Class ReactionNetworkReaction

  • All Implemented Interfaces:
    GraphEntity

    public class ReactionNetworkReaction
    extends ReactionNetworkEntity
    The Class ReactionNetworkReaction representing a reaction in a reaction network.
    Author:
    Martin Scharm
    • Constructor Detail

      • ReactionNetworkReaction

        public ReactionNetworkReaction​(ReactionNetwork rn,
                                       String labelA,
                                       String labelB,
                                       de.unirostock.sems.xmlutils.ds.DocumentNode docA,
                                       de.unirostock.sems.xmlutils.ds.DocumentNode docB,
                                       ReactionNetworkCompartment compartmentA,
                                       ReactionNetworkCompartment compartmentB,
                                       boolean reversible)
        Instantiates a new ReactionNetwork reaction.
        Parameters:
        rn - the reaction network
        labelA - the label of that reaction in the original document
        labelB - the label of that reaction in the modified document
        docA - the original document
        docB - the modified document
        compartmentA - the compartment a
        compartmentB - the compartment b
        reversible - the reversible flag
    • Method Detail

      • setCompartmentA

        public void setCompartmentA​(ReactionNetworkCompartment compartment)
        Sets the compartment in original version.
        Parameters:
        compartment - the compartment in original version
      • setCompartmentB

        public void setCompartmentB​(ReactionNetworkCompartment compartment)
        Sets the compartment in modified version.
        Parameters:
        compartment - the compartment in modified version
      • getCompartment

        public ReactionNetworkCompartment getCompartment()
        Gets the compartment. Will return:
        • the original compartment, if it's the same compartment as in the modified version
        • the compartment all substances involved in this reactions are from, if all substances originate from the same compartment
        • null, otherwise
        Returns:
        the compartment
      • addInputA

        public void addInputA​(ReactionNetworkSubstance subst,
                              SBOTerm sbo)
        Add a reactant of this reaction in its original version.
        Parameters:
        subst - the substance
        sbo - the SBOTerm describing the interaction
      • addOutputA

        public void addOutputA​(ReactionNetworkSubstance subst,
                               SBOTerm sbo)
        Add a product of this reaction in its original version.
        Parameters:
        subst - the substance
        sbo - the SBOTerm describing the interaction
      • addInputB

        public void addInputB​(ReactionNetworkSubstance subst,
                              SBOTerm sbo)
        Add a reactant of this reaction in its modified version.
        Parameters:
        subst - the substance
        sbo - the SBOTerm describing the interaction
      • addOutputB

        public void addOutputB​(ReactionNetworkSubstance subst,
                               SBOTerm sbo)
        Add a product of this reaction in its modified version.
        Parameters:
        subst - the substance
        sbo - the SBOTerm describing the interaction
      • getSBO

        public String getSBO()
        Gets the sbo.
        Returns:
        the sbo
      • isReversible

        public boolean isReversible()
        Checks if is reversible.
        Returns:
        true, if is reversible