/// <summary>
/// Get the compartment ID.
/// </summary>
/// <param name="aCompartment">the compartment object.</param>
/// <returns>the comaprtment ID.</returns>
public string getCompartmentID(CompartmentStruct aCompartment)
{
string aSystemID;
if ( aCompartment.Outside == "" )
{
if ( this.Model.Level == 1 )
aSystemID = "/:" + aCompartment.Name;
else if ( this.Model.Level == 2 )
aSystemID = "/:" + aCompartment.ID;
else
throw new EcellException("Compartment Class needs a ['ID']");
}
else
{
if( this.Model.Level == 1 )
aSystemID = this.Model.getPath(aCompartment.Outside) + ":" + aCompartment.Name;
else if (this.Model.Level == 2)
aSystemID = this.Model.getPath(aCompartment.Outside) + ":" + aCompartment.ID;
else
throw new EcellException("Compartment Class needs a ['ID']");
}
return "System:" + aSystemID;
}
private void setSizeToDictionary(CompartmentStruct aCompartment)
{
string aCompartmentID;
if (this.Model.Level == 1)
aCompartmentID = aCompartment.Name;
else if (this.Model.Level == 2)
aCompartmentID = aCompartment.ID;
else
throw new EcellException();
if (!aCompartment.Volume.Equals(double.NaN))
this.Model.CompartmentSize[aCompartmentID] = aCompartment.Volume;
else
this.Model.CompartmentSize[aCompartmentID] = this.getOutsideSize(aCompartment.Outside);
}
private void setUnitToDictionary(CompartmentStruct aCompartment)
{
string aCompartmentID;
if( this.Model.Level == 1 )
aCompartmentID = aCompartment.Name;
else if( this.Model.Level == 2 )
aCompartmentID = aCompartment.ID;
else
throw new EcellException();
if( aCompartment.Unit != "" )
this.Model.CompartmentUnit[ aCompartmentID ] = aCompartment.Unit;
else
this.Model.CompartmentUnit[ aCompartmentID ] = this.getOutsideUnit( aCompartment.Outside );
}
/// <summary>
/// Get the compartment unit.
/// </summary>
/// <param name="aCompartment">the compartment object.</param>
/// <returns>the compartment unit.</returns>
public string getCompartmentUnit(CompartmentStruct aCompartment)
{
if ( this.Model.Level == 1 )
return this.Model.CompartmentUnit[ aCompartment.Name ];
else if (this.Model.Level == 2)
return this.Model.CompartmentUnit[ aCompartment.ID ];
else
throw new EcellException();
}
/// <summary>
/// Get the compartment size.
/// </summary>
/// <param name="aCompartment">the compartment object.</param>
/// <returns>the compartment size.</returns>
public double getCompartmentSize(CompartmentStruct aCompartment)
{
if (this.Model.Level == 1)
return this.Model.CompartmentSize[aCompartment.Name];
else if (this.Model.Level == 2)
return this.Model.CompartmentSize[aCompartment.ID];
else
throw new EcellException();
}
/// <summary>
/// [ CompartmentStruct ]
/// [[ Id , Name , SpatialDimension , Size , Volume , Unit , Ouside , Constant ]]
/// </summary>
/// <param name="aSBMLmodel"></param>
/// <returns></returns>
public static List<CompartmentStruct> getCompartment(Model aSBMLmodel)
{
List<CompartmentStruct> list = new List<CompartmentStruct>();
ListOfCompartments compartments = aSBMLmodel.getListOfCompartments();
for (int i = 0; i < compartments.size(); i++ )
{
Compartment item = aSBMLmodel.getCompartment(i);
string anId = item.getId();
string aName = item.getName();
long aSpatialDimension = item.getSpatialDimensions();
double aSize = GetCompartmentSize(item);
double aVolume = GetCompartmentVolume(item);
string anUnit = item.getUnits();
string anOutside = item.getOutside();
bool aConstant = item.getConstant();
CompartmentStruct compartment = new CompartmentStruct(
anId,
aName,
aSpatialDimension,
aSize,
aVolume,
anUnit,
anOutside,
aConstant);
list.Add(compartment);
}
return list;
}
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);
}
public void TestSBML_Compartment()
{
SBMLReader reader = new SBMLReader();
SBMLDocument document = reader.readSBML(TestConstant.SBML_Oscillation);
SBML_Model model = new SBML_Model(document.getModel());
SBML_Compartment c = new SBML_Compartment(model);
CompartmentStruct cs = new CompartmentStruct();
try
{
c.getCompartmentID(cs);
}
catch (Exception)
{
}
string id;
cs.Outside = "";
cs.ID = "Test1";
id = c.getCompartmentID(cs);
Assert.AreEqual("System:/:Test1", id, "getCompartmentID returns unexpected value.");
try
{
model.Level = 1;
id = c.getCompartmentID(cs);
}
catch (Exception)
{
}
try
{
model.Level = 0;
id = c.getCompartmentID(cs);
}
catch (Exception)
{
}
model.Level = 2;
cs.Outside = "cell";
id = c.getCompartmentID(cs);
Assert.AreEqual("System:/cell:Test1", id, "getCompartmentID returns unexpected value.");
try
{
model.Level = 1;
id = c.getCompartmentID(cs);
}
catch (Exception)
{
}
try
{
model.Level = 0;
id = c.getCompartmentID(cs);
}
catch (Exception)
{
}
// GetModuleType
Type type = c.GetType();
MethodInfo info1 = type.GetMethod("setSizeToDictionary", BindingFlags.NonPublic | BindingFlags.Instance);
MethodInfo info2 = type.GetMethod("setUnitToDictionary", BindingFlags.NonPublic | BindingFlags.Instance);
try
{
info1.Invoke(c, new object[] { cs });
}
catch (Exception)
{
}
try
{
info2.Invoke(c, new object[] { cs });
}
catch (Exception)
{
}
model.Level = 1;
cs.Volume = double.NaN;
cs.Name = "Test1";
info1.Invoke(c, new object[] { cs });
info2.Invoke(c, new object[] { cs });
// getOutsideSize
model.Level = 2;
MethodInfo info3 = type.GetMethod("getOutsideSize", BindingFlags.NonPublic | BindingFlags.Instance);
double size;
size = (double)info3.Invoke(c, new object[] { "" });
Assert.AreEqual(1.0d, size, "getOutsideSize returns unexpected value.");
size = (double)info3.Invoke(c, new object[] { "cell" });
Assert.AreEqual(1.0d, size, "getOutsideSize returns unexpected value.");
// getOutsideUnit
MethodInfo info4 = type.GetMethod("getOutsideUnit", BindingFlags.NonPublic | BindingFlags.Instance);
string unit;
unit = (string)info4.Invoke(c, new object[] { "" });
Assert.AreEqual("", unit, "getCompartmentSize returns unexpected value.");
unit = (string)info4.Invoke(c, new object[] { "cell" });
Assert.AreEqual("", unit, "getCompartmentSize returns unexpected value.");
// getCompartmentSize
size = c.getCompartmentSize(cs);
Assert.AreEqual(1.0d, size, "getCompartmentSize returns unexpected value.");
model.Level = 1;
size = c.getCompartmentSize(cs);
Assert.AreEqual(1.0d, size, "getCompartmentSize returns unexpected value.");
try
{
model.Level = 0;
size = c.getCompartmentSize(cs);
}
catch (Exception)
{
}
// getCompartmentUnit
model.Level = 2;
id = c.getCompartmentUnit(cs);
Assert.AreEqual(null, id, "getCompartmentUnit returns unexpected value.");
model.Level = 1;
id = c.getCompartmentUnit(cs);
Assert.AreEqual(null, id, "getCompartmentUnit returns unexpected value.");
try
{
model.Level = 0;
id = c.getCompartmentUnit(cs);
}
catch (Exception)
{
}
}
