Examples with DiffusionDummyReactionStep cbit.vcell.mapping.DiffusionDummyReactionStep used on opensource projects

Example 1 with DiffusionDummyReactionStep

use of cbit.vcell.mapping.DiffusionDummyReactionStep in project vcell by virtualcell.

the class StructureAnalyzer method refreshTotalSpeciesContextMappings.

/**
 * This method was created in VisualAge.
 */
private void refreshTotalSpeciesContextMappings() throws java.beans.PropertyVetoException {
    if (structures == null) {
        return;
    }
    // System.out.println("StructureAnalyzer.refreshSpeciesContextMappings()");
    // GeometryContext geoContext = mathMapping.getSimulationContext().getGeometryContext();
    Model model = mathMapping_4_8.getSimulationContext().getReactionContext().getModel();
    // 
    // note, the order of species is specified such that the first species have priority
    // when the null space is solved for dependent variables.  So the order of priority
    // for elimination are as follows:
    // 
    // 1) Species involved with fast reactions.
    // 2) Species not involved with fast reactions.
    // 
    Vector<SpeciesContextMapping> scmList = new Vector<SpeciesContextMapping>();
    // 
    for (int i = 0; i < structures.length; i++) {
        SpeciesContext[] speciesContexts = model.getSpeciesContexts(structures[i]);
        for (int j = 0; j < speciesContexts.length; j++) {
            SpeciesContext sc = speciesContexts[j];
            SpeciesContextMapping scm = mathMapping_4_8.getSpeciesContextMapping(sc);
            SpeciesContextSpec scs = mathMapping_4_8.getSimulationContext().getReactionContext().getSpeciesContextSpec(sc);
            if (scm.isFastParticipant() && !scs.isConstant()) {
                scmList.addElement(scm);
            }
        }
    }
    // 
    for (int i = 0; i < structures.length; i++) {
        SpeciesContext[] speciesContexts = model.getSpeciesContexts(structures[i]);
        for (int j = 0; j < speciesContexts.length; j++) {
            SpeciesContext sc = speciesContexts[j];
            SpeciesContextMapping scm = mathMapping_4_8.getSpeciesContextMapping(sc);
            SpeciesContextSpec scs = mathMapping_4_8.getSimulationContext().getReactionContext().getSpeciesContextSpec(sc);
            if (!scm.isFastParticipant() && !scs.isConstant()) {
                scmList.addElement(scm);
            }
        }
    }
    if (scmList.size() > 0) {
        speciesContextMappings = new SpeciesContextMapping[scmList.size()];
        scmList.copyInto(speciesContextMappings);
        for (int i = 0; i < speciesContextMappings.length; i++) {
            speciesContextMappings[i].setRate(new Expression(0.0));
        // System.out.println("speciesContextMappings["+i+"] = "+speciesContextMappings[i].getSpeciesContext().getName());
        }
    } else {
        speciesContextMappings = null;
    }
    // System.out.println("StructureAnalyzer.refreshTotalSpeciesContextMapping(), speciesContextMappings.length = "+scmList.size());
    // 
    // get all reactionSteps associated with these structures
    // 
    Vector<ReactionStep> rsList = new Vector<ReactionStep>();
    ReactionSpec[] allReactionSpecs = mathMapping_4_8.getSimulationContext().getReactionContext().getReactionSpecs();
    for (int i = 0; i < allReactionSpecs.length; i++) {
        if (allReactionSpecs[i].isExcluded()) {
            continue;
        }
        ReactionStep rs = allReactionSpecs[i].getReactionStep();
        for (int j = 0; j < structures.length; j++) {
            if (rs.getStructure() == structures[j]) {
                rsList.addElement(rs);
            }
        }
    }
    // 
    for (int i = 0; i < scmList.size(); i++) {
        SpeciesContextMapping scm = (SpeciesContextMapping) scmList.elementAt(i);
        if (scm.isPDERequired()) {
            rsList.addElement(new DiffusionDummyReactionStep("DiffusionDummyReactionStep" + i, model, scm.getSpeciesContext().getStructure(), scm.getSpeciesContext()));
        }
        if (scm.hasEventAssignment()) {
            rsList.addElement(new EventDummyReactionStep("EventDummyReactionStep" + i, model, scm.getSpeciesContext().getStructure(), scm.getSpeciesContext()));
        }
        if (scm.hasHybridReaction()) {
            rsList.addElement(new HybridDummyReactionStep("HybridDummyReactionStep" + i, model, scm.getSpeciesContext().getStructure(), scm.getSpeciesContext()));
        }
        SimulationContext simContext = mathMapping_4_8.getSimulationContext();
        if (simContext.isStoch() && simContext.getGeometry().getDimension() > 0 && !simContext.getReactionContext().getSpeciesContextSpec(scm.getSpeciesContext()).isForceContinuous()) {
            rsList.addElement(new ParticleDummyReactionStep("ParticleDummyReactionStep" + i, model, scm.getSpeciesContext().getStructure(), scm.getSpeciesContext()));
        }
    }
    if (rsList.size() > 0) {
        reactionSteps = new ReactionStep[rsList.size()];
        rsList.copyInto(reactionSteps);
    } else {
        reactionSteps = null;
    }
// System.out.println("StructureAnalyzer.refreshTotalSpeciesContextMapping(), reactionSteps.length = "+scmList.size());
}