/// <summary>
///
/// </summary>
/// <param name="anUnit"></param>
/// <returns></returns>
private double getNewUnitValue(UnitStruct anUnit)
{
double aValue = 1;
// Scale
if ( anUnit.Scale != 0 )
aValue = aValue * Math.Pow( 10, anUnit.Scale );
// Multiplier
aValue = aValue * anUnit.Multiplier;
// Exponent
aValue = Math.Pow( aValue, anUnit.Exponent );
// Offset
aValue = aValue + anUnit.Offset;
return aValue;
}
public void TestConstructorOfStructs()
{
//
CompartmentStruct c = new CompartmentStruct(
"ID",
"Name",
0,
0.0,
0.0,
"Unit",
"Parent",
false);
//
EventStruct e = new EventStruct(
"ID",
"Name",
"Trigger",
"delay",
"TimeUnit",
new List<EventAssignmentStruct>());
//
EventAssignmentStruct ea = new EventAssignmentStruct(
"Variable",
"Formula");
//
FunctionDefinitionStruct fd = new FunctionDefinitionStruct(
"ID",
"Name",
"Formula");
//
ParameterStruct p = new ParameterStruct(
"ID",
"Name",
0.0,
"Unit",
false);
//
ReactionStruct r = new ReactionStruct(
"ID",
"Name",
new List<KineticLawStruct>(),
false,
false,
new List<ReactantStruct>(),
new List<ProductStruct>(),
new List<string>());
//
KineticLawStruct k = new KineticLawStruct(
"Formula",
new List<string>(),
"TimeUnit",
"Substance",
new List<ParameterStruct>(),
null);
//
ReactantStruct rs = new ReactantStruct(
"Species",
0,
"Formula",
0);
//
ProductStruct ps = new ProductStruct(
"Species",
0.0,
"Formula",
0);
//
RuleStruct rule = new RuleStruct(
0,
"Formula",
"Variable");
//
SpeciesStruct s = new SpeciesStruct(
"ID",
"Name",
"Parent",
0.0,
0.0,
"Substance",
"Spatial",
"Unit",
false,
false,
0,
false);
//
UnitDefinitionStruct ud = new UnitDefinitionStruct(
"ID",
"Name",
new List<UnitStruct>());
//
UnitStruct u = new UnitStruct(
"Kind",
0,
0,
0.0,
0.0);
//
VariableReferenceStruct v = new VariableReferenceStruct(
"Name",
"Variable",
0);
//
InitialAssignmentStruct i = new InitialAssignmentStruct(
"Name",
0.0);
}
/// <summary>
/// [ UnitDefinitionStruct ]
/// [[ Id , Name , [ UnitStruct ] ]]
/// </summary>
/// <param name="aSBMLmodel"></param>
/// <returns></returns>
public static List<UnitDefinitionStruct> getUnitDefinition(Model aSBMLmodel)
{
List<UnitDefinitionStruct> list = new List<UnitDefinitionStruct>();
ListOfUnitDefinitions listOfUnitDefinitions = aSBMLmodel.getListOfUnitDefinitions();
for (int i = 0; i < listOfUnitDefinitions.size(); i++ )
{
UnitDefinition anUnitDefinition = aSBMLmodel.getUnitDefinition(i);
string anId = anUnitDefinition.getId();
string aName = anUnitDefinition.getName();
List<UnitStruct> unitList = new List<UnitStruct>();
ListOfUnits listOfUnits = anUnitDefinition.getListOfUnits();
for (int j = 0; j < listOfUnits.size(); j++)
{
Unit anUnit = anUnitDefinition.getUnit(j);
int anUnitKind = anUnit.getKind();
string aKind = libsbml.libsbml.UnitKind_toString( anUnitKind );
int anExponent = anUnit.getExponent();
int aScale = anUnit.getScale();
double aMultiplier = anUnit.getMultiplier();
double anOffset = anUnit.getOffset();
UnitStruct unit = new UnitStruct(
aKind,
anExponent,
aScale,
aMultiplier,
anOffset );
unitList.Add( unit );
}
UnitDefinitionStruct unitDefinition = new UnitDefinitionStruct(
anId,
aName,
unitList );
list.Add(unitDefinition);
}
return list;
}
public void TestSBML_Model()
{
SBMLReader reader = new SBMLReader();
SBMLDocument document = reader.readSBML(TestConstant.SBML_Oscillation);
SBML_Model model = new SBML_Model(document.getModel());
// getSpeciesReferenceID
SpeciesStruct ss = new SpeciesStruct();
ss.Compartment = "cell";
ss.ID = "Test1";
ss.Name = "Test1";
string id;
try
{
id = model.getSpeciesReferenceID(ss.ID);
}
catch (Exception)
{
}
model.SpeciesList.Add(ss);
id = model.getSpeciesReferenceID(ss.ID);
Assert.AreEqual("/cell:Test1", id, "getEventID returns unexpected value.");
try
{
model.Level = 1;
id = model.getSpeciesReferenceID(ss.ID);
}
catch (Exception)
{
}
try
{
model.Level = 0;
id = model.getSpeciesReferenceID(ss.ID);
}
catch (Exception)
{
}
// setFunctionDefinitionToDictionary
FunctionDefinitionStruct ud = new FunctionDefinitionStruct();
ud.ID = "Function";
ud.Name = "Function";
ud.Formula = "1 * 2";
model.FunctionDefinitionList.Add(ud);
Type type = model.GetType();
MethodInfo info1 = type.GetMethod("setFunctionDefinitionToDictionary", BindingFlags.NonPublic | BindingFlags.Instance);
info1.Invoke(model, new object[] { });
// getNewUnitValue
MethodInfo info2 = type.GetMethod("getNewUnitValue", BindingFlags.NonPublic | BindingFlags.Instance);
UnitStruct unit = new UnitStruct("Kind", 2, 1, 0.5, 3);
double value = (double)info2.Invoke(model, new object[] { unit });
Assert.AreEqual(28.0d, value, "getNewUnitValue returns unexpected value.");
// convertUnit
model.Level = 2;
value = model.convertUnit("test", 0.1d);
Assert.AreEqual(0.1d, value, "convertUnit returns unexpected value.");
value = model.convertUnit("substance", 1.0d);
Assert.AreEqual(1.0d, value, "convertUnit returns unexpected value.");
model.Level = 1;
value = model.convertUnit("test", 0.1d);
Assert.AreEqual(0.1d, value, "convertUnit returns unexpected value.");
value = model.convertUnit("minute", 1.0d);
Assert.AreEqual(60.0d, value, "convertUnit returns unexpected value.");
try
{
model.Level = 0;
model.convertUnit("test", 0.1d);
}
catch (Exception)
{
}
// getPath
string path;
try
{
path = model.getPath("");
}
catch (Exception)
{
}
path = model.getPath("default");
Assert.AreEqual("/", path, "getPath returns unexpected value.");
}
