public FormulaParser(Reader.SBMLReader reader, String formula, Model model) { this.formula = formula; this.reader = reader; this.model = model; model.InterrogateModelForMissingIDs(); // Init the collection list this.formulaSpecies = new List<Species>(); this.formulaParameters = new List<Parameter>(); this.formulaUnknownEntities = new List<UnknownEntity>(); // Init the operators this.init(); this.formulaTree = this.makeFormulaTree(formula, false); }
/// <summary> /// Constructor that includes an experiment and simulation reference which is used for formulas with aggregate functions /// that use references to cell definitions, groups and species /// </summary> /// <param name="reader"> /// A <see cref="Reader.SBMLReader"/> /// </param> /// <param name="formula"> /// A <see cref="String"/> /// </param> /// <param name="model"> /// A <see cref="Model"/> /// </param> /// <param name="experiment"> /// A <see cref="Experiment"/> /// </param> /// <param name="simulation"> /// A <see cref="Simulation"/> /// </param> public FormulaParser(Reader.SBMLReader reader, String formula, Model model, Experiment experiment, Simulation simulation) { this.formula = formula; this.reader = reader; model.InterrogateModelForMissingIDs(); //create model list this.models = new List<Model>(); models.Add(model); // Init the collection list this.formulaSpecies = new List<Species>(); this.formulaParameters = new List<Parameter>(); this.formulaUnknownEntities = new List<UnknownEntity>(); // Init the operators this.init(); this.experiment = experiment; this.simulation = simulation; this.formulaTree = this.makeFormulaTree(formula, true); }