Examples with FilamentRegionEquation cbit.vcell.math.FilamentRegionEquation used on opensource projects

Example 1 with FilamentRegionEquation

use of cbit.vcell.math.FilamentRegionEquation in project vcell by virtualcell.

the class ModelOptimizationSpec method fromMath.

/**
 * Insert the method's description here.
 * Creation date: (11/1/2005 8:11:32 PM)
 * @return cbit.vcell.mapping.MathSystemHash
 * @param mathDesc cbit.vcell.math.MathDescription
 */
private static MathSystemHash fromMath(cbit.vcell.math.MathDescription mathDesc) {
    MathSystemHash hash = new MathSystemHash();
    hash.addSymbol(new MathSystemHash.IndependentVariable("t"));
    hash.addSymbol(new MathSystemHash.IndependentVariable("x"));
    hash.addSymbol(new MathSystemHash.IndependentVariable("y"));
    hash.addSymbol(new MathSystemHash.IndependentVariable("z"));
    Variable[] vars = (Variable[]) BeanUtils.getArray(mathDesc.getVariables(), Variable.class);
    for (int i = 0; i < vars.length; i++) {
        hash.addSymbol(new MathSystemHash.Variable(vars[i].getName(), vars[i].getExpression()));
    }
    SubDomain[] subDomains = (SubDomain[]) BeanUtils.getArray(mathDesc.getSubDomains(), SubDomain.class);
    for (int i = 0; i < subDomains.length; i++) {
        Equation[] equations = (Equation[]) BeanUtils.getArray(subDomains[i].getEquations(), Equation.class);
        for (int j = 0; j < equations.length; j++) {
            MathSystemHash.Variable var = (MathSystemHash.Variable) hash.getSymbol(equations[j].getVariable().getName());
            hash.addSymbol(new MathSystemHash.VariableInitial(var, equations[j].getInitialExpression()));
            if (equations[j] instanceof PdeEquation) {
                // hash.addSymbol(new MathSystemHash.VariableDerivative(var,pde.getRateExpression()));
                throw new RuntimeException("MathSystemHash doesn't yet support spatial models");
            } else if (equations[j] instanceof VolumeRegionEquation) {
                // hash.addSymbol(new MathSystemHash.VariableDerivative(var,vre.getRateExpression()));
                throw new RuntimeException("MathSystemHash doesn't yet support spatial models");
            } else if (equations[j] instanceof MembraneRegionEquation) {
                // hash.addSymbol(new MathSystemHash.VariableDerivative(var,mre.getRateExpression()));
                throw new RuntimeException("MathSystemHash doesn't yet support spatial models");
            } else if (equations[j] instanceof FilamentRegionEquation) {
                // hash.addSymbol(new MathSystemHash.VariableDerivative(var,fre.getRateExpression()));
                throw new RuntimeException("MathSystemHash doesn't yet support spatial models");
            } else if (equations[j] instanceof OdeEquation) {
                OdeEquation ode = (OdeEquation) equations[j];
                hash.addSymbol(new MathSystemHash.VariableDerivative(var, ode.getRateExpression()));
            }
        }
    }
    return hash;
}