Class SBMLSimpleSpeciesReference

  • Direct Known Subclasses:
    SBMLSpeciesReference

    public class SBMLSimpleSpeciesReference
    extends SBMLSBase
    The Class SBMLSimpleSpeciesReference representing a link to a species (mainly for modifiers, parent class for substrates and products).
    Author:
    Martin Scharm
    • Field Detail

      • id

        protected String id
        The id of this species reference.
      • name

        protected String name
        The name.
      • species

        protected SBMLSpecies species
        The species it is linking to.
    • Constructor Detail

      • SBMLSimpleSpeciesReference

        public SBMLSimpleSpeciesReference​(de.unirostock.sems.xmlutils.ds.DocumentNode documentNode,
                                          SBMLModel sbmlModel)
                                   throws BivesSBMLParseException
        Instantiates a new SBML simple species reference.
        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

      • getSpecies

        public SBMLSpecies getSpecies()
        Gets the corresponding species.
        Returns:
        the species
      • reportModification

        public String reportModification​(de.unirostock.sems.bives.algorithm.SimpleConnectionManager conMgmt,
                                         SBMLSimpleSpeciesReference a,
                                         SBMLSimpleSpeciesReference b)
        Report modification between two versions of this species reference.
        Parameters:
        conMgmt - the connection manager
        a - the original reference
        b - the modified reference
        Returns:
        the textual representation of this modification
      • reportInsert

        public String reportInsert()
        Report an insert.
        Returns:
        the string
      • reportDelete

        public String reportDelete()
        Report a delete.
        Returns:
        the string
      • report

        public String report()
        Typeset this reference.
        Returns:
        the string