public void AddProperties(SpeciesType st, Compartment c, Double iA,
Double iC, String sU, Boolean hOSU, Boolean bC, Boolean con)
{
this.speciesType = st;
this.compartment = c;
this.initialAmount = iA;
this.initialConcentration = iC;
this.substanceUnits = sU;
this.hasOnlySubstanceUnits = hOSU;
this.boundaryCondition = bC;
this.constant = con;
// Set an inital value based on whether we have a concentration or amount
// Used as an optimisation in the model for boundaryCondition species
if (this.initialAmount == -1d)
{
this.initialValue = this.initialConcentration;
}
else
{
this.initialValue = this.initialAmount;
}
}
public void AddProperties(CompartmentType cType, int sD, double size,
String units, Compartment outside, Boolean constant)
{
this.compartmentType = cType;
this.spatialDimensions = sD;
this.size = size;
this.outside = outside;
this.constant = constant;
}
public void CompartmentElement(Hashtable attrs)
{
Compartment compartment = new Compartment(attrs);
CompartmentType compartmentType = null;
int spatialDimensions = 3;
double size = 1;
String units = null; // unit enum or user-defined unit
Compartment outside = null;
Boolean constant = true;
if (attrs.ContainsKey("constant"))
{
constant = Boolean.Parse((String)attrs["constant"]);
}
if (attrs.ContainsKey("spatialdimensions"))
{
spatialDimensions = (int)(Int32.Parse((String)attrs["spatialdimensions"]));
}
if (attrs.ContainsKey("size"))
{
size = (double)(double.Parse((String)attrs["size"]));
}
else if (attrs.ContainsKey("volume")) // from SBML Level 1
{
size = (double)(double.Parse((String)attrs["volume"]));
}
if (attrs.ContainsKey("units") && this.model.IsUnits((String)attrs["units"]))
{
units = (String)attrs["units"];
}
else
{
switch (spatialDimensions)
{
case 1:
units = "length";
break;
case 2:
units = "area";
break;
case 3:
units = "volume";
break;
}
}
if (attrs.ContainsKey("compartmenttype"))
{
String cTypeId = (String)attrs["compartmenttype"];
compartmentType = (CompartmentType)this.model.findObject(cTypeId);
}
if (attrs.ContainsKey("outside"))
{
String cId = (String)attrs["outside"];
outside = (Compartment)this.model.findObject(cId);
}
compartment.AddProperties(compartmentType, spatialDimensions, size,
units, outside, constant);
if (compartment.ID != null)
{
this.model.AddId(compartment.ID, compartment);
}
this.model.listOfCompartments.Add(compartment);
}
