteractionCausalRegulatoryMechanism​(T interaction)
                                        throws IOException
        Writes interaction checksum
        Parameters:
        interaction - a T object.
        Throws:
        IOException - if any.

      • writeInteractionCausalStatement

        void writeInteractionCausalStatement​(T interaction)
                              throws IOException
        Writes interaction checksum
        Parameters:
        interaction - a T object.
        Throws:
        IOException - if any.