private static void CreateSpeciesInfoAndSpecies(string speciesName, int initialPopulation, out SpeciesDescription description, out Species species)
{
description = new SpeciesDescription(speciesName, initialPopulation);
//species = new Species(description) { Count = description.InitialValue };
species = new Species(description, new Dictionary <string, IValue>());
species.Reset();
}
public void TestSpeciesMPCount()
{
//Parameters in order to create a SpeciesMP
SpeciesDescription info1;
string speciesName = "species1";
int initialPopulation = 10;
//Species Info Object
info1 = new SpeciesDescription(speciesName, initialPopulation);
var species = new SpeciesMP(info1, new Dictionary <string, IValue>());
species.Reset();
//Test get
Assert.AreEqual(initialPopulation, species.Count);
//Test set
species.Count = 20;
Assert.AreEqual(20, species.Count);
Assert.AreEqual((double)20, species.Value);
//Test fractional value of species.
species.Value = 30.2;
Assert.AreEqual((int)30.2, species.Count);
//Test get through Update.
species.Update(30.0);
Assert.AreEqual(30, species.Count);
}
public void TestSpeciesMPValue()
{
//Parameters in order to create a SpeciesMP
SpeciesDescription info1;
string speciesName = "species1";
int initialPopulation = 10;
//Species Info Object
info1 = new SpeciesDescription(speciesName, initialPopulation);
var species = new SpeciesMP(info1, new Dictionary <string, IValue>());
species.Reset();
//Test get
Assert.AreEqual((double)initialPopulation, species.Value);
//Test set
species.Value = 20.0;
Assert.AreEqual(20.0, species.Value);
species.Value = 21.5;
Assert.AreEqual(21.5, species.Value);
//Test set via Update
species.Update(30.0);
Assert.AreEqual(30.0, species.Value);
}
public void ReactionIsLocalTest()
{
var builder = new ReactionInfo.ReactionBuilder();
ReactionInfo reaction = builder.Reaction;
var reactantA = new SpeciesDescription("reactantA", new LocaleInfo("locale1"));
var productA = new SpeciesDescription("productA", reactantA.Locale);
builder.AddReactant(reactantA);
builder.AddProduct(productA);
Console.WriteLine("Checking for reaction.IsLocal with reactants and products in same locale...");
Expect(reaction.IsLocal);
Expect(!reaction.IsDiffusion);
builder = new ReactionInfo.ReactionBuilder();
reaction = builder.Reaction;
var productB = new SpeciesDescription("productB", new LocaleInfo("locale2"));
builder.AddReactant(reactantA);
builder.AddProduct(productB);
Console.WriteLine("Checking for !reaction.IsLocal with reactants and products from different locales...");
Expect(!reaction.IsLocal);
Expect(reaction.IsDiffusion);
Console.WriteLine("");
}
public void ProcessSpeciesTestOneSpecies()
{
ModelInfo.ModelBuilder modelInfoEx = new ModelInfo.ModelBuilder("model");
var species = new SpeciesDescription("testSpecies", 10);
modelInfoEx.AddSpecies(species);
ModelInfo modelInfo = modelInfoEx.Model;
Model model = new Model(modelInfo);
MpModelBuilder modelbuilder = new MpModelBuilder();
MethodInfo processSpeciesMethod = ReflectionUtility.GetHiddenMethod("ProcessSpecies", modelbuilder);
IDictionary <string, IValue> nmap;
IDictionary <string, IBoolean> bmap;
IDictionary <string, IUpdateable> umap;
IDictionary <SpeciesDescription, Species> speciesMap = InitializeMaps(out nmap, out bmap, out umap);
var newSpecies = new SpeciesMP(species, nmap);
//Inputs to invoke hidden method ProcessSpecies (needs to be an array of objects)
var inputArray1 = new object[2];
inputArray1[0] = model;
inputArray1[1] = modelInfo;
//Test to make sure that the model has local variables that are null
var compareSpeciesMap = ReflectionUtility.GetHiddenField <IDictionary <SpeciesDescription, Species> >("_speciesMap", modelbuilder);
var compareNmap = ReflectionUtility.GetHiddenField <IDictionary <string, IValue> >("_nmap", modelbuilder);
var compareBmap = ReflectionUtility.GetHiddenField <IDictionary <string, IBoolean> >("_bmap", modelbuilder);
var compareUMap = ReflectionUtility.GetHiddenField <IDictionary <string, IUpdateable> >("_umap", modelbuilder);
Assert.AreEqual(speciesMap, compareSpeciesMap);
Assert.AreEqual(nmap, compareNmap);
Assert.AreEqual(bmap, compareBmap);
Assert.AreEqual(umap, compareUMap);
processSpeciesMethod.Invoke(modelbuilder, inputArray1);
//Begin Assertions about the species that was added to the model
Assert.AreEqual("testSpecies", model.Species[0].Name);
Assert.AreEqual(species, model.Species[0].Description);
Assert.AreEqual(1, model.Species.Count);
//Assert tests about size.
compareSpeciesMap = ReflectionUtility.GetHiddenField <IDictionary <SpeciesDescription, Species> >("_speciesMap", modelbuilder);
compareNmap = ReflectionUtility.GetHiddenField <IDictionary <string, IValue> >("_nmap", modelbuilder);
compareUMap = ReflectionUtility.GetHiddenField <IDictionary <string, IUpdateable> >("_umap", modelbuilder);
Assert.AreEqual(1, compareSpeciesMap.Count);
Assert.AreEqual(1, compareNmap.Count);
Assert.AreEqual(1, compareUMap.Count);
//Assert tests about what was actually added to the dictionary.
var testSpecies = (SpeciesMP)compareNmap["testSpecies"];
Assert.AreEqual(testSpecies.Description, newSpecies.Description);
Assert.AreEqual(testSpecies.Locale, newSpecies.Locale);
Assert.AreEqual(testSpecies.Name, newSpecies.Name);
}
public void MixedLocaleproductTest()
{
var builder = new ReactionInfo.ReactionBuilder();
var species1 = new SpeciesDescription("A-Species", new LocaleInfo("compartment-A"));
builder.AddProduct(species1);
Console.WriteLine("Checking for ArgumentException() with products from difference locales...");
Console.WriteLine("");
var species2 = new SpeciesDescription("B-Species", new LocaleInfo("compartment-B"));
builder.AddProduct(species2);
}
public void SpeciesInfoTest()
{
const string nameOne = "NameOnly";
var speciesName = new SpeciesDescription(nameOne);
Console.Write("Created species: ");
Console.WriteLine(speciesName);
Console.WriteLine("SpeciesInfoTest: testing named species Name property...");
Expect(speciesName.Name == nameOne);
Console.WriteLine("SpeciesInfoTest: testing named species Locale property...");
Expect(speciesName.Locale == null);
const string nameTwo = "NameAndPop";
const int initialPopOne = 2012;
var speciesNamePop = new SpeciesDescription(nameTwo, initialPopOne);
Console.Write("Created species: ");
Console.WriteLine(speciesNamePop);
Console.WriteLine("SpeciesInfoTest: testing name+pop species Name property...");
Expect(speciesNamePop.Name == nameTwo);
Console.WriteLine("SpeciesInfoTest: testing name+pop species Locale property...");
Expect(speciesNamePop.Locale == null);
const string nameThree = "NameAndLocale";
const string localeOneName = "univ";
var localeOne = new LocaleInfo(localeOneName);
var speciesNameLocale = new SpeciesDescription(nameThree, localeOne);
Console.Write("Created species: ");
Console.WriteLine(speciesNameLocale);
Console.WriteLine("SpeciesInfoTest: testing name+locale species Name property...");
Expect(speciesNameLocale.Name == nameThree);
Console.WriteLine("SpeciesInfoTest: testing name+locale species Locale property...");
Expect(speciesNameLocale.Locale == localeOne);
const string nameFour = "NamePopAndLocale";
const int initialPopTwo = 2112;
const string localeTwoName = "bellevue";
var localeTwo = new LocaleInfo(localeTwoName);
var speciesNamePopLocale = new SpeciesDescription(nameFour, initialPopTwo, localeTwo);
Console.Write("Created species: ");
Console.WriteLine(speciesNamePopLocale);
Console.WriteLine("SpeciesInfoTest: testing name+pop+locale species Name property...");
Expect(speciesNamePopLocale.Name == nameFour);
Console.WriteLine("SpeciesInfoTest: testing name+pop+locale species Locale property...");
Expect(speciesNamePopLocale.Locale == localeTwo);
}
public void TestSpeciesMPConstructorWithDefaults()
{
//Parameters in order to create a SpeciesMP
const string speciesName = "species1";
const int initialPopulation = 10;
//Species Info and Species Object
var info1 = new SpeciesDescription(speciesName, initialPopulation);
var species = new SpeciesMP(info1, new Dictionary <string, IValue>());
species.Reset();
//Test Constructor
Assert.AreEqual(initialPopulation, species.Count);
Assert.AreEqual(initialPopulation, (int)species.Value);
}
public void ReactionInfoTest()
{
// Add a reactant, reactant shows up in Reactants list
var builder = new ReactionInfo.ReactionBuilder();
ReactionInfo reaction = builder.Reaction;
var reactant = new SpeciesDescription("reactant", 2012);
builder.AddReactant(reactant);
Console.WriteLine("Checking for reactant added to reaction with ReactionBuilder...");
Expect(reaction.Reactants.First() == reactant);
// Add a product, product shows up in Products list
var product = new SpeciesDescription("product", 2112);
builder.AddProduct(product);
Console.WriteLine("Checking for product added to reaction with ReactionBuilder...");
Expect(reaction.Products.First() == product);
// Set rate, reaction rate is set.
var expression = new NumericExpressionTree(string.Empty,
new MultiplyOperator(new SymbolReference("reactant"),
new SymbolReference("product")));
builder.SetRate(expression);
Console.WriteLine("Checking for reaction rate set from ReactionBuilder...");
Expect(reaction.RateExpression == expression);
Console.WriteLine("Checking !reaction.HasDelay (before calling builder.SetDelay())...");
Expect(!reaction.HasDelay);
var delay = new NumericExpressionTree(string.Empty, new Constant(3.14159265f));
builder.SetDelay(delay);
Console.WriteLine("Checking reaction.HasDelay (after calling builder.SetDelay())...");
Expect(reaction.HasDelay);
Console.WriteLine("Checking reaction for correct delay...");
Expect(reaction.DelayExpression == delay);
Console.WriteLine("");
}
public void TestSpeciesMPDecrement()
{
//Parameters in order to create a SpeciesMP
SpeciesDescription info1;
string speciesName = "species1";
int initialPopulation = 20;
//Species Info Object
info1 = new SpeciesDescription(speciesName, initialPopulation);
var species = new SpeciesMP(info1, new Dictionary <string, IValue>());
species.Reset();
//Test Increment
Assert.AreEqual(initialPopulation, species.Count);
int returnCount;
double returnValue;
int deltaInt = 5;
double deltaDouble = 5.0;
returnCount = species.Decrement();
Assert.AreEqual(initialPopulation - 1, species.Count);
Assert.AreEqual(initialPopulation - 1, returnCount);
returnCount = ((Species)species).Decrement(deltaInt);
Assert.AreEqual(initialPopulation - 6, species.Count);
Assert.AreEqual(initialPopulation - 6, returnCount);
returnValue = species.Decrement(deltaDouble);
Assert.AreEqual(initialPopulation - 11, species.Value);
Assert.AreEqual(initialPopulation - 11, returnValue);
deltaInt = -5;
deltaDouble = -5.0;
returnCount = ((Species)species).Decrement(deltaInt);
Assert.AreEqual(initialPopulation - 6, species.Count);
Assert.AreEqual(initialPopulation - 6, returnCount);
returnValue = species.Decrement(deltaDouble);
Assert.AreEqual(initialPopulation - 1, species.Value);
Assert.AreEqual(initialPopulation - 1, returnValue);
}
private static Reaction CreateReaction(SpeciesDescription info1, Species reactant1, SpeciesDescription info2, Species reactant2, SpeciesDescription info3, Species product1, double rate)
{
var builder = new ReactionInfo.ReactionBuilder("theReaction");
builder.AddReactant(info1);
builder.AddReactant(info2);
builder.AddProduct(info3);
builder.SetRate(new NumericExpressionTree(new Constant(rate)));
var reactionInfo = builder.Reaction;
var speciesMap = new Dictionary <SpeciesDescription, Species>(3)
{
{ info1, reactant1 }, { info2, reactant2 }, { info3, product1 }
};
var symbolMap = new Dictionary <string, IValue>();
var reaction = new Reaction(reactionInfo, speciesMap, symbolMap);
return(reaction);
}
public void TestSpeciesMPUpdate()
{
//Parameters in order to create a SpeciesMP
SpeciesDescription info1;
string speciesName = "species1";
int initialPopulation = 10;
//Species Info Object
info1 = new SpeciesDescription(speciesName, initialPopulation);
var species = new SpeciesMP(info1, new Dictionary <string, IValue>());
species.Reset();
//Test Update
species.Update(30.0f);
Assert.AreEqual(30.0f, species.Value);
species.Update(0.0f);
Assert.AreEqual(0.0f, species.Value);
species.Update(-30.0f);
Assert.AreEqual(-30.0f, species.Value);
}
public SpeciesMP(SpeciesDescription speciesDescription, IDictionary <string, IValue> map)
: base(speciesDescription, map)
{
}
public Species(SpeciesDescription speciesDescription, IDictionary <string, IValue> map)
{
Description = speciesDescription;
_initialPopulation = speciesDescription.InitialPopulation.ResolveReferences(map);
}
public void ModelInfoTest()
{
const string modelName = "test model";
var builder = new ModelInfo.ModelBuilder(modelName);
const string constraintName = "test constraint";
const string constraintPredicateName = "constraint predicate";
var constraintExpression = new EqualToOperator(Two, Two);
var constraintPredicate = new BooleanExpressionTree(constraintPredicateName, constraintExpression);
var constraint = new ConstraintInfo(constraintName, constraintPredicate);
builder.AddConstraint(constraint);
/*
* const string eventName = "test event";
* const string eventPredicateName = "event predicate";
* var eventExpression = new GreaterThanOperator(Three, Two);
* var eventPredicate = new BooleanExpressionTree(eventPredicateName, eventExpression);
* int eventCount = 0;
* var testEvent = new EventInfo(eventName, eventPredicate, () => { eventCount++; });
* builder.AddEvent(testEvent);
*/
const string expressionName = "test expression";
var expression = new AddOperator(Three, Two);
var expressionTree = new NumericExpressionTree(expressionName, expression);
builder.AddExpression(expressionTree);
const string localeName = "test locale";
var locale = new LocaleInfo(localeName);
builder.AddLocale(locale);
const string observableName = "test observable";
const string observableExpressionName = "observable expression";
var rootOperator = new PowerOperator(Two, Three);
var observableExpressionTree = new NumericExpressionTree(observableExpressionName, rootOperator);
var observable = new ObservableInfo(observableName, observableExpressionTree);
builder.AddObservable(observable);
const string parameterName = "test parameter";
var parameter = new ParameterInfo(parameterName, 3.14159265f);
builder.AddParameter(parameter);
const string predicateName = "test predicate";
var predicateExpression = new LessThanOperator(Two, Three);
var predicate = new BooleanExpressionTree(predicateName, predicateExpression);
builder.AddPredicate(predicate);
const string speciesName = "reactant";
var reactant = new SpeciesDescription(speciesName, 2012, locale);
builder.AddSpecies(reactant);
const string reactionName = "test reaction";
var rBuilder = new ReactionInfo.ReactionBuilder(reactionName);
rBuilder.AddReactant(reactant);
var rateExpression = new MultiplyOperator(Ten, new SymbolReference(speciesName));
var reactionRate = new NumericExpressionTree(null, rateExpression);
rBuilder.SetRate(reactionRate);
var reaction = rBuilder.Reaction;
builder.AddReaction(reaction);
var modelInfo = builder.Model;
Console.WriteLine("ModelInfoTests: checking model name...");
Expect(modelInfo.Name == modelName);
Console.WriteLine("ModelInfoTests: checking constraint count (1)...");
Expect(modelInfo.Constraints.Count() == 1);
Console.WriteLine("ModelInfoTests: checking constraint...");
Expect(modelInfo.Constraints.First() == constraint);
/*
* Console.WriteLine("ModelInfoTests: checking event count (1)...");
* Expect(modelInfo.Events.Count() == 1);
* Console.WriteLine("ModelInfoTests: checking event...");
* Expect(modelInfo.Events.First() == testEvent);
*/
Console.WriteLine("ModelInfoTests: checking expression count (3)...");
Expect(modelInfo.Expressions.Count() == 3);
Console.WriteLine("ModelInfoTests: checking expressions...");
var expressions = modelInfo.Expressions.Where(net => net.Name == expressionName).ToList();
Expect(expressions.Count == 1);
Expect(expressions[0] == expressionTree);
Console.WriteLine("ModelInfoTests: checking locale count (1)...");
Expect(modelInfo.Locales.Count() == 1);
Console.WriteLine("ModelInfoTests: checking locale...");
Expect(modelInfo.Locales.First() == locale);
Console.WriteLine("ModelInfoTests: checking observable count (1)...");
Expect(modelInfo.Observables.Count() == 1);
Console.WriteLine("ModelInfoTests: checking observable...");
Expect(modelInfo.Observables.First() == observable);
Console.WriteLine("ModelInfoTests: checking parameter count (1)...");
Expect(modelInfo.Parameters.Count() == 1);
Console.WriteLine("ModelInfoTests: checking parameter...");
Expect(modelInfo.Parameters.First() == parameter);
/*
* Console.WriteLine("ModelInfoTests: checking predicate count (3)...");
* Expect(modelInfo.Predicates.Count() == 3);
*/
Console.WriteLine("ModelInfoTests: checking predicate count (2)...");
Expect(modelInfo.Predicates.Count() == 2);
Console.WriteLine("ModelInfoTests: checking predicate...");
var predicates = modelInfo.Predicates.Where(pi => pi.Name == predicateName).ToList();
Expect(predicates.Count == 1);
Expect(predicates[0] == predicate);
Console.WriteLine("ModelInfoTests: checking reaction count (1)...");
Expect(modelInfo.Reactions.Count() == 1);
Console.WriteLine("ModelInfoTests: checking reaction...");
Expect(modelInfo.Reactions.First() == reaction);
Console.WriteLine("ModelInfoTests: checking species count (1)...");
Expect(modelInfo.Species.Count() == 1);
Console.WriteLine("ModelInfoTests: checking species...");
Expect(modelInfo.Species.First() == reactant);
}
private static void CreateSpeciesInfoAndSpecies(string speciesName, int initialPopulation, out SpeciesDescription info, out SpeciesMP species)
{
info = new SpeciesDescription(speciesName, initialPopulation);
species = new SpeciesMP(info, new Dictionary <string, IValue>());
species.Reset();
}
