Class ReactionNetwork


  • public class ReactionNetwork
    extends Object
    The Class ReactionNetwork representing a reaction network.

    A ReactionNetwork contains compartments, which may contain species and reactions. There may be directed connections between species and reactions representing relationships like reactants, products, modifiers etc.
    see also ReactionNetwork

    Author:
    Martin Scharm
    • Constructor Detail

      • ReactionNetwork

        public ReactionNetwork()
        Instantiates a new reaction network.
    • Method Detail

      • getNextSubstanceID

        public int getNextSubstanceID()
        Gets the next substance id.
        Returns:
        the next substance id
      • getNextCompartmentID

        public int getNextCompartmentID()
        Gets the next compartment id.
        Returns:
        the next compartment id
      • getNextReactionID

        public int getNextReactionID()
        Gets the next reaction id.
        Returns:
        the next reaction id
      • setReaction

        public void setReaction​(de.unirostock.sems.xmlutils.ds.TreeNode node,
                                ReactionNetworkReaction react)
        Adds a reaction.
        Parameters:
        node - the node
        react - the react
      • setSubstance

        public void setSubstance​(de.unirostock.sems.xmlutils.ds.TreeNode node,
                                 ReactionNetworkSubstance subst)
        Adds a substance.
        Parameters:
        node - the node
        subst - the subst
      • setCompartment

        public void setCompartment​(de.unirostock.sems.xmlutils.ds.TreeNode node,
                                   ReactionNetworkCompartment compartment)
        Adds a compartment.
        Parameters:
        node - the node
        compartment - the compartment
      • getSubstance

        public ReactionNetworkSubstance getSubstance​(de.unirostock.sems.xmlutils.ds.TreeNode node)
        Gets a substance.
        Parameters:
        node - the node
        Returns:
        the substance
      • getReaction

        public ReactionNetworkReaction getReaction​(de.unirostock.sems.xmlutils.ds.TreeNode node)
        Gets a reaction.
        Parameters:
        node - the node
        Returns:
        the reaction
      • getCompartment

        public ReactionNetworkCompartment getCompartment​(de.unirostock.sems.xmlutils.ds.TreeNode node)
        Gets a compartment.
        Parameters:
        node - the node
        Returns:
        the compartment
      • setSingleDocument

        public void setSingleDocument()
        Sets the single document flag for non-comparison graphs.
      • modToString

        public static String modToString​(int modification)
        Convert a modification to a string representation.
        Parameters:
        modification - the modification
        Returns:
        the textual representation