public RenameEntityCommand(SBase entity, String oldID, String newID, Model.SBML.Model model)
{
this.entity = entity;
this.oldID = oldID;
this.newID = newID;
this.model = model;
}
/// <summary>
/// Add data to the ReferenceLeafNode
/// </summary>
/// <param name="text">
/// A <see cref="System.String"/>
/// </param>
/// <param name="model">
/// A <see cref="Model"/>
/// </param>
public void AddData(string text, Model model)
{
// Retrieve the object from the model
SBase reference = (SBase)model.findObject(text);
if (reference != null)
{
this.idReference = text;
this.data = reference;
}
}
public KineticLaw(Model model, Hashtable attrs)
{
this.model = model;
this.listOfParameters = new List<Parameter>();
this.setId(attrs);
if (attrs.Contains("formula"))
{
this.formula = (String)attrs["formula"];
}
}
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 KineticLaw(Model model)
{
this.model = model;
this.listOfParameters = new List<Parameter>();
formula = "";
}
public ParameterCommand(Parameter parameter, Reaction parentReaction, Model.SBML.Model model)
{
this.parameter = parameter;
this.parentReaction = parentReaction;
this.model = model;
}
public SpeciesCommand(Species species, bool adding, Model.SBML.Model model)
{
this.species = species;
this.adding = adding;
this.model = model;
}
/// <summary>
/// Checks all ReferenceLeafNodes so that they point to their SBase object.
/// Used to complete a MathTree generated from MathML after it has been parsed and
/// more about the model is known (such as paramters).
/// </summary>
/// <param name="model">
/// A <see cref="Model"/>
/// </param>
public void SetSBaseReferences(Model model)
{
root.SetSBaseReferences(model);
}
public void testWithVariables()
{
// create a formula
MuCell.Model.SBML.Reader.SBMLReader reader = new MuCell.Model.SBML.Reader.SBMLReader();
MuCell.Model.SBML.Model model = new MuCell.Model.SBML.Model();
Species s = new Species("X");
s.BoundaryCondition = false;
model.AddId(s.ID, s); // else FormulaParser can't find what X is
reader.model = model;
FormulaParser fp = new FormulaParser(reader, "10+sin(X)", model);
MathTree formulaTree = fp.getFormulaTree();
// fold the function
CellEvaluationFunction fun = formulaTree.ToCellEvaluationFunction();
// create a new CellInstance with a variable X
CellInstance cell = new CellInstance(new CellDefinition());
cell.setSpeciesAmount("X", 2.3d);
// evaluate and test that this gets the right result
Assert.AreEqual(10+Math.Sin(2.3), fun(new StateSnapshot(), cell));
}
public void testWithGroup()
{
MuCell.Model.SBML.Model model = new MuCell.Model.SBML.Model();
MuCell.Model.Experiment experiment = new MuCell.Model.Experiment("experimen1");
MuCell.Model.Simulation simulation = new MuCell.Model.Simulation("simulation1");
setupExperiment(model, experiment, simulation);
// Test parsing cell def references, group references etc.
MuCell.Model.SBML.Reader.SBMLReader reader = new MuCell.Model.SBML.Reader.SBMLReader();
FormulaParser fp = new FormulaParser(reader, "group1", model, experiment, simulation);
MathTree formulaTree = fp.getFormulaTree();
MuCell.Model.SBML.AggregateReferenceNode root = (MuCell.Model.SBML.AggregateReferenceNode)formulaTree.root;
Assert.AreEqual("group1", root.ToString());
Assert.AreEqual(null, root.CellDefinition);
Assert.AreEqual("1", root.Group.ID);
Assert.AreEqual(null, root.Species);
}
public void Setup(Experiment experiment, Simulation simulation, string speciesName)
{
// ********* INITIAL SETUP
// Hopf model
MuCell.Model.SBML.Reader.SBMLReader s = new MuCell.Model.SBML.Reader.SBMLReader("../../UnitTests/smallest.Hopf.xml");
// Cell definition 1
MuCell.Model.CellDefinition celldef1 = new MuCell.Model.CellDefinition("celldef1");
celldef1.addSBMLModel(s.model);
// Create a NEW model
MuCell.Model.SBML.Model model = new MuCell.Model.SBML.Model();
MuCell.Model.SBML.Species species1 = new MuCell.Model.SBML.Species();
MuCell.Model.SBML.Species species2 = new MuCell.Model.SBML.Species();
model.listOfSpecies = new List<MuCell.Model.SBML.Species>();
model.listOfSpecies.Add(species1);
model.listOfSpecies.Add(species2);
// Set some values for species1
species1.ID = speciesName;
species1.InitialAmount = 4.0d;
// Set some values for species2
species2.ID = "Y";
species2.InitialAmount = 0.1d;
model.AddId(speciesName, species1);
model.AddId("Y", species2);
// Set up the reaction
MuCell.Model.SBML.Reaction reaction1 = new MuCell.Model.SBML.Reaction("reaction1");
model.listOfReactions = new List<MuCell.Model.SBML.Reaction>();
model.listOfReactions.Add(reaction1);
// Set up the kinetic law
reaction1.KineticLaw = new MuCell.Model.SBML.KineticLaw(model);
reaction1.KineticLaw.Formula = speciesName.Replace(' ', '_')+"*2";
// set up the species reference for the reactants
MuCell.Model.SBML.SpeciesReference ref1 = new MuCell.Model.SBML.SpeciesReference(species1, 1);
// set up the species references for the products
MuCell.Model.SBML.SpeciesReference ref2 = new MuCell.Model.SBML.SpeciesReference(species1, 0.75);
MuCell.Model.SBML.SpeciesReference ref3 = new MuCell.Model.SBML.SpeciesReference(species2, 2);
// Add the references
reaction1.Reactants.Add(ref1);
reaction1.Products.Add(ref2);
reaction1.Products.Add(ref3);
// set up the cell definition
MuCell.Model.CellDefinition celldef2 = new MuCell.Model.CellDefinition("celldef2");
celldef2.addSBMLModel(model);
// instantiat the environment
MuCell.Model.Vector3 size = new MuCell.Model.Vector3(1, 1, 1);
MuCell.Model.Environment environment = new MuCell.Model.Environment(size);
// Cells
List<MuCell.Model.CellInstance> cells = new List<MuCell.Model.CellInstance>();
// Create 10 cells of celldef1 and 20 cells of celldef2
for(int i=0;i<10;i++){
int a = ((i+2)%3)+1;
int b = (i%3)+1;
int c = ((i+1)%3)+1;
CellInstance cell11 = celldef1.createCell();
cells.Add(cell11);
environment.AddCellToGroup(a, cell11);
CellInstance cell21 = celldef2.createCell();
CellInstance cell22 = celldef2.createCell();
cells.Add(cell21);
cells.Add(cell22);
environment.AddCellToGroup(b, cell21);
environment.AddCellToGroup(c, cell22);
}
// StateSnapshot for intial state
MuCell.Model.StateSnapshot initialState = new MuCell.Model.StateSnapshot(cells);
initialState.SimulationEnvironment = environment;
// Parameters
MuCell.Model.SimulationParameters parameters = new MuCell.Model.SimulationParameters();
parameters.InitialState = initialState;
parameters.SimulationLength = 0.01001d;
parameters.SnapshotInterval = 1;
parameters.StepTime = 0.01001d;
parameters.SolverMethod = MuCell.Model.Solver.SolverMethods.RungeKutta;
// Simulation
simulation.Parameters = parameters;
// Experiment
experiment.addCellDefinition(celldef1);
experiment.addCellDefinition(celldef2);
experiment.addSimulation(simulation);
// Start simulation
simulation.StartSimulation();
this.models = new List<MuCell.Model.SBML.Model>();
this.models.Add(s.model);
this.models.Add(model);
}
public MacroCommand rearrangeGraphFromModel(Model.SBML.Model model, IDrawingInterface drawable)
{
int modelDegree = model.listOfSpecies.Count;
//convert the model to nodes and links
List<GraphNode> nodes = new List<GraphNode>();
List<GraphLink> links = new List<GraphLink>();
foreach (Species n in model.listOfSpecies)
{
nodes.Add(new GraphNode(n, n.getPosition()));
}
foreach (Reaction n in model.listOfReactions)
{
nodes.Add(new GraphNode(n, n.getPosition()));
}
foreach (ComponentBase n in model.listOfComponents)
{
nodes.Add(new GraphNode(n, n.getPosition()));
}
foreach (Reaction r in model.listOfReactions)
{
GraphNode hubNode=findNode(r,nodes);
if (hubNode != null)
{
foreach (SimpleSpeciesReference s in r.Reactants)
{
GraphNode sNode = findNode(s.species, nodes);
if (sNode != null)
{
links.Add(new GraphLink(sNode, hubNode, modelDegree));
}
}
foreach (SimpleSpeciesReference s in r.Products)
{
GraphNode sNode = findNode(s.species, nodes);
if (sNode != null)
{
links.Add(new GraphLink(sNode, hubNode, modelDegree));
}
}
foreach (SimpleSpeciesReference s in r.Modifiers)
{
GraphNode sNode = findNode(s.species, nodes);
if (sNode != null)
{
links.Add(new GraphLink(sNode, hubNode, modelDegree));
}
}
}
}
foreach (ComponentBase c in model.listOfComponents)
{
GraphNode hubNode = findNode(c, nodes);
if (hubNode != null)
{
foreach (SimpleSpeciesReference s in c.Reactants)
{
if (s != null)
{
GraphNode sNode = findNode(s.species, nodes);
if (sNode != null)
{
links.Add(new GraphLink(sNode, hubNode, modelDegree));
}
}
}
foreach (SimpleSpeciesReference s in c.Products)
{
if (s != null)
{
GraphNode sNode = findNode(s.species, nodes);
if (sNode != null)
{
links.Add(new GraphLink(sNode, hubNode, modelDegree));
}
}
}
}
}
GraphNode[] graphNodes = nodes.ToArray();
GraphLink[] graphLinks = links.ToArray();
return resolveGraph(graphNodes, graphLinks, drawable);
}
/// <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);
}
public SBMLroot(Model model)
{
this.model = model;
this.level = model.level;
this.version = model.version;
}
/// <summary>
/// Checks all ReferenceLeafNodes so that they point to their SBase object.
/// Used to complete a MathTree generated from MathML after it has been parsed and
/// more about the model is known (such as paramters).
/// </summary>
/// <param name="model">
/// A <see cref="Model"/>
/// </param>
public override void SetSBaseReferences(Model model)
{
// Do nothing
}
public void testApproximateUnits()
{
MuCell.Model.SBML.Model model = new MuCell.Model.SBML.Model();
MuCell.Model.Experiment experiment = new MuCell.Model.Experiment("experimen1");
MuCell.Model.Simulation simulation = new MuCell.Model.Simulation("simulation1");
setupExperiment(model, experiment, simulation);
// Test parsing cell def references, group references etc.
MuCell.Model.SBML.Reader.SBMLReader reader = new MuCell.Model.SBML.Reader.SBMLReader();
FormulaParser fp = new FormulaParser(reader, "5.2", model, experiment, simulation);
MathTree formulaTree = fp.getFormulaTree();
Assert.AreEqual("No units", formulaTree.ApproximateUnits());
fp = new FormulaParser(reader, "5.2+10", model, experiment, simulation);
formulaTree = fp.getFormulaTree();
Assert.AreEqual("No units", formulaTree.ApproximateUnits());
fp = new FormulaParser(reader, "5.2-10", model, experiment, simulation);
formulaTree = fp.getFormulaTree();
Assert.AreEqual("No units", formulaTree.ApproximateUnits());
fp = new FormulaParser(reader, "5.2*10", model, experiment, simulation);
formulaTree = fp.getFormulaTree();
Assert.AreEqual("No units", formulaTree.ApproximateUnits());
fp = new FormulaParser(reader, "5.2/10", model, experiment, simulation);
formulaTree = fp.getFormulaTree();
Assert.AreEqual("No units", formulaTree.ApproximateUnits());
fp = new FormulaParser(reader, "celldef1", model, experiment, simulation);
formulaTree = fp.getFormulaTree();
Assert.AreEqual("Cells", formulaTree.ApproximateUnits());
fp = new FormulaParser(reader, "celldef1+celldef2", model, experiment, simulation);
formulaTree = fp.getFormulaTree();
Assert.AreEqual("Cells", formulaTree.ApproximateUnits());
fp = new FormulaParser(reader, "celldef1-celldef1", model, experiment, simulation);
formulaTree = fp.getFormulaTree();
Assert.AreEqual("Cells", formulaTree.ApproximateUnits());
fp = new FormulaParser(reader, "celldef1*celldef2", model, experiment, simulation);
formulaTree = fp.getFormulaTree();
Assert.AreEqual("Cells*Cells", formulaTree.ApproximateUnits());
fp = new FormulaParser(reader, "celldef1/celldef2", model, experiment, simulation);
formulaTree = fp.getFormulaTree();
Assert.AreEqual("Cells/Cells", formulaTree.ApproximateUnits());
fp = new FormulaParser(reader, "celldef1*celldef2*celldef1", model, experiment, simulation);
formulaTree = fp.getFormulaTree();
Assert.AreEqual("Cells*Cells*Cells", formulaTree.ApproximateUnits());
fp = new FormulaParser(reader, "celldef1+10", model, experiment, simulation);
formulaTree = fp.getFormulaTree();
Assert.AreEqual("Cells", formulaTree.ApproximateUnits());
fp = new FormulaParser(reader, "celldef1*10", model, experiment, simulation);
formulaTree = fp.getFormulaTree();
Assert.AreEqual("Cells", formulaTree.ApproximateUnits());
fp = new FormulaParser(reader, "celldef1 / 34.2", model, experiment, simulation);
formulaTree = fp.getFormulaTree();
Assert.AreEqual("Cells", formulaTree.ApproximateUnits());
fp = new FormulaParser(reader, "4/celldef1", model, experiment, simulation);
formulaTree = fp.getFormulaTree();
Assert.AreEqual("1/Cells", formulaTree.ApproximateUnits());
fp = new FormulaParser(reader, "24/(celldef1*celldef1)", model, experiment, simulation);
formulaTree = fp.getFormulaTree();
Assert.AreEqual("1/Cells*Cells", formulaTree.ApproximateUnits());
fp = new FormulaParser(reader, "celldef1.group1/(celldef1*celldef1)", model, experiment, simulation);
formulaTree = fp.getFormulaTree();
Assert.AreEqual("Cells/Cells*Cells", formulaTree.ApproximateUnits());
fp = new FormulaParser(reader, "celldef1/celldef1+10", model, experiment, simulation);
formulaTree = fp.getFormulaTree();
Assert.AreEqual("Cells/Cells", formulaTree.ApproximateUnits());
fp = new FormulaParser(reader, "celldef1.group1", model, experiment, simulation);
formulaTree = fp.getFormulaTree();
Assert.AreEqual("Cells", formulaTree.ApproximateUnits());
fp = new FormulaParser(reader, "celldef1.group2 + celldef1.group1", model, experiment, simulation);
formulaTree = fp.getFormulaTree();
Assert.AreEqual("Cells", formulaTree.ApproximateUnits());
fp = new FormulaParser(reader, "celldef1.group1/celldef1.group2", model, experiment, simulation);
formulaTree = fp.getFormulaTree();
Assert.AreEqual("Cells/Cells", formulaTree.ApproximateUnits());
fp = new FormulaParser(reader, "143/celldef1.group1", model, experiment, simulation);
formulaTree = fp.getFormulaTree();
Assert.AreEqual("1/Cells", formulaTree.ApproximateUnits());
fp = new FormulaParser(reader, "s1", model, experiment, simulation);
formulaTree = fp.getFormulaTree();
Assert.AreEqual("Concentration", formulaTree.ApproximateUnits());
fp = new FormulaParser(reader, "s1*4", model, experiment, simulation);
formulaTree = fp.getFormulaTree();
Assert.AreEqual("Concentration", formulaTree.ApproximateUnits());
fp = new FormulaParser(reader, "s1*s2", model, experiment, simulation);
formulaTree = fp.getFormulaTree();
Assert.AreEqual("Concentration*Concentration", formulaTree.ApproximateUnits());
fp = new FormulaParser(reader, "s1*s2*celldef1.s1", model, experiment, simulation);
formulaTree = fp.getFormulaTree();
Assert.AreEqual("Concentration*Concentration*Concentration", formulaTree.ApproximateUnits());
fp = new FormulaParser(reader, "s1*celldef1.group1.s1", model, experiment, simulation);
formulaTree = fp.getFormulaTree();
Assert.AreEqual("Concentration*Concentration", formulaTree.ApproximateUnits());
fp = new FormulaParser(reader, "group2.s2*celldef1.group1.s1", model, experiment, simulation);
formulaTree = fp.getFormulaTree();
Assert.AreEqual("Concentration*Concentration", formulaTree.ApproximateUnits());
fp = new FormulaParser(reader, "s1/s2", model, experiment, simulation);
formulaTree = fp.getFormulaTree();
Assert.AreEqual("Concentration/Concentration", formulaTree.ApproximateUnits());
fp = new FormulaParser(reader, "4.345/s1", model, experiment, simulation);
formulaTree = fp.getFormulaTree();
Assert.AreEqual("1/Concentration", formulaTree.ApproximateUnits());
fp = new FormulaParser(reader, "s1+celldef1", model, experiment, simulation);
formulaTree = fp.getFormulaTree();
Assert.AreEqual("No units", formulaTree.ApproximateUnits());
fp = new FormulaParser(reader, "4.345/s1+celldef1", model, experiment, simulation);
formulaTree = fp.getFormulaTree();
Assert.AreEqual("No units", formulaTree.ApproximateUnits());
fp = new FormulaParser(reader, "celldef1*celldef1.group1.s1", model, experiment, simulation);
formulaTree = fp.getFormulaTree();
Assert.AreEqual("Cells*Concentration", formulaTree.ApproximateUnits());
fp = new FormulaParser(reader, "s2/celldef1", model, experiment, simulation);
formulaTree = fp.getFormulaTree();
Assert.AreEqual("Concentration/Cells", formulaTree.ApproximateUnits());
fp = new FormulaParser(reader, "s2/celldef1+s1", model, experiment, simulation);
formulaTree = fp.getFormulaTree();
Assert.AreEqual("No units", formulaTree.ApproximateUnits());
fp = new FormulaParser(reader, "s2/celldef1+celldef2", model, experiment, simulation);
formulaTree = fp.getFormulaTree();
Assert.AreEqual("No units", formulaTree.ApproximateUnits());
fp = new FormulaParser(reader, "celldef1/celldef1.group1.s1", model, experiment, simulation);
formulaTree = fp.getFormulaTree();
Assert.AreEqual("Cells/Concentration", formulaTree.ApproximateUnits());
fp = new FormulaParser(reader, "Abs(s1)", model, experiment, simulation);
formulaTree = fp.getFormulaTree();
Assert.AreEqual("Concentration", formulaTree.ApproximateUnits());
}
/// <summary>
/// Checks all ReferenceLeafNodes so that they point to their SBase object.
/// Used to complete a MathTree generated from MathML after it has been parsed and
/// more about the model is known (such as paramters).
/// </summary>
/// <param name="model">
/// A <see cref="Model"/>
/// </param>
public override void SetSBaseReferences(Model model)
{
if (this.idReference != null)
{
SBase reference = (SBase)model.findObject(this.idReference);
if (reference != null)
{
this.data = reference;
}
}
}
public void testWithCellDefWithSpaces()
{
MuCell.Model.SBML.Model model = new MuCell.Model.SBML.Model();
MuCell.Model.Experiment experiment = new MuCell.Model.Experiment("experimen1");
MuCell.Model.Simulation simulation = new MuCell.Model.Simulation("simulation1");
setupExperiment(model, experiment, simulation);
experiment.GetCellDefinition("celldef1").Name = "cell def1";
Assert.That(experiment.ContainsCellDefinition("cell_def1"));
// Test parsing cell def references, group references etc.
MuCell.Model.SBML.Reader.SBMLReader reader = new MuCell.Model.SBML.Reader.SBMLReader();
FormulaParser fp = new FormulaParser(reader, "cell_def1", model, experiment, simulation);
MathTree formulaTree = fp.getFormulaTree();
MuCell.Model.SBML.AggregateReferenceNode root = (MuCell.Model.SBML.AggregateReferenceNode)formulaTree.root;
Assert.AreEqual("cell def1", root.ToString());
Assert.AreEqual(experiment.getCellDefinitions()[0], root.CellDefinition);
Assert.AreEqual(null, root.Group);
Assert.AreEqual(null, root.Species);
}
/// <summary>
/// Base constructor
/// </summary>
public CellDefinition()
{
sbmlModel = new MuCell.Model.SBML.Model();
}
public void testWithSpecies()
{
MuCell.Model.SBML.Model model = new MuCell.Model.SBML.Model();
MuCell.Model.Experiment experiment = new MuCell.Model.Experiment("experimen1");
MuCell.Model.Simulation simulation = new MuCell.Model.Simulation("simulation1");
setupExperiment(model, experiment, simulation);
// Test parsing cell def references, group references etc.
MuCell.Model.SBML.Reader.SBMLReader reader = new MuCell.Model.SBML.Reader.SBMLReader();
FormulaParser fp = new FormulaParser(reader, "5.2+s2", model, experiment, simulation);
MathTree formulaTree = fp.getFormulaTree();
MuCell.Model.SBML.InnerNode root = (InnerNode)formulaTree.root;
Assert.AreEqual(BinaryMathOperators.Plus, root.data);
Assert.AreEqual(5.2, ((MuCell.Model.SBML.NumberLeafNode)(root.subtree.ToArray()[0])).data);
Assert.AreEqual("5.2+s2", root.ToString());
MuCell.Model.SBML.AggregateReferenceNode right = (MuCell.Model.SBML.AggregateReferenceNode)(root.subtree.ToArray()[1]);
Assert.AreEqual("s2", right.ToString());
Assert.AreEqual(null, right.CellDefinition);
Assert.AreEqual(null, right.Group);
Assert.AreEqual("s2", right.Species.ID);
}
public ReactionCommand(Reaction reaction, bool adding, Model.SBML.Model model)
{
this.reaction = reaction;
this.adding = adding;
this.model = model;
}
/// <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;
}
}
public void ModelElement(Hashtable attrs)
{
if (attrs.ContainsKey("name"))
{
this.model = new Model((String)attrs["name"]);
}
else if (attrs.ContainsKey("id"))
{
this.model = new Model((string)attrs["id"]);
}
else
this.model = new Model();
}
/// <summary>
/// Given a filePath parse and add the SBML model defined
/// by the file at the filepath and sets the SBML model
/// </summary>
/// <param name="filePath">
/// A <see cref="System.String"/>
/// </param>
/// <returns>
/// A <see cref="bool"/> denoting success of failure as a boolean
/// </returns>
/// <summary>
/// Adds an SBML model from the object
/// </summary>
/// <param name="model">
/// A <see cref="Model.SBML.Model"/>
/// </param>
/// <returns>
/// A <see cref="System.Boolean"/>
/// </returns>
public bool addSBMLModel(Model.SBML.Model model)
{
this.sbmlModel = model;
return true;
}
/// <summary>
/// Checks all ReferenceLeafNodes so that they point to their SBase object.
/// Used to complete a MathTree generated from MathML after it has been parsed and
/// more about the model is known (such as paramters).
/// </summary>
/// <param name="model">
/// A <see cref="Model"/>
/// </param>
public virtual void SetSBaseReferences(Model model)
{
}