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

Example 36 with Structure

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

the class DiffEquMathMapping method refreshVariables.

/**
 * This method was created in VisualAge.
 */
private void refreshVariables() throws MappingException {
    // System.out.println("MathMapping.refreshVariables()");
    // 
    // non-constant dependent variables require a function
    // 
    Enumeration<SpeciesContextMapping> enum1 = getSpeciesContextMappings();
    while (enum1.hasMoreElements()) {
        SpeciesContextMapping scm = enum1.nextElement();
        SpeciesContextSpec scs = simContext.getReactionContext().getSpeciesContextSpec(scm.getSpeciesContext());
        if (scm.getDependencyExpression() != null && !scs.isConstant()) {
            // scm.setVariable(new Function(scm.getSpeciesContext().getName(),scm.getDependencyExpression()));
            scm.setVariable(null);
        }
        if (getSimulationContext().hasEventAssignment(scs.getSpeciesContext())) {
            scm.setDependencyExpression(null);
        }
    }
    // 
    // non-constant independent variables require either a membrane or volume variable
    // 
    enum1 = getSpeciesContextMappings();
    while (enum1.hasMoreElements()) {
        SpeciesContextMapping scm = (SpeciesContextMapping) enum1.nextElement();
        SpeciesContextSpec scs = simContext.getReactionContext().getSpeciesContextSpec(scm.getSpeciesContext());
        if (scm.getDependencyExpression() == null && (!scs.isConstant() || getSimulationContext().hasEventAssignment(scs.getSpeciesContext()))) {
            StructureMapping sm = simContext.getGeometryContext().getStructureMapping(scm.getSpeciesContext().getStructure());
            Structure struct = scm.getSpeciesContext().getStructure();
            Domain domain = null;
            if (sm.getGeometryClass() != null) {
                domain = new Domain(sm.getGeometryClass());
            }
            if (struct instanceof Feature || struct instanceof Membrane) {
                if (sm.getGeometryClass() instanceof SurfaceClass) {
                    if (scs.isWellMixed()) {
                        scm.setVariable(new MembraneRegionVariable(scm.getSpeciesContext().getName(), domain));
                    } else if (getSimulationContext().isStoch() && getSimulationContext().getGeometry().getDimension() > 0 && !scs.isForceContinuous()) {
                        scm.setVariable(new MemVariable(scm.getSpeciesContext().getName() + "_conc", domain));
                    } else {
                        scm.setVariable(new MemVariable(scm.getSpeciesContext().getName(), domain));
                    }
                } else {
                    if (scs.isWellMixed()) {
                        scm.setVariable(new VolumeRegionVariable(scm.getSpeciesContext().getName(), domain));
                    } else if (getSimulationContext().isStoch() && getSimulationContext().getGeometry().getDimension() > 0 && !scs.isForceContinuous()) {
                        scm.setVariable(new VolVariable(scm.getSpeciesContext().getName() + "_conc", domain));
                    } else {
                        scm.setVariable(new VolVariable(scm.getSpeciesContext().getName(), domain));
                    }
                }
            } else {
                throw new MappingException("class " + scm.getSpeciesContext().getStructure().getClass() + " not supported");
            }
            mathSymbolMapping.put(scm.getSpeciesContext(), scm.getVariable().getName());
        }
    }
}

Example 37 with Structure

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

the class StructureAnalyzer method refreshFastMatrices.

/**
 * This method was created in VisualAge.
 */
private void refreshFastMatrices() throws Exception {
    // System.out.println("StructureAnalyzer.refreshFastMatrices()");
    // 
    // update scheme matrix for fast system
    // 
    fastSchemeMatrix = new RationalNumberMatrix(fastSpeciesContextMappings.length, fastReactionSteps.length);
    for (int i = 0; i < fastSpeciesContextMappings.length; i++) {
        for (int j = 0; j < fastReactionSteps.length; j++) {
            fastSchemeMatrix.set_elem(i, j, fastReactionSteps[j].getStoichiometry(fastSpeciesContextMappings[i].getSpeciesContext()));
        }
    }
    // 
    for (int i = 0; i < fastSpeciesContextMappings.length; i++) {
        SpeciesContextMapping scm = fastSpeciesContextMappings[i];
        SpeciesContext sc = scm.getSpeciesContext();
        // 
        // collect fast rate expression
        // 
        Expression exp = new Expression(0.0);
        for (int j = 0; j < fastReactionSteps.length; j++) {
            int stoichiometry = fastReactionSteps[j].getStoichiometry(sc);
            ReactionSpec reactionSpec = mathMapping_4_8.getSimulationContext().getReactionContext().getReactionSpec(fastReactionSteps[j]);
            if (stoichiometry != 0) {
                if (!reactionSpec.isFast()) {
                    throw new Exception("expected only fast rates");
                }
                if (reactionSpec.isExcluded()) {
                    throw new Exception("expected only included rates");
                }
                ReactionParticipant[] rps = fastReactionSteps[j].getReactionParticipants();
                ReactionParticipant rp0 = null;
                for (ReactionParticipant rp : rps) {
                    if (rp.getSpeciesContext() == sc) {
                        rp0 = rp;
                        break;
                    }
                }
                // 
                if (rp0 != null) {
                    Structure structure = fastReactionSteps[j].getStructure();
                    Expression fastRateExpression = getReactionRateExpression(fastReactionSteps[j], rp0).renameBoundSymbols(mathMapping_4_8.getNameScope());
                    if ((structure instanceof Membrane) && (rp0.getStructure() != structure)) {
                        Membrane membrane = (Membrane) structure;
                        MembraneMapping membraneMapping = (MembraneMapping) mathMapping_4_8.getSimulationContext().getGeometryContext().getStructureMapping(membrane);
                        Expression fluxCorrection = new Expression(mathMapping_4_8.getFluxCorrectionParameter(membraneMapping, (Feature) rp0.getStructure()), mathMapping_4_8.getNameScope());
                        exp = Expression.add(exp, Expression.mult(fluxCorrection, fastRateExpression));
                    } else {
                        exp = Expression.add(exp, new Expression(fastRateExpression));
                    }
                }
            }
        }
        // exp.bindExpression(mathMapping);
        scm.setFastRate(exp.flatten());
    }
    // System.out.println("StructureAnalyzer.refreshFastMatrices(), scheme matrix:");
    // fastSchemeMatrix.show();
    // 
    // update null space matrix
    // 
    fastNullSpaceMatrix = fastSchemeMatrix.findNullSpace();
// if (fastNullSpaceMatrix==null){
// System.out.println("fast system has full rank");
// }else{
// System.out.println("StructureAnalyzer.refreshFastMatrices(), nullSpace matrix:");
// fastNullSpaceMatrix.show();
// }
}

Example 38 with Structure

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

the class VolumeStructureAnalyzer method refreshStructures.

/**
 * Build list of structures that are mapped to this volume subdomain
 */
protected void refreshStructures() {
    // 
    // get all structures that are mapped to this subvolume (subdomain)
    // 
    Structure[] structs = mathMapping_4_8.getStructures(subVolume);
    Vector<Structure> structList = new Vector<Structure>();
    if (structs != null) {
        for (int i = 0; i < structs.length; i++) {
            // 
            if (structs[i] instanceof Membrane) {
                Membrane membrane = (Membrane) structs[i];
                MembraneMapping membraneMapping = (MembraneMapping) mathMapping_4_8.getSimulationContext().getGeometryContext().getStructureMapping(membrane);
                if (mathMapping_4_8.getResolved(membraneMapping)) {
                    continue;
                }
            }
            // 
            // add all others to the structure list
            // 
            structList.addElement(structs[i]);
        }
    }
    // 
    if (structList.size() > 0) {
        structures = new Structure[structList.size()];
        structList.copyInto(structures);
    } else {
        structures = null;
    }
}

Example 39 with Structure

use of cbit.vcell.model.Structure 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 40 with Structure

use of cbit.vcell.model.Structure 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);
    }
}