Examples with KeyValue org.vcell.util.document.KeyValue used on opensource projects

Example 21 with KeyValue

use of org.vcell.util.document.KeyValue in project vcell by virtualcell.

the class FrapDataUtils method getVCSimulationIdentifierFromVCellSimulationData.

public static VCSimulationIdentifier getVCSimulationIdentifierFromVCellSimulationData(File vcellSimLogFile) {
    final String SIMID_PREFIX = "SimID_";
    String simulationKeyS = vcellSimLogFile.getName().substring(SIMID_PREFIX.length(), vcellSimLogFile.getName().indexOf('_', SIMID_PREFIX.length()));
    KeyValue simulationKey = new KeyValue(simulationKeyS);
    return new VCSimulationIdentifier(simulationKey, getDotUser());
}

Example 22 with KeyValue

use of org.vcell.util.document.KeyValue in project vcell by virtualcell.

the class MathModelWindowManager method simStatusChanged.

/**
 * Insert the method's description here.
 * Creation date: (5/14/2004 11:08:35 AM)
 * @param newMathModel cbit.vcell.mathmodel.MathModel
 */
// private void setMathModel(MathModel newMathModel) {
// resetGeometryListeners((getMathModel() != null?(getMathModel().getMathDescription() != null?getMathModel().getMathDescription().getGeometry():null):null),
// (newMathModel != null?(newMathModel.getMathDescription() != null?newMathModel.getMathDescription().getGeometry():null):null));
// 
// resetMathDescriptionListeners(
// (getMathModel() != null?getMathModel().getMathDescription():null),
// (newMathModel != null?newMathModel.getMathDescription():null));
// if (getMathModel() != null) {
// getMathModel().removePropertyChangeListener(this);
// }
// mathModel = newMathModel;
// if (getMathModel() != null) {
// getMathModel().addPropertyChangeListener(this);
// }
// }
// private void resetMathDescriptionListeners(MathDescription oldMathDescription,MathDescription newMathDescription){
// if(oldMathDescription != null){
// oldMathDescription.removePropertyChangeListener(this);
// }
// if(newMathDescription != null){
// newMathDescription.addPropertyChangeListener(this);
// }
// }
// /**
// * Insert the method's description here.
// * Creation date: (6/14/2004 10:55:40 PM)
// * @param newDocument cbit.vcell.document.VCDocument
// */
// private void showDataViewerPlotsFrame(final javax.swing.JInternalFrame plotFrame) {
// dataViewerPlotsFramesVector.add(plotFrame);
// showFrame(plotFrame);
// plotFrame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter() {
// public void internalFrameClosing(javax.swing.event.InternalFrameEvent e) {
// dataViewerPlotsFramesVector.remove(plotFrame);
// }
// });
// }
// /**
// * Insert the method's description here.
// * Creation date: (6/14/2004 10:55:40 PM)
// * @param newDocument cbit.vcell.document.VCDocument
// */
// public void showDataViewerPlotsFrames(javax.swing.JInternalFrame[] plotFrames) {
// for (int i = 0; i < plotFrames.length; i++){
// showDataViewerPlotsFrame(plotFrames[i]);
// }
// }
/**
 * Insert the method's description here.
 * Creation date: (6/9/2004 3:58:21 PM)
 * @param newJobStatus cbit.vcell.messaging.db.SimulationJobStatus
 * @param progress java.lang.Double
 * @param timePoint java.lang.Double
 */
public void simStatusChanged(SimStatusEvent simStatusEvent) {
    // ** events are only generated from server side job statuses **
    KeyValue simKey = simStatusEvent.getVCSimulationIdentifier().getSimulationKey();
    // do we have the sim?
    Simulation[] sims = getMathModel().getSimulations();
    if (sims == null) {
        // we don't have it
        return;
    }
    Simulation simulation = null;
    for (int i = 0; i < sims.length; i++) {
        if (simKey.equals(sims[i].getKey()) || ((sims[i].getSimulationVersion() != null) && simKey.equals(sims[i].getSimulationVersion().getParentSimulationReference()))) {
            simulation = sims[i];
            break;
        }
    }
    if (simulation == null) {
        // we don't have it
        return;
    }
    // we have it; get current server side status
    SimulationStatus simStatus = getRequestManager().getServerSimulationStatus(simulation.getSimulationInfo());
    // if failed, notify
    if (simStatusEvent.isNewFailureEvent()) {
        String qualifier = "";
        if (simulation.getScanCount() > 1) {
            qualifier += "One job from ";
        }
        PopupGenerator.showErrorDialog(this, qualifier + "Simulation '" + simulation.getName() + "' failed\n" + simStatus.getDetails());
    }
    // update status display
    ClientSimManager simManager = simulationWorkspace.getClientSimManager();
    simManager.updateStatusFromServer(simulation);
    // is there new data?
    if (simStatusEvent.isNewDataEvent()) {
        fireNewData(new DataEvent(this, new VCSimulationDataIdentifier(simulation.getSimulationInfo().getAuthoritativeVCSimulationIdentifier(), simStatusEvent.getJobIndex())));
    }
}

Example 23 with KeyValue

use of org.vcell.util.document.KeyValue 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 24 with KeyValue

use of org.vcell.util.document.KeyValue in project vcell by virtualcell.

the class TestingFrameworkWindowManager method queryTCritCrossRef.

@SuppressWarnings("serial")
public void queryTCritCrossRef(final TestSuiteInfoNew tsin, final TestCriteriaNew tcrit, final String varName) {
    try {
        QueryTestCriteriaCrossRefOP queryTestCriteriaCrossRefOP = new QueryTestCriteriaCrossRefOP(tsin.getTSKey(), tcrit.getTCritKey(), varName);
        TestCriteriaCrossRefOPResults testCriteriaCrossRefOPResults = (TestCriteriaCrossRefOPResults) getRequestManager().getDocumentManager().doTestSuiteOP(queryTestCriteriaCrossRefOP);
        final Vector<TestCriteriaCrossRefOPResults.CrossRefData> xrefDataV = testCriteriaCrossRefOPResults.getCrossRefData();
        final TestSuiteInfoNew[] testSuiteInfos = getRequestManager().getDocumentManager().getTestSuiteInfos();
        Vector<TestSuiteInfoNew> missingTestSuites = new Vector<TestSuiteInfoNew>();
        for (int i = 0; i < testSuiteInfos.length; i++) {
            boolean bFound = false;
            for (int j = 0; j < xrefDataV.size(); j++) {
                if (xrefDataV.elementAt(j).tsVersion.equals(testSuiteInfos[i].getTSID())) {
                    bFound = true;
                    break;
                }
            }
            if (!bFound) {
                missingTestSuites.add(testSuiteInfos[i]);
            }
        }
        TestCriteriaCrossRefOPResults.CrossRefData xrefDataSource = null;
        for (int i = 0; i < xrefDataV.size(); i++) {
            if (xrefDataV.elementAt(i).tcritKey.equals(tcrit.getTCritKey())) {
                xrefDataSource = xrefDataV.elementAt(i);
                break;
            }
        }
        if (xrefDataSource == null) {
            throw new RuntimeException("Couldn't find source Test Criteria in query results.");
        }
        final int numColumns = 8;
        final int XREFDATA_ALLOWANCE = 1;
        final int TSKEY_ALLOWANCE = 1;
        final int XREFDATA_OFFSET = numColumns;
        final int TSDATE_OFFSET = 1;
        final int VARNAME_OFFSET = 3;
        final int TSKEYMISSING_OFFSET = numColumns + 1;
        final String[] colNames = new String[numColumns];
        final Object[][] sourceRows = new Object[xrefDataV.size() + missingTestSuites.size()][numColumns + XREFDATA_ALLOWANCE + TSKEY_ALLOWANCE];
        String sourceTestSuite = null;
        colNames[0] = "tsVersion";
        colNames[1] = "tsDate";
        colNames[2] = "tsBaseVersion";
        colNames[3] = "varName";
        colNames[4] = "RelErorr";
        colNames[5] = "limitRelErorr";
        colNames[6] = "limitAbsErorr";
        colNames[7] = "AbsErorr";
        for (int i = 0; i < xrefDataV.size(); i++) {
            sourceRows[i][colNames.length] = xrefDataV.elementAt(i);
            if (xrefDataV.elementAt(i).tcritKey.equals(queryTestCriteriaCrossRefOP.getTestCriterium())) {
                sourceTestSuite = xrefDataV.elementAt(i).tsVersion;
            }
            sourceRows[i][0] = xrefDataV.elementAt(i).tsVersion;
            sourceRows[i][2] = (xrefDataV.elementAt(i).tsRefVersion == null ? (xrefDataV.elementAt(i).regressionModelID == null ? /* && xrefDataV.elementAt(i).regressionMMref==null*/
            "" : "Ref Model exist BUT outside of TestSuites") : xrefDataV.elementAt(i).tsRefVersion);
            sourceRows[i][6] = xrefDataV.elementAt(i).maxAbsErorr;
            sourceRows[i][5] = xrefDataV.elementAt(i).maxRelErorr;
            if (xrefDataV.elementAt(i).varName != null) {
                sourceRows[i][VARNAME_OFFSET] = xrefDataV.elementAt(i).varName;
                sourceRows[i][4] = xrefDataV.elementAt(i).varCompSummary.getRelativeError();
                sourceRows[i][7] = xrefDataV.elementAt(i).varCompSummary.getAbsoluteError();
            } else {
                sourceRows[i][VARNAME_OFFSET] = "-No Report-";
                // "No Report";
                sourceRows[i][4] = null;
                // "No Report";
                sourceRows[i][7] = null;
            }
            for (int j = 0; j < testSuiteInfos.length; j++) {
                if (xrefDataV.elementAt(i).tsVersion.equals(testSuiteInfos[j].getTSID())) {
                    sourceRows[i][1] = testSuiteInfos[j].getTSDate();
                    break;
                }
            }
        }
        for (int i = xrefDataV.size(); i < sourceRows.length; i++) {
            sourceRows[i][0] = missingTestSuites.elementAt(i - xrefDataV.size()).getTSID();
            sourceRows[i][TSDATE_OFFSET] = missingTestSuites.elementAt(i - xrefDataV.size()).getTSDate();
            sourceRows[i][TSKEYMISSING_OFFSET] = missingTestSuites.elementAt(i - xrefDataV.size()).getTSKey();
        }
        // Arrays.sort(rows,
        // new Comparator<Object[]>(){
        // public int compare(Object[] o1, Object[] o2) {
        // return ((String)o1[0]).compareToIgnoreCase((String)o2[0]);
        // //						if(o1[0].equals(o2[0])){
        // //							return o1[3].compareToIgnoreCase(o2[3]);
        // //						}
        // //						return o1[0].compareToIgnoreCase(o2[0]);
        // }
        // }
        // );
        final VCellSortTableModel<Object[]> tableModel = new VCellSortTableModel<Object[]>(colNames) {

            public Class<?> getColumnClass(int columnIndex) {
                if (columnIndex == TSDATE_OFFSET) {
                    return Date.class;
                } else if (columnIndex >= 4 && columnIndex <= 7) {
                    return Double.class;
                }
                return String.class;
            }

            public boolean isCellEditable(int row, int column) {
                return false;
            }

            public Object getValueAt(int rowIndex, int columnIndex) {
                return getValueAt(rowIndex)[columnIndex];
            }

            public Comparator<Object[]> getComparator(final int col, final boolean ascending) {
                return new Comparator<Object[]>() {

                    public int compare(Object[] o1, Object[] o2) {
                        if (o1[col] == null && o2[col] == null) {
                            return 0;
                        }
                        // if(ascending){
                        if (o1[col] == null) {
                            return 1;
                        }
                        if (o2[col] == null) {
                            return -1;
                        }
                        // }
                        if (getColumnClass(col).equals(String.class)) {
                            if (ascending) {
                                return ((String) o1[col]).compareToIgnoreCase(((String) o2[col]));
                            } else {
                                return ((String) o2[col]).compareToIgnoreCase(((String) o1[col]));
                            }
                        } else if (getColumnClass(col).equals(Date.class)) {
                            if (ascending) {
                                return ((Date) o1[col]).compareTo(((Date) o2[col]));
                            }
                            return ((Date) o2[col]).compareTo(((Date) o1[col]));
                        } else if (getColumnClass(col).equals(Double.class)) {
                            if (ascending) {
                                return ((Double) o1[col]).compareTo(((Double) o2[col]));
                            }
                            return ((Double) o2[col]).compareTo(((Double) o1[col]));
                        }
                        throw new RuntimeException("TestSuite XRef Query unexpecte column class " + getColumnClass(col).getName());
                    }
                };
            }
        };
        tableModel.setData(Arrays.asList(sourceRows));
        // Create table
        final JSortTable table = new JSortTable();
        table.setModel(tableModel);
        table.setSelectionMode(ListSelectionModel.MULTIPLE_INTERVAL_SELECTION);
        final JScrollPane scrollPaneContentPane = new JScrollPane(table);
        table.setPreferredScrollableViewportSize(new Dimension(500, 250));
        table.getColumnModel().getColumn(TSDATE_OFFSET).setCellRenderer(new DefaultTableCellRenderer() {

            // DateFormat formatter = DateFormat.getDateTimeInstance();
            public Component getTableCellRendererComponent(JTable table, Object value, boolean isSelected, boolean hasFocus, int row, int column) {
                return super.getTableCellRendererComponent(table, (value == null ? null : ((Date) value).toString()), /*formatter.format((Date)value)*/
                isSelected, hasFocus, row, column);
            }
        });
        DefaultTableCellRenderer dtcr = new DefaultTableCellRenderer() {

            public Component getTableCellRendererComponent(JTable table, Object value, boolean isSelected, boolean hasFocus, int row, int column) {
                return super.getTableCellRendererComponent(table, (value == null ? null : ((Double) value).toString()), /*formatter.format((Date)value)*/
                isSelected, hasFocus, row, column);
            }
        };
        table.getColumnModel().getColumn(4).setCellRenderer(dtcr);
        table.getColumnModel().getColumn(5).setCellRenderer(dtcr);
        table.getColumnModel().getColumn(6).setCellRenderer(dtcr);
        table.getColumnModel().getColumn(7).setCellRenderer(dtcr);
        // table.getColumnModel().getColumn(4).setCellRenderer(
        // new DefaultTableCellRenderer(){
        // public Component getTableCellRendererComponent(JTable table, Object value, boolean isSelected, boolean hasFocus, int row, int column) {
        // return super.getTableCellRendererComponent(table,(value == null?null:((Double)value).toString())/*formatter.format((Date)value)*/, isSelected, hasFocus, row, column);
        // }
        // }
        // );
        // table.getTableHeader().setReorderingAllowed(false);
        // Popup Menu
        final TestCriteriaCrossRefOPResults.CrossRefData xrefDataSourceFinal = xrefDataSource;
        final JPopupMenu queryPopupMenu = new JPopupMenu();
        final JMenuItem changeLimitsMenuItem = new JMenuItem("Change Selected Error Limits...");
        final String OPEN_MODEL = "Open Model(s)";
        final JMenuItem openModelMenuItem = new JMenuItem(OPEN_MODEL);
        final String OPEN_REGRREFMODEL = "Open Regr Ref Model(s)";
        final JMenuItem openRegrRefModelMenuItem = new JMenuItem(OPEN_REGRREFMODEL);
        final String SELECT_REF_IN_TREE = "Select in Tree View";
        final JMenuItem showInTreeMenuItem = new JMenuItem(SELECT_REF_IN_TREE);
        final String SELECT_REGR_REF_IN_TREE = "Select RegrRef TCase in Tree View";
        final JMenuItem showRegrRefInTreeMenuItem = new JMenuItem(SELECT_REGR_REF_IN_TREE);
        queryPopupMenu.add(changeLimitsMenuItem);
        queryPopupMenu.add(openModelMenuItem);
        queryPopupMenu.add(openRegrRefModelMenuItem);
        queryPopupMenu.add(showInTreeMenuItem);
        queryPopupMenu.add(showRegrRefInTreeMenuItem);
        ActionListener showInTreeActionListener = new ActionListener() {

            public void actionPerformed(ActionEvent actionEvent) {
                int[] selectedRows = table.getSelectedRows();
                if (selectedRows == null || selectedRows.length != 1) {
                    PopupGenerator.showErrorDialog(TestingFrameworkWindowManager.this, "Action " + actionEvent.getActionCommand() + " accepts only single selection!");
                    return;
                }
                TestCriteriaCrossRefOPResults.CrossRefData xrefData = (TestCriteriaCrossRefOPResults.CrossRefData) tableModel.getValueAt(selectedRows[0], XREFDATA_OFFSET);
                BigDecimal missingTSKey = (BigDecimal) tableModel.getValueAt(selectedRows[0], TSKEYMISSING_OFFSET);
                if (actionEvent.getActionCommand().equals(SELECT_REF_IN_TREE)) {
                    getTestingFrameworkWindowPanel().selectInTreeView((xrefData != null ? xrefData.tsKey : missingTSKey), (xrefData != null ? xrefData.tcaseKey : null), (xrefData != null ? xrefData.tcritKey : null));
                } else if (actionEvent.getActionCommand().equals(SELECT_REGR_REF_IN_TREE)) {
                    if (xrefData == null) {
                        PopupGenerator.showErrorDialog(getComponent(), "No Regression Reference info available.");
                        return;
                    }
                    getTestingFrameworkWindowPanel().selectInTreeView((xrefData != null ? xrefData.regressionModelTSuiteID : null), (xrefData != null ? xrefData.regressionModelTCaseID : null), (xrefData != null ? xrefData.regressionModelTCritID : null));
                }
                ChildWindow childWindow = TFWFinder.findChildWindowManager(getComponent()).getChildWindowFromContentPane(scrollPaneContentPane);
                if (childWindow != null) {
                    childWindow.show();
                }
            }
        };
        showInTreeMenuItem.addActionListener(showInTreeActionListener);
        showRegrRefInTreeMenuItem.addActionListener(showInTreeActionListener);
        ActionListener openModelsActionListener = new ActionListener() {

            public void actionPerformed(ActionEvent actionEvent) {
                int[] selectedRows = table.getSelectedRows();
                String failureS = "";
                TestCriteriaCrossRefOPResults.CrossRefData xrefData = null;
                int openCount = 0;
                for (int i = 0; i < selectedRows.length; i++) {
                    try {
                        xrefData = (TestCriteriaCrossRefOPResults.CrossRefData) tableModel.getValueAt(selectedRows[i], XREFDATA_OFFSET);
                        if (xrefData != null && (actionEvent.getActionCommand().equals(OPEN_REGRREFMODEL) ? xrefData.regressionModelID != null : true)) {
                            openCount += 1;
                            VCDocumentInfo vcDocInfo = null;
                            if (xrefData.isBioModel) {
                                vcDocInfo = getRequestManager().getDocumentManager().getBioModelInfo(new KeyValue((actionEvent.getActionCommand().equals(OPEN_REGRREFMODEL) ? xrefData.regressionModelID : xrefData.modelID)));
                            } else {
                                vcDocInfo = getRequestManager().getDocumentManager().getMathModelInfo(new KeyValue((actionEvent.getActionCommand().equals(OPEN_REGRREFMODEL) ? xrefData.regressionModelID : xrefData.modelID)));
                            }
                            getRequestManager().openDocument(vcDocInfo, TestingFrameworkWindowManager.this, true);
                        }
                    } catch (Exception e) {
                        failureS += failureS + "key=" + xrefData.modelID + " " + e.getMessage() + "\n";
                        e.printStackTrace();
                    }
                }
                if (failureS.length() > 0 || openCount == 0) {
                    PopupGenerator.showErrorDialog(TestingFrameworkWindowManager.this, "Failed to open some models\n" + failureS + (openCount == 0 ? "Selection(s) had no model(s)" : ""));
                }
                ChildWindow childWindow = TFWFinder.findChildWindowManager(getComponent()).getChildWindowFromContentPane(scrollPaneContentPane);
                if (childWindow != null) {
                    childWindow.show();
                }
            }
        };
        openModelMenuItem.addActionListener(openModelsActionListener);
        openRegrRefModelMenuItem.addActionListener(openModelsActionListener);
        changeLimitsMenuItem.addActionListener(new ActionListener() {

            public void actionPerformed(ActionEvent actionEvent) {
                int[] selectedRows = table.getSelectedRows();
                Vector<TestCriteriaCrossRefOPResults.CrossRefData> changeTCritV = new Vector<TestCriteriaCrossRefOPResults.CrossRefData>();
                for (int i = 0; i < selectedRows.length; i++) {
                    TestCriteriaCrossRefOPResults.CrossRefData xrefData = (TestCriteriaCrossRefOPResults.CrossRefData) tableModel.getValueAt(selectedRows[i], XREFDATA_OFFSET);
                    if (xrefData != null) {
                        boolean bFound = false;
                        for (int j = 0; j < changeTCritV.size(); j++) {
                            if (changeTCritV.elementAt(j).tcritKey.equals(xrefData.tcritKey)) {
                                bFound = true;
                                break;
                            }
                        }
                        if (!bFound) {
                            changeTCritV.add(xrefData);
                        }
                    }
                }
                if (changeTCritV.size() > 0) {
                    Double relativeErrorLimit = null;
                    Double absoluteErrorLimit = null;
                    while (true) {
                        try {
                            String ret = PopupGenerator.showInputDialog(getComponent(), "Enter new TestCriteria Error Limits for '" + xrefDataSourceFinal.simName + "'.  '-'(dash) to keep original value.", "RelativeErrorLimit,AbsoluteErrorLimit");
                            int commaPosition = ret.indexOf(',');
                            if (commaPosition == -1) {
                                throw new Exception("No comma found separating RelativeErrorLimit AbsoluteErrorLimit");
                            }
                            if (commaPosition != ret.lastIndexOf(',')) {
                                throw new Exception("Only 1 comma allowed separating RelativeErrorLimit and AbsoluteErrorLimit");
                            }
                            final String KEEP_ORIGINAL_VALUE = "-";
                            String relativeErrorS = ret.substring(0, commaPosition);
                            String absoluteErrorS = ret.substring(commaPosition + 1, ret.length());
                            if (!relativeErrorS.equals(KEEP_ORIGINAL_VALUE)) {
                                relativeErrorLimit = Double.parseDouble(relativeErrorS);
                            }
                            if (!absoluteErrorS.equals(KEEP_ORIGINAL_VALUE)) {
                                absoluteErrorLimit = Double.parseDouble(absoluteErrorS);
                            }
                            if ((relativeErrorLimit != null && relativeErrorLimit <= 0) || (absoluteErrorLimit != null && absoluteErrorLimit <= 0)) {
                                throw new Exception("Error limits must be greater than 0");
                            }
                            break;
                        } catch (UserCancelException e) {
                            ChildWindow childWindow = TFWFinder.findChildWindowManager(getComponent()).getChildWindowFromContentPane(scrollPaneContentPane);
                            if (childWindow != null) {
                                childWindow.show();
                            }
                            return;
                        } catch (Exception e) {
                            PopupGenerator.showErrorDialog(TestingFrameworkWindowManager.this, "Error parsing Error Limits\n" + e.getMessage());
                        }
                    }
                    double[] relErrorLimitArr = new double[changeTCritV.size()];
                    double[] absErrorLimitArr = new double[changeTCritV.size()];
                    Object[][] rows = new Object[changeTCritV.size()][5];
                    for (int j = 0; j < changeTCritV.size(); j++) {
                        relErrorLimitArr[j] = (relativeErrorLimit != null ? relativeErrorLimit.doubleValue() : changeTCritV.elementAt(j).maxRelErorr);
                        absErrorLimitArr[j] = (absoluteErrorLimit != null ? absoluteErrorLimit.doubleValue() : changeTCritV.elementAt(j).maxAbsErorr);
                        rows[j][2] = new Double(relErrorLimitArr[j]);
                        rows[j][4] = new Double(absErrorLimitArr[j]);
                        rows[j][1] = new Double(changeTCritV.elementAt(j).maxRelErorr);
                        rows[j][3] = new Double(changeTCritV.elementAt(j).maxAbsErorr);
                        rows[j][0] = changeTCritV.elementAt(j).tsVersion;
                    }
                    try {
                        PopupGenerator.showComponentOKCancelTableList(getComponent(), "Confirm Error Limit Changes", new String[] { "TSVersion", "Orig RelErrorLimit", "New RelErrorLimit", "Orig AbsErrorLimit", "New AbsErrorLimit" }, rows, null);
                    } catch (UserCancelException e) {
                        ChildWindow childWindow = TFWFinder.findChildWindowManager(getComponent()).getChildWindowFromContentPane(scrollPaneContentPane);
                        if (childWindow != null) {
                            childWindow.show();
                        }
                        return;
                    }
                    // Get information needed to generate new TestCriteria Reports
                    final String YES_ANSWER = "Yes";
                    Hashtable<TestSuiteInfoNew, Vector<TestCriteriaCrossRefOPResults.CrossRefData>> genReportHash = null;
                    String genRepResult = PopupGenerator.showWarningDialog(getComponent(), "Generate Reports for changed Test Criterias?", new String[] { YES_ANSWER, "No" }, YES_ANSWER);
                    if (genRepResult != null && genRepResult.equals(YES_ANSWER)) {
                        genReportHash = new Hashtable<TestSuiteInfoNew, Vector<TestCriteriaCrossRefOPResults.CrossRefData>>();
                        for (int i = 0; i < changeTCritV.size(); i++) {
                            boolean bFound = false;
                            for (int j = 0; j < testSuiteInfos.length; j++) {
                                if (changeTCritV.elementAt(i).tsVersion.equals(testSuiteInfos[j].getTSID())) {
                                    bFound = true;
                                    Vector<TestCriteriaCrossRefOPResults.CrossRefData> tempV = genReportHash.get(testSuiteInfos[j]);
                                    if (tempV == null) {
                                        tempV = new Vector<TestCriteriaCrossRefOPResults.CrossRefData>();
                                        genReportHash.put(testSuiteInfos[j], tempV);
                                    }
                                    tempV.add(changeTCritV.elementAt(i));
                                }
                            }
                            if (!bFound) {
                                PopupGenerator.showErrorDialog(TestingFrameworkWindowManager.this, "Couldn't find testsuiteinfo for testcriteria");
                                return;
                            }
                        }
                    }
                    BigDecimal[] changeTCritBDArr = new BigDecimal[changeTCritV.size()];
                    for (int i = 0; i < changeTCritV.size(); i++) {
                        changeTCritBDArr[i] = changeTCritV.elementAt(i).tcritKey;
                    }
                    ChangeTestCriteriaErrorLimitOP changeTestCriteriaErrorLimitOP = new ChangeTestCriteriaErrorLimitOP(changeTCritBDArr, absErrorLimitArr, relErrorLimitArr);
                    try {
                        getTestingFrameworkWindowPanel().getDocumentManager().doTestSuiteOP(changeTestCriteriaErrorLimitOP);
                    } catch (Exception e) {
                        PopupGenerator.showErrorDialog(TestingFrameworkWindowManager.this, "Failed Changing Error limits for selected " + xrefDataSourceFinal.simName + "\n" + e.getMessage());
                        return;
                    }
                    ChildWindow childWindow = TFWFinder.findChildWindowManager(getComponent()).getChildWindowFromContentPane(scrollPaneContentPane);
                    if (childWindow != null) {
                        childWindow.close();
                    }
                    getTestingFrameworkWindowPanel().refreshTree((TestSuiteInfoNew) null);
                    if (genReportHash != null) {
                        updateReports(genReportHash);
                    } else {
                        new Thread(new Runnable() {

                            public void run() {
                                TestingFrameworkWindowManager.this.queryTCritCrossRef(tsin, tcrit, varName);
                            }
                        }).start();
                    }
                } else {
                    PopupGenerator.showErrorDialog(TestingFrameworkWindowManager.this, "No selected rows contain Test Criteria.");
                }
            }
        });
        table.addMouseListener(new MouseAdapter() {

            @Override
            public void mouseClicked(MouseEvent e) {
                super.mouseClicked(e);
                checkPopup(e);
            }

            @Override
            public void mousePressed(MouseEvent e) {
                super.mousePressed(e);
                checkPopup(e);
            }

            @Override
            public void mouseReleased(MouseEvent e) {
                super.mouseReleased(e);
                checkPopup(e);
            }

            private void checkPopup(MouseEvent mouseEvent) {
                if (mouseEvent.isPopupTrigger()) {
                    // Not use because popupmenu will not show at edge
                    // if(table.getSelectedRowCount() <= 1){
                    // table.getSelectionModel().setSelectionInterval(table.rowAtPoint(mouseEvent.getPoint()),table.rowAtPoint(mouseEvent.getPoint()));
                    // }
                    doPopup(mouseEvent);
                } else {
                    queryPopupMenu.setVisible(false);
                }
            }

            private void doPopup(MouseEvent mouseEvent) {
                // queryPopupMenu.add(showInTreeMenuItem);
                if (table.getSelectedRowCount() == 0) {
                    changeLimitsMenuItem.setEnabled(false);
                    openModelMenuItem.setEnabled(false);
                    openRegrRefModelMenuItem.setEnabled(false);
                    showInTreeMenuItem.setEnabled(false);
                    showRegrRefInTreeMenuItem.setEnabled(false);
                } else {
                    changeLimitsMenuItem.setEnabled(true);
                    openModelMenuItem.setEnabled(true);
                    openRegrRefModelMenuItem.setEnabled(true);
                    showInTreeMenuItem.setEnabled(true);
                    if (table.getSelectedRowCount() == 1) {
                        TestCriteriaCrossRefOPResults.CrossRefData xrefData = (TestCriteriaCrossRefOPResults.CrossRefData) tableModel.getValueAt(table.getSelectedRow(), numColumns);
                        showRegrRefInTreeMenuItem.setEnabled(xrefData != null && xrefData.regressionModelID != null && xrefData.tsRefVersion != null);
                    }
                }
                queryPopupMenu.show(mouseEvent.getComponent(), mouseEvent.getPoint().x, mouseEvent.getPoint().y);
            }
        });
        String title = (xrefDataSource.isBioModel ? "BM" : "MM") + " " + xrefDataSource.tcSolutionType + " (" + sourceTestSuite + ") " + " \"" + (xrefDataSource.isBioModel ? xrefDataSource.bmName : xrefDataSource.mmName) + "\"  ::  " + (xrefDataSource.isBioModel ? "app=\"" + xrefDataSource.bmAppName + "\"  ::  sim=\"" + xrefDataSource.simName + "\"" : "sim=\"" + xrefDataSource.simName + "\"");
        ChildWindow childWindow = TFWFinder.findChildWindowManager(getComponent()).addChildWindow(scrollPaneContentPane, scrollPaneContentPane, title);
        // childWindow.setSize(600,400);
        childWindow.setIsCenteredOnParent();
        childWindow.pack();
        childWindow.setResizable(true);
        childWindow.show();
    } catch (DataAccessException e) {
        e.printStackTrace();
        PopupGenerator.showErrorDialog(TestingFrameworkWindowManager.this, "Error Query TestCriteria Cross Ref:\n" + e.getMessage());
    }
}

Example 25 with KeyValue

use of org.vcell.util.document.KeyValue in project vcell by virtualcell.

the class DBReactionWizardPanel method bfnActionPerformed.

/**
 * Comment
 */
private void bfnActionPerformed(java.awt.event.ActionEvent actionEvent) {
    try {
        // 
        javax.swing.DefaultListModel pndlm = (javax.swing.DefaultListModel) getParameterNamesJList().getModel();
        // 
        if (actionEvent.getSource().equals(getBackJButton())) {
            if (getResolverJPanel().isVisible() && pndlm.size() == 0 && getSearchDictionaryJRadioButton().isSelected() == false) {
                // skip Parameters if there are none
                ((java.awt.CardLayout) getCardLayoutJPanel().getLayout()).previous(getCardLayoutJPanel());
            }
            ((java.awt.CardLayout) getCardLayoutJPanel().getLayout()).previous(getCardLayoutJPanel());
        } else if (actionEvent.getSource().equals(getNextJButton())) {
            if (getSearchCriteriaJPanel().isVisible()) {
                if (getSearchDictionaryJRadioButton().isSelected()) {
                    getParameterJPanel().setVisible(false);
                } else {
                    getParameterJPanel().setVisible(true);
                }
                if (!lastSearchIsSameAsCurrent()) {
                    search();
                    lastReactionSelection = null;
                    return;
                }
            } else if (getParameterJPanel().isVisible()) {
                if (lastReactStepSelection == null || !lastReactStepSelection.equals(getReactionStep0())) {
                    lastReactStepSelection = getReactionStep0();
                    ReactionType rxType = null;
                    if (getReactionStep0() instanceof FluxReaction) {
                        if (getReactionStep0().isReversible()) {
                            rxType = ReactionType.REACTTYPE_FLUX_REVERSIBLE;
                        } else {
                            rxType = ReactionType.REACTTYPE_FLUX_IRREVERSIBLE;
                        }
                    } else {
                        if (getReactionStep0().isReversible()) {
                            rxType = ReactionType.REACTTYPE_SIMPLE_REVERSIBLE;
                        } else {
                            rxType = ReactionType.REACTTYPE_SIMPLE_IRREVERSIBLE;
                        }
                    }
                    KeyValue bmid = mapRXIDtoBMIDs.get(lastReactStepSelection.getKey());
                    KeyValue structRef = mapRXIDtoStructRefIDs.get(lastReactStepSelection.getKey());
                    ReactionDescription dbfr = new ReactionDescription(getReactionStep0().getName(), rxType, getReactionStep0().getKey(), bmid, structRef);
                    // 
                    ReactionParticipant[] rpArr = getReactionStep0().getReactionParticipants();
                    for (int i = 0; i < rpArr.length; i += 1) {
                        DBNonFormalUnboundSpecies dbnfu = new DBNonFormalUnboundSpecies(rpArr[i].getSpecies().getCommonName());
                        char role;
                        if (rpArr[i] instanceof Reactant) {
                            role = ReactionDescription.RX_ELEMENT_REACTANT;
                        } else if (rpArr[i] instanceof Product) {
                            role = ReactionDescription.RX_ELEMENT_PRODUCT;
                        } else if (rpArr[i] instanceof Catalyst) {
                            role = ReactionDescription.RX_ELEMENT_CATALYST;
                        } else {
                            throw new RuntimeException("Unsupported ReationParticiapnt=" + rpArr[i].getClass().getName());
                        }
                        dbfr.addReactionElement(dbnfu, rpArr[i].getSpeciesContext().getName(), rpArr[i].getStoichiometry(), role);
                    }
                    if (dbfr.isFluxReaction()) {
                        // make sure flux is in right direction
                        Structure outsideStruct = getModel().getStructureTopology().getOutsideFeature((Membrane) getReactionStep0().getStructure());
                        String defaultOutsideSCName = dbfr.getOrigSpeciesContextName(dbfr.getFluxIndexOutside());
                        for (int i = 0; i < rpArr.length; i += 1) {
                            if (rpArr[i].getSpeciesContext().getName().equals(defaultOutsideSCName)) {
                                if (!rpArr[i].getStructure().equals(outsideStruct)) {
                                    dbfr.swapFluxSCNames();
                                }
                                break;
                            }
                        }
                    }
                    setupRX(dbfr);
                }
            }
            // 
            ((java.awt.CardLayout) getCardLayoutJPanel().getLayout()).next(getCardLayoutJPanel());
        } else if (actionEvent.getSource().equals(getFinishJButton())) {
            applySelectedReactionElements();
        }
        // 
        configureBFN();
    } catch (Exception e) {
        e.printStackTrace();
        DialogUtils.showErrorDialog(this, "DBReactionWizard failed\n" + e.getMessage(), e);
    }
}