Class ReactionNetworkSubstanceRef

    • Field Detail

      • modTermA

        public SBOTerm modTermA
        The optional modification terms in original doc.
      • modTermB

        public SBOTerm modTermB
        The optional modification terms in modified doc.
      • singleDoc

        protected boolean singleDoc
        The single doc flag if in single-doc-operation-mode.
    • Constructor Detail

      • ReactionNetworkSubstanceRef

        public ReactionNetworkSubstanceRef​(ReactionNetworkSubstance subst,
                                           boolean flagA,
                                           boolean flagB,
                                           SBOTerm modTermA,
                                           SBOTerm modTermB)
                                    throws BivesUnsupportedException
        Instantiates a new substance reference.
        Parameters:
        subst - the substance
        flagA - the existence flag for the original version
        flagB - the existence flag for the modified version
        modTermA - the modification type in the original version
        modTermB - the modification type in the original version
        Throws:
        BivesUnsupportedException
    • Method Detail

      • setSboA

        public void setSboA​(SBOTerm modTermA)
                     throws BivesUnsupportedException
        Sets the SBOTerm as defined in the original version.
        Parameters:
        modTermA - the SBOTerm of version A
        Throws:
        BivesUnsupportedException - indicating that this edge has two different modification properties.
      • setSboB

        public void setSboB​(SBOTerm modTermB)
                     throws BivesUnsupportedException
        Sets the SBOTerm as defined in the modified version.
        Parameters:
        modTermB - the SBOTerm of version B
        Throws:
        BivesUnsupportedException - indicating that this edge has two different modification properties.
      • setFlagA

        public void setFlagA​(boolean flagA)
        Sets the existence flag for the original version.
        Parameters:
        flagA - the flag for doc A
      • setFlagB

        public void setFlagB​(boolean flagB)
        Sets the existence flag for the modified version.
        Parameters:
        flagB - the flag for doc B
      • getSBO

        public String getSBO()
        Gets the SBOTerm.
        Returns:
        the SBOTerm
      • getModTerm

        public String getModTerm()
        Gets the modifier term.
        Returns:
        the modifier term
      • getModification

        public int getModification()
        Gets the modification.
        Returns:
        the modification
      • setSingleDocument

        public void setSingleDocument()
        Sets the single document flag.