Examples with SpeciesContextSpec cbit.vcell.mapping.SpeciesContextSpec used on opensource projects

Example 61 with SpeciesContextSpec

use of cbit.vcell.mapping.SpeciesContextSpec in project vcell by virtualcell.

the class RuleBasedTest method checkNonspatialStochasticSimContext.

private static void checkNonspatialStochasticSimContext(SimulationContext srcSimContext, File baseDirectory, int numTrials) throws Exception {
    if (!srcSimContext.getApplicationType().equals(Application.NETWORK_STOCHASTIC) || srcSimContext.getGeometry().getDimension() != 0) {
        throw new RuntimeException("simContext is of type " + srcSimContext.getApplicationType() + " and geometry dimension of " + srcSimContext.getGeometry().getDimension() + ", expecting nonspatial stochastic");
    }
    BioModel origBioModel = srcSimContext.getBioModel();
    BioModel bioModel = XmlHelper.XMLToBioModel(new XMLSource(XmlHelper.bioModelToXML(origBioModel)));
    bioModel.refreshDependencies();
    // create ODE and RuleBased
    SimulationContext newODEApp = SimulationContext.copySimulationContext(srcSimContext, "aUniqueNewODEApp", false, Application.NETWORK_DETERMINISTIC);
    SimulationContext newRuleBasedApp = SimulationContext.copySimulationContext(srcSimContext, "aUniqueNewRuleBasedApp", false, Application.RULE_BASED_STOCHASTIC);
    newODEApp.setBioModel(bioModel);
    newRuleBasedApp.setBioModel(bioModel);
    ArrayList<AnnotatedFunction> outputFunctionsList = srcSimContext.getOutputFunctionContext().getOutputFunctionsList();
    // OutputContext outputContext = new OutputContext(outputFunctionsList.toArray(new AnnotatedFunction[outputFunctionsList.size()]));
    newODEApp.getOutputFunctionContext().setOutputFunctions(outputFunctionsList);
    newRuleBasedApp.getOutputFunctionContext().setOutputFunctions(outputFunctionsList);
    NetworkGenerationRequirements networkGenerationRequirements = NetworkGenerationRequirements.AllowTruncatedStandardTimeout;
    bioModel.addSimulationContext(newODEApp);
    newODEApp.refreshMathDescription(new MathMappingCallbackTaskAdapter(null), networkGenerationRequirements);
    bioModel.addSimulationContext(newRuleBasedApp);
    newRuleBasedApp.refreshMathDescription(new MathMappingCallbackTaskAdapter(null), networkGenerationRequirements);
    srcSimContext.refreshMathDescription(new MathMappingCallbackTaskAdapter(null), networkGenerationRequirements);
    // Create non-spatialStoch, ODE and RuleBased sims
    Simulation nonspatialStochAppNewSim = srcSimContext.addNewSimulation(STOCH_SIM_NAME, /*SimulationOwner.DEFAULT_SIM_NAME_PREFIX*/
    new MathMappingCallbackTaskAdapter(null), networkGenerationRequirements);
    Simulation newODEAppNewSim = newODEApp.addNewSimulation(ODE_SIM_NAME, new MathMappingCallbackTaskAdapter(null), networkGenerationRequirements);
    Simulation newRuleBasedAppNewSim = newRuleBasedApp.addNewSimulation(NFS_SIM_NAME, new MathMappingCallbackTaskAdapter(null), networkGenerationRequirements);
    nonspatialStochAppNewSim.setSimulationOwner(srcSimContext);
    newODEAppNewSim.setSimulationOwner(newODEApp);
    newRuleBasedAppNewSim.setSimulationOwner(newRuleBasedApp);
    try {
        bioModel.getModel().getSpeciesContexts();
        ArrayList<String> varNameList = new ArrayList<String>();
        for (SpeciesContextSpec scs : srcSimContext.getReactionContext().getSpeciesContextSpecs()) {
            varNameList.add(scs.getSpeciesContext().getName());
        }
        String[] varNames = varNameList.toArray(new String[0]);
        OutputTimeSpec outputTimeSpec = nonspatialStochAppNewSim.getSolverTaskDescription().getOutputTimeSpec();
        ArrayList<Double> sampleTimeList = new ArrayList<Double>();
        if (outputTimeSpec instanceof UniformOutputTimeSpec) {
            double endingTime = nonspatialStochAppNewSim.getSolverTaskDescription().getTimeBounds().getEndingTime();
            double dT = ((UniformOutputTimeSpec) outputTimeSpec).getOutputTimeStep();
            int currTimeIndex = 0;
            while (currTimeIndex * dT <= (endingTime + 1e-8)) {
                sampleTimeList.add(currTimeIndex * dT);
                currTimeIndex++;
            }
        }
        double[] sampleTimes = new double[sampleTimeList.size()];
        for (int i = 0; i < sampleTimes.length; i++) {
            sampleTimes[i] = sampleTimeList.get(i);
        }
        TimeSeriesMultitrialData sampleDataStoch1 = new TimeSeriesMultitrialData("stochastic1", varNames, sampleTimes, numTrials);
        TimeSeriesMultitrialData sampleDataStoch2 = new TimeSeriesMultitrialData("stochastic2", varNames, sampleTimes, numTrials);
        TimeSeriesMultitrialData sampleDataDeterministic = new TimeSeriesMultitrialData("determinstic", varNames, sampleTimes, 1);
        runsolver(nonspatialStochAppNewSim, baseDirectory, numTrials, sampleDataStoch1);
        runsolver(newODEAppNewSim, baseDirectory, 1, sampleDataDeterministic);
        runsolver(newRuleBasedAppNewSim, baseDirectory, numTrials, sampleDataStoch2);
        writeVarDiffData(baseDirectory, sampleDataStoch1, sampleDataStoch2);
        writeKolmogorovSmirnovTest(baseDirectory, sampleDataStoch1, sampleDataStoch2);
        writeChiSquareTest(baseDirectory, sampleDataStoch1, sampleDataStoch2);
        writeData(baseDirectory, sampleDataStoch1);
        writeData(baseDirectory, sampleDataStoch2);
        writeData(baseDirectory, sampleDataDeterministic);
    } finally {
        srcSimContext.removeSimulation(nonspatialStochAppNewSim);
        newODEApp.removeSimulation(newODEAppNewSim);
        newRuleBasedApp.removeSimulation(newRuleBasedAppNewSim);
    }
}

Example 62 with SpeciesContextSpec

use of cbit.vcell.mapping.SpeciesContextSpec in project vcell by virtualcell.

the class IssuePanel method invokeHyperlink.

private void invokeHyperlink(Issue issue) {
    if (selectionManager != null) {
        // followHyperlink is no-op if selectionManger null, so no point in proceeding if it is
        IssueContext issueContext = issue.getIssueContext();
        IssueSource object = issue.getSource();
        if (object instanceof DecoratedIssueSource) {
            DecoratedIssueSource dis = (DecoratedIssueSource) object;
            dis.activateView(selectionManager);
        } else if (object instanceof Parameter) {
            followHyperlink(new ActiveView(null, DocumentEditorTreeFolderClass.BIOMODEL_PARAMETERS_NODE, ActiveViewID.parameters_functions), new Object[] { object });
        } else if (object instanceof StructureMapping) {
            StructureMapping structureMapping = (StructureMapping) object;
            StructureMappingNameScope structureMappingNameScope = (StructureMappingNameScope) structureMapping.getNameScope();
            SimulationContext simulationContext = ((SimulationContextNameScope) (structureMappingNameScope.getParent())).getSimulationContext();
            followHyperlink(new ActiveView(simulationContext, DocumentEditorTreeFolderClass.GEOMETRY_NODE, ActiveViewID.structure_mapping), new Object[] { object });
        } else if (object instanceof SpatialObject) {
            SpatialObject spatialObject = (SpatialObject) object;
            SimulationContext simulationContext = spatialObject.getSimulationContext();
            followHyperlink(new ActiveView(simulationContext, DocumentEditorTreeFolderClass.GEOMETRY_NODE, ActiveViewID.spatial_objects), new Object[] { object });
        } else if (object instanceof SpatialProcess) {
            SpatialProcess spatialProcess = (SpatialProcess) object;
            SimulationContext simulationContext = spatialProcess.getSimulationContext();
            followHyperlink(new ActiveView(simulationContext, DocumentEditorTreeFolderClass.GEOMETRY_NODE, ActiveViewID.spatial_processes), new Object[] { object });
        } else if (object instanceof GeometryContext.UnmappedGeometryClass) {
            UnmappedGeometryClass unmappedGeometryClass = (UnmappedGeometryClass) object;
            SimulationContext simulationContext = unmappedGeometryClass.getSimulationContext();
            followHyperlink(new ActiveView(simulationContext, DocumentEditorTreeFolderClass.GEOMETRY_NODE, ActiveViewID.structure_mapping), new Object[] { object });
        } else if (object instanceof MicroscopeMeasurement) {
            SimulationContext simulationContext = ((MicroscopeMeasurement) object).getSimulationContext();
            followHyperlink(new ActiveView(simulationContext, DocumentEditorTreeFolderClass.PROTOCOLS_NODE, ActiveViewID.microscope_measuremments), new Object[] { object });
        } else if (object instanceof BioEvent) {
            BioEvent be = (BioEvent) object;
            SimulationContext simulationContext = be.getSimulationContext();
            followHyperlink(new ActiveView(simulationContext, DocumentEditorTreeFolderClass.PROTOCOLS_NODE, ActiveViewID.events), new Object[] { object });
        } else if (object instanceof OutputFunctionIssueSource) {
            SimulationOwner simulationOwner = ((OutputFunctionIssueSource) object).getOutputFunctionContext().getSimulationOwner();
            if (simulationOwner instanceof SimulationContext) {
                SimulationContext simulationContext = (SimulationContext) simulationOwner;
                followHyperlink(new ActiveView(simulationContext, DocumentEditorTreeFolderClass.SIMULATIONS_NODE, ActiveViewID.output_functions), new Object[] { ((OutputFunctionIssueSource) object).getAnnotatedFunction() });
            } else if (simulationOwner instanceof MathModel) {
                followHyperlink(new ActiveView(null, DocumentEditorTreeFolderClass.MATH_OUTPUT_FUNCTIONS_NODE, ActiveViewID.math_output_functions), new Object[] { ((OutputFunctionIssueSource) object).getAnnotatedFunction() });
            }
        } else if (object instanceof Simulation) {
            Simulation simulation = (Simulation) object;
            SimulationOwner simulationOwner = simulation.getSimulationOwner();
            if (simulationOwner instanceof SimulationContext) {
                SimulationContext simulationContext = (SimulationContext) simulationOwner;
                followHyperlink(new ActiveView(simulationContext, DocumentEditorTreeFolderClass.SIMULATIONS_NODE, ActiveViewID.simulations), new Object[] { simulation });
            } else if (simulationOwner instanceof MathModel) {
                followHyperlink(new ActiveView(null, DocumentEditorTreeFolderClass.MATH_SIMULATIONS_NODE, ActiveViewID.math_simulations), new Object[] { simulation });
            }
        } else if (object instanceof AssignmentRule) {
            AssignmentRule ar = (AssignmentRule) object;
            SimulationContext sc = ar.getSimulationContext();
            followHyperlink(new ActiveView(sc, DocumentEditorTreeFolderClass.PROTOCOLS_NODE, ActiveViewID.assignmentRules), new Object[] { ar });
        } else if (object instanceof RateRule) {
            RateRule rr = (RateRule) object;
            SimulationContext sc = rr.getSimulationContext();
            followHyperlink(new ActiveView(sc, DocumentEditorTreeFolderClass.PROTOCOLS_NODE, ActiveViewID.rateRules), new Object[] { rr });
        } else if (object instanceof GeometryContext) {
            setActiveView(new ActiveView(((GeometryContext) object).getSimulationContext(), DocumentEditorTreeFolderClass.GEOMETRY_NODE, ActiveViewID.geometry_definition));
        } else if (object instanceof Structure) {
            followHyperlink(new ActiveView(null, DocumentEditorTreeFolderClass.STRUCTURES_NODE, ActiveViewID.structures), new Object[] { object });
        } else if (object instanceof MolecularType) {
            followHyperlink(new ActiveView(null, DocumentEditorTreeFolderClass.MOLECULAR_TYPES_NODE, ActiveViewID.structures), new Object[] { object });
        } else if (object instanceof ReactionStep) {
            followHyperlink(new ActiveView(null, DocumentEditorTreeFolderClass.REACTIONS_NODE, ActiveViewID.reactions), new Object[] { object });
        } else if (object instanceof ReactionRule) {
            followHyperlink(new ActiveView(null, DocumentEditorTreeFolderClass.REACTIONS_NODE, ActiveViewID.reactions), new Object[] { object });
        } else if (object instanceof SpeciesContextSpec) {
            SpeciesContextSpec scs = (SpeciesContextSpec) object;
            ActiveView av = new ActiveView(scs.getSimulationContext(), DocumentEditorTreeFolderClass.SPECIFICATIONS_NODE, ActiveViewID.species_settings);
            followHyperlink(av, new Object[] { object });
        } else if (object instanceof ReactionCombo) {
            ReactionCombo rc = (ReactionCombo) object;
            followHyperlink(new ActiveView(rc.getReactionContext().getSimulationContext(), DocumentEditorTreeFolderClass.SPECIFICATIONS_NODE, ActiveViewID.reaction_setting), new Object[] { ((ReactionCombo) object).getReactionSpec() });
        } else if (object instanceof SpeciesContext) {
            followHyperlink(new ActiveView(null, DocumentEditorTreeFolderClass.SPECIES_NODE, ActiveViewID.species), new Object[] { object });
        } else if (object instanceof RbmObservable) {
            followHyperlink(new ActiveView(null, DocumentEditorTreeFolderClass.OBSERVABLES_NODE, ActiveViewID.observables), new Object[] { object });
        } else if (object instanceof MathDescription) {
            // followHyperlink(new ActiveView(null, DocumentEditorTreeFolderClass.MATH_SIMULATIONS_NODE, ActiveViewID.generated_math), new Object[] {object});
            followHyperlink(new ActiveView(null, DocumentEditorTreeFolderClass.GEOMETRY_NODE, ActiveViewID.structure_mapping), new Object[] { object });
        } else if (object instanceof SpeciesPattern) {
            // if (issue.getIssueContext().hasContextType(ContextType.SpeciesContext)){
            // SpeciesContext thing = (SpeciesContext)issue.getIssueContext().getContextObject(ContextType.SpeciesContext);
            // followHyperlink(new ActiveView(null, DocumentEditorTreeFolderClass.SPECIES_NODE, ActiveViewID.species), new Object[] {thing});
            // }else if(issue.getIssueContext().hasContextType(ContextType.ReactionRule)) {
            // ReactionRule thing = (ReactionRule)issue.getIssueContext().getContextObject(ContextType.ReactionRule);
            // followHyperlink(new ActiveView(null, DocumentEditorTreeFolderClass.REACTIONS_NODE, ActiveViewID.reactions), new Object[] {thing});
            // }else if(issue.getIssueContext().hasContextType(ContextType.RbmObservable)) {
            // RbmObservable thing = (RbmObservable)issue.getIssueContext().getContextObject(ContextType.RbmObservable);
            // followHyperlink(new ActiveView(null, DocumentEditorTreeFolderClass.OBSERVABLES_NODE, ActiveViewID.observables), new Object[] {thing});
            // } else {
            System.err.println("SpeciesPattern object missing a proper issue context.");
        // }
        } else if (object instanceof SimulationContext) {
            SimulationContext sc = (SimulationContext) object;
            IssueCategory ic = issue.getCategory();
            switch(ic) {
                case RbmNetworkConstraintsBad:
                    NetworkConstraints nc = sc.getNetworkConstraints();
                    if (issue.getMessage() == SimulationContext.IssueInsufficientMolecules) {
                        NetworkConstraintsEntity nce = new NetworkConstraintsEntity(NetworkConstraintsTableModel.sMaxMoleculesName, nc.getMaxMoleculesPerSpecies() + "", NetworkTransformer.defaultMaxMoleculesPerSpecies + "");
                        followHyperlink(new ActiveView(sc, DocumentEditorTreeFolderClass.SPECIFICATIONS_NODE, ActiveViewID.network_setting), new Object[] { nce });
                    } else {
                        NetworkConstraintsEntity nce = new NetworkConstraintsEntity(NetworkConstraintsTableModel.sMaxIterationName, nc.getMaxIteration() + "", NetworkTransformer.defaultMaxIteration + "");
                        followHyperlink(new ActiveView(sc, DocumentEditorTreeFolderClass.SPECIFICATIONS_NODE, ActiveViewID.network_setting), new Object[] { nce });
                    }
                    break;
                default:
                    followHyperlink(new ActiveView(sc, DocumentEditorTreeFolderClass.SPECIFICATIONS_NODE, ActiveViewID.network_setting), new Object[] { object });
                    break;
            }
        } else if (object instanceof Geometry) {
            if (issueContext.hasContextType(ContextType.SimContext)) {
                SimulationContext simContext = (SimulationContext) issueContext.getContextObject(ContextType.SimContext);
                followHyperlink(new ActiveView(simContext, DocumentEditorTreeFolderClass.GEOMETRY_NODE, ActiveViewID.geometry_definition), new Object[] { object });
            } else if (issueContext.hasContextType(ContextType.MathModel)) {
                followHyperlink(new ActiveView(null, DocumentEditorTreeFolderClass.MATH_GEOMETRY_NODE, ActiveViewID.math_geometry), new Object[] { object });
            } else if (issueContext.hasContextType(ContextType.MathDescription)) {
                followHyperlink(new ActiveView(null, DocumentEditorTreeFolderClass.GEOMETRY_NODE, ActiveViewID.geometry_definition), new Object[] { object });
            }
        } else {
            System.err.println("unknown object type in IssuePanel.invokeHyperlink(): " + object.getClass() + ", context type: " + issueContext.getContextType());
        }
    }
}

Example 63 with SpeciesContextSpec

use of cbit.vcell.mapping.SpeciesContextSpec in project vcell by virtualcell.

the class BioModelParametersTableModel method getApplicationEditableSymbolTableEntryList.

private List<EditableSymbolTableEntry> getApplicationEditableSymbolTableEntryList(SimulationContext simulationContext) {
    ArrayList<EditableSymbolTableEntry> parameterList = new ArrayList<EditableSymbolTableEntry>();
    Map<String, SymbolTableEntry> entryMap = new HashMap<String, SymbolTableEntry>();
    simulationContext.getEntries(entryMap);
    for (SymbolTableEntry ste : entryMap.values()) {
        if (ste instanceof EditableSymbolTableEntry && ste.getNameScope() == simulationContext.getNameScope()) {
            parameterList.add((EditableSymbolTableEntry) ste);
        }
    }
    for (StructureMapping mapping : simulationContext.getGeometryContext().getStructureMappings()) {
        parameterList.addAll(mapping.computeApplicableParameterList());
    }
    for (SpeciesContextSpec spec : simulationContext.getReactionContext().getSpeciesContextSpecs()) {
        parameterList.addAll(spec.computeApplicableParameterList());
    }
    for (ElectricalStimulus elect : simulationContext.getElectricalStimuli()) {
        parameterList.addAll(Arrays.asList(elect.getParameters()));
    }
    for (SpatialProcess sp : simulationContext.getSpatialProcesses()) {
        parameterList.addAll(Arrays.asList(sp.getParameters()));
    }
    return parameterList;
}

Example 64 with SpeciesContextSpec

use of cbit.vcell.mapping.SpeciesContextSpec 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);
            }
        }
    }
}