Examples with LocalParameter cbit.vcell.mapping.ParameterContext.LocalParameter used on opensource projects

Example 16 with LocalParameter

use of cbit.vcell.mapping.ParameterContext.LocalParameter in project vcell by virtualcell.

the class RulebasedTransformer method transform.

private void transform(SimulationContext originalSimContext, SimulationContext transformedSimulationContext, ArrayList<ModelEntityMapping> entityMappings, MathMappingCallback mathMappingCallback) throws PropertyVetoException {
    Model newModel = transformedSimulationContext.getModel();
    Model originalModel = originalSimContext.getModel();
    ModelEntityMapping em = null;
    // list of rules created from the reactions; we apply the symmetry factor computed by bionetgen only to these
    Set<ReactionRule> fromReactions = new HashSet<>();
    for (SpeciesContext newSpeciesContext : newModel.getSpeciesContexts()) {
        final SpeciesContext originalSpeciesContext = originalModel.getSpeciesContext(newSpeciesContext.getName());
        // map new and old species contexts
        em = new ModelEntityMapping(originalSpeciesContext, newSpeciesContext);
        entityMappings.add(em);
        if (newSpeciesContext.hasSpeciesPattern()) {
            // it's perfect already and can't be improved
            continue;
        }
        try {
            MolecularType newmt = newModel.getRbmModelContainer().createMolecularType();
            newModel.getRbmModelContainer().addMolecularType(newmt, false);
            MolecularTypePattern newmtp_sc = new MolecularTypePattern(newmt);
            SpeciesPattern newsp_sc = new SpeciesPattern();
            newsp_sc.addMolecularTypePattern(newmtp_sc);
            newSpeciesContext.setSpeciesPattern(newsp_sc);
            RbmObservable newo = new RbmObservable(newModel, "O0_" + newmt.getName() + "_tot", newSpeciesContext.getStructure(), RbmObservable.ObservableType.Molecules);
            MolecularTypePattern newmtp_ob = new MolecularTypePattern(newmt);
            SpeciesPattern newsp_ob = new SpeciesPattern();
            newsp_ob.addMolecularTypePattern(newmtp_ob);
            newo.addSpeciesPattern(newsp_ob);
            newModel.getRbmModelContainer().addObservable(newo);
            // map new observable to old species context
            em = new ModelEntityMapping(originalSpeciesContext, newo);
            entityMappings.add(em);
        } catch (ModelException e) {
            e.printStackTrace();
            throw new RuntimeException("unable to transform species context: " + e.getMessage());
        } catch (PropertyVetoException e) {
            // TODO Auto-generated catch block
            e.printStackTrace();
        }
    }
    ReactionSpec[] reactionSpecs = transformedSimulationContext.getReactionContext().getReactionSpecs();
    for (ReactionSpec reactionSpec : reactionSpecs) {
        if (reactionSpec.isExcluded()) {
            // we create rules only from those reactions which are not excluded
            continue;
        }
        ReactionStep rs = reactionSpec.getReactionStep();
        String name = rs.getName();
        String mangled = TokenMangler.fixTokenStrict(name);
        mangled = newModel.getReactionName(mangled);
        Kinetics k = rs.getKinetics();
        if (!(k instanceof MassActionKinetics)) {
            throw new RuntimeException("Only Mass Action Kinetics supported at this time, reaction \"" + rs.getName() + "\" uses kinetic law type \"" + rs.getKinetics().getName() + "\"");
        }
        boolean bReversible = rs.isReversible();
        ReactionRule rr = new ReactionRule(newModel, mangled, rs.getStructure(), bReversible);
        fromReactions.add(rr);
        MassActionKinetics massActionKinetics = (MassActionKinetics) k;
        List<Reactant> rList = rs.getReactants();
        List<Product> pList = rs.getProducts();
        // counting the stoichiometry - 2A+B means 3 reactants
        int numReactants = 0;
        for (Reactant r : rList) {
            numReactants += r.getStoichiometry();
            if (numReactants > 2) {
                String message = "NFSim doesn't support more than 2 reactants within a reaction: " + name;
                throw new RuntimeException(message);
            }
        }
        int numProducts = 0;
        for (Product p : pList) {
            numProducts += p.getStoichiometry();
            if (bReversible && numProducts > 2) {
                String message = "NFSim doesn't support more than 2 products within a reversible reaction: " + name;
                throw new RuntimeException(message);
            }
        }
        RateLawType rateLawType = RateLawType.MassAction;
        RbmKineticLaw kineticLaw = new RbmKineticLaw(rr, rateLawType);
        try {
            String forwardRateName = massActionKinetics.getForwardRateParameter().getName();
            Expression forwardRateExp = massActionKinetics.getForwardRateParameter().getExpression();
            String reverseRateName = massActionKinetics.getReverseRateParameter().getName();
            Expression reverseRateExp = massActionKinetics.getReverseRateParameter().getExpression();
            LocalParameter fR = kineticLaw.getLocalParameter(RbmKineticLawParameterType.MassActionForwardRate);
            fR.setName(forwardRateName);
            LocalParameter rR = kineticLaw.getLocalParameter(RbmKineticLawParameterType.MassActionReverseRate);
            rR.setName(reverseRateName);
            if (rs.hasReactant()) {
                kineticLaw.setParameterValue(fR, forwardRateExp, true);
            }
            if (rs.hasProduct()) {
                kineticLaw.setParameterValue(rR, reverseRateExp, true);
            }
            // 
            for (KineticsParameter reaction_p : massActionKinetics.getKineticsParameters()) {
                if (reaction_p.getRole() == Kinetics.ROLE_UserDefined) {
                    LocalParameter rule_p = kineticLaw.getLocalParameter(reaction_p.getName());
                    if (rule_p == null) {
                        // 
                        // after lazy parameter creation we didn't find a user-defined rule parameter with this same name.
                        // 
                        // there must be a global symbol with the same name, that the local reaction parameter has overridden.
                        // 
                        ParameterContext.LocalProxyParameter rule_proxy_parameter = null;
                        for (ProxyParameter proxyParameter : kineticLaw.getProxyParameters()) {
                            if (proxyParameter.getName().equals(reaction_p.getName())) {
                                rule_proxy_parameter = (LocalProxyParameter) proxyParameter;
                            }
                        }
                        if (rule_proxy_parameter != null) {
                            // we want to convert to local
                            boolean bConvertToGlobal = false;
                            kineticLaw.convertParameterType(rule_proxy_parameter, bConvertToGlobal);
                        } else {
                            // could find neither local parameter nor proxy parameter
                            throw new RuntimeException("user defined parameter " + reaction_p.getName() + " from reaction " + rs.getName() + " didn't map to a reactionRule parameter");
                        }
                    } else if (rule_p.getRole() == RbmKineticLawParameterType.UserDefined) {
                        kineticLaw.setParameterValue(rule_p, reaction_p.getExpression(), true);
                        rule_p.setUnitDefinition(reaction_p.getUnitDefinition());
                    } else {
                        throw new RuntimeException("user defined parameter " + reaction_p.getName() + " from reaction " + rs.getName() + " mapped to a reactionRule parameter with unexpected role " + rule_p.getRole().getDescription());
                    }
                }
            }
        } catch (ExpressionException e) {
            e.printStackTrace();
            throw new RuntimeException("Problem attempting to set RbmKineticLaw expression: " + e.getMessage());
        }
        rr.setKineticLaw(kineticLaw);
        KineticsParameter[] kpList = k.getKineticsParameters();
        ModelParameter[] mpList = rs.getModel().getModelParameters();
        ModelParameter mp = rs.getModel().getModelParameter(kpList[0].getName());
        ReactionParticipant[] rpList = rs.getReactionParticipants();
        for (ReactionParticipant p : rpList) {
            if (p instanceof Reactant) {
                int stoichiometry = p.getStoichiometry();
                for (int i = 0; i < stoichiometry; i++) {
                    SpeciesPattern speciesPattern = new SpeciesPattern(rs.getModel(), p.getSpeciesContext().getSpeciesPattern());
                    ReactantPattern reactantPattern = new ReactantPattern(speciesPattern, p.getStructure());
                    rr.addReactant(reactantPattern);
                }
            } else if (p instanceof Product) {
                int stoichiometry = p.getStoichiometry();
                for (int i = 0; i < stoichiometry; i++) {
                    SpeciesPattern speciesPattern = new SpeciesPattern(rs.getModel(), p.getSpeciesContext().getSpeciesPattern());
                    ProductPattern productPattern = new ProductPattern(speciesPattern, p.getStructure());
                    rr.addProduct(productPattern);
                }
            }
        }
        // commented code below is probably obsolete, we verify (above) in the reaction the number of participants,
        // no need to do it again in the corresponding rule
        // if(rr.getReactantPatterns().size() > 2) {
        // String message = "NFSim doesn't support more than 2 reactants within a reaction: " + name;
        // throw new RuntimeException(message);
        // }
        // if(rr.getProductPatterns().size() > 2) {
        // String message = "NFSim doesn't support more than 2 products within a reaction: " + name;
        // throw new RuntimeException(message);
        // }
        newModel.removeReactionStep(rs);
        newModel.getRbmModelContainer().addReactionRule(rr);
    }
    for (ReactionRuleSpec rrs : transformedSimulationContext.getReactionContext().getReactionRuleSpecs()) {
        if (rrs == null) {
            continue;
        }
        ReactionRule rr = rrs.getReactionRule();
        if (rrs.isExcluded()) {
            // delete those rules which are disabled (excluded) in the Specifications / Reaction table
            newModel.getRbmModelContainer().removeReactionRule(rr);
            continue;
        }
    }
    // now that we generated the rules we can delete the reaction steps they're coming from
    for (ReactionStep rs : newModel.getReactionSteps()) {
        newModel.removeReactionStep(rs);
    }
    try {
        // we invoke bngl just for the purpose of generating the xml file, which we'll then use to extract the symmetry factor
        generateNetwork(transformedSimulationContext, fromReactions, mathMappingCallback);
    } catch (ClassNotFoundException | IOException e) {
        // TODO Auto-generated catch block
        e.printStackTrace();
    }
    System.out.println("Finished RuleBased Transformer.");
}

Example 17 with LocalParameter

use of cbit.vcell.mapping.ParameterContext.LocalParameter in project vcell by virtualcell.

the class ITextWriter method writeMembraneMapping.

protected void writeMembraneMapping(Section simContextSection, SimulationContext simContext) throws DocumentException {
    GeometryContext geoContext = simContext.getGeometryContext();
    if (geoContext == null) {
        return;
    }
    Section memMapSection = null;
    Table memMapTable = null;
    StructureMapping[] structMappings = geoContext.getStructureMappings();
    for (int i = 0; i < structMappings.length; i++) {
        MembraneMapping memMapping = null;
        if (structMappings[i] instanceof FeatureMapping) {
            continue;
        } else {
            memMapping = (MembraneMapping) structMappings[i];
        }
        String structName = memMapping.getStructure().getName();
        String initVoltage = "";
        Expression tempExp = memMapping.getInitialVoltageParameter().getExpression();
        VCUnitDefinition tempUnit = memMapping.getInitialVoltageParameter().getUnitDefinition();
        if (tempExp != null) {
            initVoltage = tempExp.infix();
            if (tempUnit != null) {
                initVoltage += "   " + tempUnit.getSymbolUnicode();
            }
        }
        String spCap = "";
        tempExp = memMapping.getSpecificCapacitanceParameter().getExpression();
        tempUnit = memMapping.getSpecificCapacitanceParameter().getUnitDefinition();
        if (tempExp != null) {
            spCap = tempExp.infix();
            if (tempUnit != null) {
                spCap += "   " + tempUnit.getSymbolUnicode();
            }
        }
        if (memMapTable == null) {
            memMapTable = getTable(4, 100, 1, 3, 3);
            memMapTable.addCell(createCell("Electrical Mapping - Membrane Potential", getBold(DEF_HEADER_FONT_SIZE), 4, 1, Element.ALIGN_CENTER, true));
            memMapTable.addCell(createHeaderCell("Membrane", getBold(), 1));
            memMapTable.addCell(createHeaderCell("Calculate V (T/F)", getBold(), 1));
            memMapTable.addCell(createHeaderCell("V initial", getBold(), 1));
            memMapTable.addCell(createHeaderCell("Specific Capacitance", getBold(), 1));
            memMapTable.endHeaders();
        }
        memMapTable.addCell(createCell(structName, getFont()));
        memMapTable.addCell(createCell((memMapping.getCalculateVoltage() ? " T " : " F "), getFont()));
        memMapTable.addCell(createCell(initVoltage, getFont()));
        memMapTable.addCell(createCell(spCap, getFont()));
    }
    if (memMapTable != null) {
        memMapSection = simContextSection.addSection("Membrane Mapping For " + simContext.getName(), simContextSection.numberDepth() + 1);
        memMapSection.add(memMapTable);
    }
    int[] widths = { 1, 1, 1, 5, 8 };
    Table electTable = null;
    ElectricalStimulus[] electricalStimuli = simContext.getElectricalStimuli();
    for (int j = 0; j < electricalStimuli.length; j++) {
        if (j == 0) {
            electTable = getTable(5, 100, 1, 3, 3);
            electTable.addCell(createCell("Electrical Mapping - Electrical Stimulus", getBold(DEF_HEADER_FONT_SIZE), 5, 1, Element.ALIGN_CENTER, true));
            electTable.addCell(createHeaderCell("Stimulus Name", getBold(), 1));
            electTable.addCell(createHeaderCell("Current Name", getBold(), 1));
            electTable.addCell(createHeaderCell("Clamp Type", getBold(), 1));
            electTable.addCell(createHeaderCell("Voltage/Current Density", getBold(), 1));
            electTable.addCell(createHeaderCell("Clamp Device", getBold(), 1));
            electTable.endHeaders();
        }
        String stimName = electricalStimuli[j].getName();
        String currName = "";
        String clampType = "", expStr = "";
        Expression tempExp = null;
        VCUnitDefinition tempUnit = null;
        if (electricalStimuli[j] instanceof CurrentDensityClampStimulus) {
            CurrentDensityClampStimulus stimulus = (CurrentDensityClampStimulus) electricalStimuli[j];
            LocalParameter currentDensityParameter = stimulus.getCurrentDensityParameter();
            tempExp = currentDensityParameter.getExpression();
            tempUnit = currentDensityParameter.getUnitDefinition();
            clampType = "Current Density (deprecated)";
        } else if (electricalStimuli[j] instanceof TotalCurrentClampStimulus) {
            TotalCurrentClampStimulus stimulus = (TotalCurrentClampStimulus) electricalStimuli[j];
            LocalParameter totalCurrentParameter = stimulus.getCurrentParameter();
            tempExp = totalCurrentParameter.getExpression();
            tempUnit = totalCurrentParameter.getUnitDefinition();
            clampType = "Current";
        } else if (electricalStimuli[j] instanceof VoltageClampStimulus) {
            VoltageClampStimulus stimulus = (VoltageClampStimulus) electricalStimuli[j];
            Parameter voltageParameter = stimulus.getVoltageParameter();
            tempExp = voltageParameter.getExpression();
            tempUnit = voltageParameter.getUnitDefinition();
            clampType = "Voltage";
        }
        if (tempExp != null) {
            expStr = tempExp.infix();
            if (tempUnit != null) {
                expStr += "   " + tempUnit.getSymbolUnicode();
            }
        }
        electTable.addCell(createCell(stimName, getFont()));
        electTable.addCell(createCell(currName, getFont()));
        electTable.addCell(createCell(clampType, getFont()));
        electTable.addCell(createCell(expStr, getFont()));
        // add electrode info
        Electrode electrode = electricalStimuli[j].getElectrode();
        if (electrode == null) {
            electTable.addCell(createCell("N/A", getFont()));
        } else {
            Coordinate c = electrode.getPosition();
            String location = c.getX() + ", " + c.getY() + ", " + c.getZ();
            String featureName = electrode.getFeature().getName();
            electTable.addCell(createCell("(" + location + ") in " + featureName, getFont()));
        }
    }
    if (electTable != null) {
        if (memMapSection == null) {
            memMapSection = simContextSection.addSection("Membrane Mapping For " + simContext.getName(), 1);
        }
        electTable.setWidths(widths);
        memMapSection.add(electTable);
    }
    // add temperature
    Table tempTable = getTable(1, 75, 1, 3, 3);
    tempTable.setAlignment(Table.ALIGN_LEFT);
    tempTable.addCell(createCell("Temperature: " + simContext.getTemperatureKelvin() + " K", getFont()));
    if (memMapSection != null) {
        memMapSection.add(tempTable);
    }
}

Example 18 with LocalParameter

use of cbit.vcell.mapping.ParameterContext.LocalParameter in project vcell by virtualcell.

the class ReactionRule method deriveDirectRule.

public static ReactionRule deriveDirectRule(ReactionRule oldRule) throws ExpressionBindingException, PropertyVetoException {
    Model m = oldRule.getModel();
    Structure s = oldRule.getStructure();
    boolean bR = false;
    String newName = oldRule.getDisplayName() + DirectHalf;
    ReactionRule newRule = new ReactionRule(m, newName, s, bR);
    RbmKineticLaw oldLaw = oldRule.getKineticLaw();
    RateLawType rateLawType = oldLaw.getRateLawType();
    if (rateLawType != RateLawType.MassAction) {
        throw new RuntimeException("Only Mass Action Kinetics supported at this time, " + ReactionRule.typeName + " \"" + oldRule.getName() + "\" uses kinetic law type \"" + rateLawType.toString() + "\"");
    }
    RbmKineticLaw newLaw = new RbmKineticLaw(newRule, rateLawType);
    newRule.setKineticLaw(newLaw);
    LocalParameter oldfr = oldLaw.getLocalParameter(RbmKineticLawParameterType.MassActionForwardRate);
    Expression exp = new Expression(oldfr.getExpression());
    newLaw.setLocalParameterValue(RbmKineticLawParameterType.MassActionForwardRate, exp);
    for (ReactantPattern oldrp : oldRule.getReactantPatterns()) {
        SpeciesPattern newsp = new SpeciesPattern(m, oldrp.getSpeciesPattern());
        ReactantPattern newrp = new ReactantPattern(newsp, oldrp.getStructure());
        // don't try to resolve matches or bonds, we want to mirror whatever is in the old rule
        newRule.addReactant(newrp, false, false);
    }
    for (ProductPattern oldpp : oldRule.getProductPatterns()) {
        SpeciesPattern newsp = new SpeciesPattern(m, oldpp.getSpeciesPattern());
        ProductPattern newpp = new ProductPattern(newsp, oldpp.getStructure());
        newRule.addProduct(newpp, false, false);
    }
    newLaw.bind(newRule);
    return newRule;
}

Example 19 with LocalParameter

use of cbit.vcell.mapping.ParameterContext.LocalParameter in project vcell by virtualcell.

the class ReactionRulePropertiesTableModel method isCellEditable.

/**
 * Insert the method's description here.
 * Creation date: (2/24/01 12:27:46 AM)
 * @return boolean
 * @param rowIndex int
 * @param columnIndex int
 */
public boolean isCellEditable(int rowIndex, int columnIndex) {
    if (!bEditable) {
        return false;
    }
    Object o = getValueAt(rowIndex);
    if (!(o instanceof Parameter)) {
        return false;
    }
    Parameter parameter = (Parameter) o;
    if (reactionRule != null && reactionRule.getKineticLaw().getLocalParameter(RbmKineticLawParameterType.MassActionReverseRate) == parameter) {
        if (!reactionRule.isReversible()) {
            // disable Kr if rule is not reversible
            return false;
        }
    }
    switch(columnIndex) {
        case COLUMN_NAME:
            return parameter.isNameEditable();
        case COLUMN_DESCRIPTION:
            return false;
        case COLUMN_IS_GLOBAL:
            // if the parameter is reaction rate param or a ReservedSymbol in the model, it should not be editable
            if ((parameter instanceof LocalParameter) && (((LocalParameter) parameter).getRole() != RbmKineticLaw.RbmKineticLawParameterType.UserDefined)) {
                return false;
            }
            if (parameter instanceof UnresolvedParameter) {
                return false;
            }
            if (parameter instanceof LocalProxyParameter) {
                LocalProxyParameter kpp = (LocalProxyParameter) parameter;
                SymbolTableEntry ste = kpp.getTarget();
                if ((ste instanceof Model.ReservedSymbol) || (ste instanceof SpeciesContext) || (ste instanceof ModelQuantity)) {
                    return false;
                }
            }
            return true;
        case COLUMN_VALUE:
            return parameter.isExpressionEditable();
        case COLUMN_UNITS:
            return parameter.isUnitEditable();
    }
    return false;
}

Example 20 with LocalParameter

use of cbit.vcell.mapping.ParameterContext.LocalParameter in project vcell by virtualcell.

the class ReactionRulePropertiesTableModel method setValueAt.

public void setValueAt(Object aValue, int rowIndex, int columnIndex) {
    Object o = getValueAt(rowIndex);
    if (!(o instanceof Parameter)) {
        return;
    }
    Parameter parameter = (Parameter) o;
    // try {
    switch(columnIndex) {
        case COLUMN_NAME:
            {
                try {
                    if (aValue instanceof String) {
                        String newName = (String) aValue;
                        if (!parameter.getName().equals(newName)) {
                            if (parameter instanceof LocalParameter) {
                                reactionRule.getKineticLaw().renameParameter(parameter.getName(), newName);
                            } else if (parameter instanceof LocalProxyParameter) {
                                parameter.setName(newName);
                            }
                            fireTableRowsUpdated(rowIndex, rowIndex);
                        }
                    }
                } catch (ExpressionException e) {
                    e.printStackTrace(System.out);
                    PopupGenerator.showErrorDialog(ownerTable, "Error changing parameter name:\n" + e.getMessage());
                } catch (PropertyVetoException e) {
                    e.printStackTrace(System.out);
                    PopupGenerator.showErrorDialog(ownerTable, "Error changing parameter name:\n" + e.getMessage());
                }
                break;
            }
        case COLUMN_IS_GLOBAL:
            {
                if (aValue.equals(Boolean.FALSE)) {
                    // check box has been <unset> (<true> to <false>) : change param from global to local
                    if ((parameter instanceof LocalProxyParameter) && ((((LocalProxyParameter) parameter).getTarget() instanceof Model.ReservedSymbol) || (((LocalProxyParameter) parameter).getTarget() instanceof SpeciesContext) || (((LocalProxyParameter) parameter).getTarget() instanceof ModelQuantity))) {
                        PopupGenerator.showErrorDialog(ownerTable, "Parameter : \'" + parameter.getName() + "\' is a " + ((LocalProxyParameter) parameter).getTarget().getClass() + " in the model; cannot convert it to a local kinetic parameter.");
                    } else {
                        try {
                            reactionRule.getKineticLaw().convertParameterType(parameter, false);
                        } catch (PropertyVetoException pve) {
                            pve.printStackTrace(System.out);
                            PopupGenerator.showErrorDialog(ownerTable, "Unable to convert parameter : \'" + parameter.getName() + "\' to local kinetics parameter : " + pve.getMessage());
                        } catch (ExpressionBindingException e) {
                            e.printStackTrace(System.out);
                            PopupGenerator.showErrorDialog(ownerTable, "Unable to convert parameter : \'" + parameter.getName() + "\' to local kinetics parameter : " + e.getMessage());
                        }
                    }
                } else {
                    // check box has been <set> (<false> to <true>) : change param from local to global
                    if ((parameter instanceof LocalParameter) && (((LocalParameter) parameter).getRole() != RbmKineticLaw.RbmKineticLawParameterType.UserDefined)) {
                        PopupGenerator.showErrorDialog(ownerTable, "Parameter : \'" + parameter.getName() + "\' is a pre-defined kinetics parameter (not user-defined); cannot convert it to a model level (global) parameter.");
                    } else {
                        ModelParameter mp = reactionRule.getModel().getModelParameter(parameter.getName());
                        // model already had the model parameter 'param', but check if 'param' value is different from
                        // model parameter with same name. If it is, the local value will be overridden by global (model) param
                        // value, and user should be warned.
                        String choice = "Ok";
                        if (mp != null && !(mp.getExpression().compareEqual(parameter.getExpression()))) {
                            String msgStr = "Model already has a global parameter named : \'" + parameter.getName() + "\'; with value = \'" + mp.getExpression().infix() + "\'; This local parameter \'" + parameter.getName() + "\' with value = \'" + parameter.getExpression().infix() + "\' will be overridden by the global value. \nPress \'Ok' to override " + "local value with global value of \'" + parameter.getName() + "\'. \nPress \'Cancel\' to retain new local value.";
                            choice = PopupGenerator.showWarningDialog(ownerTable, msgStr, new String[] { "Ok", "Cancel" }, "Ok");
                        }
                        if (choice.equals("Ok")) {
                            try {
                                // Now 'parameter' is a local kinetic parameter. If it is not numeric, and if its expression
                                // contains other local kinetic parameters, warn user that 'parameter' cannot be promoted because
                                // of its expression containing other local parameters.
                                boolean bPromoteable = true;
                                if (!parameter.getExpression().isNumeric()) {
                                    String[] symbols = parameter.getExpression().getSymbols();
                                    for (int i = 0; i < symbols.length; i++) {
                                        if (reactionRule.getKineticLaw().getLocalParameter(symbols[i]) != null) {
                                            PopupGenerator.showErrorDialog(ownerTable, "Parameter \'" + parameter.getName() + "\' contains other local kinetic parameters; Cannot convert it to global until the referenced parameters are global.");
                                            bPromoteable = false;
                                        }
                                    }
                                }
                                if (bPromoteable) {
                                    reactionRule.getKineticLaw().convertParameterType(parameter, true);
                                }
                            } catch (PropertyVetoException pve) {
                                pve.printStackTrace(System.out);
                                PopupGenerator.showErrorDialog(ownerTable, "Cannot convert parameter \'" + parameter.getName() + "\' to global parameter : " + pve.getMessage());
                            } catch (ExpressionBindingException e) {
                                e.printStackTrace(System.out);
                                PopupGenerator.showErrorDialog(ownerTable, "Cannot convert parameter \'" + parameter.getName() + "\' to global parameter : " + e.getMessage());
                            }
                        }
                    }
                }
                fireTableRowsUpdated(rowIndex, rowIndex);
                break;
            }
        case COLUMN_VALUE:
            {
                try {
                    if (aValue instanceof ScopedExpression) {
                        // }
                        throw new RuntimeException("unexpected value type ScopedExpression");
                    } else if (aValue instanceof String) {
                        String newExpressionString = (String) aValue;
                        if (parameter instanceof LocalParameter) {
                            LocalParameter localParameter = (LocalParameter) parameter;
                            reactionRule.getKineticLaw().setParameterValue(localParameter, new Expression(newExpressionString), true);
                        } else if (parameter instanceof LocalProxyParameter) {
                            parameter.setExpression(new Expression(newExpressionString));
                        }
                    }
                    reactionRule.getKineticLaw().resolveUndefinedUnits();
                    fireTableRowsUpdated(rowIndex, rowIndex);
                } catch (java.beans.PropertyVetoException e) {
                    e.printStackTrace(System.out);
                    PopupGenerator.showErrorDialog(ownerTable, "Error:\n" + e.getMessage());
                } catch (ExpressionException e) {
                    e.printStackTrace(System.out);
                    PopupGenerator.showErrorDialog(ownerTable, "Expression error:\n" + e.getMessage());
                }
                break;
            }
        case COLUMN_UNITS:
            {
                try {
                    if (aValue instanceof String && parameter instanceof LocalParameter && ((LocalParameter) parameter).getRole() == RbmKineticLaw.RbmKineticLawParameterType.UserDefined) {
                        String newUnitString = (String) aValue;
                        LocalParameter kineticsParm = (LocalParameter) parameter;
                        ModelUnitSystem modelUnitSystem = reactionRule.getModel().getUnitSystem();
                        if (!kineticsParm.getUnitDefinition().getSymbol().equals(newUnitString)) {
                            kineticsParm.setUnitDefinition(modelUnitSystem.getInstance(newUnitString));
                            reactionRule.getKineticLaw().resolveUndefinedUnits();
                            fireTableRowsUpdated(rowIndex, rowIndex);
                        }
                    }
                } catch (VCUnitException e) {
                    e.printStackTrace(System.out);
                    PopupGenerator.showErrorDialog(ownerTable, "Error changing parameter unit:\n" + e.getMessage());
                }
                break;
            }
    }
// }catch (java.beans.PropertyVetoException e){
// e.printStackTrace(System.out);
// }
}