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

Example 1 with ProxyParameter

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

the class BioModelParametersTableModel method propertyChange.

@Override
public void propertyChange(java.beans.PropertyChangeEvent evt) {
    super.propertyChange(evt);
    if (evt.getSource() instanceof EditableSymbolTableEntry) {
        int changeRow = getRowIndex((EditableSymbolTableEntry) evt.getSource());
        if (changeRow >= 0) {
            fireTableRowsUpdated(changeRow, changeRow);
        }
    } else {
        String propertyName = evt.getPropertyName();
        if (evt.getSource() == bioModel.getModel()) {
            if (propertyName.equals(Model.PROPERTY_NAME_MODEL_PARAMETERS)) {
                ModelParameter[] oldValue = (ModelParameter[]) evt.getOldValue();
                if (oldValue != null) {
                    for (EditableSymbolTableEntry parameter : oldValue) {
                        parameter.removePropertyChangeListener(this);
                    }
                }
                ModelParameter[] newValue = (ModelParameter[]) evt.getNewValue();
                if (newValue != null) {
                    for (EditableSymbolTableEntry parameter : newValue) {
                        parameter.addPropertyChangeListener(this);
                    }
                }
                refreshData();
            } else if (propertyName.equals(Model.PROPERTY_NAME_SPECIES_CONTEXTS)) {
                SpeciesContext[] oldValue = (SpeciesContext[]) evt.getOldValue();
                if (oldValue != null) {
                    for (SpeciesContext sc : oldValue) {
                        sc.removePropertyChangeListener(this);
                    }
                }
                SpeciesContext[] newValue = (SpeciesContext[]) evt.getNewValue();
                if (newValue != null) {
                    for (SpeciesContext sc : newValue) {
                        sc.addPropertyChangeListener(this);
                    }
                }
                refreshData();
            } else if (propertyName.equals(Model.PROPERTY_NAME_REACTION_STEPS)) {
                ReactionStep[] oldValue = (ReactionStep[]) evt.getOldValue();
                if (oldValue != null) {
                    for (ReactionStep reactionStep : oldValue) {
                        reactionStep.removePropertyChangeListener(this);
                        reactionStep.getKinetics().removePropertyChangeListener(this);
                        for (KineticsParameter kineticsEditableSymbolTableEntry : reactionStep.getKinetics().getKineticsParameters()) {
                            kineticsEditableSymbolTableEntry.removePropertyChangeListener(this);
                        }
                        for (ProxyParameter proxyEditableSymbolTableEntry : reactionStep.getKinetics().getProxyParameters()) {
                            proxyEditableSymbolTableEntry.removePropertyChangeListener(this);
                        }
                        for (UnresolvedParameter unresolvedEditableSymbolTableEntry : reactionStep.getKinetics().getUnresolvedParameters()) {
                            unresolvedEditableSymbolTableEntry.removePropertyChangeListener(this);
                        }
                    }
                }
                ReactionStep[] newValue = (ReactionStep[]) evt.getNewValue();
                if (newValue != null) {
                    for (ReactionStep reactionStep : newValue) {
                        reactionStep.addPropertyChangeListener(this);
                        reactionStep.getKinetics().addPropertyChangeListener(this);
                        for (KineticsParameter kineticsEditableSymbolTableEntry : reactionStep.getKinetics().getKineticsParameters()) {
                            kineticsEditableSymbolTableEntry.addPropertyChangeListener(this);
                        }
                        for (ProxyParameter proxyEditableSymbolTableEntry : reactionStep.getKinetics().getProxyParameters()) {
                            proxyEditableSymbolTableEntry.addPropertyChangeListener(this);
                        }
                        for (UnresolvedParameter unresolvedEditableSymbolTableEntry : reactionStep.getKinetics().getUnresolvedParameters()) {
                            unresolvedEditableSymbolTableEntry.addPropertyChangeListener(this);
                        }
                    }
                }
                refreshData();
            } else if (evt.getPropertyName().equals(RbmModelContainer.PROPERTY_NAME_REACTION_RULE_LIST)) {
                List<ReactionRule> oldValue = (List<ReactionRule>) evt.getOldValue();
                if (oldValue != null) {
                    for (ReactionRule rs : oldValue) {
                        rs.removePropertyChangeListener(this);
                    }
                }
                List<ReactionRule> newValue = (List<ReactionRule>) evt.getNewValue();
                if (newValue != null) {
                    for (ReactionRule rs : newValue) {
                        rs.addPropertyChangeListener(this);
                    }
                }
                refreshData();
            }
        } else if (evt.getSource() == bioModel) {
            if (propertyName.equals(BioModel.PROPERTY_NAME_SIMULATION_CONTEXTS)) {
                SimulationContext[] oldValue = (SimulationContext[]) evt.getOldValue();
                for (SimulationContext simulationContext : oldValue) {
                    simulationContext.removePropertyChangeListener(this);
                    simulationContext.getGeometryContext().removePropertyChangeListener(this);
                    for (StructureMapping mapping : simulationContext.getGeometryContext().getStructureMappings()) {
                        mapping.removePropertyChangeListener(this);
                        for (EditableSymbolTableEntry parameter : mapping.getParameters()) {
                            parameter.removePropertyChangeListener(this);
                        }
                    }
                    simulationContext.getReactionContext().removePropertyChangeListener(this);
                    for (SpeciesContextSpec spec : simulationContext.getReactionContext().getSpeciesContextSpecs()) {
                        spec.removePropertyChangeListener(this);
                        for (EditableSymbolTableEntry parameter : spec.getParameters()) {
                            parameter.removePropertyChangeListener(this);
                        }
                    }
                    for (ElectricalStimulus elect : simulationContext.getElectricalStimuli()) {
                        elect.removePropertyChangeListener(this);
                        for (EditableSymbolTableEntry parameter : elect.getParameters()) {
                            parameter.removePropertyChangeListener(this);
                        }
                    }
                    for (SpatialObject spatialObject : simulationContext.getSpatialObjects()) {
                        spatialObject.removePropertyChangeListener(this);
                    }
                    for (SpatialProcess spatialProcess : simulationContext.getSpatialProcesses()) {
                        spatialProcess.removePropertyChangeListener(this);
                        for (LocalParameter p : spatialProcess.getParameters()) {
                            p.removePropertyChangeListener(this);
                        }
                    }
                    for (SimulationContextParameter p : simulationContext.getSimulationContextParameters()) {
                        p.removePropertyChangeListener(this);
                    }
                }
                SimulationContext[] newValue = (SimulationContext[]) evt.getNewValue();
                for (SimulationContext simulationContext : newValue) {
                    simulationContext.addPropertyChangeListener(this);
                    simulationContext.getGeometryContext().addPropertyChangeListener(this);
                    for (StructureMapping mapping : simulationContext.getGeometryContext().getStructureMappings()) {
                        mapping.addPropertyChangeListener(this);
                        for (EditableSymbolTableEntry parameter : mapping.getParameters()) {
                            parameter.addPropertyChangeListener(this);
                        }
                    }
                    simulationContext.getReactionContext().addPropertyChangeListener(this);
                    for (SpeciesContextSpec spec : simulationContext.getReactionContext().getSpeciesContextSpecs()) {
                        spec.addPropertyChangeListener(this);
                        for (EditableSymbolTableEntry parameter : spec.getParameters()) {
                            parameter.addPropertyChangeListener(this);
                        }
                    }
                    for (ElectricalStimulus elect : simulationContext.getElectricalStimuli()) {
                        elect.addPropertyChangeListener(this);
                        for (EditableSymbolTableEntry parameter : elect.getParameters()) {
                            parameter.addPropertyChangeListener(this);
                        }
                    }
                    for (SpatialObject spatialObject : simulationContext.getSpatialObjects()) {
                        spatialObject.addPropertyChangeListener(this);
                    }
                    for (SpatialProcess spatialProcess : simulationContext.getSpatialProcesses()) {
                        spatialProcess.addPropertyChangeListener(this);
                        for (LocalParameter p : spatialProcess.getParameters()) {
                            p.addPropertyChangeListener(this);
                        }
                    }
                    for (SimulationContextParameter p : simulationContext.getSimulationContextParameters()) {
                        p.addPropertyChangeListener(this);
                    }
                }
                refreshData();
            }
        } else if (evt.getSource() instanceof GeometryContext && evt.getPropertyName().equals(GeometryContext.PROPERTY_STRUCTURE_MAPPINGS)) {
            StructureMapping[] oldValue = (StructureMapping[]) evt.getOldValue();
            if (oldValue != null) {
                for (StructureMapping mapping : oldValue) {
                    mapping.removePropertyChangeListener(this);
                    for (EditableSymbolTableEntry parameter : mapping.getParameters()) {
                        parameter.removePropertyChangeListener(this);
                    }
                }
            }
            StructureMapping[] newValue = (StructureMapping[]) evt.getNewValue();
            if (newValue != null) {
                for (StructureMapping mapping : newValue) {
                    mapping.addPropertyChangeListener(this);
                    for (EditableSymbolTableEntry parameter : mapping.getParameters()) {
                        parameter.addPropertyChangeListener(this);
                    }
                }
            }
            refreshData();
        } else if (evt.getSource() instanceof ReactionStep && (evt.getPropertyName().equals(ReactionStep.PROPERTY_NAME_KINETICS))) {
            Kinetics oldValue = (Kinetics) evt.getOldValue();
            if (oldValue != null) {
                oldValue.removePropertyChangeListener(this);
                for (KineticsParameter kineticsEditableSymbolTableEntry : oldValue.getKineticsParameters()) {
                    kineticsEditableSymbolTableEntry.removePropertyChangeListener(this);
                }
                for (ProxyParameter proxyEditableSymbolTableEntry : oldValue.getProxyParameters()) {
                    proxyEditableSymbolTableEntry.removePropertyChangeListener(this);
                }
                for (UnresolvedParameter unresolvedEditableSymbolTableEntry : oldValue.getUnresolvedParameters()) {
                    unresolvedEditableSymbolTableEntry.removePropertyChangeListener(this);
                }
            }
            Kinetics newValue = (Kinetics) evt.getNewValue();
            if (newValue != null) {
                newValue.addPropertyChangeListener(this);
                for (KineticsParameter kineticsEditableSymbolTableEntry : newValue.getKineticsParameters()) {
                    kineticsEditableSymbolTableEntry.addPropertyChangeListener(this);
                }
                for (ProxyParameter proxyEditableSymbolTableEntry : newValue.getProxyParameters()) {
                    proxyEditableSymbolTableEntry.addPropertyChangeListener(this);
                }
                for (UnresolvedParameter unresolvedEditableSymbolTableEntry : newValue.getUnresolvedParameters()) {
                    unresolvedEditableSymbolTableEntry.addPropertyChangeListener(this);
                }
            }
            refreshData();
        } else if (evt.getSource() instanceof SimulationContext && evt.getPropertyName().equals(SimulationContext.PROPERTY_NAME_SPATIALPROCESSES)) {
            SpatialProcess[] oldValue = (SpatialProcess[]) evt.getOldValue();
            if (oldValue != null) {
                for (SpatialProcess process : oldValue) {
                    process.removePropertyChangeListener(this);
                    for (EditableSymbolTableEntry parameter : process.getParameters()) {
                        parameter.removePropertyChangeListener(this);
                    }
                }
            }
            SpatialProcess[] newValue = (SpatialProcess[]) evt.getNewValue();
            if (newValue != null) {
                for (SpatialProcess process : newValue) {
                    process.addPropertyChangeListener(this);
                    for (EditableSymbolTableEntry parameter : process.getParameters()) {
                        parameter.addPropertyChangeListener(this);
                    }
                }
            }
            refreshData();
        } else if (evt.getSource() instanceof SimulationContext && evt.getPropertyName().equals(SimulationContext.PROPERTY_NAME_SPATIALOBJECTS)) {
            SpatialObject[] oldValue = (SpatialObject[]) evt.getOldValue();
            if (oldValue != null) {
                for (SpatialObject spatialObject : oldValue) {
                    spatialObject.removePropertyChangeListener(this);
                }
            }
            SpatialObject[] newValue = (SpatialObject[]) evt.getNewValue();
            if (newValue != null) {
                for (SpatialObject spatialObject : newValue) {
                    spatialObject.addPropertyChangeListener(this);
                }
            }
            refreshData();
        } else if (evt.getSource() instanceof SpatialObject && evt.getPropertyName().equals(SpatialObject.PROPERTY_NAME_QUANTITYCATEGORIESENABLED)) {
            refreshData();
        } else if (evt.getSource() instanceof SimulationContext && evt.getPropertyName().equals(SimulationContext.PROPERTY_NAME_SIMULATIONCONTEXTPARAMETERS)) {
            SimulationContextParameter[] oldValue = (SimulationContextParameter[]) evt.getOldValue();
            if (oldValue != null) {
                for (SimulationContextParameter param : oldValue) {
                    param.removePropertyChangeListener(this);
                }
            }
            SimulationContextParameter[] newValue = (SimulationContextParameter[]) evt.getNewValue();
            if (newValue != null) {
                for (SimulationContextParameter param : newValue) {
                    param.addPropertyChangeListener(this);
                }
            }
            refreshData();
        } else if (evt.getSource() instanceof Kinetics && (evt.getPropertyName().equals(Kinetics.PROPERTY_NAME_KINETICS_PARAMETERS))) {
            EditableSymbolTableEntry[] oldValue = (EditableSymbolTableEntry[]) evt.getOldValue();
            if (oldValue != null) {
                for (int i = 0; i < oldValue.length; i++) {
                    oldValue[i].removePropertyChangeListener(this);
                }
            }
            EditableSymbolTableEntry[] newValue = (EditableSymbolTableEntry[]) evt.getNewValue();
            if (newValue != null) {
                for (int i = 0; i < newValue.length; i++) {
                    newValue[i].addPropertyChangeListener(this);
                }
            }
            refreshData();
        // } else if(evt.getSource() instanceof ReactionRuleEmbedded) {
        // ReactionRuleEmbedded reactionRule = (ReactionRuleEmbedded) evt.getSource();
        // int changeRow = getRowIndex(reactionRule);
        // if (changeRow >= 0) {
        // fireTableRowsUpdated(changeRow, changeRow);
        // }
        }
    }
}

Example 2 with ProxyParameter

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

the class ParameterTableModel 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("reactionStep")) {
        ReactionStep oldValue = (ReactionStep) evt.getOldValue();
        if (oldValue != null) {
            oldValue.removePropertyChangeListener(this);
            oldValue.getKinetics().removePropertyChangeListener(this);
            for (int i = 0; i < oldValue.getKinetics().getKineticsParameters().length; i++) {
                oldValue.getKinetics().getKineticsParameters()[i].removePropertyChangeListener(this);
            }
            for (int i = 0; i < oldValue.getKinetics().getProxyParameters().length; i++) {
                oldValue.getKinetics().getProxyParameters()[i].removePropertyChangeListener(this);
            }
        }
        ReactionStep newValue = (ReactionStep) evt.getNewValue();
        if (newValue != null) {
            newValue.addPropertyChangeListener(this);
            newValue.getKinetics().addPropertyChangeListener(this);
            for (int i = 0; i < newValue.getKinetics().getKineticsParameters().length; i++) {
                newValue.getKinetics().getKineticsParameters()[i].removePropertyChangeListener(this);
                newValue.getKinetics().getKineticsParameters()[i].addPropertyChangeListener(this);
            }
            for (int i = 0; i < newValue.getKinetics().getProxyParameters().length; i++) {
                newValue.getKinetics().getProxyParameters()[i].removePropertyChangeListener(this);
                newValue.getKinetics().getProxyParameters()[i].addPropertyChangeListener(this);
            }
            autoCompleteSymbolFilter = reactionStep.getAutoCompleteSymbolFilter();
        }
        refreshData();
    }
    if (evt.getSource() == reactionStep && evt.getPropertyName().equals(ReactionStep.PROPERTY_NAME_KINETICS)) {
        Kinetics oldValue = (Kinetics) evt.getOldValue();
        if (oldValue != null) {
            oldValue.removePropertyChangeListener(this);
            for (int i = 0; i < oldValue.getKineticsParameters().length; i++) {
                oldValue.getKineticsParameters()[i].removePropertyChangeListener(this);
            }
            for (int i = 0; i < oldValue.getProxyParameters().length; i++) {
                oldValue.getProxyParameters()[i].removePropertyChangeListener(this);
            }
        }
        Kinetics newValue = (Kinetics) evt.getNewValue();
        if (newValue != null) {
            newValue.addPropertyChangeListener(this);
            for (int i = 0; i < newValue.getKineticsParameters().length; i++) {
                newValue.getKineticsParameters()[i].removePropertyChangeListener(this);
                newValue.getKineticsParameters()[i].addPropertyChangeListener(this);
            }
            for (int i = 0; i < newValue.getProxyParameters().length; i++) {
                newValue.getProxyParameters()[i].removePropertyChangeListener(this);
                newValue.getProxyParameters()[i].addPropertyChangeListener(this);
            }
        }
        // get rid of all Catalysts when changing kynetic type
        if (reactionStep != null && reactionStep.hasCatalyst() && newValue != null && newValue != oldValue) {
            List<ReactionParticipant> rpList = new ArrayList<>(Arrays.asList(reactionStep.getReactionParticipants()));
            for (ReactionParticipant rp : rpList) {
                if (rp instanceof Catalyst) {
                    try {
                        reactionStep.removeReactionParticipant(rp);
                    } catch (PropertyVetoException | ExpressionException | ModelException e) {
                        // do nothing if it fails
                        e.printStackTrace();
                    }
                }
            }
        }
        refreshData();
    }
    if (evt.getSource() instanceof Kinetics && (evt.getPropertyName().equals("kineticsParameters") || 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].removePropertyChangeListener(this);
            newParams[i].addPropertyChangeListener(this);
        }
        if (evt.getPropertyName().equals("proxyParameters")) {
            List<Parameter> addedList = new ArrayList<>(Arrays.asList(newParams));
            addedList.removeAll(Arrays.asList(oldParams));
            List<Parameter> removedList = new ArrayList<>(Arrays.asList(oldParams));
            removedList.removeAll(Arrays.asList(newParams));
            if (reactionStep != null) {
                for (Parameter removed : removedList) {
                    if (removed instanceof ProxyParameter && ((ProxyParameter) removed).getTarget() instanceof SpeciesContext) {
                        SpeciesContext sc = (SpeciesContext) ((ProxyParameter) removed).getTarget();
                        if (reactionStep.getReactant(sc.getName()) == null && reactionStep.getProduct(sc.getName()) == null && reactionStep.getCatalyst(sc.getName()) != null) {
                            try {
                                reactionStep.removeReactionParticipant(reactionStep.getCatalyst(sc.getName()));
                            } catch (PropertyVetoException | ExpressionException | ModelException e) {
                                // we do nothing
                                e.printStackTrace();
                            }
                        }
                    }
                }
                for (Parameter added : addedList) {
                    if (added instanceof ProxyParameter && ((ProxyParameter) added).getTarget() instanceof SpeciesContext) {
                        SpeciesContext sc = (SpeciesContext) ((ProxyParameter) added).getTarget();
                        if (reactionStep.getReactant(sc.getName()) == null && reactionStep.getProduct(sc.getName()) == null && reactionStep.getCatalyst(sc.getName()) == null) {
                            try {
                                reactionStep.addCatalyst(sc);
                            } catch (PropertyVetoException | ModelException e) {
                                // we do nothing
                                e.printStackTrace();
                            }
                        }
                    }
                }
            }
        }
        refreshData();
    }
    if (evt.getSource() instanceof Parameter) {
        fireTableRowsUpdated(0, getRowCount() - 1);
    }
}

Example 3 with ProxyParameter

use of cbit.vcell.model.ProxyParameter 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 4 with ProxyParameter

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

the class MathMapping_4_8 method getMathSymbol0.

/**
 * Substitutes appropriate variables for speciesContext bindings
 *
 * @return cbit.vcell.parser.Expression
 * @param origExp cbit.vcell.parser.Expression
 * @param structureMapping cbit.vcell.mapping.StructureMapping
 */
private String getMathSymbol0(SymbolTableEntry ste, StructureMapping structureMapping) throws MappingException {
    String steName = ste.getName();
    if (ste instanceof Kinetics.KineticsParameter) {
        Integer count = localNameCountHash.get(steName);
        if (count == null) {
            throw new MappingException("KineticsParameter " + steName + " not found in local name count");
        }
        if (count > 1 || steName.equals("J")) {
            return steName + "_" + ste.getNameScope().getName();
        // return getNameScope().getSymbolName(ste);
        } else {
            return steName;
        }
    }
    if (ste instanceof MathMapping_4_8.ProbabilityParameter) {
        // be careful here, to see if we need mangle the reaction name
        MathMapping_4_8.ProbabilityParameter probParm = (MathMapping_4_8.ProbabilityParameter) ste;
        return probParm.getName();
    }
    if (ste instanceof MathMapping_4_8.SpeciesConcentrationParameter) {
        MathMapping_4_8.SpeciesConcentrationParameter concParm = (MathMapping_4_8.SpeciesConcentrationParameter) ste;
        return concParm.getSpeciesContextSpec().getSpeciesContext().getName() + MATH_FUNC_SUFFIX_SPECIES_CONCENTRATION;
    }
    if (ste instanceof MathMapping_4_8.SpeciesCountParameter) {
        MathMapping_4_8.SpeciesCountParameter countParm = (MathMapping_4_8.SpeciesCountParameter) ste;
        return countParm.getSpeciesContextSpec().getSpeciesContext().getName() + MATH_VAR_SUFFIX_SPECIES_COUNT;
    }
    if (ste instanceof MathMapping_4_8.EventAssignmentInitParameter) {
        MathMapping_4_8.EventAssignmentInitParameter eventInitParm = (MathMapping_4_8.EventAssignmentInitParameter) ste;
        return eventInitParm.getName() + MATH_FUNC_SUFFIX_EVENTASSIGN_INIT;
    }
    if (ste instanceof Model.ReservedSymbol) {
        return steName;
    }
    if (ste instanceof Membrane.MembraneVoltage) {
        return steName;
    }
    if (ste instanceof Structure.StructureSize) {
        Structure structure = ((Structure.StructureSize) ste).getStructure();
        StructureMapping.StructureMappingParameter sizeParameter = simContext.getGeometryContext().getStructureMapping(structure).getSizeParameter();
        return getMathSymbol(sizeParameter, structureMapping);
    }
    if (ste instanceof ProxyParameter) {
        ProxyParameter pp = (ProxyParameter) ste;
        return getMathSymbol0(pp.getTarget(), structureMapping);
    }
    // 
    Model model = simContext.getModel();
    if (ste instanceof ModelParameter) {
        ModelParameter mp = (ModelParameter) ste;
        if (simContext.getGeometry().getDimension() == 0) {
            return mp.getName();
        } else {
            if (mp.getExpression().getSymbols() == null) {
                return mp.getName();
            }
            // check if global param variant name exists in globalVarsHash. If so, return it, else, throw exception.
            Hashtable<String, Expression> smVariantsHash = globalParamVariantsHash.get(mp);
            String variantName = mp.getName() + "_" + TokenMangler.fixTokenStrict(structureMapping.getStructure().getName());
            if (smVariantsHash.get(variantName) != null) {
                return variantName;
            } else {
                // global param variant doesn't exist in the hash, so get the substituted expression for global param and
                // gather all symbols (speciesContexts) that do not match with arg 'structureMapping' to display a proper error message.
                Expression expr = null;
                try {
                    expr = substituteGlobalParameters(mp.getExpression());
                } catch (ExpressionException e) {
                    e.printStackTrace(System.out);
                    throw new RuntimeException("Could not substitute expression for global parameter '" + mp.getName() + "' with expression '" + "'" + e.getMessage());
                }
                // find symbols (typically speciesContexts) in 'exp' that do not match with the arg 'structureMapping'
                String[] symbols = expr.getSymbols();
                String msg = "";
                if (symbols != null) {
                    Vector<String> spContextNamesVector = new Vector<String>();
                    for (int j = 0; j < symbols.length; j++) {
                        SpeciesContext sc = model.getSpeciesContext(symbols[j]);
                        if (sc != null) {
                            if (!sc.getStructure().compareEqual(structureMapping.getStructure())) {
                                spContextNamesVector.addElement(sc.getName());
                            }
                        }
                    }
                    for (int i = 0; (spContextNamesVector != null && i < spContextNamesVector.size()); i++) {
                        if (i == 0) {
                            msg += "'" + spContextNamesVector.elementAt(i) + ", ";
                        } else if (i == spContextNamesVector.size() - 1) {
                            msg += spContextNamesVector.elementAt(i) + "'";
                        } else {
                            msg += spContextNamesVector.elementAt(i) + ", ";
                        }
                    }
                }
                throw new RuntimeException("Global parameter '" + mp.getName() + "' is not defined in compartment '" + structureMapping.getStructure().getName() + "', but was referenced in that compartment." + "\n\nExpression '" + mp.getExpression().infix() + "' for global parameter '" + mp.getName() + "' expands to '" + expr.infix() + "' " + "and contains species " + msg + " that is/are not in adjacent compartments.");
            }
        // return (mp.getName()+"_"+TokenMangler.fixTokenStrict(structureMapping.getStructure().getName()));
        }
    }
    if (ste instanceof SpeciesContextSpec.SpeciesContextSpecParameter) {
        SpeciesContextSpec.SpeciesContextSpecParameter scsParm = (SpeciesContextSpec.SpeciesContextSpecParameter) ste;
        if (scsParm.getRole() == SpeciesContextSpec.ROLE_InitialConcentration) {
            return ((SpeciesContextSpec) (scsParm.getNameScope().getScopedSymbolTable())).getSpeciesContext().getName() + MATH_FUNC_SUFFIX_SPECIES_INIT_CONCENTRATION;
        }
        if (scsParm.getRole() == SpeciesContextSpec.ROLE_InitialCount) {
            return ((SpeciesContextSpec) (scsParm.getNameScope().getScopedSymbolTable())).getSpeciesContext().getName() + MATH_FUNC_SUFFIX_SPECIES_INIT_COUNT;
        }
        if (scsParm.getRole() == SpeciesContextSpec.ROLE_DiffusionRate) {
            return ((SpeciesContextSpec) (scsParm.getNameScope().getScopedSymbolTable())).getSpeciesContext().getName() + "_diffusionRate";
        }
        if (scsParm.getRole() == SpeciesContextSpec.ROLE_BoundaryValueXm) {
            return ((SpeciesContextSpec) (scsParm.getNameScope().getScopedSymbolTable())).getSpeciesContext().getName() + "_boundaryXm";
        }
        if (scsParm.getRole() == SpeciesContextSpec.ROLE_BoundaryValueXp) {
            return ((SpeciesContextSpec) (scsParm.getNameScope().getScopedSymbolTable())).getSpeciesContext().getName() + "_boundaryXp";
        }
        if (scsParm.getRole() == SpeciesContextSpec.ROLE_BoundaryValueYm) {
            return ((SpeciesContextSpec) (scsParm.getNameScope().getScopedSymbolTable())).getSpeciesContext().getName() + "_boundaryYm";
        }
        if (scsParm.getRole() == SpeciesContextSpec.ROLE_BoundaryValueYp) {
            return ((SpeciesContextSpec) (scsParm.getNameScope().getScopedSymbolTable())).getSpeciesContext().getName() + "_boundaryYp";
        }
        if (scsParm.getRole() == SpeciesContextSpec.ROLE_BoundaryValueZm) {
            return ((SpeciesContextSpec) (scsParm.getNameScope().getScopedSymbolTable())).getSpeciesContext().getName() + "_boundaryZm";
        }
        if (scsParm.getRole() == SpeciesContextSpec.ROLE_BoundaryValueZp) {
            return ((SpeciesContextSpec) (scsParm.getNameScope().getScopedSymbolTable())).getSpeciesContext().getName() + "_boundaryZp";
        }
        if (scsParm.getRole() == SpeciesContextSpec.ROLE_VelocityX) {
            return ((SpeciesContextSpec) (scsParm.getNameScope().getScopedSymbolTable())).getSpeciesContext().getName() + "_velocityX";
        }
        if (scsParm.getRole() == SpeciesContextSpec.ROLE_VelocityY) {
            return ((SpeciesContextSpec) (scsParm.getNameScope().getScopedSymbolTable())).getSpeciesContext().getName() + "_velocityY";
        }
        if (scsParm.getRole() == SpeciesContextSpec.ROLE_VelocityZ) {
            return ((SpeciesContextSpec) (scsParm.getNameScope().getScopedSymbolTable())).getSpeciesContext().getName() + "_velocityZ";
        }
    }
    if (ste instanceof ElectricalDevice.ElectricalDeviceParameter) {
        ElectricalDevice.ElectricalDeviceParameter edParm = (ElectricalDevice.ElectricalDeviceParameter) ste;
        ElectricalDevice electricalDevice = (ElectricalDevice) edParm.getNameScope().getScopedSymbolTable();
        if (electricalDevice instanceof MembraneElectricalDevice) {
            String nameWithScope = ((MembraneElectricalDevice) electricalDevice).getMembraneMapping().getMembrane().getNameScope().getName();
            if (edParm.getRole() == ElectricalDevice.ROLE_TotalCurrent) {
                return "I_" + nameWithScope;
            }
            if (edParm.getRole() == ElectricalDevice.ROLE_TransmembraneCurrent) {
                return "F_" + nameWithScope;
            }
        // }else if (electricalDevice instanceof CurrentClampElectricalDevice) {
        // if (edParm.getRole()==ElectricalDevice.ROLE_TotalCurrentDensity){
        // return "I_"+((CurrentClampElectricalDevice)electricalDevice).getCurrentClampStimulus().getNameScope().getName();
        // }
        // if (edParm.getRole()==ElectricalDevice.ROLE_TransmembraneCurrentDensity){
        // return "F_"+((CurrentClampElectricalDevice)electricalDevice).getCurrentClampStimulus().getNameScope().getName();
        // }
        // }else if (electricalDevice instanceof VoltageClampElectricalDevice) {
        // if (edParm.getRole()==ElectricalDevice.ROLE_TotalCurrentDensity){
        // return "I_"+((VoltageClampElectricalDevice)electricalDevice).getVoltageClampStimulus().getNameScope().getName();
        // }
        // if (edParm.getRole()==ElectricalDevice.ROLE_TransmembraneCurrentDensity){
        // return "F_"+((VoltageClampElectricalDevice)electricalDevice).getVoltageClampStimulus().getNameScope().getName();
        // }
        }
    }
    if (ste instanceof LocalParameter && ((LocalParameter) ste).getNameScope() instanceof ElectricalStimulus.ElectricalStimulusNameScope) {
        LocalParameter esParm = (LocalParameter) ste;
        String nameWithScope = esParm.getNameScope().getName();
        if (esParm.getRole() == ElectricalStimulusParameterType.TotalCurrent) {
            return "I_" + nameWithScope;
        } else if (esParm.getRole() == ElectricalStimulusParameterType.Voltage) {
            return "V_" + nameWithScope;
        }
    }
    StructureTopology structTopology = model.getStructureTopology();
    if (ste instanceof StructureMapping.StructureMappingParameter) {
        StructureMapping.StructureMappingParameter smParm = (StructureMapping.StructureMappingParameter) ste;
        Structure structure = ((StructureMapping) (smParm.getNameScope().getScopedSymbolTable())).getStructure();
        int role = smParm.getRole();
        if (role == StructureMapping.ROLE_VolumeFraction) {
            return "VolFract_" + (structTopology.getInsideFeature((Membrane) structure)).getNameScope().getName();
        } else {
            String nameWithScope = structure.getNameScope().getName();
            if (role == StructureMapping.ROLE_SurfaceToVolumeRatio) {
                return "SurfToVol_" + nameWithScope;
            } else if (role == StructureMapping.ROLE_InitialVoltage) {
                return smParm.getName();
            } else if (role == StructureMapping.ROLE_SpecificCapacitance) {
                return "C_" + nameWithScope;
            } else if (role == StructureMapping.ROLE_AreaPerUnitArea) {
                return "AreaPerUnitArea_" + nameWithScope;
            } else if (role == StructureMapping.ROLE_AreaPerUnitVolume) {
                return "AreaPerUnitVolume_" + nameWithScope;
            } else if (role == StructureMapping.ROLE_VolumePerUnitArea) {
                return "VolumePerUnitArea_" + nameWithScope;
            } else if (role == StructureMapping.ROLE_VolumePerUnitVolume) {
                return "VolumePerUnitVolume_" + nameWithScope;
            } else if (role == StructureMapping.ROLE_Size) {
                if (simContext.getGeometry().getDimension() == 0) {
                    // if geometry is compartmental, make sure compartment sizes are set if referenced in model.
                    if (smParm.getExpression() == null || smParm.getExpression().isZero()) {
                        throw new MappingException("\nIn non-spatial application '" + getSimulationContext().getName() + "', " + "size of structure '" + structure.getName() + "' must be assigned a " + "positive value if referenced in the model.\n\nPlease go to 'Structure Mapping' tab to check the size.");
                    }
                }
                return "Size_" + nameWithScope;
            }
        }
    }
    // 
    if (ste instanceof SpeciesContext) {
        SpeciesContext sc = (SpeciesContext) ste;
        SpeciesContextMapping scm = getSpeciesContextMapping(sc);
        // 
        if (structureMapping instanceof FeatureMapping) {
            // 
            if (scm.getVariable() != null && !scm.getVariable().getName().equals(steName)) {
                return scm.getVariable().getName();
            }
        // 
        // for reactions within a spatially resolved membrane, may need "_INSIDE" or "_OUTSIDE" for jump condition
        // 
        // if the membrane is distributed, then always use the plain variable.
        // 
        } else if (structureMapping instanceof MembraneMapping) {
            Membrane membrane = ((MembraneMapping) structureMapping).getMembrane();
            // 
            if (sc.getStructure() instanceof Membrane || getResolved(structureMapping) == false) {
                if (scm.getVariable() != null && !(scm.getVariable().getName().equals(steName))) {
                    return scm.getVariable().getName();
                }
            // 
            // if the speciesContext is outside the membrane
            // 
            } else {
                SpeciesContextSpec scs = simContext.getReactionContext().getSpeciesContextSpec(sc);
                if (sc.getStructure() == structTopology.getInsideFeature(membrane) || sc.getStructure() == structTopology.getOutsideFeature(membrane)) {
                    if (getResolved(structureMapping) && !scs.isConstant()) {
                        if (!scs.isDiffusing()) {
                            throw new MappingException("Enable diffusion in Application '" + simContext.getName() + "'. This must be done for any species (e.g '" + sc.getName() + "') in flux reactions.\n\n" + "To save or run simulations, set the diffusion rate to a non-zero " + "value in Initial Conditions or disable those reactions in Specifications->Reactions.");
                        }
                        return scm.getVariable().getName() + (sc.getStructure() == structTopology.getInsideFeature(membrane) ? "_INSIDE" : "_OUTSIDE");
                    } else {
                        return scm.getSpeciesContext().getName();
                    }
                } else {
                    throw new MappingException(sc.getName() + " shouldn't be involved with structure " + structureMapping.getStructure().getName());
                }
            }
        }
    }
    return getNameScope().getSymbolName(ste);
}

Example 5 with ProxyParameter

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

the class BioModelParametersTableModel method bioModelChange.

@Override
protected void bioModelChange(PropertyChangeEvent evt) {
    super.bioModelChange(evt);
    BioModel oldValue = (BioModel) evt.getOldValue();
    if (oldValue != null) {
        for (EditableSymbolTableEntry parameter : oldValue.getModel().getModelParameters()) {
            parameter.removePropertyChangeListener(this);
        }
        for (SpeciesContext sc : oldValue.getModel().getSpeciesContexts()) {
            sc.removePropertyChangeListener(this);
        }
        for (ReactionStep reactionStep : oldValue.getModel().getReactionSteps()) {
            reactionStep.removePropertyChangeListener(this);
            Kinetics kinetics = reactionStep.getKinetics();
            kinetics.removePropertyChangeListener(this);
            for (KineticsParameter kineticsEditableSymbolTableEntry : kinetics.getKineticsParameters()) {
                kineticsEditableSymbolTableEntry.removePropertyChangeListener(this);
            }
            for (ProxyParameter proxyEditableSymbolTableEntry : kinetics.getProxyParameters()) {
                proxyEditableSymbolTableEntry.removePropertyChangeListener(this);
            }
            for (UnresolvedParameter unresolvedEditableSymbolTableEntry : kinetics.getUnresolvedParameters()) {
                unresolvedEditableSymbolTableEntry.removePropertyChangeListener(this);
            }
        }
        for (SimulationContext simulationContext : oldValue.getSimulationContexts()) {
            simulationContext.removePropertyChangeListener(this);
            simulationContext.getGeometryContext().removePropertyChangeListener(this);
            for (StructureMapping mapping : simulationContext.getGeometryContext().getStructureMappings()) {
                mapping.removePropertyChangeListener(this);
                for (EditableSymbolTableEntry parameter : mapping.getParameters()) {
                    parameter.removePropertyChangeListener(this);
                }
            }
            simulationContext.getReactionContext().removePropertyChangeListener(this);
            for (SpeciesContextSpec spec : simulationContext.getReactionContext().getSpeciesContextSpecs()) {
                spec.removePropertyChangeListener(this);
                for (EditableSymbolTableEntry parameter : spec.getParameters()) {
                    parameter.removePropertyChangeListener(this);
                }
            }
            for (ElectricalStimulus elect : simulationContext.getElectricalStimuli()) {
                elect.removePropertyChangeListener(this);
                for (EditableSymbolTableEntry parameter : elect.getParameters()) {
                    parameter.removePropertyChangeListener(this);
                }
            }
            for (SpatialObject spatialObject : simulationContext.getSpatialObjects()) {
                spatialObject.removePropertyChangeListener(this);
            }
            for (SpatialProcess spatialProcess : simulationContext.getSpatialProcesses()) {
                spatialProcess.removePropertyChangeListener(this);
                for (LocalParameter p : spatialProcess.getParameters()) {
                    p.removePropertyChangeListener(this);
                }
            }
            for (SimulationContextParameter p : simulationContext.getSimulationContextParameters()) {
                p.removePropertyChangeListener(this);
            }
        }
    }
    BioModel newValue = (BioModel) evt.getNewValue();
    if (newValue != null) {
        for (ModelParameter modelEditableSymbolTableEntry : newValue.getModel().getModelParameters()) {
            modelEditableSymbolTableEntry.addPropertyChangeListener(this);
        }
        for (SpeciesContext sc : newValue.getModel().getSpeciesContexts()) {
            sc.addPropertyChangeListener(this);
        }
        for (ReactionStep reactionStep : newValue.getModel().getReactionSteps()) {
            reactionStep.addPropertyChangeListener(this);
            Kinetics kinetics = reactionStep.getKinetics();
            kinetics.addPropertyChangeListener(this);
            for (KineticsParameter kineticsEditableSymbolTableEntry : kinetics.getKineticsParameters()) {
                kineticsEditableSymbolTableEntry.addPropertyChangeListener(this);
            }
            for (ProxyParameter proxyEditableSymbolTableEntry : kinetics.getProxyParameters()) {
                proxyEditableSymbolTableEntry.addPropertyChangeListener(this);
            }
            for (UnresolvedParameter unresolvedEditableSymbolTableEntry : kinetics.getUnresolvedParameters()) {
                unresolvedEditableSymbolTableEntry.addPropertyChangeListener(this);
            }
        }
        for (SimulationContext simulationContext : newValue.getSimulationContexts()) {
            simulationContext.addPropertyChangeListener(this);
            simulationContext.getGeometryContext().addPropertyChangeListener(this);
            for (StructureMapping mapping : simulationContext.getGeometryContext().getStructureMappings()) {
                mapping.addPropertyChangeListener(this);
                for (EditableSymbolTableEntry parameter : mapping.getParameters()) {
                    parameter.addPropertyChangeListener(this);
                }
            }
            simulationContext.getReactionContext().addPropertyChangeListener(this);
            for (SpeciesContextSpec spec : simulationContext.getReactionContext().getSpeciesContextSpecs()) {
                spec.addPropertyChangeListener(this);
                for (EditableSymbolTableEntry parameter : spec.getParameters()) {
                    parameter.addPropertyChangeListener(this);
                }
            }
            for (ElectricalStimulus elect : simulationContext.getElectricalStimuli()) {
                elect.addPropertyChangeListener(this);
                for (EditableSymbolTableEntry parameter : elect.getParameters()) {
                    parameter.addPropertyChangeListener(this);
                }
            }
            for (SpatialObject spatialObject : simulationContext.getSpatialObjects()) {
                spatialObject.addPropertyChangeListener(this);
            }
            for (SpatialProcess spatialProcess : simulationContext.getSpatialProcesses()) {
                spatialProcess.addPropertyChangeListener(this);
                for (LocalParameter p : spatialProcess.getParameters()) {
                    p.addPropertyChangeListener(this);
                }
            }
            for (SimulationContextParameter p : simulationContext.getSimulationContextParameters()) {
                p.addPropertyChangeListener(this);
            }
        }
    }
}