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

Example 16 with ReactionStep

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

the class BioPaxRelationshipTableModel method refreshData.

private void refreshData() {
    ArrayList<BioPaxRelationshipTableRow> entityRows = new ArrayList<BioPaxRelationshipTableRow>();
    if (bioModel != null) {
        HashSet<RelationshipObject> relationshipObjects = null;
        if (bioPaxObject != null) {
            relationshipObjects = bioModel.getRelationshipModel().getRelationshipObjects(bioPaxObject);
        }
        List<BioPaxRelationshipTableRow> allEntityRows = new ArrayList<BioPaxRelationshipTableRow>();
        if (bioPaxObject instanceof Conversion) {
            for (ReactionStep rs : bioModel.getModel().getReactionSteps()) {
                BioPaxRelationshipTableRow entityRow = new BioPaxRelationshipTableRow(rs);
                if (relationshipObjects != null) {
                    for (RelationshipObject ro : relationshipObjects) {
                        if (ro.getBioModelEntityObject() == rs) {
                            entityRow.setSelected(true);
                            break;
                        }
                    }
                }
                if (!bShowLinkOnly || entityRow.selected) {
                    allEntityRows.add(entityRow);
                }
            }
            for (ReactionRule rr : bioModel.getModel().getRbmModelContainer().getReactionRuleList()) {
                BioPaxRelationshipTableRow entityRow = new BioPaxRelationshipTableRow(rr);
                if (relationshipObjects != null) {
                    for (RelationshipObject ro : relationshipObjects) {
                        if (ro.getBioModelEntityObject() == rr) {
                            entityRow.setSelected(true);
                            break;
                        }
                    }
                }
                if (!bShowLinkOnly || entityRow.selected) {
                    allEntityRows.add(entityRow);
                }
            }
        } else if (bioPaxObject instanceof PhysicalEntity) {
            for (SpeciesContext rs : bioModel.getModel().getSpeciesContexts()) {
                BioPaxRelationshipTableRow entityRow = new BioPaxRelationshipTableRow(rs);
                if (relationshipObjects != null) {
                    for (RelationshipObject ro : relationshipObjects) {
                        if (ro.getBioModelEntityObject() == rs) {
                            entityRow.setSelected(true);
                            break;
                        }
                    }
                }
                if (!bShowLinkOnly || entityRow.selected) {
                    allEntityRows.add(entityRow);
                }
            }
            for (MolecularType mt : bioModel.getModel().getRbmModelContainer().getMolecularTypeList()) {
                BioPaxRelationshipTableRow entityRow = new BioPaxRelationshipTableRow(mt);
                if (relationshipObjects != null) {
                    for (RelationshipObject ro : relationshipObjects) {
                        if (ro.getBioModelEntityObject() == mt) {
                            entityRow.setSelected(true);
                            break;
                        }
                    }
                }
                if (!bShowLinkOnly || entityRow.selected) {
                    allEntityRows.add(entityRow);
                }
            }
        }
        if (searchText == null || searchText.length() == 0) {
            entityRows.addAll(allEntityRows);
        } else {
            for (BioPaxRelationshipTableRow rs : allEntityRows) {
                BioModelEntityObject object = rs.getBioModelEntityObject();
                String lowerCaseSearchText = searchText.toLowerCase();
                if (object.getName().toLowerCase().contains(lowerCaseSearchText) || object.getTypeLabel().toLowerCase().contains(lowerCaseSearchText)) {
                    entityRows.add(rs);
                }
            }
        }
    }
    setData(entityRows);
    GuiUtils.flexResizeTableColumns(ownerTable);
}

Example 17 with ReactionStep

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

the class IssueTableModel method getSourceObjectPathDescription.

private String getSourceObjectPathDescription(VCDocument vcDocument, Issue issue) {
    VCAssert.assertValid(issue);
    Object source = issue.getSource();
    {
        IssueOrigin io = BeanUtils.downcast(IssueOrigin.class, source);
        if (io != null) {
            return io.getDescription();
        }
    }
    if (vcDocument instanceof BioModel) {
        BioModel bioModel = (BioModel) vcDocument;
        String description = "";
        if (source instanceof SymbolTableEntry) {
            if (source instanceof SpeciesContext) {
                description = "Model / Species";
            } else if (source instanceof RbmObservable) {
                description = "Model / Observables";
            } else {
                description = ((SymbolTableEntry) source).getNameScope().getPathDescription();
            }
        } else if (source instanceof MolecularType) {
            description = "Model / Molecules";
        } else if (source instanceof ReactionStep) {
            ReactionStep reactionStep = (ReactionStep) source;
            description = ((ReactionNameScope) reactionStep.getNameScope()).getPathDescription();
        } else if (source instanceof ReactionRule) {
            ReactionRule reactionRule = (ReactionRule) source;
            description = ((ReactionRuleNameScope) reactionRule.getNameScope()).getPathDescription();
        } else if (source instanceof SpeciesPattern) {
            // if (issue.getIssueContext().hasContextType(ContextType.SpeciesContext)){
            // description = "Model / Species";
            // }else if(issue.getIssueContext().hasContextType(ContextType.ReactionRule)) {
            // ReactionRule thing = (ReactionRule)issue.getIssueContext().getContextObject(ContextType.ReactionRule);
            // description = ((ReactionRuleNameScope)thing.getNameScope()).getPathDescription();
            // }else if(issue.getIssueContext().hasContextType(ContextType.RbmObservable)) {
            // description = "Model / Observables";
            // } else {
            System.err.println("Bad issue context for " + ((SpeciesPattern) source).toString());
            description = ((SpeciesPattern) source).toString();
        // }
        } else if (source instanceof Structure) {
            Structure structure = (Structure) source;
            description = "Model / " + structure.getTypeName() + "(" + structure.getName() + ")";
        } else if (source instanceof StructureMapping) {
            StructureMapping structureMapping = (StructureMapping) source;
            description = ((StructureMappingNameScope) structureMapping.getNameScope()).getPathDescription();
        } else if (source instanceof OutputFunctionIssueSource) {
            SimulationContext simulationContext = (SimulationContext) ((OutputFunctionIssueSource) source).getOutputFunctionContext().getSimulationOwner();
            description = "App(" + simulationContext.getName() + ") / " + "Simulations" + " / " + "Output Functions";
        } else if (source instanceof RateRule) {
            SimulationContext simulationContext = ((RateRule) source).getSimulationContext();
            description = "App(" + simulationContext.getName() + ") / " + "Protocols / " + RateRule.typeName;
        } else if (source instanceof AssignmentRule) {
            SimulationContext simulationContext = ((AssignmentRule) source).getSimulationContext();
            description = "App(" + simulationContext.getName() + ") / " + "Protocols / " + AssignmentRule.typeName;
        } else if (source instanceof Simulation) {
            Simulation simulation = (Simulation) source;
            try {
                SimulationContext simulationContext = bioModel.getSimulationContext(simulation);
                description = "App(" + simulationContext.getName() + ") / Simulations";
            } catch (ObjectNotFoundException e) {
                e.printStackTrace();
                description = "App(" + "unknown" + ") / Simulations";
            }
        } else if (source instanceof UnmappedGeometryClass) {
            UnmappedGeometryClass unmappedGC = (UnmappedGeometryClass) source;
            description = "App(" + unmappedGC.getSimulationContext().getName() + ") / Subdomain(" + unmappedGC.getGeometryClass().getName() + ")";
        } else if (source instanceof GeometryContext) {
            description = "App(" + ((GeometryContext) source).getSimulationContext().getName() + ")";
        } else if (source instanceof ModelOptimizationSpec) {
            description = "App(" + ((ModelOptimizationSpec) source).getSimulationContext().getName() + ") / Parameter Estimation";
        } else if (source instanceof MicroscopeMeasurement) {
            description = "App(" + ((MicroscopeMeasurement) source).getSimulationContext().getName() + ") / Microscope Measurements";
        } else if (source instanceof SpatialObject) {
            description = "App(" + ((SpatialObject) source).getSimulationContext().getName() + ") / Spatial Objects";
        } else if (source instanceof SpatialProcess) {
            description = "App(" + ((SpatialProcess) source).getSimulationContext().getName() + ") / Spatial Processes";
        } else if (source instanceof SpeciesContextSpec) {
            SpeciesContextSpec scs = (SpeciesContextSpec) source;
            description = "App(" + scs.getSimulationContext().getName() + ") / Specifications / Species";
        } else if (source instanceof ReactionCombo) {
            ReactionCombo rc = (ReactionCombo) source;
            description = "App(" + rc.getReactionContext().getSimulationContext().getName() + ") / Specifications / Reactions";
        } else if (source instanceof RbmModelContainer) {
            IssueCategory ic = issue.getCategory();
            switch(ic) {
                case RbmMolecularTypesTableBad:
                    description = "Model / " + MolecularType.typeName + "s";
                    break;
                case RbmReactionRulesTableBad:
                    description = "Model / Reactions";
                    break;
                case RbmObservablesTableBad:
                    description = "Model / Observables";
                    break;
                case RbmNetworkConstraintsBad:
                    description = "Network Constrains";
                    break;
                default:
                    description = "Model";
                    break;
            }
        } else if (source instanceof SimulationContext) {
            SimulationContext sc = (SimulationContext) source;
            IssueCategory ic = issue.getCategory();
            switch(ic) {
                case RbmNetworkConstraintsBad:
                    description = "Specifications / Network";
                    break;
                default:
                    description = "Application";
                    break;
            }
        } else if (source instanceof Model) {
            description = "Model";
        } else if (source instanceof BioEvent) {
            return "Protocols / Events";
        } else if (source instanceof MathDescription) {
            return "Math Description";
        } else {
            System.err.println("unknown source type in IssueTableModel.getSourceObjectPathDescription(): " + source.getClass());
        }
        return description;
    } else if (vcDocument instanceof MathModel) {
        if (source instanceof Geometry) {
            return GuiConstants.DOCUMENT_EDITOR_FOLDERNAME_MATH_GEOMETRY;
        } else if (source instanceof OutputFunctionIssueSource) {
            return GuiConstants.DOCUMENT_EDITOR_FOLDERNAME_MATH_OUTPUTFUNCTIONS;
        } else if (source instanceof Simulation) {
            return "Simulation(" + ((Simulation) source).getName() + ")";
        } else {
            return GuiConstants.DOCUMENT_EDITOR_FOLDERNAME_MATH_VCML;
        }
    } else {
        System.err.println("unknown document type in IssueTableModel.getSourceObjectPathDescription()");
        return "";
    }
}

Example 18 with ReactionStep

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

the class IssueTableModel method getSourceObjectDescription.

private String getSourceObjectDescription(VCDocument vcDocument, Issue issue) {
    if (vcDocument instanceof BioModel) {
        Object object = issue.getSource();
        {
            DecoratedIssueSource dis = BeanUtils.downcast(DecoratedIssueSource.class, object);
            if (dis != null) {
                return dis.getSourcePath();
            }
        }
        String description = "";
        if (object instanceof SymbolTableEntry) {
            description = ((SymbolTableEntry) object).getName();
        } else if (object instanceof ReactionStep) {
            description = ((ReactionStep) object).getName();
        } else if (object instanceof ReactionRule) {
            description = ((ReactionRule) object).getName();
        } else if (object instanceof SpeciesPattern) {
            // Object parent = issue.getIssueContext().getContextObject();
            // if (parent instanceof SpeciesContext){
            // description = ((SpeciesContext)parent).getName();
            // }
            // if (issue.getIssueContext().hasContextType(ContextType.SpeciesContext)){
            // SpeciesContext thing = (SpeciesContext)issue.getIssueContext().getContextObject(ContextType.SpeciesContext);
            // description = thing.getName();
            // }else if(issue.getIssueContext().hasContextType(ContextType.ReactionRule)) {
            // ReactionRule thing = (ReactionRule)issue.getIssueContext().getContextObject(ContextType.ReactionRule);
            // description = thing.getName();
            // }else if(issue.getIssueContext().hasContextType(ContextType.RbmObservable)) {
            // RbmObservable thing = (RbmObservable)issue.getIssueContext().getContextObject(ContextType.RbmObservable);
            // description = thing.getName();
            // } else {
            System.err.println("Bad issue context for " + ((SpeciesPattern) object).toString());
            description = ((SpeciesPattern) object).toString();
        // }
        } else if (object instanceof MolecularType) {
            description = ((MolecularType) object).getName();
        } else if (object instanceof MolecularComponent) {
            description = ((MolecularComponent) object).getName();
        } else if (object instanceof ComponentStateDefinition) {
            description = ((ComponentStateDefinition) object).getName();
        } else if (object instanceof Structure) {
            description = ((Structure) object).getName();
        } else if (object instanceof SubDomain) {
            description = ((SubDomain) object).getName();
        } else if (object instanceof Geometry) {
            description = ((Geometry) object).getName();
        } else if (object instanceof StructureMapping) {
            description = ((StructureMapping) object).getStructure().getName();
        } else if (object instanceof OutputFunctionIssueSource) {
            description = ((OutputFunctionIssueSource) object).getAnnotatedFunction().getName();
        } else if (object instanceof UnmappedGeometryClass) {
            description = ((UnmappedGeometryClass) object).getGeometryClass().getName();
        } else if (object instanceof MicroscopeMeasurement) {
            description = ((MicroscopeMeasurement) object).getName();
        } else if (object instanceof SpatialObject) {
            description = ((SpatialObject) object).getName();
        } else if (object instanceof SpatialProcess) {
            description = ((SpatialProcess) object).getName();
        } else if (object instanceof GeometryContext) {
            description = "Geometry";
        } else if (object instanceof ModelOptimizationSpec) {
            description = ((ModelOptimizationSpec) object).getParameterEstimationTask().getName();
        } else if (object instanceof Simulation) {
            description = ((Simulation) object).getName();
        } else if (object instanceof SpeciesContextSpec) {
            SpeciesContextSpec scs = (SpeciesContextSpec) object;
            description = scs.getSpeciesContext().getName();
        } else if (object instanceof ReactionCombo) {
            ReactionSpec rs = ((ReactionCombo) object).getReactionSpec();
            description = rs.getReactionStep().getName();
        } else if (object instanceof RbmModelContainer) {
            // RbmModelContainer mc = (RbmModelContainer)object;
            description = "Rules validator";
        } else if (object instanceof SimulationContext) {
            SimulationContext sc = (SimulationContext) object;
            description = sc.getName();
        } else if (object instanceof Model) {
            Model m = (Model) object;
            description = m.getName();
        } else if (object instanceof BioEvent) {
            return ((BioEvent) object).getName() + "";
        } else if (object instanceof MathDescription) {
            return ((MathDescription) object).getName() + "";
        } else if (object instanceof AssignmentRule) {
            return ((AssignmentRule) object).getDisplayName() + "";
        } else if (object instanceof RateRule) {
            return ((RateRule) object).getDisplayName() + "";
        } else {
            System.err.println("unknown object type in IssueTableModel.getSourceObjectDescription(): " + object.getClass());
        }
        return description;
    } else if (vcDocument instanceof MathModel) {
        Object object = issue.getSource();
        String description = "";
        if (object instanceof Variable) {
            description = ((Variable) object).getName();
        } else if (object instanceof SubDomain) {
            description = ((SubDomain) object).getName();
        } else if (object instanceof Geometry) {
            description = "Geometry";
        } else if (object instanceof OutputFunctionIssueSource) {
            description = ((OutputFunctionIssueSource) object).getAnnotatedFunction().getName();
        } else if (object instanceof MathDescription) {
            return "math";
        } else if (object instanceof Simulation) {
            return "Simulation " + ((Simulation) object).getName() + "";
        }
        return description;
    } else {
        System.err.println("unknown document type in IssueTableModel.getSourceObjectDescription()");
        return "";
    }
}

Example 19 with ReactionStep

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

the class BioModelParametersTableModel method computeData.

/**
 * Insert the method's description here.
 * Creation date: (9/23/2003 1:24:52 PM)
 * @return cbit.vcell.model.EditableSymbolTableEntry
 * @param row int
 */
protected List<EditableSymbolTableEntry> computeData() {
    ArrayList<EditableSymbolTableEntry> allEditableSymbolTableEntryList = new ArrayList<EditableSymbolTableEntry>();
    if (bioModel == null) {
        return null;
    }
    if (bGlobal) {
        Map<String, SymbolTableEntry> entryMap = new HashMap<String, SymbolTableEntry>();
        bioModel.getModel().getEntries(entryMap);
        for (SymbolTableEntry ste : entryMap.values()) {
            if (ste instanceof EditableSymbolTableEntry && !(ste instanceof ReservedSymbol)) {
                allEditableSymbolTableEntryList.add((EditableSymbolTableEntry) ste);
            }
        }
    }
    if (bReactions) {
        for (ReactionStep reactionStep : bioModel.getModel().getReactionSteps()) {
            allEditableSymbolTableEntryList.addAll(Arrays.asList(reactionStep.getKinetics().getUnresolvedParameters()));
            allEditableSymbolTableEntryList.addAll(Arrays.asList(reactionStep.getKinetics().getKineticsParameters()));
        }
        if (!bioModel.getModel().getRbmModelContainer().isEmpty()) {
            for (ReactionRule reactionRule : bioModel.getModel().getRbmModelContainer().getReactionRuleList()) {
                allEditableSymbolTableEntryList.addAll(Arrays.asList(reactionRule.getKineticLaw().getLocalParameters()));
                allEditableSymbolTableEntryList.addAll(Arrays.asList(reactionRule.getKineticLaw().getProxyParameters()));
                allEditableSymbolTableEntryList.addAll(Arrays.asList(reactionRule.getKineticLaw().getUnresolvedParameters()));
            }
        }
    }
    if (bApplications) {
        for (SimulationContext simContext : bioModel.getSimulationContexts()) {
            if (applicationSelection != null && (applicationSelection.isAll() || applicationSelection.getSimulationContext() == simContext)) {
                allEditableSymbolTableEntryList.addAll(getApplicationEditableSymbolTableEntryList(simContext));
            }
        }
    }
    boolean bSearchInactive = searchText == null || searchText.length() == 0;
    String lowerCaseSearchText = bSearchInactive ? null : searchText.toLowerCase();
    ArrayList<EditableSymbolTableEntry> parameterList = new ArrayList<EditableSymbolTableEntry>();
    for (EditableSymbolTableEntry parameter : allEditableSymbolTableEntryList) {
        boolean bNumeric = parameter.getExpression() == null || parameter.getExpression().isNumeric();
        if (bConstants && bNumeric || bFunctions && !bNumeric) {
            if (bSearchInactive || parameter.getNameScope().getPathDescription().toLowerCase().contains(lowerCaseSearchText) || parameter.getName().toLowerCase().contains(lowerCaseSearchText) || parameter.getExpression() != null && parameter.getExpression().infix().toLowerCase().contains(lowerCaseSearchText) || parameter.getDescription().toLowerCase().contains(lowerCaseSearchText)) {
                parameterList.add(parameter);
            }
        }
    }
    return parameterList;
}

Example 20 with ReactionStep

use of cbit.vcell.model.ReactionStep 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);
        // }
        }
    }
}