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

Example 1 with GeometryContext

use of cbit.vcell.mapping.GeometryContext 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 GeometryContext

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

the class TestingFrameworkWindowManager method addTestCases.

/**
 * Insert the method's description here.
 * Creation date: (4/10/2003 11:27:32 AM)
 * @param testCase cbit.vcell.numericstestingframework.TestCase
 */
public String addTestCases(final TestSuiteInfoNew tsInfo, final TestCaseNew[] testCaseArray, int regrRefFlag, ClientTaskStatusSupport pp) {
    if (tsInfo == null) {
        throw new IllegalArgumentException("TestSuiteInfo cannot be null");
    }
    if (testCaseArray == null || testCaseArray.length == 0) {
        throw new IllegalArgumentException("TestCases cannot be null / empty");
    }
    // make modifiable list
    List<TestCaseNew> testCases = new ArrayList<>(Arrays.asList(testCaseArray));
    StringBuffer errors = new StringBuffer();
    // When a testCase (mathmodel/biomodel) is added to a testSuite, a new version of the mathModel/biomodel should be created.
    // Also, the simulations in the original mathmodel/biomodel should be rid of their parent simulation reference.
    pp.setMessage("Getting testSuite");
    pp.setProgress(1);
    TestSuiteNew testSuite = null;
    try {
        testSuite = getRequestManager().getDocumentManager().getTestSuite(tsInfo.getTSKey());
    } catch (Throwable e) {
        throw new RuntimeException("couldn't get test suite " + tsInfo.getTSID() + "\n" + e.getClass().getName() + " mesg=" + e.getMessage() + "\n");
    }
    if (testSuite != null && testSuite.getTSInfoNew().isLocked()) {
        throw new RuntimeException("Cannot addTestCases to locked table");
    }
    if (testSuite != null) {
        // Saving BioModels
        TestCaseNew[] existingTestCases = testSuite.getTestCases();
        java.util.HashMap<KeyValue, BioModel> bioModelHashMap = new java.util.HashMap<KeyValue, BioModel>();
        // if(existingTestCases != null){
        // Find BioModels, Using the same BM reference for sibling Applications
        int pcounter = 0;
        // use iterator to allow removal of test case from collection if exception
        Iterator<TestCaseNew> iter = testCases.iterator();
        while (iter.hasNext()) {
            TestCaseNew testCase = iter.next();
            pp.setProgress(Math.max(1, ((int) ((pcounter++ / (double) (testCases.size() * 3)) * 100))));
            pp.setMessage("Checking " + testCase.getVersion().getName());
            try {
                if (testCase instanceof TestCaseNewBioModel) {
                    TestCaseNewBioModel bioTestCase = (TestCaseNewBioModel) testCase;
                    // 
                    if (bioModelHashMap.get(bioTestCase.getBioModelInfo().getVersion().getVersionKey()) == null) {
                        pp.setMessage("Getting BM " + testCase.getVersion().getName());
                        BioModel bioModel = getRequestManager().getDocumentManager().getBioModel(bioTestCase.getBioModelInfo().getVersion().getVersionKey());
                        if (!bioModel.getVersion().getOwner().equals(getRequestManager().getDocumentManager().getUser())) {
                            throw new Exception("BioModel does not belong to VCELLTESTACCOUNT, cannot proceed with test!");
                        }
                        // 
                        // if biomodel already exists in same testsuite, then use this BioModel edition
                        // 
                        BioModel newBioModel = null;
                        if (existingTestCases != null) {
                            for (int j = 0; newBioModel == null && j < existingTestCases.length; j++) {
                                if (existingTestCases[j] instanceof TestCaseNewBioModel) {
                                    TestCaseNewBioModel existingTestCaseBioModel = (TestCaseNewBioModel) existingTestCases[j];
                                    // 
                                    if (existingTestCaseBioModel.getBioModelInfo().getVersion().getBranchID().equals(bioTestCase.getBioModelInfo().getVersion().getBranchID())) {
                                        // 
                                        if (existingTestCaseBioModel.getBioModelInfo().getVersion().getVersionKey().equals(bioTestCase.getBioModelInfo().getVersion().getVersionKey())) {
                                            // 
                                            // same, store this "unchanged" in bioModelHashMap
                                            // 
                                            newBioModel = bioModel;
                                        } else {
                                            // 
                                            throw new Exception("can't add new test case using (" + bioTestCase.getBioModelInfo().getVersion().getName() + " " + bioTestCase.getBioModelInfo().getVersion().getDate() + ")\n" + "a test case already exists with different edition of same BioModel dated " + existingTestCaseBioModel.getBioModelInfo().getVersion().getDate());
                                        }
                                    }
                                }
                            }
                        }
                        if (newBioModel == null) {
                            pp.setMessage("Saving BM " + testCase.getVersion().getName());
                            // 
                            // some older models have membrane voltage variable names which are not unique
                            // (e.g. membranes 'pm' and 'nm' both have membrane voltage variables named 'Voltage_Membrane0')
                            // 
                            // if this is the case, we will try to repair the conflict (for math testing purposes only) by renaming the voltage variables to their default values.
                            // 
                            // Ordinarily, the conflict will be identified as an "Error" issue and the user will be prompted to repair before saving or math generation.
                            // 
                            bioModel.refreshDependencies();
                            boolean bFoundIdentifierConflictUponLoading = hasDuplicateIdentifiers(bioModel);
                            if (bFoundIdentifierConflictUponLoading) {
                                // 
                                // look for two MembraneVoltage instances with same variable name, rename all
                                // 
                                HashSet<String> membraneVoltageVarNames = new HashSet<String>();
                                ArrayList<MembraneVoltage> membraneVoltageVars = new ArrayList<MembraneVoltage>();
                                for (Structure struct : bioModel.getModel().getStructures()) {
                                    if (struct instanceof Membrane) {
                                        MembraneVoltage membraneVoltage = ((Membrane) struct).getMembraneVoltage();
                                        if (membraneVoltage != null) {
                                            membraneVoltageVars.add(membraneVoltage);
                                            membraneVoltageVarNames.add(membraneVoltage.getName());
                                        }
                                    }
                                }
                                if (membraneVoltageVars.size() != membraneVoltageVarNames.size()) {
                                    // rename them all to the default names
                                    for (MembraneVoltage memVoltage : membraneVoltageVars) {
                                        memVoltage.setName(Membrane.getDefaultMembraneVoltageName(memVoltage.getMembrane().getName()));
                                    }
                                }
                            }
                            SimulationContext[] simContexts = bioModel.getSimulationContexts();
                            for (int j = 0; j < simContexts.length; j++) {
                                simContexts[j].clearVersion();
                                GeometrySurfaceDescription gsd = simContexts[j].getGeometry().getGeometrySurfaceDescription();
                                if (gsd != null) {
                                    GeometricRegion[] grArr = gsd.getGeometricRegions();
                                    if (grArr == null) {
                                        gsd.updateAll();
                                    }
                                }
                                MathMapping mathMapping = simContexts[j].createNewMathMapping();
                                // for older models that do not have absolute compartment sizes set, but have relative sizes (SVR/VF); or if there is only one compartment with size not set,
                                // compute absolute compartment sizes using relative sizes and assuming a default value of '1' for one of the compartments.
                                // Otherwise, the math generation will fail, since for the relaxed topology (VCell 5.3 and later) absolute compartment sizes are required.
                                GeometryContext gc = simContexts[j].getGeometryContext();
                                if (simContexts[j].getGeometry().getDimension() == 0 && ((gc.isAllSizeSpecifiedNull() && !gc.isAllVolFracAndSurfVolSpecifiedNull()) || (gc.getModel().getStructures().length == 1 && gc.isAllSizeSpecifiedNull()))) {
                                    // choose the first structure in model and set its size to '1'.
                                    Structure struct = simContexts[j].getModel().getStructure(0);
                                    double structSize = 1.0;
                                    StructureSizeSolver.updateAbsoluteStructureSizes(simContexts[j], struct, structSize, struct.getStructureSize().getUnitDefinition());
                                }
                                simContexts[j].setMathDescription(mathMapping.getMathDescription());
                            }
                            Simulation[] sims = bioModel.getSimulations();
                            String[] simNames = new String[sims.length];
                            for (int j = 0; j < sims.length; j++) {
                                // prevents parent simulation (from the original mathmodel) reference connection
                                // Otherwise it will refer to data from previous (parent) simulation.
                                sims[j].clearVersion();
                                simNames[j] = sims[j].getName();
                            // if(sims[j].getSolverTaskDescription().getSolverDescription().equals(SolverDescription.FiniteVolume)){
                            // sims[j].getSolverTaskDescription().setSolverDescription(SolverDescription.FiniteVolumeStandalone);
                            // }
                            }
                            newBioModel = getRequestManager().getDocumentManager().save(bioModel, simNames);
                        }
                        bioModelHashMap.put(bioTestCase.getBioModelInfo().getVersion().getVersionKey(), newBioModel);
                    }
                }
            } catch (Throwable e) {
                String identifier = testCase.getVersion() != null ? "Name=" + testCase.getVersion().getName() : "TCKey=" + testCase.getTCKey();
                if (lg.isInfoEnabled()) {
                    lg.info(identifier, e);
                }
                errors.append("Error collecting BioModel for TestCase " + identifier + '\n' + e.getClass().getName() + " " + e.getMessage() + '\n');
                // remove to avoid further processing attempts
                iter.remove();
            }
        }
        // }
        // then process each BioModelTestCase individually
        // if(bioModelHashMap != null){
        pcounter = 0;
        for (TestCaseNew testCase : testCases) {
            pp.setProgress(Math.max(1, ((int) ((pcounter++ / (double) (testCases.size() * 3)) * 100))));
            pp.setMessage("Checking " + testCase.getVersion().getName());
            try {
                AddTestCasesOP testCaseOP = null;
                if (testCase instanceof TestCaseNewBioModel) {
                    pp.setMessage("Processing BM " + testCase.getVersion().getName());
                    TestCaseNewBioModel bioTestCase = (TestCaseNewBioModel) testCase;
                    BioModel newBioModel = (BioModel) bioModelHashMap.get(bioTestCase.getBioModelInfo().getVersion().getVersionKey());
                    if (newBioModel == null) {
                        throw new Exception("BioModel not found");
                    }
                    SimulationContext simContext = null;
                    for (int j = 0; j < newBioModel.getSimulationContexts().length; j++) {
                        if (newBioModel.getSimulationContext(j).getName().equals(bioTestCase.getSimContextName())) {
                            simContext = newBioModel.getSimulationContext(j);
                        }
                    }
                    Simulation[] newSimulations = simContext.getSimulations();
                    AddTestCriteriaOPBioModel[] testCriteriaOPs = new AddTestCriteriaOPBioModel[newSimulations.length];
                    for (int j = 0; j < newSimulations.length; j++) {
                        TestCriteriaNewBioModel tcritOrigForSimName = null;
                        for (int k = 0; bioTestCase.getTestCriterias() != null && k < bioTestCase.getTestCriterias().length; k += 1) {
                            if (bioTestCase.getTestCriterias()[k].getSimInfo().getName().equals(newSimulations[j].getName())) {
                                tcritOrigForSimName = (TestCriteriaNewBioModel) bioTestCase.getTestCriterias()[k];
                                break;
                            }
                        }
                        KeyValue regressionBioModelKey = null;
                        KeyValue regressionBioModelSimKey = null;
                        if (bioTestCase.getType().equals(TestCaseNew.REGRESSION)) {
                            if (regrRefFlag == TestingFrameworkWindowManager.COPY_REGRREF) {
                                regressionBioModelKey = (tcritOrigForSimName != null && tcritOrigForSimName.getRegressionBioModelInfo() != null ? tcritOrigForSimName.getRegressionBioModelInfo().getVersion().getVersionKey() : null);
                                regressionBioModelSimKey = (tcritOrigForSimName != null && tcritOrigForSimName.getRegressionSimInfo() != null ? tcritOrigForSimName.getRegressionSimInfo().getVersion().getVersionKey() : null);
                            } else if (regrRefFlag == TestingFrameworkWindowManager.ASSIGNORIGINAL_REGRREF) {
                                regressionBioModelKey = (tcritOrigForSimName != null ? bioTestCase.getBioModelInfo().getVersion().getVersionKey() : null);
                                regressionBioModelSimKey = (tcritOrigForSimName != null ? tcritOrigForSimName.getSimInfo().getVersion().getVersionKey() : null);
                            } else if (regrRefFlag == TestingFrameworkWindowManager.ASSIGNNEW_REGRREF) {
                                regressionBioModelKey = newBioModel.getVersion().getVersionKey();
                                regressionBioModelSimKey = newSimulations[j].getVersion().getVersionKey();
                            } else {
                                throw new IllegalArgumentException(this.getClass().getName() + ".addTestCases(...) BIOMODEL Unknown Regression Operation Flag");
                            }
                        }
                        testCriteriaOPs[j] = new AddTestCriteriaOPBioModel(testCase.getTCKey(), newSimulations[j].getVersion().getVersionKey(), regressionBioModelKey, regressionBioModelSimKey, (tcritOrigForSimName != null ? tcritOrigForSimName.getMaxAbsError() : new Double(1e-16)), (tcritOrigForSimName != null ? tcritOrigForSimName.getMaxRelError() : new Double(1e-9)), null);
                    }
                    testCaseOP = new AddTestCasesOPBioModel(new BigDecimal(tsInfo.getTSKey().toString()), newBioModel.getVersion().getVersionKey(), simContext.getKey(), bioTestCase.getType(), bioTestCase.getAnnotation(), testCriteriaOPs);
                    getRequestManager().getDocumentManager().doTestSuiteOP(testCaseOP);
                }
            } catch (Throwable e) {
                errors.append("Error processing Biomodel for TestCase " + (testCase.getVersion() != null ? "Name=" + testCase.getVersion().getName() : "TCKey=" + testCase.getTCKey()) + "\n" + e.getClass().getName() + " " + e.getMessage() + "\n");
            }
        }
        // }
        // Process MathModels
        pcounter = 0;
        for (TestCaseNew testCase : testCases) {
            pp.setProgress(Math.max(1, ((int) ((pcounter++ / (double) (testCases.size() * 3)) * 100))));
            pp.setMessage("Checking " + testCase.getVersion().getName());
            try {
                AddTestCasesOP testCaseOP = null;
                if (testCase instanceof TestCaseNewMathModel) {
                    TestCaseNewMathModel mathTestCase = (TestCaseNewMathModel) testCase;
                    pp.setMessage("Getting MathModel " + testCase.getVersion().getName());
                    MathModel mathModel = getRequestManager().getDocumentManager().getMathModel(mathTestCase.getMathModelInfo().getVersion().getVersionKey());
                    if (!mathModel.getVersion().getOwner().equals(getRequestManager().getDocumentManager().getUser())) {
                        throw new Exception("MathModel does not belong to VCELLTESTACCOUNT, cannot proceed with test!");
                    }
                    Simulation[] sims = mathModel.getSimulations();
                    String[] simNames = new String[sims.length];
                    for (int j = 0; j < sims.length; j++) {
                        // prevents parent simulation (from the original mathmodel) reference connection
                        // Otherwise it will refer to data from previous (parent) simulation.
                        sims[j].clearVersion();
                        simNames[j] = sims[j].getName();
                    // if(sims[j].getSolverTaskDescription().getSolverDescription().equals(SolverDescription.FiniteVolume)){
                    // sims[j].getSolverTaskDescription().setSolverDescription(SolverDescription.FiniteVolumeStandalone);
                    // }
                    }
                    pp.setMessage("Saving MathModel " + testCase.getVersion().getName());
                    MathModel newMathModel = getRequestManager().getDocumentManager().save(mathModel, simNames);
                    Simulation[] newSimulations = newMathModel.getSimulations();
                    AddTestCriteriaOPMathModel[] testCriteriaOPs = new AddTestCriteriaOPMathModel[newSimulations.length];
                    for (int j = 0; j < newSimulations.length; j++) {
                        TestCriteriaNewMathModel tcritOrigForSimName = null;
                        for (int k = 0; mathTestCase.getTestCriterias() != null && k < mathTestCase.getTestCriterias().length; k += 1) {
                            if (mathTestCase.getTestCriterias()[k].getSimInfo().getName().equals(newSimulations[j].getName())) {
                                tcritOrigForSimName = (TestCriteriaNewMathModel) mathTestCase.getTestCriterias()[k];
                                break;
                            }
                        }
                        KeyValue regressionMathModelKey = null;
                        KeyValue regressionMathModelSimKey = null;
                        if (mathTestCase.getType().equals(TestCaseNew.REGRESSION)) {
                            if (regrRefFlag == TestingFrameworkWindowManager.COPY_REGRREF) {
                                regressionMathModelKey = (tcritOrigForSimName != null && tcritOrigForSimName.getRegressionMathModelInfo() != null ? tcritOrigForSimName.getRegressionMathModelInfo().getVersion().getVersionKey() : null);
                                regressionMathModelSimKey = (tcritOrigForSimName != null && tcritOrigForSimName.getRegressionSimInfo() != null ? tcritOrigForSimName.getRegressionSimInfo().getVersion().getVersionKey() : null);
                            } else if (regrRefFlag == TestingFrameworkWindowManager.ASSIGNORIGINAL_REGRREF) {
                                regressionMathModelKey = (tcritOrigForSimName != null ? mathTestCase.getMathModelInfo().getVersion().getVersionKey() : null);
                                regressionMathModelSimKey = (tcritOrigForSimName != null ? tcritOrigForSimName.getSimInfo().getVersion().getVersionKey() : null);
                            } else if (regrRefFlag == TestingFrameworkWindowManager.ASSIGNNEW_REGRREF) {
                                regressionMathModelKey = newMathModel.getVersion().getVersionKey();
                                regressionMathModelSimKey = newSimulations[j].getVersion().getVersionKey();
                            } else {
                                throw new IllegalArgumentException(this.getClass().getName() + ".addTestCases(...) MATHMODEL Unknown Regression Operation Flag");
                            }
                        }
                        testCriteriaOPs[j] = new AddTestCriteriaOPMathModel(testCase.getTCKey(), newSimulations[j].getVersion().getVersionKey(), regressionMathModelKey, regressionMathModelSimKey, (tcritOrigForSimName != null ? tcritOrigForSimName.getMaxAbsError() : new Double(1e-16)), (tcritOrigForSimName != null ? tcritOrigForSimName.getMaxRelError() : new Double(1e-9)), null);
                    }
                    testCaseOP = new AddTestCasesOPMathModel(new BigDecimal(tsInfo.getTSKey().toString()), newMathModel.getVersion().getVersionKey(), mathTestCase.getType(), mathTestCase.getAnnotation(), testCriteriaOPs);
                    getRequestManager().getDocumentManager().doTestSuiteOP(testCaseOP);
                }
            } catch (Throwable e) {
                errors.append("Error processing MathModel for TestCase " + (testCase.getVersion() != null ? "Name=" + testCase.getVersion().getName() : "TCKey=" + testCase.getTCKey()) + "\n" + e.getClass().getName() + " " + e.getMessage() + "\n");
            }
        }
    }
    if (errors.length() > 0) {
        return errors.toString();
    }
    return null;
}

Example 3 with GeometryContext

use of cbit.vcell.mapping.GeometryContext 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 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 4 with GeometryContext

use of cbit.vcell.mapping.GeometryContext 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 {
            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 5 with GeometryContext

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

the class SbmlExtensionFilter method askUser.

@Override
public void askUser(ChooseContext c) throws UserCancelException {
    BioModel bioModel = c.chosenContext.getBioModel();
    JFrame currentWindow = c.currentWindow;
    selectedSimWOSBE = null;
    selectedSimContext = c.chosenContext;
    // get user choice of structure and its size and computes absolute sizes of compartments using the StructureSizeSolver.
    Structure[] structures = bioModel.getModel().getStructures();
    // get the nonspatial simulationContexts corresponding to names in applicableAppNameList
    // This is needed in ApplnSelectionAndStructureSizeInputPanel
    String strucName = null;
    double structSize = 1.0;
    int structSelection = -1;
    int option = JOptionPane.CANCEL_OPTION;
    ApplnSelectionAndStructureSizeInputPanel applnStructInputPanel = null;
    while (structSelection < 0) {
        applnStructInputPanel = new ApplnSelectionAndStructureSizeInputPanel();
        applnStructInputPanel.setSimContext(c.chosenContext);
        applnStructInputPanel.setStructures(structures);
        if (applnStructInputPanel.isNeedStructureSizes()) {
            applnStructInputPanel.setPreferredSize(new java.awt.Dimension(350, 400));
            applnStructInputPanel.setMaximumSize(new java.awt.Dimension(350, 400));
            option = DialogUtils.showComponentOKCancelDialog(currentWindow, applnStructInputPanel, "Specify Structure Size to Export:");
            structSelection = applnStructInputPanel.getStructSelectionIndex();
            if (option == JOptionPane.CANCEL_OPTION || option == JOptionPane.CLOSED_OPTION) {
                break;
            } else if (option == JOptionPane.OK_OPTION && structSelection < 0) {
                DialogUtils.showErrorDialog(currentWindow, "Please select a structure and set its size");
            }
        } else {
            // adapt to legacy logic ...
            structSelection = 0;
            option = JOptionPane.OK_OPTION;
        }
    }
    if (option == JOptionPane.OK_OPTION) {
        applnStructInputPanel.applyStructureNameAndSizeValues();
        strucName = applnStructInputPanel.getSelectedStructureName();
        selectedSimContext = applnStructInputPanel.getSelectedSimContext();
        GeometryContext geoContext = selectedSimContext.getGeometryContext();
        if (!isSpatial) {
            // calculate structure Sizes only if appln is not spatial
            structSize = applnStructInputPanel.getStructureSize();
            // Invoke StructureSizeEvaluator to compute absolute sizes of compartments if all sizes are not set
            if ((geoContext.isAllSizeSpecifiedNull() && geoContext.isAllVolFracAndSurfVolSpecifiedNull()) || ((strucName == null || structSize <= 0.0) && (geoContext.isAllSizeSpecifiedNull() && geoContext.isAllVolFracAndSurfVolSpecified())) || (!geoContext.isAllSizeSpecifiedPositive() && geoContext.isAllVolFracAndSurfVolSpecifiedNull()) || (!geoContext.isAllSizeSpecifiedPositive() && !geoContext.isAllVolFracAndSurfVolSpecified()) || (geoContext.isAllSizeSpecifiedNull() && !geoContext.isAllVolFracAndSurfVolSpecified())) {
                DialogUtils.showErrorDialog(currentWindow, "Cannot export to SBML without compartment sizes being set. This can be automatically " + " computed if the absolute size of at least one compartment and the relative sizes (Surface-to-volume-ratio/Volume-fraction) " + " of all compartments are known. Sufficient information is not available to perform this computation." + "\n\nThis can be fixed by going back to the application '" + selectedSimContext.getName() + "' and setting structure sizes in the 'StructureMapping' tab.");
                throw UserCancelException.CANCEL_XML_TRANSLATION;
            }
            if (!geoContext.isAllSizeSpecifiedPositive() && geoContext.isAllVolFracAndSurfVolSpecified()) {
                Structure chosenStructure = selectedSimContext.getModel().getStructure(strucName);
                StructureMapping chosenStructMapping = selectedSimContext.getGeometryContext().getStructureMapping(chosenStructure);
                try {
                    StructureSizeSolver.updateAbsoluteStructureSizes(selectedSimContext, chosenStructure, structSize, chosenStructMapping.getSizeParameter().getUnitDefinition());
                } catch (Exception e) {
                    throw new ProgrammingException("exception updating sizes", e);
                }
            }
        } else {
            if (!geoContext.isAllUnitSizeParameterSetForSpatial()) {
                DialogUtils.showErrorDialog(currentWindow, "Cannot export to SBML without compartment size ratios being set." + "\n\nThis can be fixed by going back to the application '" + selectedSimContext.getName() + "' and setting structure" + " size ratios in the 'StructureMapping' tab.");
                throw UserCancelException.CANCEL_XML_TRANSLATION;
            }
        }
        // Select simulation whose overrides need to be exported
        // If simContext doesn't have simulations, don't pop up simulationSelectionPanel
        Simulation[] sims = bioModel.getSimulations(selectedSimContext);
        // display only those simulations that have overrides in the simulationSelectionPanel.
        Vector<Simulation> orSims = new Vector<Simulation>();
        for (int s = 0; (sims != null) && (s < sims.length); s++) {
            if (sims[s].getMathOverrides().hasOverrides()) {
                orSims.addElement(sims[s]);
            }
        }
        Simulation[] overriddenSims = orSims.toArray(new Simulation[orSims.size()]);
        if (overriddenSims.length > 0) {
            SimulationSelectionPanel simSelectionPanel = new SimulationSelectionPanel();
            simSelectionPanel.setPreferredSize(new java.awt.Dimension(600, 400));
            simSelectionPanel.setMaximumSize(new java.awt.Dimension(600, 400));
            simSelectionPanel.setSimulations(overriddenSims);
            int simOption = DialogUtils.showComponentOKCancelDialog(currentWindow, simSelectionPanel, "Select Simulation whose overrides should be exported:");
            if (simOption == JOptionPane.OK_OPTION) {
                selectedSimWOSBE = simSelectionPanel.getSelectedSimulation();
            // if (chosenSimulation != null) {
            // CARRY						hashTable.put("selectedSimulation", chosenSimulation);
            // }
            } else if (simOption == JOptionPane.CANCEL_OPTION || simOption == JOptionPane.CLOSED_OPTION) {
                // Hence canceling the entire export to SBML operation.
                throw UserCancelException.CANCEL_XML_TRANSLATION;
            }
        }
    } else if (option == JOptionPane.CANCEL_OPTION || option == JOptionPane.CLOSED_OPTION) {
        // Hence canceling the entire export to SBML operation.
        throw UserCancelException.CANCEL_XML_TRANSLATION;
    }
    if (selectedSimWOSBE != null) {
        String selectedFileName = c.filename;
        // rename file to contain exported simulation.
        String ext = FilenameUtils.getExtension(selectedFileName);
        String base = FilenameUtils.getBaseName(selectedFileName);
        String path = FilenameUtils.getPath(selectedFileName);
        base += "_" + TokenMangler.mangleToSName(selectedSimWOSBE.getName());
        selectedFileName = path + base + ext;
        c.selectedFile.renameTo(new File(selectedFileName));
    }
}