Class SBMLReaction

  • All Implemented Interfaces:
    de.unirostock.sems.bives.algorithm.DiffReporter

    public class SBMLReaction
    extends SBMLGenericIdNameObject
    implements de.unirostock.sems.bives.algorithm.DiffReporter
    The Class SBMLReaction represents any kind of process that can change the quantity of one or more species in a model.
    Author:
    Martin Scharm
    • Constructor Detail

      • SBMLReaction

        public SBMLReaction​(de.unirostock.sems.xmlutils.ds.DocumentNode documentNode,
                            SBMLModel sbmlModel)
                     throws BivesSBMLParseException
        Instantiates a new SBML reaction.
        Parameters:
        documentNode - the document node encoding this entity in the corresponding XML tree
        sbmlModel - the SBML model
        Throws:
        BivesSBMLParseException - the bives sbml parse exception
    • Method Detail

      • getCompartment

        public SBMLCompartment getCompartment()
        Gets the compartment.
        Returns:
        the compartment
      • isReversible

        public boolean isReversible()
        Checks if this reaction is reversible.
        Returns:
        true, if it is reversible
      • isFast

        public boolean isFast()
        Checks if this reaction is fast.
        Returns:
        true, if it is fast
      • getKineticLaw

        public SBMLKineticLaw getKineticLaw()
        Gets the kinetic law.
        Returns:
        the kinetic law
      • getListOfReactantsNode

        public SBMLListOf getListOfReactantsNode()
        Gets the list of reactants node.
        Returns:
        the list of reactants node
      • getListOfProductsNode

        public SBMLListOf getListOfProductsNode()
        Gets the list of products node.
        Returns:
        the list of products node
      • getListOfModifiersNode

        public SBMLListOf getListOfModifiersNode()
        Gets the list of modifiers node.
        Returns:
        the list of modifiers node
      • reportModification

        public de.unirostock.sems.bives.markup.MarkupElement reportModification​(de.unirostock.sems.bives.algorithm.SimpleConnectionManager conMgmt,
                                                                                de.unirostock.sems.bives.algorithm.DiffReporter docA,
                                                                                de.unirostock.sems.bives.algorithm.DiffReporter docB)
        Specified by:
        reportModification in interface de.unirostock.sems.bives.algorithm.DiffReporter
      • reportInsert

        public de.unirostock.sems.bives.markup.MarkupElement reportInsert()
        Specified by:
        reportInsert in interface de.unirostock.sems.bives.algorithm.DiffReporter
      • reportDelete

        public de.unirostock.sems.bives.markup.MarkupElement reportDelete()
        Specified by:
        reportDelete in interface de.unirostock.sems.bives.algorithm.DiffReporter
      • report

        public void report​(de.unirostock.sems.bives.markup.MarkupElement me,
                           boolean insert)
        Typeset this reaction.
        Parameters:
        me - the markup element
        insert - is that an insert? otherwise we report a delete