public void TestSerialization()
{
EventBuilder x1 = CreateObject <EventBuilder>().WithName("Eve.Builder").WithDimension(DimensionLength);
x1.Formula = CreateObject <ConstantFormula>().WithDimension(DimensionLength).WithValue(23.4);
x1.OneTime = true;
IFormula f1 = CreateObject <ExplicitFormula>().WithDimension(DimensionLength).WithFormulaString("3*Patty");
IFormulaUsablePath fup = new FormulaUsablePath(new string[] { "Patricia" }).WithAlias("Patty").WithDimension(DimensionLength);
f1.AddObjectPath(fup);
IFormula f2 = CreateObject <ConstantFormula>().WithDimension(DimensionLength).WithValue(23.4);
IParameter p1 = WithExtensions.WithValue <Parameter>(CreateObject <Parameter>().WithName("Patricia").WithFormula(f1), 3.1);
IParameter p2 = WithExtensions.WithValue <Parameter>(CreateObject <Parameter>().WithName("Pascal").WithFormula(f1), 3.2);
x1.AddParameter(p1);
x1.AddParameter(p2);
IEventAssignmentBuilder eab1 = CreateObject <EventAssignmentBuilder>().WithDimension(DimensionLength).WithFormula(f1).WithName("eab1");
IEventAssignmentBuilder eab2 = CreateObject <EventAssignmentBuilder>().WithFormula(f2).WithName("eab2");
x1.AddAssignment(eab1);
x1.AddAssignment(eab2);
var x2 = SerializeAndDeserialize(x1);
AssertForSpecs.AreEqualEventBuilder(x1, x2);
}
/// <summary>
/// Creates the Mobi Event Assignment for one SBML Event Assignment.
/// </summary>
internal void CreateEventAssignment(EventAssignment eventAssignment)
{
_counter++;
var assignmentVar = eventAssignment.getVariable();
var alias = _sbmlInformation.AliasCreator.CreateAliasFrom(assignmentVar) + _counter;
var description = String.Empty;
if (eventAssignment.isSetNotes())
{
description += eventAssignment.getNotesString();
}
if (eventAssignment.isSetSBOTerm())
{
description += (SBMLConstants.SPACE + eventAssignment.getSBOTerm());
}
IEventAssignmentBuilder eab = new EventAssignmentBuilder()
.WithId(eventAssignment.getId() + SBMLConstants.SPACE + eventAssignment.getName() + SBMLConstants.SPACE + alias)
.WithName(SBMLConstants.SBML_EVENT_ASSIGNMENT + eventAssignment.getId())
.WithDescription(description);
var formula = _astHandler.Parse(eventAssignment.getMath(), eab, assignmentVar, _sbmlProject, _sbmlInformation) ??
ObjectBaseFactory.Create <ExplicitFormula>().WithFormulaString(String.Empty).WithName(SBMLConstants.DEFAULT_FORMULA_NAME);
eab.Formula = formula;
EventGroupBuildingBlock.FormulaCache.Add(formula);
EventBuilder.AddAssignment(eab);
}
protected override void Context()
{
base.Context();
var e1 = new EventBuilder().WithName("Event");
e1.OneTime = true;
var eventAssignmentBuilder1 = new EventAssignmentBuilder();
eventAssignmentBuilder1.ObjectPath = new ObjectPath("Sim|A|B|C");
eventAssignmentBuilder1.Name = "EAB";
eventAssignmentBuilder1.Formula = new ExplicitFormula("a+b");
e1.AddAssignment(eventAssignmentBuilder1);
e1.AddParameter(new Parameter().WithName("P1"));
var e2 = new EventBuilder().WithName("Event");
e2.OneTime = true;
var eventAssignmentBuilder2 = new EventAssignmentBuilder();
eventAssignmentBuilder2.ObjectPath = new ObjectPath("Sim|A|B|C");
eventAssignmentBuilder2.Name = "EAB";
eventAssignmentBuilder2.Formula = new ExplicitFormula("a+b");
e2.AddAssignment(eventAssignmentBuilder2);
_object1 = e1;
_object2 = e2;
}
protected override void Context()
{
base.Context();
var e1 = new EventBuilder().WithName("Event");
e1.OneTime = true;
var eventAssignmentBuilder1 = new EventAssignmentBuilder();
eventAssignmentBuilder1.ObjectPath = new ObjectPath("Sim|A|B|C");
eventAssignmentBuilder1.Name = "EAB1";
e1.AddAssignment(eventAssignmentBuilder1);
var e2 = new EventBuilder().WithName("Event");
e2.OneTime = true;
var eventAssignmentBuilder2 = new EventAssignmentBuilder();
eventAssignmentBuilder2.ObjectPath = new ObjectPath("Sim|A|B|C");
eventAssignmentBuilder2.Name = "EAB2";
e2.AddAssignment(eventAssignmentBuilder2);
_object1 = e1;
_object2 = e2;
_comparerSettings.OnlyComputingRelevant = false;
}
protected override void Context()
{
base.Context();
var e1 = new EventBuilder().WithName("Event");
e1.OneTime = true;
var eventAssignmentBuilder1 = new EventAssignmentBuilder();
eventAssignmentBuilder1.ObjectPath = new ObjectPath("Sim|A|B|C");
eventAssignmentBuilder1.Name = "EAB";
e1.AddAssignment(eventAssignmentBuilder1);
var e2 = new EventBuilder().WithName("Event");
e2.OneTime = true;
var eventAssignmentBuilder2 = new EventAssignmentBuilder();
eventAssignmentBuilder2.ObjectPath = new ObjectPath("Sim|A|B|D");
eventAssignmentBuilder2.Name = "EAB";
e2.AddAssignment(eventAssignmentBuilder2);
_object1 = e1;
_object2 = e2;
}
protected override void Context()
{
base.Context();
_eventGroupBuildingBlock = new EventGroupBuildingBlock();
var eventGroup = new EventGroupBuilder().WithName("EG");
_eventGroupBuildingBlock.Add(eventGroup);
var ehcStartEvent = new EventBuilder().WithName(Converter321To331.EHCStartEvent);
eventGroup.Add(ehcStartEvent);
var eabOldStart = new EventAssignmentBuilder().WithName("EAB1").WithFormula(new ExplicitFormula("ln(2) / EHC_Halftime * M * EHC_EjectionFraction"));
eabOldStart.UseAsValue = false;
eabOldStart.ObjectPath = new ObjectPath(new[] { "Organism", "Gallbladder", "Gallbladder emptying rate" });
ehcStartEvent.AddAssignment(eabOldStart);
var assignmentBuilder = new EventAssignmentBuilder().WithName("EAB2").WithFormula(new ExplicitFormula("DontChange"));
assignmentBuilder.ObjectPath = new ObjectPath(new[] { "PATH" });
ehcStartEvent.AddAssignment(assignmentBuilder);
var ehcStopEvent = new EventBuilder().WithName(Converter321To331.EHCStopEvent);
var eabOldStop = new EventAssignmentBuilder().WithName("EAB1").WithFormula(new ConstantFormula(0));
eabOldStop.UseAsValue = false;
eabOldStop.ObjectPath = new ObjectPath(new[] { "Organism", "Gallbladder", "Gallbladder emptying rate" });
ehcStopEvent.AddAssignment(eabOldStop);
assignmentBuilder = new EventAssignmentBuilder().WithName("EAB2").WithFormula(new ExplicitFormula("DontChange"));
assignmentBuilder.ObjectPath = new ObjectPath(new[] { "PATH" });
ehcStopEvent.AddAssignment(assignmentBuilder);
eventGroup.Add(ehcStopEvent);
var protocolSchemaItem = new Container().WithName("ProtocolSchemaItem").WithParentContainer(eventGroup);
_drugMassParameter = new Parameter().WithName("DrugMass").WithParentContainer(protocolSchemaItem).WithValue(1);
applications = new EventGroupBuilder().WithName("Applications");
applications.Add(new Parameter().WithName("TotalDrugMass"));
_eventGroupBuildingBlock.Add(applications);
}
protected override void Context()
{
base.Context();
var eg1 = new EventGroupBuilder().WithName("Events");
var app1 = new ApplicationBuilder().WithName("App").WithParentContainer(eg1);
app1.MoleculeName = "Drug";
var c1 = new Container().WithName("ProtocolSchemaItem").WithParentContainer(app1);
_e1 = new EventBuilder().WithName("Event").WithParentContainer(app1);
_eventAssignmentBuilder1 = new EventAssignmentBuilder();
_eventAssignmentBuilder1.ObjectPath = new ObjectPath("Sim|A|B|C");
_eventAssignmentBuilder1.Name = "EAB";
_eventAssignmentBuilder1.UseAsValue = true;
_eventAssignmentBuilder1.Formula = new ExplicitFormula("a+b");
_e1.AddAssignment(_eventAssignmentBuilder1);
_explicitFormula1 = new ExplicitFormula("1+2");
_p1 = new Parameter().WithName("P").WithFormula(_explicitFormula1).WithParentContainer(c1);
var eg2 = new EventGroupBuilder().WithName("Events");
var app2 = new ApplicationBuilder().WithName("App").WithParentContainer(eg2);
app2.MoleculeName = "Drug";
var c2 = new Container().WithName("ProtocolSchemaItem").WithParentContainer(app2);
var e2 = new EventBuilder().WithName("Event").WithParentContainer(app2);
var eventAssignmentBuilder2 = new EventAssignmentBuilder();
eventAssignmentBuilder2.ObjectPath = new ObjectPath("Sim|A|B|C");
eventAssignmentBuilder2.Name = "EAB";
eventAssignmentBuilder2.UseAsValue = false;
eventAssignmentBuilder2.Formula = new ExplicitFormula("a+b");
e2.AddAssignment(eventAssignmentBuilder2);
var p2 = new Parameter().WithName("P").WithFormula(new ExplicitFormula("2+1")).WithParentContainer(c2);
_object1 = eg1;
_object2 = eg2;
}
