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);
}
public FormulaParser(Reader.SBMLReader reader, String formula)
{
this.formula = formula;
this.reader = reader;
// Init the collection list
this.formulaSpecies = new List<Species>();
this.formulaParameters = new List<Parameter>();
this.formulaUnknownEntities = new List<UnknownEntity>();
// Init the operators
this.init();
// Make the formula tree
this.formulaTree = this.makeFormulaTree(formula, false);
// no Model, so can't look up ID references
// (mainly for testing purposes)
}
/// <summary>
/// Adds an SBML model from a file
/// </summary>
/// <param name="filePath">
/// A <see cref="System.String"/>
/// </param>
/// <returns>
/// A <see cref="System.Boolean"/>
/// </returns>
public bool addSBMLModel(string filePath)
{
SBML.Reader.SBMLReader reader = new SBML.Reader.SBMLReader();
if (reader.Parse(filePath))
{
// Add the model
// sbmlModels.Add(read.model);
this.sbmlModel = reader.model;
return true;
}
else
{
// Else fail
return 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);
}
/// <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 and also a list of all models used
/// </summary>
/// <param name="reader">
/// A <see cref="Reader.SBMLReader"/>
/// </param>
/// <param name="formula">
/// A <see cref="String"/>
/// </param>
/// <param name="models">
/// A <see cref="List`1"/>
/// </param>
/// <param name="experiment">
/// A <see cref="Experiment"/>
/// </param>
/// <param name="simulation">
/// A <see cref="Simulation"/>
/// </param>
public FormulaParser(Reader.SBMLReader reader, String formula, List<Model> models, Experiment experiment, Simulation simulation)
{
this.formula = formula;
this.reader = reader;
this.models = models;
foreach (Model model in models)
{
model.InterrogateModelForMissingIDs();
}
// Init the operators
this.init();
this.experiment = experiment;
this.simulation = simulation;
this.formulaTree = this.makeFormulaTree(formula, true);
}
