Class ReactionNetworkSubstance

  • All Implemented Interfaces:
    GraphEntity

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

      • ReactionNetworkSubstance

        public ReactionNetworkSubstance​(ReactionNetwork rn,
                                        String labelA,
                                        String labelB,
                                        de.unirostock.sems.xmlutils.ds.DocumentNode docA,
                                        de.unirostock.sems.xmlutils.ds.DocumentNode docB,
                                        ReactionNetworkCompartment compartmentA,
                                        ReactionNetworkCompartment compartmentB)
        Instantiates a new substance in a reaction network.
        Parameters:
        rn - the reaction network
        labelA - the label of that compartment in the original document
        labelB - the label of that compartment in the modified document
        docA - the original document
        docB - the modified document
        compartmentA - the compartment a
        compartmentB - the compartment b
    • 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
        • null, otherwise
        Returns:
        the compartment
      • getSBO

        public String getSBO()
        Gets the SBOTerm describing this substance.
        Returns:
        the SBOTerm