Examples with Parameter cbit.vcell.model.Parameter used on opensource projects

Example 46 with Parameter

use of cbit.vcell.model.Parameter in project vcell by virtualcell.

the class ParticleMathMapping method combineHybrid.

private void combineHybrid() throws MappingException, ExpressionException, MatrixException, MathException, ModelException {
    ArrayList<SpeciesContext> continuousSpecies = new ArrayList<SpeciesContext>();
    ArrayList<ParticleVariable> continuousSpeciesParticleVars = new ArrayList<ParticleVariable>();
    ArrayList<SpeciesContext> stochSpecies = new ArrayList<SpeciesContext>();
    // 
    // categorize speciesContexts as continuous and stochastic
    // 
    SpeciesContextSpec[] scsArray = getSimulationContext().getReactionContext().getSpeciesContextSpecs();
    continuousSpecies = new ArrayList<SpeciesContext>();
    stochSpecies = new ArrayList<SpeciesContext>();
    for (SpeciesContextSpec speciesContextSpec : scsArray) {
        if (!getSimulationContext().isStoch() || speciesContextSpec.isForceContinuous()) {
            continuousSpecies.add(speciesContextSpec.getSpeciesContext());
            Variable variable = getMathSymbolMapping().getVariable(speciesContextSpec.getSpeciesContext());
            if (variable instanceof ParticleVariable) {
                continuousSpeciesParticleVars.add((ParticleVariable) variable);
            }
        } else {
            stochSpecies.add(speciesContextSpec.getSpeciesContext());
        }
    }
    if (continuousSpecies.isEmpty()) {
        return;
    }
    // 
    // create continuous mathDescription ... add stochastic variables and processes to the continuous Math and use this.
    // 
    DiffEquMathMapping mathMapping = new DiffEquMathMapping(getSimulationContext(), callback, networkGenerationRequirements);
    mathMapping.refresh(null);
    MathDescription contMathDesc = mathMapping.getMathDescription();
    // 
    // get list of all continuous variables
    // 
    HashMap<String, Variable> allContinuousVars = new HashMap<String, Variable>();
    Enumeration<Variable> enumVar = contMathDesc.getVariables();
    while (enumVar.hasMoreElements()) {
        Variable var = enumVar.nextElement();
        allContinuousVars.put(var.getName(), var);
    }
    // 
    // replace those continuous variables and equations for stochastic speciesContexts
    // with the particleVariables and particleProperties
    // (ParticleJumpProcesses removed later)
    // 
    ModelUnitSystem unitSystem = getSimulationContext().getModel().getUnitSystem();
    for (SpeciesContext stochSpeciesContext : stochSpecies) {
        Variable contVar = mathMapping.getMathSymbolMapping().getVariable(stochSpeciesContext);
        Variable stochVar = getMathSymbolMapping().getVariable(stochSpeciesContext);
        allContinuousVars.put(stochVar.getName(), stochVar);
        // 
        // replace continuous "concentration" VolVariable/MemVariable for this particle with a Function for concentration
        // 
        allContinuousVars.remove(contVar);
        VCUnitDefinition sizeUnit = unitSystem.getLengthUnit().raiseTo(new RationalNumber(stochSpeciesContext.getStructure().getDimension()));
        VCUnitDefinition stochasticDensityUnit = unitSystem.getStochasticSubstanceUnit().divideBy(sizeUnit);
        VCUnitDefinition continuousDensityUnit = unitSystem.getConcentrationUnit(stochSpeciesContext.getStructure());
        if (stochasticDensityUnit.isEquivalent(continuousDensityUnit)) {
            allContinuousVars.put(contVar.getName(), new Function(contVar.getName(), new Expression(stochVar, getNameScope()), contVar.getDomain()));
        } else {
            Expression conversionFactorExp = getUnitFactor(continuousDensityUnit.divideBy(stochasticDensityUnit));
            allContinuousVars.put(contVar.getName(), new Function(contVar.getName(), Expression.mult(new Expression(stochVar, getNameScope()), conversionFactorExp), contVar.getDomain()));
        }
        // 
        // remove continuous equation
        // 
        Enumeration<SubDomain> contSubDomains = contMathDesc.getSubDomains();
        while (contSubDomains.hasMoreElements()) {
            SubDomain contSubDomain = contSubDomains.nextElement();
            contSubDomain.removeEquation(contVar);
            if (contSubDomain instanceof MembraneSubDomain) {
                ((MembraneSubDomain) contSubDomain).removeJumpCondition(contVar);
            }
        }
        // 
        // remove all continuous variables for speciesContextSpec parameters (e.g. initial conditions, diffusion rates, boundary conditions, velocities)
        // 
        SpeciesContextSpec scs = getSimulationContext().getReactionContext().getSpeciesContextSpec(stochSpeciesContext);
        Parameter[] scsParameters = scs.getParameters();
        for (Parameter parameter : scsParameters) {
            Variable continuousScsParmVariable = mathMapping.getMathSymbolMapping().getVariable(parameter);
            allContinuousVars.remove(continuousScsParmVariable);
        }
        // 
        // copy ParticleJumpProcess and ParticleProperties to the continuous math
        // 
        SubDomain contSubDomain = contMathDesc.getSubDomain(contVar.getDomain().getName());
        SubDomain stochSubDomain = mathDesc.getSubDomain(stochVar.getDomain().getName());
        ParticleProperties particleProperties = stochSubDomain.getParticleProperties(stochVar);
        contSubDomain.addParticleProperties(particleProperties);
    }
    // 
    // add all ParticleJumpProcesses to the continuous model
    // 
    Enumeration<SubDomain> enumStochSubdomains = mathDesc.getSubDomains();
    while (enumStochSubdomains.hasMoreElements()) {
        SubDomain stochSubdomain = enumStochSubdomains.nextElement();
        SubDomain contSubdomain = contMathDesc.getSubDomain(stochSubdomain.getName());
        for (ParticleJumpProcess particleJumpProcess : stochSubdomain.getParticleJumpProcesses()) {
            // 
            // modify "selection list" (particleVariables), probability rate, and actions if referenced particleVariable is to be "forced continuous"
            // 
            ParticleVariable[] selectedParticles = particleJumpProcess.getParticleVariables();
            for (ParticleVariable particleVariable : selectedParticles) {
                if (continuousSpeciesParticleVars.contains(particleVariable)) {
                    particleJumpProcess.remove(particleVariable);
                    JumpProcessRateDefinition jumpProcessRateDefinition = particleJumpProcess.getParticleRateDefinition();
                    if (jumpProcessRateDefinition instanceof MacroscopicRateConstant) {
                        MacroscopicRateConstant macroscopicRateConstant = (MacroscopicRateConstant) jumpProcessRateDefinition;
                        macroscopicRateConstant.setExpression(Expression.mult(macroscopicRateConstant.getExpression(), new Expression(particleVariable, null)));
                    } else if (jumpProcessRateDefinition instanceof InteractionRadius) {
                        throw new MappingException("cannot adjust interaction radius for reaction process " + particleJumpProcess.getName() + ", particle " + particleVariable.getName() + " is continuous");
                    } else {
                        throw new MappingException("rate definition type " + jumpProcessRateDefinition.getClass().getSimpleName() + " not yet implemented for hybrid PDE/Particle math generation");
                    }
                }
                Iterator<Action> iterAction = particleJumpProcess.getActions().iterator();
                while (iterAction.hasNext()) {
                    Action action = iterAction.next();
                    if (continuousSpeciesParticleVars.contains(action.getVar())) {
                        iterAction.remove();
                    }
                }
            }
            if (!particleJumpProcess.getActions().isEmpty()) {
                contSubdomain.addParticleJumpProcess(particleJumpProcess);
            }
        }
    }
    // 
    for (MathMappingParameter mathMappingParameter : fieldMathMappingParameters) {
        if (mathMappingParameter instanceof UnitFactorParameter) {
            String name = mathMappingParameter.getName();
            if (!allContinuousVars.containsKey(name)) {
                allContinuousVars.put(name, newFunctionOrConstant(name, mathMappingParameter.getExpression(), null));
            }
        }
    }
    // 
    // add constants and functions from the particle math that aren't already defined in the continuous math
    // 
    Enumeration<Variable> enumVars = mathDesc.getVariables();
    while (enumVars.hasMoreElements()) {
        Variable var = enumVars.nextElement();
        if (var instanceof Constant || var instanceof Function) {
            String name = var.getName();
            if (!allContinuousVars.containsKey(name)) {
                allContinuousVars.put(name, var);
            }
        }
    }
    contMathDesc.setAllVariables(allContinuousVars.values().toArray(new Variable[0]));
    mathDesc = contMathDesc;
    // 
    for (int i = 0; i < fieldMathMappingParameters.length; i++) {
        if (fieldMathMappingParameters[i] instanceof UnitFactorParameter) {
            GeometryClass geometryClass = fieldMathMappingParameters[i].getGeometryClass();
            Variable variable = newFunctionOrConstant(getMathSymbol(fieldMathMappingParameters[i], geometryClass), getIdentifierSubstitutions(fieldMathMappingParameters[i].getExpression(), fieldMathMappingParameters[i].getUnitDefinition(), geometryClass), fieldMathMappingParameters[i].getGeometryClass());
            if (mathDesc.getVariable(variable.getName()) == null) {
                mathDesc.addVariable(variable);
            }
        }
    }
    if (!mathDesc.isValid()) {
        System.out.println(mathDesc.getVCML_database());
        throw new MappingException("generated an invalid mathDescription: " + mathDesc.getWarning());
    }
    System.out.println("]]]]]]]]]]]]]]]]]]]]]] VCML string begin ]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]");
    System.out.println(mathDesc.getVCML());
    System.out.println("]]]]]]]]]]]]]]]]]]]]]] VCML string end ]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]");
}

Example 47 with Parameter

use of cbit.vcell.model.Parameter in project vcell by virtualcell.

the class RulebasedMathMapping method addStrictMassActionParticleJumpProcess.

private void addStrictMassActionParticleJumpProcess(VariableHash varHash, GeometryClass geometryClass, SubDomain subDomain, ReactionRule reactionRule, String jpName, ArrayList<ParticleVariable> reactantParticles, ArrayList<ParticleVariable> productParticles, ArrayList<Action> forwardActions, ArrayList<Action> reverseActions) throws ExpressionException, ExpressionBindingException, PropertyVetoException, MathException, MappingException {
    String reactionRuleName = reactionRule.getName();
    RbmKineticLaw kinetics = reactionRule.getKineticLaw();
    RulebasedTransformation ruleBasedTransformation = ((RulebasedTransformation) getTransformation());
    if (kinetics.getRateLawType() != RbmKineticLaw.RateLawType.MassAction) {
        throw new RuntimeException("expecting mass action kinetics for reaction rule " + reactionRuleName);
    }
    // 
    // construct stochastic forward or reverse rate expression (separately).  Transform from
    // original expression of "concentrationRate" in terms of rateParameter and reactants/products in concentrations
    // to
    // new stochastic expression of "molecularRate" in terms of forwardRateParameter, reactants/products in molecules, structure sizes, and unit conversions.
    // 
    // (1)  concentrationRate = K * [s0] * [s1]    [uM.s-1]  or   [molecules.um-3.s-1]   or   [molecules.um-2.s-1]  (or other)
    // (2)  molecularRate = P * <s0> * <s1>        [molecules.s-1]
    // 
    // in this math description, we are using <s_i> [molecules], but original kinetics were in [s_i] [uM or molecules.um-2].
    // so through a change in variable to get things in terms of <s_i>.  <<<< Here P is the desired stochastic rate coefficient. >>>
    // 
    // (3)  let [s_i] = <s_i>/structsize(s_i)*unitConversionFactor(substanceunit([s_i])/substanceunit(<s_i>))
    // 
    // in addition to the change in variables, we need to transform the entire expression from concentration/time to molecules/time
    // 
    // (4)  let molecularRate = concentrationRate * structSize(reaction) * unitConversionFactor(substanceunit(molecularRate)/substanceunit(concentrationRate))
    // 
    // (5)  in general, concentationRate = K * PRODUCT([s_i])
    // 
    // change of variables into stochastic variables used in MathDescription, substituting (3) into (5)
    // 
    // (6)  concentrationRate = K * PRODUCT(<s_i>/structsize(s_i)*unitConversionFactor(substanceunit([s_i])/substanceunit(<s_i>)))
    // 
    // reordering to separate the sizes, the unit conversions and the <s_i>
    // 
    // (7)  concentrationRate = K * PRODUCT(<s_i>) * PRODUCT(1/structsize(s_i)) * unitConversionFactor(PRODUCT(substanceunit([s_i])/substanceunit(<s_i>)))
    // 
    // combining (4) and (7)
    // 
    // (8) molecularRate = K * PRODUCT(<s_i>) * PRODUCT(1/structsize(s_i)) * unitConversionFactor(PRODUCT(substanceunit([s_i])/substanceunit(<s_i>))) * structSize(reaction) * unitConversionFactor(substanceunit(molecularRate)/substanceunit(concentrationRate))
    // 
    // collecting terms of sizes and unit conversions
    // 
    // (9)  molecularRate = K * PRODUCT(<s_i>) * structSize(reaction) / PRODUCT(structsize(s_i)) * unitConversionFactor(substanceunit(molecularRate)/substanceunit(concentrationRate) * PRODUCT(substanceunit([s_i])/substanceunit(<s_i>)))
    // 
    // (10) molecularRate = K * PRODUCT(<s_i>) * sizeFactor * unitConversionFactor(substanceConversionUnit)
    // 
    // where
    // 
    // (11) sizeFactor = structSize(reaction) / PRODUCT(structsize(s_i))
    // (12) substanceConversionUnit = substanceunit(molecularRate)/substanceunit(concentrationRate) * PRODUCT(substanceunit([s_i])/substanceunit(<s_i>))
    // 
    // The ParticleJumpCondition wants a single new rate stochastic, P from equation (2).  Note that PRODUCT(<s_i>) will be captured separately the the reactantPatterns.
    // comparing (2) and (10) we have found P.
    // 
    // (13) P = K * sizeFactor * unitConversionFactor(substanceConversionUnit)
    // 
    // the framework also needs the proper unit for P
    // 
    // (14) Unit(P) = Unit(K) * Unit(sizeFactor) * substanceConversionUnit
    // 
    // 
    ModelUnitSystem modelUnitSystem = getSimulationContext().getModel().getUnitSystem();
    VCUnitDefinition stochasticSubstanceUnit = modelUnitSystem.getStochasticSubstanceUnit();
    VCUnitDefinition reactionRuleSubstanceUnit = modelUnitSystem.getSubstanceUnit(reactionRule.getStructure());
    int forwardRuleIndex = 0;
    // 
    // get forward rate parameter and make sure it is constant valued.
    // 
    Parameter forward_rateParameter = kinetics.getLocalParameter(RbmKineticLawParameterType.MassActionForwardRate);
    Expression substitutedForwardRate = MathUtilities.substituteModelParameters(forward_rateParameter.getExpression(), reactionRule.getNameScope().getScopedSymbolTable());
    if (!substitutedForwardRate.flatten().isNumeric()) {
        throw new MappingException("forward rate constant for reaction rule " + reactionRule.getName() + " is not constant");
    }
    // 
    // create forward sizeExp and forward unitFactor
    // 
    VCUnitDefinition forward_substanceConversionUnit = stochasticSubstanceUnit.divideBy(reactionRuleSubstanceUnit);
    VCUnitDefinition forward_sizeFactorUnit = reactionRule.getStructure().getStructureSize().getUnitDefinition();
    Expression forward_sizeFactor = new Expression(reactionRule.getStructure().getStructureSize(), getNameScope());
    for (ReactantPattern reactantPattern : reactionRule.getReactantPatterns()) {
        Expression reactantSizeExp = new Expression(reactantPattern.getStructure().getStructureSize(), getNameScope());
        VCUnitDefinition reactantSizeUnit = reactantPattern.getStructure().getStructureSize().getUnitDefinition();
        VCUnitDefinition reactantSubstanceUnit = modelUnitSystem.getSubstanceUnit(reactantPattern.getStructure());
        forward_sizeFactor = Expression.div(forward_sizeFactor, reactantSizeExp);
        forward_sizeFactorUnit = forward_sizeFactorUnit.divideBy(reactantSizeUnit);
        forward_substanceConversionUnit = forward_substanceConversionUnit.multiplyBy(reactantSubstanceUnit).divideBy(stochasticSubstanceUnit);
    }
    // simplify sizeFactor (often has size/size/size)
    try {
        forward_sizeFactor = RationalExpUtils.getRationalExp(forward_sizeFactor).simplifyAsExpression();
        forward_sizeFactor.bindExpression(getSimulationContext().getModel());
    } catch (ParseException e) {
        e.printStackTrace();
    }
    Expression forward_rateExp = Expression.mult(new Expression(forward_rateParameter, getNameScope()), forward_sizeFactor, getUnitFactor(forward_substanceConversionUnit)).flatten();
    VCUnitDefinition forward_rateUnit = forward_rateParameter.getUnitDefinition().multiplyBy(forward_sizeFactorUnit).multiplyBy(forward_substanceConversionUnit);
    ProbabilityParameter forward_probParm = addProbabilityParameter(PARAMETER_PROBABILITYRATE_PREFIX + jpName, forward_rateExp, PARAMETER_ROLE_P, forward_rateUnit, reactionRule);
    // add probability to function or constant
    varHash.addVariable(newFunctionOrConstant(getMathSymbol(forward_probParm, geometryClass), getIdentifierSubstitutions(forward_rateExp, forward_rateUnit, geometryClass), geometryClass));
    // add forward ParticleJumpProcess
    String forward_name = reactionRuleName;
    Expression forward_rate = getIdentifierSubstitutions(new Expression(forward_probParm, getNameScope()), forward_probParm.getUnitDefinition(), geometryClass);
    JumpProcessRateDefinition forward_rateDefinition = new MacroscopicRateConstant(forward_rate);
    ReactionRuleAnalysisReport rrarBiomodelForward = ruleBasedTransformation.getRulesForwardMap().get(reactionRule);
    ProcessSymmetryFactor forwardSymmetryFactor = new ProcessSymmetryFactor(rrarBiomodelForward.getSymmetryFactor());
    ParticleJumpProcess forward_particleJumpProcess = new ParticleJumpProcess(forward_name, reactantParticles, forward_rateDefinition, forwardActions, forwardSymmetryFactor);
    subDomain.addParticleJumpProcess(forward_particleJumpProcess);
    // 
    for (ReactionRule rr : getSimulationContext().getModel().getRbmModelContainer().getReactionRuleList()) {
        if (rr == reactionRule) {
            break;
        }
        forwardRuleIndex++;
        if (rr.isReversible()) {
            forwardRuleIndex++;
        }
    }
    // 
    if (reactionRule.isReversible()) {
        Parameter reverse_rateParameter = kinetics.getLocalParameter(RbmKineticLawParameterType.MassActionReverseRate);
        if (reverse_rateParameter == null || reverse_rateParameter.getExpression() == null) {
            throw new MappingException("reverse rate constant for reaction rule " + reactionRule.getName() + " is missing");
        }
        {
            Expression substitutedReverseRate = MathUtilities.substituteModelParameters(reverse_rateParameter.getExpression(), reactionRule.getNameScope().getScopedSymbolTable());
            if (!substitutedReverseRate.flatten().isNumeric()) {
                throw new MappingException("reverse rate constant for reaction rule " + reactionRule.getName() + " is not constant");
            }
        }
        // 
        // create reverse sizeExp and reverse unitFactor
        // 
        VCUnitDefinition reverse_substanceConversionUnit = stochasticSubstanceUnit.divideBy(reactionRuleSubstanceUnit);
        VCUnitDefinition reverse_sizeFactorUnit = reactionRule.getStructure().getStructureSize().getUnitDefinition();
        Expression reverse_sizeFactor = new Expression(reactionRule.getStructure().getStructureSize(), getNameScope());
        for (ProductPattern productPattern : reactionRule.getProductPatterns()) {
            Expression reactantSizeExp = new Expression(productPattern.getStructure().getStructureSize(), getNameScope());
            VCUnitDefinition reactantSizeUnit = productPattern.getStructure().getStructureSize().getUnitDefinition();
            VCUnitDefinition reactantSubstanceUnit = modelUnitSystem.getSubstanceUnit(productPattern.getStructure());
            reverse_sizeFactor = Expression.div(reverse_sizeFactor, reactantSizeExp);
            reverse_sizeFactorUnit = reverse_sizeFactorUnit.divideBy(reactantSizeUnit);
            reverse_substanceConversionUnit = reverse_substanceConversionUnit.multiplyBy(reactantSubstanceUnit).divideBy(stochasticSubstanceUnit);
        }
        // simplify sizeFactor (often has size/size/size)
        try {
            reverse_sizeFactor = RationalExpUtils.getRationalExp(reverse_sizeFactor).simplifyAsExpression();
            reverse_sizeFactor.bindExpression(getSimulationContext().getModel());
        } catch (ParseException e) {
            e.printStackTrace();
        }
        Expression reverse_rateExp = Expression.mult(new Expression(reverse_rateParameter, getNameScope()), reverse_sizeFactor, getUnitFactor(reverse_substanceConversionUnit)).flatten();
        VCUnitDefinition reverse_rateUnit = reverse_rateParameter.getUnitDefinition().multiplyBy(reverse_sizeFactorUnit).multiplyBy(reverse_substanceConversionUnit);
        // if the reaction has forward rate (Mass action,HMMs), or don't have either forward or reverse rate (some other rate laws--like general)
        // we process it as forward reaction
        // get jump process name
        ProbabilityParameter reverse_probParm = addProbabilityParameter(PARAMETER_PROBABILITYRATE_PREFIX + jpName + "_reverse", reverse_rateExp, PARAMETER_ROLE_P_reverse, reverse_rateUnit, reactionRule);
        // add probability to function or constant
        varHash.addVariable(newFunctionOrConstant(getMathSymbol(reverse_probParm, geometryClass), getIdentifierSubstitutions(reverse_rateExp, reverse_rateUnit, geometryClass), geometryClass));
        // add reverse ParticleJumpProcess
        Expression reverse_rate = getIdentifierSubstitutions(new Expression(reverse_probParm, getNameScope()), reverse_probParm.getUnitDefinition(), geometryClass);
        String reverse_name = reactionRuleName + "_reverse";
        JumpProcessRateDefinition reverse_rateDefinition = new MacroscopicRateConstant(reverse_rate);
        ReactionRuleAnalysisReport rrarBiomodelReverse = ruleBasedTransformation.getRulesReverseMap().get(reactionRule);
        ProcessSymmetryFactor reverseSymmetryFactor = new ProcessSymmetryFactor(rrarBiomodelReverse.getSymmetryFactor());
        ParticleJumpProcess reverse_particleJumpProcess = new ParticleJumpProcess(reverse_name, productParticles, reverse_rateDefinition, reverseActions, reverseSymmetryFactor);
        subDomain.addParticleJumpProcess(reverse_particleJumpProcess);
        // 
        // check reverse direction mapping and operations with RuleAnalysis.
        // 
        int reverseRuleIndex = forwardRuleIndex + 1;
        ReactionRuleAnalysisReport rrar = ruleBasedTransformation.getRulesReverseMap().get(reactionRule);
        jumpProcessMap.put(reverse_particleJumpProcess, rrar);
    }
}

Example 48 with Parameter

use of cbit.vcell.model.Parameter in project vcell by virtualcell.

the class AbstractStochMathMapping method getSubstitutedExpr.

/**
 * @param expr
 * @param bConcentration
 * @return
 * @throws ExpressionException
 */
protected Expression getSubstitutedExpr(Expression expr, boolean bConcentration, boolean bIsInitialCondn) throws ExpressionException {
    expr = new Expression(expr);
    String[] symbols = expr.getSymbols();
    // Check if 'expr' has other speciesContexts in its expression, need to replace it with 'spContext_init'
    for (int j = 0; symbols != null && j < symbols.length; j++) {
        // if symbol is a speciesContext, replacing it with a reference to initial condition for that speciesContext.
        SpeciesContext spC = null;
        SymbolTableEntry ste = expr.getSymbolBinding(symbols[j]);
        if (ste instanceof ProxyParameter) {
            // if expression is for speciesContextSpec or Kinetics, ste will be a ProxyParameter instance.
            ProxyParameter spspp = (ProxyParameter) ste;
            if (spspp.getTarget() instanceof SpeciesContext) {
                spC = (SpeciesContext) spspp.getTarget();
            }
        } else if (ste instanceof SpeciesContext) {
            // if expression is for a global parameter, ste will be a SpeciesContext instance.
            spC = (SpeciesContext) ste;
        }
        if (spC != null) {
            SpeciesContextSpec spcspec = getSimulationContext().getReactionContext().getSpeciesContextSpec(spC);
            Parameter spCParm = null;
            if (bConcentration && bIsInitialCondn) {
                // speciesContext has initConcentration set, so need to replace 'spContext' in 'expr' 'spContext_init'
                spCParm = spcspec.getParameterFromRole(SpeciesContextSpec.ROLE_InitialConcentration);
            } else if (!bConcentration && bIsInitialCondn) {
                // speciesContext has initCount set, so need to replace 'spContext' in 'expr' 'spContext_initCount'
                spCParm = spcspec.getParameterFromRole(SpeciesContextSpec.ROLE_InitialCount);
            } else if (bConcentration && !bIsInitialCondn) {
                // need to replace 'spContext' in 'expr' 'spContext_Conc'
                spCParm = getSpeciesConcentrationParameter(spC);
            } else if (!bConcentration && !bIsInitialCondn) {
                // need to replace 'spContext' in 'expr' 'spContext_Count'
                spCParm = getSpeciesCountParameter(spC);
            }
            // need to get init condn expression, but can't get it from getMathSymbol() (mapping between bio and math), hence get it as below.
            Expression scsInitExpr = new Expression(spCParm, getNameScope());
            // scsInitExpr.bindExpression(this);
            expr.substituteInPlace(new Expression(spC.getName()), scsInitExpr);
        }
    }
    return expr;
}

Example 49 with Parameter

use of cbit.vcell.model.Parameter in project vcell by virtualcell.

the class BioModelParametersPanel method deleteButtonPressed.

protected void deleteButtonPressed() {
    try {
        int[] rows = parametersFunctionsTable.getSelectedRows();
        if (rows == null) {
            return;
        }
        String deleteListText = "";
        ArrayList<Parameter> deleteList = new ArrayList<Parameter>();
        for (int r : rows) {
            if (r < parametersFunctionsTableModel.getRowCount()) {
                EditableSymbolTableEntry parameter = parametersFunctionsTableModel.getValueAt(r);
                if (parameter instanceof ModelParameter) {
                    ModelParameter modelParameter = (ModelParameter) parameter;
                    deleteList.add(modelParameter);
                    deleteListText += "\tGlobal Parameter " + modelParameter.getName() + "\n";
                }
                if (parameter instanceof SimulationContextParameter) {
                    SimulationContextParameter simulationContextParameter = (SimulationContextParameter) parameter;
                    deleteList.add(simulationContextParameter);
                    deleteListText += "\tApplication(" + simulationContextParameter.getSimulationContext().getName() + ") Parameter " + simulationContextParameter.getName() + "\n";
                }
            }
        }
        String confirm = PopupGenerator.showOKCancelWarningDialog(this, "Deleting global and/or application parameters", "You are going to delete the following global/application parameter(s):\n\n " + deleteListText + "\n Continue?");
        if (confirm.equals(UserMessage.OPTION_CANCEL)) {
            return;
        }
        for (Parameter param : deleteList) {
            if (param instanceof ModelParameter) {
                bioModel.getModel().removeModelParameter((ModelParameter) param);
            }
            if (param instanceof SimulationContextParameter) {
                SimulationContextParameter simContextParameter = (SimulationContextParameter) param;
                SimulationContext simContext = simContextParameter.getSimulationContext();
                simContext.removeSimulationContextParameter(simContextParameter);
            }
        }
    } catch (Exception ex) {
        ex.printStackTrace();
        DialogUtils.showErrorDialog(this, ex.getMessage());
    }
}

Example 50 with Parameter

use of cbit.vcell.model.Parameter in project vcell by virtualcell.

the class ReactionRulePropertiesTableModel method propertyChange.

/**
 * This method gets called when a bound property is changed.
 * @param evt A PropertyChangeEvent object describing the event source
 *   and the property that has changed.
 */
public void propertyChange(java.beans.PropertyChangeEvent evt) {
    if (evt.getSource() == this && evt.getPropertyName().equals("reactionRule")) {
        ReactionRule oldValue = (ReactionRule) evt.getOldValue();
        if (oldValue != null) {
            oldValue.removePropertyChangeListener(this);
            oldValue.getKineticLaw().removePropertyChangeListener(this);
            for (int i = 0; i < oldValue.getKineticLaw().getLocalParameters().length; i++) {
                oldValue.getKineticLaw().getLocalParameters()[i].removePropertyChangeListener(this);
            }
            for (int i = 0; i < oldValue.getKineticLaw().getProxyParameters().length; i++) {
                oldValue.getKineticLaw().getProxyParameters()[i].removePropertyChangeListener(this);
            }
        }
        ReactionRule newValue = (ReactionRule) evt.getNewValue();
        if (newValue != null) {
            newValue.addPropertyChangeListener(this);
            newValue.getKineticLaw().addPropertyChangeListener(this);
            for (int i = 0; i < newValue.getKineticLaw().getLocalParameters().length; i++) {
                newValue.getKineticLaw().getLocalParameters()[i].addPropertyChangeListener(this);
            }
            for (int i = 0; i < newValue.getKineticLaw().getProxyParameters().length; i++) {
                newValue.getKineticLaw().getProxyParameters()[i].addPropertyChangeListener(this);
            }
            autoCompleteSymbolFilter = reactionRule.getAutoCompleteSymbolFilter();
        }
        refreshData();
    }
    if (evt.getSource() == reactionRule && evt.getPropertyName().equals(ReactionRule.PROPERTY_NAME_KINETICLAW)) {
        RbmKineticLaw oldValue = (RbmKineticLaw) evt.getOldValue();
        if (oldValue != null) {
            oldValue.removePropertyChangeListener(this);
            for (int i = 0; i < oldValue.getLocalParameters().length; i++) {
                oldValue.getLocalParameters()[i].removePropertyChangeListener(this);
            }
            for (int i = 0; i < oldValue.getProxyParameters().length; i++) {
                oldValue.getProxyParameters()[i].removePropertyChangeListener(this);
            }
        }
        RbmKineticLaw newValue = (RbmKineticLaw) evt.getNewValue();
        if (newValue != null) {
            newValue.addPropertyChangeListener(this);
            for (int i = 0; i < newValue.getLocalParameters().length; i++) {
                newValue.getLocalParameters()[i].addPropertyChangeListener(this);
            }
            for (int i = 0; i < newValue.getProxyParameters().length; i++) {
                newValue.getProxyParameters()[i].addPropertyChangeListener(this);
            }
        }
        refreshData();
    }
    if (evt.getSource() instanceof RbmKineticLaw && (evt.getPropertyName().equals("localParameters") || evt.getPropertyName().equals("proxyParameters"))) {
        Parameter[] oldParams = (Parameter[]) evt.getOldValue();
        Parameter[] newParams = (Parameter[]) evt.getNewValue();
        for (int i = 0; oldParams != null && i < oldParams.length; i++) {
            oldParams[i].removePropertyChangeListener(this);
        }
        for (int i = 0; newParams != null && i < newParams.length; i++) {
            newParams[i].addPropertyChangeListener(this);
        }
        refreshData();
    }
    if (evt.getSource() instanceof LocalParameter || evt.getSource() instanceof LocalProxyParameter) {
        refreshData();
    }
    if (evt.getSource() instanceof Parameter) {
        fireTableRowsUpdated(0, getRowCount() - 1);
    }
}