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

Example 26 with Membrane

use of cbit.vcell.model.Membrane 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 27 with Membrane

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

the class DBReactionWizardPanel method setupRX.

/**
 * Insert the method's description here.
 * Creation date: (8/5/2003 2:50:56 PM)
 * @param dbfr cbit.vcell.dictionary.ReactionDescription
 */
private void setupRX(ReactionDescription dbfr) {
    resolvedReaction = dbfr;
    if (resolvedReaction != null) {
        if (speciesAssignmentJCB != null) {
            for (int i = 0; i < speciesAssignmentJCB.length; i += 1) {
                speciesAssignmentJCB[i].removeActionListener(this);
            }
        }
        if (structureAssignmentJCB != null) {
            for (int i = 0; i < structureAssignmentJCB.length; i += 1) {
                structureAssignmentJCB[i].removeActionListener(this);
            }
        }
        getReactionCanvas1().setReactionCanvasDisplaySpec(resolvedReaction.toReactionCanvasDisplaySpec());
        getRXParticipantsJPanel().removeAll();
        // java.awt.Insets zeroInsets = new java.awt.Insets(0,0,0,0);
        java.awt.Insets fourInsets = new java.awt.Insets(4, 4, 4, 4);
        java.awt.GridBagConstraints gbc = new java.awt.GridBagConstraints();
        gbc.fill = java.awt.GridBagConstraints.HORIZONTAL;
        gbc.insets = fourInsets;
        gbc.gridx = 0;
        gbc.gridy = 0;
        javax.swing.JLabel rxjlabel = new javax.swing.JLabel("RX Elements");
        // rxjlabel.setForeground(java.awt.Color.white);
        // rxjlabel.setOpaque(true);
        // rxjlabel.setBackground(java.awt.Color.white);
        getRXParticipantsJPanel().add(rxjlabel, gbc);
        // gbc.insets = zeroInsets;
        for (int i = 0; i < resolvedReaction.elementCount(); i += 1) {
            gbc.gridy = i + 1;
            javax.swing.JLabel jlabel = new javax.swing.JLabel(resolvedReaction.getReactionElement(i).getPreferredName() + (resolvedReaction.isFluxReaction() && resolvedReaction.getFluxIndexOutside() == i ? " (Outside)" : "") + (resolvedReaction.isFluxReaction() && resolvedReaction.getFluxIndexInside() == i ? " (Inside)" : ""));
            // jlabel.setOpaque(true);
            // jlabel.setBackground(java.awt.Color.white);
            // jlabel.setForeground(java.awt.Color.black);
            getRXParticipantsJPanel().add(jlabel, gbc);
        }
        // gbc.insets = fourInsets;
        gbc.gridx = 1;
        gbc.gridy = 0;
        speciesAssignmentJCB = new javax.swing.JComboBox[resolvedReaction.elementCount()];
        DefaultListCellRenderer speciesListCellRenderer = new DefaultListCellRenderer() {

            @Override
            public Component getListCellRendererComponent(JList list, Object value, int index, boolean isSelected, boolean cellHasFocus) {
                // TODO Auto-generated method stub
                return super.getListCellRendererComponent(list, (value instanceof Species ? "Existing " + ((Species) value).getCommonName() : value), index, isSelected, cellHasFocus);
            }
        };
        javax.swing.JLabel rspjlabel = new javax.swing.JLabel("Assign to Model Species");
        // rspjlabel.setForeground(java.awt.Color.white);
        // rspjlabel.setOpaque(true);
        // rspjlabel.setBackground(java.awt.Color.white);
        getRXParticipantsJPanel().add(rspjlabel, gbc);
        // getRXParticipantsJPanel().add(new javax.swing.JLabel("Resolve to Model Species"),gbc);
        speciesOrder = new Species[getModel().getSpecies().length + 1];
        speciesOrder[0] = null;
        for (int j = 0; j < getModel().getSpecies().length; j += 1) {
            speciesOrder[j + 1] = getModel().getSpecies(j);
        }
        for (int i = 0; i < resolvedReaction.elementCount(); i += 1) {
            javax.swing.JComboBox jcb = new javax.swing.JComboBox();
            jcb.setRenderer(speciesListCellRenderer);
            speciesAssignmentJCB[i] = jcb;
            jcb.addItem("New Species");
            for (int j = 1; j < speciesOrder.length; j += 1) {
                jcb.addItem(/*"Existing "+*/
                speciesOrder[j]);
            }
            gbc.gridy = i + 1;
            getRXParticipantsJPanel().add(jcb, gbc);
            jcb.setEnabled(false);
        }
        gbc.gridx = 2;
        gbc.gridy = 0;
        structureAssignmentJCB = new javax.swing.JComboBox[resolvedReaction.elementCount()];
        DefaultListCellRenderer structureListCellRenderer = new DefaultListCellRenderer() {

            @Override
            public Component getListCellRendererComponent(JList list, Object value, int index, boolean isSelected, boolean cellHasFocus) {
                // TODO Auto-generated method stub
                return super.getListCellRendererComponent(list, (value instanceof Structure ? ((Structure) value).getName() : value), index, isSelected, cellHasFocus);
            }
        };
        javax.swing.JLabel rstjlabel = new javax.swing.JLabel("Assign to Model Compartment");
        // rstjlabel.setForeground(java.awt.Color.white);
        // rstjlabel.setOpaque(true);
        // rstjlabel.setBackground(java.awt.Color.white);
        getRXParticipantsJPanel().add(rstjlabel, gbc);
        // getRXParticipantsJPanel().add(new javax.swing.JLabel("Resolve to Model Compartment"),gbc);
        StructureTopology structTopology = getModel().getStructureTopology();
        for (int i = 0; i < resolvedReaction.elementCount(); i += 1) {
            javax.swing.JComboBox jcb = new javax.swing.JComboBox();
            jcb.setRenderer(structureListCellRenderer);
            structureAssignmentJCB[i] = jcb;
            if (resolvedReaction.isFluxReaction() && resolvedReaction.isFlux(i) && resolvedReaction.getFluxIndexOutside() == i) {
                jcb.addItem(structTopology.getOutsideFeature((Membrane) getStructure()));
                jcb.setEnabled(false);
            } else if (resolvedReaction.isFluxReaction() && resolvedReaction.isFlux(i) && resolvedReaction.getFluxIndexInside() == i) {
                jcb.addItem((structTopology).getInsideFeature((Membrane) getStructure()));
                jcb.setEnabled(false);
            } else {
                jcb.addItem(getStructure());
                if (getStructure() instanceof Membrane) {
                    jcb.addItem(structTopology.getOutsideFeature((Membrane) getStructure()));
                    jcb.addItem(structTopology.getInsideFeature((Membrane) getStructure()));
                } else {
                    jcb.setEnabled(false);
                }
            }
            gbc.gridy = i + 1;
            getRXParticipantsJPanel().add(jcb, gbc);
        }
        for (int i = 0; i < resolvedReaction.elementCount(); i += 1) {
            speciesAssignmentJCB[i].addActionListener(this);
            structureAssignmentJCB[i].addActionListener(this);
        }
    }
}

Example 28 with Membrane

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

the class DBReactionWizardPanel method searchUserReactions.

/**
 * Insert the method's description here.
 * Creation date: (7/12/2003 2:45:44 PM)
 */
private void searchUserReactions(final ReactionQuerySpec reactionQuerySpec) {
    if (getDocumentManager() != null) {
        final DocumentManager docManager = getDocumentManager();
        final JList jlist = getReactionsJList();
        // 
        final String RXSTRING_VALUE_KEY = "rxString";
        // 
        AsynchClientTask searchReactions = new AsynchClientTask("searching reactions", AsynchClientTask.TASKTYPE_NONSWING_BLOCKING) {

            public void run(Hashtable<String, Object> hash) {
                try {
                    mapRXStringtoRXIDs.clear();
                    // 
                    ReactionDescription[] dbrd = docManager.getUserReactionDescriptions(reactionQuerySpec);
                    // 
                    if (dbrd != null && !(getStructure() instanceof Membrane)) {
                        Vector<ReactionDescription> noflux = new Vector<ReactionDescription>();
                        for (int i = 0; i < dbrd.length; i += 1) {
                            if (!dbrd[i].isFluxReaction()) {
                                noflux.add(dbrd[i]);
                            }
                        }
                        if (noflux.size() > 0) {
                            dbrd = new ReactionDescription[noflux.size()];
                            noflux.copyInto(dbrd);
                        }
                    }
                    // 
                    String[] dbrdS = null;
                    if (dbrd != null) {
                        // if(mapRXStringtoRXIDs == null){mapRXStringtoRXIDs = new java.util.Hashtable();}
                        for (int i = 0; i < dbrd.length; i += 1) {
                            String rxString = dbrd[i].toString();
                            if (!mapRXStringtoRXIDs.containsKey(rxString)) {
                                mapRXStringtoRXIDs.put(rxString, new Vector<String>());
                            }
                            mapRXStringtoRXIDs.get(rxString).add(dbrd[i].getVCellRXID().toString());
                            mapRXIDtoBMIDs.put(dbrd[i].getVCellRXID(), dbrd[i].getVCellBioModelID());
                            mapRXIDtoStructRefIDs.put(dbrd[i].getVCellRXID(), dbrd[i].getVCellStructRef());
                        }
                        dbrdS = (String[]) mapRXStringtoRXIDs.keySet().toArray(new String[0]);
                    }
                    // 
                    if (dbrd != null && dbrd.length > 0) {
                        hash.put(RXSTRING_VALUE_KEY, dbrdS);
                    }
                } catch (DataAccessException e) {
                    PopupGenerator.showErrorDialog(DBReactionWizardPanel.this, e.getMessage());
                }
            }
        };
        // 
        AsynchClientTask updateRXList = new AsynchClientTask("updateRXList", AsynchClientTask.TASKTYPE_SWING_BLOCKING) {

            public void run(Hashtable<String, Object> hash) {
                String[] dbrdS = (String[]) hash.get(RXSTRING_VALUE_KEY);
                if (dbrdS != null) {
                    jlist.setListData(dbrdS);
                } else {
                    jlist.setListData(new String[0]);
                }
                afterSearchConfigure();
            }
        };
        // 
        Hashtable<String, Object> hashTemp = new Hashtable<String, Object>();
        ClientTaskDispatcher.dispatch(this, hashTemp, new AsynchClientTask[] { searchReactions, updateRXList }, false);
    }
}

Example 29 with Membrane

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

the class KineticsTypeTemplatePanel method getKineticsTypeComboBox.

private javax.swing.JComboBox getKineticsTypeComboBox() {
    if (kineticsTypeComboBox == null) {
        try {
            kineticsTypeComboBox = new javax.swing.JComboBox();
            kineticsTypeComboBox.setName("JComboBox1");
            kineticsTypeComboBox.setRenderer(new DefaultListCellRenderer() {

                private static final String MU = "\u03BC";

                private static final String MICROMOLAR = MU + "M";

                private static final String SQUARED = "\u00B2";

                private static final String SQUAREMICRON = MU + "m" + SQUARED;

                public Component getListCellRendererComponent(JList list, Object value, int index, boolean isSelected, boolean cellHasFocus) {
                    java.awt.Component component = super.getListCellRendererComponent(list, value, index, isSelected, cellHasFocus);
                    if (value instanceof KineticsDescription) {
                        KineticsDescription kineticsDescription = (KineticsDescription) value;
                        if (getKinetics() != null && getKinetics().getReactionStep() != null) {
                            if (getKinetics().getReactionStep().getStructure() instanceof Feature) {
                                if (kineticsDescription.equals(KineticsDescription.General)) {
                                    setText("General [" + MICROMOLAR + "/s]");
                                } else if (kineticsDescription.equals(KineticsDescription.MassAction)) {
                                    setText("Mass Action [" + MICROMOLAR + "/s] (recommended for stochastic application)");
                                } else if (kineticsDescription.equals(KineticsDescription.GeneralLumped)) {
                                    setText("General [molecules/s]");
                                } else if (kineticsDescription.equals(KineticsDescription.HMM_irreversible)) {
                                    setText("Henri-Michaelis-Menten (Irreversible) [" + MICROMOLAR + "/s]");
                                } else if (kineticsDescription.equals(KineticsDescription.HMM_reversible)) {
                                    setText("Henri-Michaelis-Menten (Reversible) [" + MICROMOLAR + "/s]");
                                } else {
                                    setText(kineticsDescription.getDescription());
                                }
                            } else if (getKinetics().getReactionStep().getStructure() instanceof Membrane) {
                                if (kineticsDescription.equals(KineticsDescription.General)) {
                                    setText("General [molecules/(" + SQUAREMICRON + " s)]");
                                } else if (kineticsDescription.equals(KineticsDescription.MassAction)) {
                                    setText("Mass Action [molecules/(" + SQUAREMICRON + " s)]");
                                } else if (kineticsDescription.equals(KineticsDescription.GeneralLumped)) {
                                    setText("General [molecules/s)]");
                                } else if (kineticsDescription.equals(KineticsDescription.HMM_irreversible)) {
                                    setText("Henri-Michaelis-Menten (Irreversible) [molecules/(" + SQUAREMICRON + " s)]");
                                } else if (kineticsDescription.equals(KineticsDescription.HMM_reversible)) {
                                    setText("Henri-Michaelis-Menten (Reversible) [molecules/(" + SQUAREMICRON + " s)]");
                                } else if (kineticsDescription.equals(KineticsDescription.Macroscopic_irreversible)) {
                                    setText("Macroscopic (Irreversible) [molecules/(" + SQUAREMICRON + " s)]");
                                } else if (kineticsDescription.equals(KineticsDescription.Microscopic_irreversible)) {
                                    setText("Microscopic (Irreversible) [molecules/(" + SQUAREMICRON + " s)]");
                                } else {
                                    setText(kineticsDescription.getDescription());
                                }
                            }
                        } else {
                            setText(kineticsDescription.getDescription());
                        }
                    }
                    return component;
                }
            });
        // user code begin {1}
        // user code end
        } catch (java.lang.Throwable ivjExc) {
            // user code begin {2}
            // user code end
            handleException(ivjExc);
        }
    }
    return kineticsTypeComboBox;
}

Example 30 with Membrane

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

the class SimpleReactionPanel method setTornOffSimpleReaction.

/**
 * Set the TornOffSimpleReaction to a new value.
 * @param newValue cbit.vcell.model.SimpleReaction
 */
/* WARNING: THIS METHOD WILL BE REGENERATED. */
private void setTornOffSimpleReaction(SimpleReaction newValue) {
    if (ivjTornOffSimpleReaction != newValue) {
        try {
            SimpleReaction oldValue = getTornOffSimpleReaction();
            /* Stop listening for events from the current object */
            if (ivjTornOffSimpleReaction != null) {
                ivjTornOffSimpleReaction.removePropertyChangeListener(ivjEventHandler);
            }
            ivjTornOffSimpleReaction = newValue;
            /* Listen for events from the new object */
            if (ivjTornOffSimpleReaction != null) {
                ivjTornOffSimpleReaction.addPropertyChangeListener(ivjEventHandler);
            }
            connPtoP1SetSource();
            getReactionCanvas().setReactionStep(ivjTornOffSimpleReaction);
            if (ivjTornOffSimpleReaction != null) {
                getSimpleReactionNameTextField().setText(getTornOffSimpleReaction().getName());
            }
            getReactionElectricalPropertiesPanel1().setKinetics(ivjTornOffSimpleReaction.getKinetics());
            boolean electricalPropertiesVisible = ivjTornOffSimpleReaction != null && ivjTornOffSimpleReaction.getStructure() instanceof Membrane;
            getReactionElectricalPropertiesPanel1().setVisible(electricalPropertiesVisible);
            getKineticsTypeTemplatePanel().setReactionStep(getSimpleReaction());
            firePropertyChange("simpleReaction", oldValue, newValue);
        // user code begin {1}
        // user code end
        } catch (java.lang.Throwable ivjExc) {
            // user code begin {2}
            // user code end
            handleException(ivjExc);
        }
    }
    ;
// user code begin {3}
// user code end
}