public void TestWithSpecies()
{
// Create a 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 = "s1";
species1.InitialAmount = 4.0d;
// Set some values for species2
species2.ID = "s2";
species2.InitialAmount = 0.1d;
model.AddId("s1", species1);
model.AddId("s2", 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 = "(s1)*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 celldef1 = new MuCell.Model.CellDefinition("cell1");
celldef1.addSBMLModel(model);
// set up a cell
MuCell.Model.CellInstance cell1 = celldef1.createCell();
cell1.localSpeciesDelta.Add("s1", 0.0d);
cell1.localSpeciesDelta.Add("s2", 0.0d);
cell1.localSpeciesVariables.Add("s1", 4.0d);
cell1.localSpeciesVariables.Add("s2", 0.1d);
// set up the statesnaphost
MuCell.Model.StateSnapshot state1 = new MuCell.Model.StateSnapshot();
state1.Cells.Add(cell1);
// get the eval function
MuCell.Model.EffectReactionEvaluationFunction fun1 = reaction1.ToEffectReactionEvaluationFunction();
// Evaluate
fun1(state1, cell1);
cell1.setSpeciesAmount("s1", cell1.UnitTestGetSpeciesAmountsAndDeltas("s1"));
cell1.setSpeciesAmount("s2", cell1.UnitTestGetSpeciesAmountsAndDeltas("s2"));
cell1.UnitTestClearDeltas();
Assert.AreEqual(2.0d, cell1.getLocalSimulationSpeciesAmount("s1"));
Assert.AreEqual(16.1d, cell1.getLocalSimulationSpeciesAmount("s2"));
// Evaluate again
fun1(state1, cell1);
cell1.setSpeciesAmount("s1", cell1.UnitTestGetSpeciesAmountsAndDeltas("s1"));
cell1.setSpeciesAmount("s2", cell1.UnitTestGetSpeciesAmountsAndDeltas("s2"));
cell1.UnitTestClearDeltas();
Assert.AreEqual(1.0d, cell1.getLocalSimulationSpeciesAmount("s1"));
Assert.AreEqual(24.1d, cell1.getLocalSimulationSpeciesAmount("s2"));
}
public void TestWithParameters()
{
// Create a 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();
MuCell.Model.SBML.Parameter parameter = new MuCell.Model.SBML.Parameter();
parameter.ID = "k_1";
parameter.Value = 0.07d;
model.listOfParameters = new List<MuCell.Model.SBML.Parameter>();
model.listOfParameters.Add(parameter);
model.listOfSpecies = new List<MuCell.Model.SBML.Species>();
model.listOfSpecies.Add(species1);
model.listOfSpecies.Add(species2);
// Set some values for species1
species1.ID = "s1";
species1.InitialAmount = 1.0d;
// Set some values for species2
species2.ID = "s2";
species2.InitialAmount = 12.0d;
model.AddId("s1", species1);
model.AddId("s2", species2);
model.AddId("k_1", parameter);
// Set up the reaction
MuCell.Model.SBML.Reaction reaction1 = new MuCell.Model.SBML.Reaction("reaction1");
// Set up the kinetic law
reaction1.KineticLaw = new MuCell.Model.SBML.KineticLaw(model);
reaction1.KineticLaw.Formula = "s1*s2*k_1";
// 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(species2, 3);
// Add the references
reaction1.Reactants.Add(ref1);
reaction1.Products.Add(ref2);
// set up the cell definition
MuCell.Model.CellDefinition celldef1 = new MuCell.Model.CellDefinition("cell1");
celldef1.addSBMLModel(model);
// set up a cell
MuCell.Model.CellInstance cell1 = celldef1.createCell();
cell1.localSpeciesDelta.Add("s1", 0.0d);
cell1.localSpeciesDelta.Add("s2", 0.0d);
cell1.localSpeciesVariables.Add("s1", 1.0d);
cell1.localSpeciesVariables.Add("s2", 12.0d);
// set up the statesnaphost
MuCell.Model.StateSnapshot state1 = new MuCell.Model.StateSnapshot();
state1.Cells.Add(cell1);
// get the eval function
MuCell.Model.EffectReactionEvaluationFunction fun1 = reaction1.ToEffectReactionEvaluationFunction();
// Evaluate
fun1(state1, cell1);
cell1.setSpeciesAmount("s1", cell1.UnitTestGetSpeciesAmountsAndDeltas("s1"));
cell1.setSpeciesAmount("s2", cell1.UnitTestGetSpeciesAmountsAndDeltas("s2"));
cell1.UnitTestClearDeltas();
AssertDouble.AreEqual(1.0d-0.84d, cell1.getLocalSimulationSpeciesAmount("s1"));
AssertDouble.AreEqual(12.0d+0.84d*3.0d, cell1.getLocalSimulationSpeciesAmount("s2"));
System.Console.WriteLine("about to eval");
// Evaluate again
fun1(state1, cell1);
cell1.setSpeciesAmount("s1", cell1.UnitTestGetSpeciesAmountsAndDeltas("s1"));
cell1.setSpeciesAmount("s2", cell1.UnitTestGetSpeciesAmountsAndDeltas("s2"));
cell1.UnitTestClearDeltas();
AssertDouble.AreEqual(0.16d-0.162624d, cell1.getLocalSimulationSpeciesAmount("s1"));
AssertDouble.AreEqual(14.52d+0.162624d*3.0d, cell1.getLocalSimulationSpeciesAmount("s2"));
// Check the param is the same
Assert.AreEqual(0.07m, parameter.Value);
}
public void treeStructureTest()
{
MuCell.Model.SBML.Model model = new MuCell.Model.SBML.Model();
MuCell.Model.SBML.Reaction reaction1 = new MuCell.Model.SBML.Reaction();
model.listOfReactions = new List<MuCell.Model.SBML.Reaction>();
model.listOfReactions.Add(reaction1);
MuCell.Model.SBML.KineticLaw kw1 = new MuCell.Model.SBML.KineticLaw(model);
kw1.math = new MuCell.Model.SBML.MathTree();
kw1.math.root = new MuCell.Model.SBML.InnerNode(MuCell.Model.SBML.BinaryMathOperators.Times);
reaction1.KineticLaw = kw1;
model.AddId("reaction1", kw1);
MuCell.Model.SBML.Reaction[] reactions = model.listOfReactions.ToArray();
Assert.AreEqual(1, reactions.Length);
Assert.AreEqual(MuCell.Model.SBML.BinaryMathOperators.Times, ((MuCell.Model.SBML.InnerNode)(reactions[0].KineticLaw.math.root)).data);
}
public void TestSerializationEquality()
{
String filename = "../../UnitTests/expt1.serialized.xml";
MuCell.Model.Experiment experiment = new MuCell.Model.Experiment("experiment1");
Simulation simulation1 = new Simulation("simulation1");
Results results = new Results();
MuCell.Model.SBML.Model model = new MuCell.Model.SBML.Model();
CellDefinition cellDef1 = new CellDefinition("cellDef1");
cellDef1.addSBMLModel(model);
for (int i = 0; i < 5; i++)
{
StateSnapshot snapshot = new StateSnapshot();
for (int j = 0; j < 10; j++)
{
CellInstance cell = new CellInstance(cellDef1);
cell.GroupID = j;
cell.CellInstanceSpatialContext.Position = new Vector3(1*j, 1+i, 2+j);
cell.CellInstanceSpatialContext.Velocity = new Vector3(4*i, 5+j, 3+i);
cell.CellInstanceSpatialContext.Volume = new Vector3(10+j, 14*i, 15*i);
cell.CellInstanceSpatialContext.Orientation = new Vector3(2+i, 3*j, 4*j);
snapshot.Cells.Add(cell);
}
MuCell.Model.Environment environment = new MuCell.Model.Environment(new Vector3(10 * i, 14 * i, 15 * i));
SerializableDictionary<int, MuCell.Model.SBML.Group> dict = new SerializableDictionary<int, MuCell.Model.SBML.Group>();
// create new groups x3
MuCell.Model.SBML.Group group1 = new MuCell.Model.SBML.Group(1);
group1.Col = System.Drawing.Color.Beige;
MuCell.Model.SBML.Group group2 = new MuCell.Model.SBML.Group(2);
group2.Col = System.Drawing.Color.Brown;
MuCell.Model.SBML.Group group3 = new MuCell.Model.SBML.Group(3);
group3.Col = System.Drawing.Color.Green;
dict.Add(1, group1); dict.Add(2, group2); dict.Add(3, group3);
environment.Groups = dict;
//SerializableDictionary<int, MuCell.Model.NutrientField> nutDict = new SerializableDictionary<int, MuCell.Model.NutrientField>();
//// create new nutrients x2
//MuCell.Model.NutrientField nut1 = new MuCell.Model.NutrientField(1);
//MuCell.Model.NutrientField nut2 = new MuCell.Model.NutrientField(2);
//nut2.Col = System.Drawing.Color.Fuchsia;
//nutDict.Add(1,nut1); nutDict.Add(2,nut2);
//environment.Nutrients = nutDict;
snapshot.SimulationEnvironment = environment;
results.StateSnapshots.Add(snapshot);
}
results.CurrentState = results.StateSnapshots[4];
for (int i = 0; i < 3; i++)
{
TimeSeries timeSeries = new TimeSeries("Function" + i, 1.2 * i);
for (int j = 0; j < 20; j++)
{
timeSeries.Series.Add(0.43+i*j+0.031*j);
}
results.TimeSeries.Add(timeSeries);
}
results.FilePath = "some-file-path";
simulation1.SimulationResults = results;
SimulationParameters simulationParams1 = new SimulationParameters();
simulationParams1.TimeSeries = results.TimeSeries;
simulationParams1.InitialState = results.StateSnapshots[0];
// add to simulation
simulation1.Parameters = simulationParams1;
// expt.addSimulation
experiment.addSimulation(simulation1);
XmlSerializer s = new XmlSerializer(typeof(MuCell.Model.Experiment));
TextWriter w = new StreamWriter(filename);
s.Serialize(w, experiment);
w.Close();
TextReader tr = new StreamReader(filename);
Experiment deserializedExpt = (Experiment)s.Deserialize(tr);
tr.Close();
Assert.IsTrue(experiment.exptEquals(deserializedExpt));
}
public void testRenaming()
{
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 = "species1";
species1.InitialAmount = 4.0d;
species1.InitialConcentration = 7.0d;
species1.xPosition = 2.0f;
// Set some values for species2 that has the same id and same values
species2.ID = "species2";
species2.InitialAmount = 4.0d;
species2.InitialConcentration = 7.0d;
species2.xPosition = 2.0f;
// Add to the model
model.AddId(species1.ID, species1);
model.AddId(species2.ID, species2);
// Rename
species1.ID = "new_species1";
// Check the id in the species object
Assert.AreEqual("new_species1", species1.ID);
Assert.AreEqual("species1", species1.getOldID());
model.updateID(species1);
// Check the ids in the model
Assert.IsTrue(model.idExists("new_species1"));
Assert.IsTrue(model.idExists("species2"));
Assert.IsFalse(model.idExists("species1"));
}
public void testNonDataDuplicate()
{
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();
MuCell.Model.SBML.Species species3 = new MuCell.Model.SBML.Species();
model.listOfSpecies = new List<MuCell.Model.SBML.Species>();
model.listOfSpecies.Add(species1);
model.listOfSpecies.Add(species2);
model.listOfSpecies.Add(species3);
// Set some values for species1
species1.ID = "species1";
species1.InitialAmount = 4.0d;
species1.InitialConcentration = 7.0d;
species1.xPosition = 2.0f;
// Set some values for species2 that has the same id and same values
species2.ID = "species1";
species2.InitialAmount = 4.0d;
species2.InitialConcentration = 7.0d;
species2.xPosition = 2.0f;
// Set some values for species3 that has the same id but DIFFERENT values
species3.ID = "species1";
// Difference
species3.InitialAmount = 5.0d;
species3.InitialConcentration = 7.0d;
species3.xPosition = 2.0f;
// Add to the model
model.AddId(species1.ID, species1);
model.AddId(species2.ID, species2);
model.AddId(species3.ID, species3);
try
{
model.processDuplicates();
}
catch (MuCell.Model.SBML.DuplicateSBMLObjectIdException e)
{
// Assert that an exception has been thrown
Assert.IsTrue(true);
}
}
public void testInterrogateModelForIDs()
{
MuCell.Model.SBML.Model model = new MuCell.Model.SBML.Model();
model.listOfReactions = new List<MuCell.Model.SBML.Reaction>();
model.listOfSpecies = new List<MuCell.Model.SBML.Species>();
MuCell.Model.SBML.Species species1 = new MuCell.Model.SBML.Species();
MuCell.Model.SBML.Species species2 = new MuCell.Model.SBML.Species();
MuCell.Model.SBML.Species species3 = new MuCell.Model.SBML.Species();
species1.ID = "species1";
species2.ID = "species2";
species3.ID = "species 3";
model.AddId("species1", species1);
MuCell.Model.SBML.Reaction r1 = new MuCell.Model.SBML.Reaction();
MuCell.Model.SBML.SpeciesReference sp1r = new MuCell.Model.SBML.SpeciesReference();
sp1r.species = species1;
MuCell.Model.SBML.SpeciesReference sp2r = new MuCell.Model.SBML.SpeciesReference();
sp2r.species = species2;
MuCell.Model.SBML.SpeciesReference sp3r = new MuCell.Model.SBML.SpeciesReference();
sp3r.species = species3;
r1.Reactants.Add(sp1r);
r1.Reactants.Add(sp2r);
r1.Products.Add(sp3r);
MuCell.Model.SBML.KineticLaw kl = new MuCell.Model.SBML.KineticLaw(model);
r1.KineticLaw = kl;
MuCell.Model.SBML.Parameter k1 = new MuCell.Model.SBML.Parameter();
k1.ID = "k1";
r1.Parameters.Add(k1);
r1.Formula = "species1*species_3*k1";
model.listOfSpecies.Add(species1);
model.listOfReactions.Add(r1);
// Assert the unknown entities
Assert.AreEqual(2, r1.KineticLaw.UnknownEntitiesFromFormula().Count);
Assert.AreEqual("species_3", r1.KineticLaw.UnknownEntitiesFromFormula().ToArray()[0].ID);
Assert.AreEqual("k1", r1.KineticLaw.UnknownEntitiesFromFormula().ToArray()[1].ID);
// Assert missing items in model
Assert.IsTrue(model.idExists("species1"));
Assert.IsFalse(model.idExists("species2"));
Assert.IsFalse(model.idExists("species 3"));
Assert.IsFalse(model.idExists("k1"));
model.InterrogateModelForMissingIDs();
// redo formula
r1.Formula = "species1*species_3*k1";
// assert no unknown entities
Assert.AreEqual(0, r1.KineticLaw.UnknownEntitiesFromFormula().Count);
// Assert everything is in the model
Assert.IsTrue(model.idExists("species1"));
Assert.IsTrue(model.idExists("species2"));
Assert.IsTrue(model.idExists("species 3"));
Assert.IsTrue(model.idExists("k1"));
}
public void testDataDuplicate()
{
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 = "species1";
species1.InitialAmount = 4.0d;
species1.InitialConcentration = 7.0d;
species1.xPosition = 2.0f;
// Set some values for species2 that has the same id and same values
species2.ID = "species1";
species2.InitialAmount = 4.0d;
species2.InitialConcentration = 7.0d;
species2.xPosition = 2.0f;
// Add to the model
model.AddId(species1.ID, species1);
model.AddId(species2.ID, species2);
// Check that we have two species
Assert.AreEqual(2, model.listOfSpecies.Count);
// Should remove species2
model.processDuplicates();
// Check there is now only 1 species in the model
Assert.AreEqual(1, model.listOfSpecies.Count);
// Check that it is species1
Assert.AreEqual(species1, model.listOfSpecies.ToArray()[0]);
}
public void serializeXandYPositions()
{
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 = "species1";
species1.InitialAmount = 4.0;
species1.InitialConcentration = 7.0;
species1.xPosition = 2.0f;
species1.yPosition = 3.0f;
// Set some values for species2
species2.ID = "species2";
species2.InitialAmount = 1.0;
species2.InitialConcentration = 3.0;
species2.xPosition = 5.0f;
species2.yPosition = 6.0f;
// Add to the model
model.AddId(species1.ID, species1);
model.AddId(species2.ID, species2);
model.saveToXml("../../UnitTests/xy.serialized.xml");
}
