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

Example 6 with SpeciesContextMapping

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

the class StructureAnalyzer method substituteIntoFastSystem.

/**
 * This method was created in VisualAge.
 */
private void substituteIntoFastSystem() throws Exception {
    // 
    for (int j = 0; j < speciesContextMappings.length; j++) {
        if (speciesContextMappings[j].getDependencyExpression() != null) {
            Expression dependentVar = new Expression(speciesContextMappings[j].getSpeciesContext(), mathMapping_4_8.getNameScope());
            Expression dependentExp = new Expression(speciesContextMappings[j].getDependencyExpression());
            // System.out.println("trying to substitute '"+dependentExp.toString()+"' for variable '"+dependentVar.toString()+"'");
            for (int i = 0; i < fastSpeciesContextMappings.length; i++) {
                SpeciesContextMapping scm = fastSpeciesContextMappings[i];
                if (scm.getFastInvariant() != null) {
                    scm.getFastInvariant().substituteInPlace(dependentVar, dependentExp);
                    scm.setFastInvariant(scm.getFastInvariant().flatten());
                } else {
                    scm.getFastRate().substituteInPlace(dependentVar, dependentExp);
                    scm.setFastRate(scm.getFastRate().flatten());
                }
            }
        }
    }
// for (int i=0;i<fastSpeciesContextMappings.length;i++){
// SpeciesContextMapping scm = fastSpeciesContextMappings[i];
// if (scm.fastInvariant!=null){
// System.out.println("fastInvariant for "+scm.getSpeciesContext().getName()+" = "+scm.fastInvariant.toString());
// }else{
// System.out.println("fastRate for "+scm.getSpeciesContext().getName()+" = "+scm.fastRate.toString());
// }
// }
}

Example 7 with SpeciesContextMapping

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

the class StructureAnalyzer method refreshFastSystem.

/**
 * Find which species are fast-independent, use their rates as the "fastRate"s.
 * null space rows correspond to "fastInvariant".
 */
private void refreshFastSystem() throws Exception {
    // 
    for (int v = 0; v < fastSpeciesContextMappings.length; v++) {
        fastSpeciesContextMappings[v].setFastInvariant(null);
    }
    if (fastNullSpaceMatrix == null) {
        // System.out.println("the fast matrix has full rank, there are no fast invariants");
        return;
    }
    if (fastSpeciesContextMappings.length != fastNullSpaceMatrix.getNumCols()) {
        throw new Exception("varName array not same dimension as b matrix");
    }
    StructureAnalyzer.Dependency[] dependencies = refreshTotalDependancies(fastNullSpaceMatrix, fastSpeciesContextMappings, mathMapping_4_8, true);
    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 fastInvariant (e.g. (K_fast_total= xyz + wzy)
        // 
        constantExp.bindExpression(mathMapping_4_8);
        firstSCM.setFastInvariant(constantExp.flatten());
    }
}

Example 8 with SpeciesContextMapping

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

the class MathMapping_4_8 method getResolvedVolVariable.

/**
 * Find the defined variable (VolVariable) for the resolved compartments.
 * This method is used to assure only one variable is created.
 * @return cbit.vcell.math.VolVariable
 * @param species cbit.vcell.model.Species
 */
private VolVariable getResolvedVolVariable(Species species) {
    Enumeration<SpeciesContextMapping> enum1 = getSpeciesContextMappings();
    while (enum1.hasMoreElements()) {
        SpeciesContextMapping scm = enum1.nextElement();
        if (scm.getSpeciesContext().getSpecies() == species) {
            Variable var = scm.getVariable();
            if (var instanceof VolVariable) {
                Structure structure = scm.getSpeciesContext().getStructure();
                StructureMapping sm = simContext.getGeometryContext().getStructureMapping(structure);
                if (structure instanceof Feature && getResolved(sm)) {
                    return (VolVariable) var;
                }
            }
        }
    }
    return new VolVariable(TokenMangler.fixTokenStrict(species.getCommonName()), nullDomain);
}

Example 9 with SpeciesContextMapping

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

the class MathMapping_4_8 method refreshVariables.

/**
 * This method was created in VisualAge.
 */
private void refreshVariables() throws MappingException {
    // System.out.println("MathMapping.refreshVariables()");
    // 
    // non-constant dependent variables require a function
    // 
    Enumeration<SpeciesContextMapping> enum1 = getSpeciesContextMappings();
    while (enum1.hasMoreElements()) {
        SpeciesContextMapping scm = enum1.nextElement();
        SpeciesContextSpec scs = simContext.getReactionContext().getSpeciesContextSpec(scm.getSpeciesContext());
        if (scm.getDependencyExpression() != null && !scs.isConstant()) {
            // scm.setVariable(new Function(scm.getSpeciesContext().getName(),scm.getDependencyExpression()));
            scm.setVariable(null);
        }
    }
    enum1 = getSpeciesContextMappings();
    while (enum1.hasMoreElements()) {
        SpeciesContextMapping scm = enum1.nextElement();
        SpeciesContextSpec scs = simContext.getReactionContext().getSpeciesContextSpec(scm.getSpeciesContext());
        if (getSimulationContext().hasEventAssignment(scs.getSpeciesContext())) {
            scm.setDependencyExpression(null);
        }
    }
    // 
    // non-constant independent variables require either a membrane or volume variable
    // 
    enum1 = getSpeciesContextMappings();
    while (enum1.hasMoreElements()) {
        SpeciesContextMapping scm = (SpeciesContextMapping) enum1.nextElement();
        SpeciesContextSpec scs = simContext.getReactionContext().getSpeciesContextSpec(scm.getSpeciesContext());
        if (scm.getDependencyExpression() == null && (!scs.isConstant() || getSimulationContext().hasEventAssignment(scs.getSpeciesContext()))) {
            StructureMapping sm = simContext.getGeometryContext().getStructureMapping(scm.getSpeciesContext().getStructure());
            Structure struct = scm.getSpeciesContext().getStructure();
            if (struct instanceof Feature) {
                if (getResolved(sm)) {
                    scm.setVariable(getResolvedVolVariable(scm.getSpeciesContext().getSpecies()));
                } else {
                    scm.setVariable(new VolVariable(scm.getSpeciesContext().getName(), nullDomain));
                }
            } else if (struct instanceof Membrane) {
                if (getResolved(sm)) {
                    scm.setVariable(new MemVariable(scm.getSpeciesContext().getName(), nullDomain));
                } else {
                    scm.setVariable(new VolVariable(scm.getSpeciesContext().getName(), nullDomain));
                }
            } else {
                throw new MappingException("class " + scm.getSpeciesContext().getStructure().getClass() + " not supported");
            }
            mathSymbolMapping.put(scm.getSpeciesContext(), scm.getVariable().getName());
        }
    }
}

Example 10 with SpeciesContextMapping

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

the class MathMapping_4_8 method refreshSpeciesContextMappings.

/**
 * This method was created in VisualAge.
 */
private void refreshSpeciesContextMappings() throws ExpressionException, MappingException, MathException {
    // 
    // create a SpeciesContextMapping for each speciesContextSpec.
    // 
    // set initialExpression from SpeciesContextSpec.
    // set diffusing
    // set variable (only if "Constant" or "Function", else leave it as null)
    // 
    speciesContextMappingList.removeAllElements();
    SpeciesContextSpec[] speciesContextSpecs = simContext.getReactionContext().getSpeciesContextSpecs();
    for (int i = 0; i < speciesContextSpecs.length; i++) {
        SpeciesContextSpec scs = speciesContextSpecs[i];
        SpeciesContextMapping scm = new SpeciesContextMapping(scs.getSpeciesContext());
        scm.setPDERequired(simContext.isPDERequired(scs.getSpeciesContext()));
        scm.setHasEventAssignment(simContext.hasEventAssignment(scs.getSpeciesContext()));
        scm.setHasHybridReaction(false);
        for (ReactionSpec reactionSpec : getSimulationContext().getReactionContext().getReactionSpecs()) {
            if (!reactionSpec.isExcluded() && reactionSpec.hasHybrid(getSimulationContext(), scs.getSpeciesContext())) {
                scm.setHasHybridReaction(true);
            }
        }
        // scm.setAdvecting(isAdvectionRequired(scs.getSpeciesContext()));
        if (scs.isConstant()) {
            Expression initCond = scs.getInitialConditionParameter() == null ? null : scs.getInitialConditionParameter().getExpression();
            scm.setDependencyExpression(initCond);
        // //
        // // determine if a Function is necessary
        // //
        // boolean bNeedFunction = false;
        // if (initCond.getSymbols()!=null){
        // bNeedFunction = true;
        // }
        // if (bNeedFunction){
        // scm.setVariable(new Function(scm.getSpeciesContext().getName(),initCond));
        // }else{
        // scm.setVariable(new Constant(scm.getSpeciesContext().getName(),initCond));
        // }
        }
        // 
        // test if participant in fast reaction step, request elimination if possible
        // 
        scm.setFastParticipant(false);
        ReactionSpec[] reactionSpecs = simContext.getReactionContext().getReactionSpecs();
        for (int j = 0; j < reactionSpecs.length; j++) {
            ReactionSpec reactionSpec = reactionSpecs[j];
            if (reactionSpec.isExcluded()) {
                continue;
            }
            ReactionStep rs = reactionSpec.getReactionStep();
            if (rs instanceof SimpleReaction && rs.countNumReactionParticipants(scs.getSpeciesContext()) > 0) {
                if (reactionSpec.isFast()) {
                    scm.setFastParticipant(true);
                }
            }
        }
        speciesContextMappingList.addElement(scm);
    }
}