Examples with VCUnitException cbit.vcell.units.VCUnitException used on opensource projects

Example 1 with VCUnitException

use of cbit.vcell.units.VCUnitException in project vcell by virtualcell.

the class VCUnitEvaluator method computeUnit.

// public VCUnitDefinition computeUnit(VCUnitDefinition units []) throws VCUnitException {
// return computeUnit(units, false);
// }
public VCUnitDefinition computeUnit(SimpleNode parent, VCUnitDefinition[] units, boolean assignTBDs) throws VCUnitException {
    if (units == null || units.length == 0)
        return null;
    VCUnitDefinition unit = unitSystem.getInstance_TBD();
    boolean first = true;
    for (int i = 0; i < units.length; i++) {
        if (units[i].isTBD()) {
            continue;
        } else {
            if (first) {
                unit = units[i];
                first = false;
                continue;
            }
        }
        if (!unit.isEquivalent(units[i])) {
            throw new VCUnitException("Incompatible units [" + unit.getSymbol() + "] and [" + units[i].getSymbol() + "] in Expression: " + parent.infixString(SimpleNode.LANGUAGE_DEFAULT));
        }
    }
    if (assignTBDs && unit != null) {
        for (int i = 0; i < units.length; i++) {
            if (units[i].isTBD()) {
                units[i] = unit;
            }
        }
    }
    return unit;
}

Example 2 with VCUnitException

use of cbit.vcell.units.VCUnitException in project vcell by virtualcell.

the class Model method gatherIssues.

/**
 * Insert the method's description here.
 * Creation date: (5/12/2004 10:38:12 PM)
 * @param issueList java.util.Vector
 */
public void gatherIssues(IssueContext issueContext, List<Issue> issueList) {
    issueContext = issueContext.newChildContext(ContextType.Model, this);
    // 
    try {
        for (ModelParameter modelParameter : fieldModelParameters) {
            Expression exp = modelParameter.getExpression();
            String[] symbols = exp.getSymbols();
            if (symbols != null) {
                String issueMsgPrefix = "Global parameter '" + modelParameter.getName() + "' ";
                for (int j = 0; j < symbols.length; j++) {
                    SymbolTableEntry ste = exp.getSymbolBinding(symbols[j]);
                    if (ste == null) {
                        issueList.add(new Issue(modelParameter, issueContext, IssueCategory.ModelParameterExpressionError, issueMsgPrefix + "references undefined symbol '" + symbols[j] + "'", Issue.SEVERITY_ERROR));
                    } else if (ste instanceof SpeciesContext) {
                        if (!contains((SpeciesContext) ste)) {
                            issueList.add(new Issue(modelParameter, issueContext, IssueCategory.ModelParameterExpressionError, issueMsgPrefix + "references undefined species '" + symbols[j] + "'", Issue.SEVERITY_ERROR));
                        }
                    } else if (ste instanceof ModelParameter) {
                        if (!contains((ModelParameter) ste)) {
                            issueList.add(new Issue(modelParameter, issueContext, IssueCategory.ModelParameterExpressionError, issueMsgPrefix + "references undefined global parameter '" + symbols[j] + "'", Issue.SEVERITY_ERROR));
                        }
                    }
                }
            }
        }
        // 
        for (int i = 0; i < fieldModelParameters.length; i++) {
            try {
                VCUnitEvaluator unitEvaluator = new VCUnitEvaluator(getUnitSystem());
                VCUnitDefinition paramUnitDef = fieldModelParameters[i].getUnitDefinition();
                VCUnitDefinition expUnitDef = unitEvaluator.getUnitDefinition(fieldModelParameters[i].getExpression());
                if (paramUnitDef == null) {
                    issueList.add(new Issue(fieldModelParameters[i], issueContext, IssueCategory.Units, "defined unit is null", Issue.SEVERITY_WARNING));
                } else if (expUnitDef == null) {
                    issueList.add(new Issue(fieldModelParameters[i], issueContext, IssueCategory.Units, "computed unit is null", Issue.SEVERITY_WARNING));
                } else if (paramUnitDef.isTBD()) {
                    issueList.add(new Issue(fieldModelParameters[i], issueContext, IssueCategory.Units, "unit is undefined (" + unitSystem.getInstance_TBD().getSymbol() + ")", Issue.SEVERITY_WARNING));
                } else if (!paramUnitDef.isEquivalent(expUnitDef) && !expUnitDef.isTBD()) {
                    issueList.add(new Issue(fieldModelParameters[i], issueContext, IssueCategory.Units, "unit mismatch, computed = [" + expUnitDef.getSymbol() + "]", Issue.SEVERITY_WARNING));
                }
            } catch (VCUnitException e) {
                issueList.add(new Issue(fieldModelParameters[i], issueContext, IssueCategory.Units, "units inconsistent: " + e.getMessage(), Issue.SEVERITY_WARNING));
            } catch (ExpressionException e) {
                issueList.add(new Issue(fieldModelParameters[i], issueContext, IssueCategory.Units, "units inconsistent: " + e.getMessage(), Issue.SEVERITY_WARNING));
            }
        }
    } catch (Throwable e) {
        e.printStackTrace(System.out);
        issueList.add(new Issue(this, issueContext, IssueCategory.Units, "unexpected exception: " + e.getMessage(), Issue.SEVERITY_WARNING));
    }
    // 
    for (Structure struct : fieldStructures) {
        struct.gatherIssues(issueContext, issueList);
    }
    // 
    for (int i = 0; i < fieldReactionSteps.length; i++) {
        fieldReactionSteps[i].gatherIssues(issueContext, issueList);
    }
    // 
    // get issues from species contexts (species patterns)
    // 
    int seedSpeciesCount = 0;
    for (int i = 0; i < fieldSpeciesContexts.length; i++) {
        if (fieldSpeciesContexts[i].hasSpeciesPattern()) {
            seedSpeciesCount++;
        }
        fieldSpeciesContexts[i].gatherIssues(issueContext, issueList);
    }
    if (seedSpeciesCount == 0 && !rbmModelContainer.getReactionRuleList().isEmpty()) {
        String msg = "At least one seed species is required.";
        issueList.add(new Issue(this, issueContext, IssueCategory.Identifiers, msg, Issue.Severity.WARNING));
    }
    // 
    // get issues for symbol name clashes (specifically structures with same voltage names or structure names)
    // 
    HashSet<SymbolTableEntry> steHashSet = new HashSet<SymbolTableEntry>();
    gatherLocalEntries(steHashSet);
    Iterator<SymbolTableEntry> iter = steHashSet.iterator();
    Hashtable<String, SymbolTableEntry> symbolHashtable = new Hashtable<String, SymbolTableEntry>();
    while (iter.hasNext()) {
        SymbolTableEntry ste = iter.next();
        SymbolTableEntry existingSTE = symbolHashtable.get(ste.getName());
        if (existingSTE != null) {
            issueList.add(new Issue(this, issueContext, IssueCategory.Identifiers, "model symbol \"" + ste.getName() + "\" is used within \"" + ste.getNameScope().getName() + "\" and \"" + existingSTE.getNameScope().getName() + "\"", Issue.SEVERITY_ERROR));
        } else {
            symbolHashtable.put(ste.getName(), ste);
        }
    }
    // 
    // gather issues for electrical topology (unspecified +ve or -ve features, or +ve feature == -ve feature
    // 
    getElectricalTopology().gatherIssues(issueContext, issueList);
    // 
    if (rbmModelContainer == null) {
        issueList.add(new Issue(this, issueContext, IssueCategory.InternalError, "Rbm Model Container is null", Issue.SEVERITY_WARNING));
    } else {
        rbmModelContainer.gatherIssues(issueContext, issueList);
    }
}

Example 3 with VCUnitException

use of cbit.vcell.units.VCUnitException in project vcell by virtualcell.

the class ParameterContext method gatherIssues.

public void gatherIssues(IssueContext issueContext, List<Issue> issueList, ParameterRoleEnum userDefinedRole) {
    // 
    for (int i = 0; fieldUnresolvedParameters != null && i < fieldUnresolvedParameters.length; i++) {
        issueList.add(new Issue(fieldUnresolvedParameters[i], issueContext, IssueCategory.UnresolvedParameter, "Unresolved parameter '" + fieldUnresolvedParameters[i].getName(), Issue.SEVERITY_ERROR));
    }
    // 
    for (int i = 0; fieldParameters != null && i < fieldParameters.length; i++) {
        if (fieldParameters[i].getRole() == userDefinedRole) {
            try {
                if (!isReferenced(fieldParameters[i], 0)) {
                    issueList.add(new Issue(fieldParameters[i], issueContext, IssueCategory.KineticsUnreferencedParameter, "Unreferenced Kinetic Parameter '" + fieldParameters[i].getName(), Issue.SEVERITY_WARNING));
                }
            } catch (ExpressionException e) {
                issueList.add(new Issue(fieldParameters[i], issueContext, IssueCategory.KineticsExpressionError, "error resolving expression " + e.getMessage(), Issue.SEVERITY_WARNING));
            }
        }
    }
    // 
    if (fieldParameters != null) {
        for (LocalParameter parameter : this.fieldParameters) {
            if (parameter.getExpression() == null) {
                issueList.add(new Issue(parameter, issueContext, IssueCategory.KineticsExpressionMissing, "expression is missing", Issue.SEVERITY_INFO));
            } else {
                Expression exp = parameter.getExpression();
                String[] symbols = exp.getSymbols();
                String issueMessagePrefix = "parameter '" + parameter.getName() + "' ";
                if (symbols != null) {
                    for (int j = 0; j < symbols.length; j++) {
                        SymbolTableEntry ste = exp.getSymbolBinding(symbols[j]);
                        if (ste instanceof LocalProxyParameter) {
                            ste = ((LocalProxyParameter) ste).getTarget();
                        }
                        if (ste == null) {
                            issueList.add(new Issue(parameter, issueContext, IssueCategory.KineticsExpressionUndefinedSymbol, issueMessagePrefix + "references undefined symbol '" + symbols[j] + "'", Issue.SEVERITY_ERROR));
                        // } else if (ste instanceof SpeciesContext) {
                        // if (!getReactionStep().getModel().contains((SpeciesContext)ste)) {
                        // issueList.add(new Issue(parameter,issueContext,IssueCategory.KineticsExpressionUndefinedSymbol, issueMessagePrefix + "references undefined species '"+symbols[j]+"'",Issue.SEVERITY_ERROR));
                        // }
                        // if (reactionStep.countNumReactionParticipants((SpeciesContext)ste) == 0){
                        // issueList.add(new Issue(parameter,issueContext,IssueCategory.KineticsExpressionNonParticipantSymbol, issueMessagePrefix + "references species context '"+symbols[j]+"', but it is not a reactant/product/catalyst of this reaction",Issue.SEVERITY_WARNING));
                        // }
                        // } else if (ste instanceof ModelParameter) {
                        // if (!getReactionStep().getModel().contains((ModelParameter)ste)) {
                        // issueList.add(new Issue(parameter,issueContext,IssueCategory.KineticsExpressionUndefinedSymbol, issueMessagePrefix + "references undefined global parameter '"+symbols[j]+"'",Issue.SEVERITY_ERROR));
                        // }
                        }
                    }
                }
            }
        }
        // looking for local param which masks a global and issueing a warning
        for (LocalParameter parameter : fieldParameters) {
            String name = parameter.getName();
            SymbolTableEntry ste = nameScope.getExternalEntry(name, this);
            String steName;
            if (ste != null) {
                if (ste instanceof Displayable) {
                    steName = ((Displayable) ste).getDisplayType() + " " + ste.getName();
                } else {
                    steName = ste.getClass().getSimpleName() + " " + ste.getName();
                }
                String msg = steName + " is overriden by a local parameter " + name;
                issueList.add(new Issue(parameter, issueContext, IssueCategory.Identifiers, msg, Issue.SEVERITY_WARNING));
            }
        }
    }
    try {
        // 
        // determine unit consistency for each expression
        // 
        VCUnitSystem unitSystem = unitSystemProvider.getUnitSystem();
        VCUnitEvaluator unitEvaluator = new VCUnitEvaluator(unitSystem);
        for (int i = 0; i < fieldParameters.length; i++) {
            if (fieldParameters[i].getExpression() == null) {
                continue;
            }
            try {
                VCUnitDefinition paramUnitDef = fieldParameters[i].getUnitDefinition();
                VCUnitDefinition expUnitDef = unitEvaluator.getUnitDefinition(fieldParameters[i].getExpression());
                if (paramUnitDef == null) {
                    issueList.add(new Issue(fieldParameters[i], issueContext, IssueCategory.Units, "defined unit is null", Issue.SEVERITY_WARNING));
                } else if (paramUnitDef.isTBD()) {
                    issueList.add(new Issue(fieldParameters[i], issueContext, IssueCategory.Units, "undefined unit " + unitSystem.getInstance_TBD().getSymbol(), Issue.SEVERITY_WARNING));
                } else if (expUnitDef == null) {
                    issueList.add(new Issue(fieldParameters[i], issueContext, IssueCategory.Units, "computed unit is null", Issue.SEVERITY_WARNING));
                } else if (paramUnitDef.isTBD() || (!paramUnitDef.isEquivalent(expUnitDef) && !expUnitDef.isTBD())) {
                    issueList.add(new Issue(fieldParameters[i], issueContext, IssueCategory.Units, "inconsistent units, defined=[" + fieldParameters[i].getUnitDefinition().getSymbol() + "], computed=[" + expUnitDef.getSymbol() + "]", Issue.SEVERITY_WARNING));
                }
            } catch (VCUnitException e) {
                issueList.add(new Issue(fieldParameters[i], issueContext, IssueCategory.Units, e.getMessage(), Issue.SEVERITY_WARNING));
            } catch (ExpressionException e) {
                issueList.add(new Issue(fieldParameters[i], issueContext, IssueCategory.Units, e.getMessage(), Issue.SEVERITY_WARNING));
            }
        }
    } catch (Throwable e) {
        issueList.add(new Issue(parameterPolicy.getIssueSource(), issueContext, IssueCategory.Units, "unexpected exception: " + e.getMessage(), Issue.SEVERITY_INFO));
    }
    // 
    for (int i = 0; i < fieldParameters.length; i++) {
        RealInterval simpleBounds = parameterPolicy.getConstraintBounds(fieldParameters[i].getRole());
        if (simpleBounds != null) {
            String parmName = fieldParameters[i].getName();
            issueList.add(new SimpleBoundsIssue(fieldParameters[i], issueContext, simpleBounds, "parameter " + parmName + ": must be within " + simpleBounds.toString()));
        }
    }
}

Example 4 with VCUnitException

use of cbit.vcell.units.VCUnitException 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);
// }
}

Example 5 with VCUnitException

use of cbit.vcell.units.VCUnitException in project vcell by virtualcell.

the class ParameterTableModel method setValueAt.

public void setValueAt(Object aValue, int rowIndex, int columnIndex) {
    Parameter parameter = getValueAt(rowIndex);
    // try {
    switch(columnIndex) {
        case COLUMN_NAME:
            {
                try {
                    if (aValue instanceof String) {
                        String newName = (String) aValue;
                        if (!parameter.getName().equals(newName)) {
                            if (parameter instanceof Kinetics.KineticsParameter) {
                                reactionStep.getKinetics().renameParameter(parameter.getName(), newName);
                            } else if (parameter instanceof Kinetics.KineticsProxyParameter) {
                                parameter.setName(newName);
                            }
                            fireTableRowsUpdated(rowIndex, rowIndex);
                        }
                    }
                } catch (ExpressionException e) {
                    e.printStackTrace(System.out);
                    PopupGenerator.showErrorDialog(ownerTable, "Error changing parameter name:\n" + e.getMessage());
                } catch (java.beans.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 KineticsProxyParameter) && ((((KineticsProxyParameter) parameter).getTarget() instanceof Model.ReservedSymbol) || (((KineticsProxyParameter) parameter).getTarget() instanceof SpeciesContext) || (((KineticsProxyParameter) parameter).getTarget() instanceof ModelQuantity))) {
                        PopupGenerator.showErrorDialog(ownerTable, "Parameter : \'" + parameter.getName() + "\' is a " + ((KineticsProxyParameter) parameter).getTarget().getClass() + " in the model; cannot convert it to a local kinetic parameter.");
                    } else {
                        try {
                            reactionStep.getKinetics().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 KineticsParameter) && (((KineticsParameter) parameter).getRole() != Kinetics.ROLE_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 = reactionStep.getKinetics().getReactionStep().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 (reactionStep.getKinetics().getKineticsParameter(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) {
                                    reactionStep.getKinetics().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 Kinetics.KineticsParameter) {
                            reactionStep.getKinetics().setParameterValue((Kinetics.KineticsParameter) parameter, new Expression(newExpressionString));
                        } else if (parameter instanceof Kinetics.KineticsProxyParameter) {
                            parameter.setExpression(new Expression(newExpressionString));
                        }
                    }
                    reactionStep.getKinetics().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 Kinetics.KineticsParameter && ((Kinetics.KineticsParameter) parameter).getRole() == Kinetics.ROLE_UserDefined) {
                        String newUnitString = (String) aValue;
                        Kinetics.KineticsParameter kineticsParm = (Kinetics.KineticsParameter) parameter;
                        ModelUnitSystem modelUnitSystem = reactionStep.getModel().getUnitSystem();
                        if (!kineticsParm.getUnitDefinition().getSymbol().equals(newUnitString)) {
                            kineticsParm.setUnitDefinition(modelUnitSystem.getInstance(newUnitString));
                            reactionStep.getKinetics().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);
// }
}