Examples with ApplnSelectionAndStructureSizeInputPanel org.vcell.sbml.gui.ApplnSelectionAndStructureSizeInputPanel used on opensource projects

Example 1 with ApplnSelectionAndStructureSizeInputPanel

use of org.vcell.sbml.gui.ApplnSelectionAndStructureSizeInputPanel in project vcell by virtualcell.

the class SbmlExtensionFilter method askUser.

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