Examples with MathMappingParameter cbit.vcell.mapping.AbstractMathMapping.MathMappingParameter used on opensource projects

Example 1 with MathMappingParameter

use of cbit.vcell.mapping.AbstractMathMapping.MathMappingParameter in project vcell by virtualcell.

the class StructureAnalyzer method refreshTotalDependancies.

/**
 * This method was created by a SmartGuide.
 * @param b cbit.vcell.math.Matrix
 * @param vars java.lang.String[]
 */
private void refreshTotalDependancies() throws Exception {
    // 
    for (int v = 0; v < speciesContextMappings.length; v++) {
        speciesContextMappings[v].setDependencyExpression(null);
    }
    if (totalNullSpaceMatrix == null) {
        // System.out.println("the matrix has full rank, there are no dependencies");
        return;
    }
    if (speciesContextMappings.length != totalNullSpaceMatrix.getNumCols()) {
        throw new Exception("varName array not same dimension as b matrix");
    }
    StructureAnalyzer.Dependency[] dependencies = refreshTotalDependancies(totalNullSpaceMatrix, speciesContextMappings, mathMapping, false);
    VCUnitDefinition totalMassUnit = null;
    boolean bIsSpatial = mathMapping.getSimulationContext().getGeometry().getDimension() > 0;
    ModelUnitSystem modelUnitSystem = mathMapping.getSimulationContext().getModel().getUnitSystem();
    if (this instanceof VolumeStructureAnalyzer) {
        if (!bIsSpatial) {
            // VCUnitDefinition.UNIT_umol_um3_per_L; -> VCell vol substance unit
            totalMassUnit = modelUnitSystem.getVolumeSubstanceUnit();
        } else {
            // VCUnitDefinition.UNIT_uM;
            totalMassUnit = modelUnitSystem.getVolumeConcentrationUnit();
        }
    } else if (this instanceof MembraneStructureAnalyzer) {
        if (!bIsSpatial) {
            // VCUnitDefinition.UNIT_molecules;
            totalMassUnit = modelUnitSystem.getMembraneSubstanceUnit();
        } else {
            // VCUnitDefinition.UNIT_molecules_per_um2;
            totalMassUnit = modelUnitSystem.getMembraneConcentrationUnit();
        }
    }
    for (int i = 0; i < dependencies.length; i++) {
        String constantName = dependencies[i].invariantSymbolName;
        Expression constantExp = dependencies[i].conservedMoietyExpression;
        SpeciesContextMapping firstSCM = dependencies[i].speciesContextMapping;
        Expression exp = dependencies[i].dependencyExpression;
        // 
        // store totalMass parameter (e.g. K_xyz_total = xyz_init + wzy_init)
        // 
        GeometryClass geometryClass = mathMapping.getSimulationContext().getGeometryContext().getStructureMapping(firstSCM.getSpeciesContext().getStructure()).getGeometryClass();
        MathMappingParameter totalMassParameter = mathMapping.addMathMappingParameter(constantName, constantExp.flatten(), DiffEquMathMapping.PARAMETER_ROLE_TOTALMASS, totalMassUnit, geometryClass);
        // 
        // store dependency parameter (e.g. xyz = K_xyz_total - wzy)
        // 
        exp.bindExpression(mathMapping);
        firstSCM.setDependencyExpression(exp);
    }
}