Examples with VCFileChooser org.vcell.util.gui.VCFileChooser used on opensource projects

Example 11 with VCFileChooser

use of org.vcell.util.gui.VCFileChooser in project vcell by virtualcell.

the class ChooseFile method showGeometryModelXMLFileChooser.

// // Check structure sized and select a simulation to export to SBML
// if (isSbml) {
// // 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
// 
// SimulationContext[] applicableSimContexts = applicableSimContext.toArray(new SimulationContext[applicableSimContext.size()]);
// 
// String strucName = null;
// double structSize = 1.0;
// int structSelection = -1;
// int option = JOptionPane.CANCEL_OPTION;
// Simulation chosenSimulation = null;
// 
// ApplnSelectionAndStructureSizeInputPanel applnStructInputPanel = null;
// while (structSelection < 0) {
// applnStructInputPanel = new ApplnSelectionAndStructureSizeInputPanel();
// applnStructInputPanel.setSimContexts(applicableSimContexts);
// applnStructInputPanel.setStructures(structures);
// applnStructInputPanel.setPreferredSize(new java.awt.Dimension(350, 400));
// applnStructInputPanel.setMaximumSize(new java.awt.Dimension(350, 400));
// option = DialogUtils.showComponentOKCancelDialog(currentWindow, applnStructInputPanel, "Select Application and 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");
// }
// }
// 
// if (option == JOptionPane.OK_OPTION) {
// applnStructInputPanel.applyStructureNameAndSizeValues();
// strucName = applnStructInputPanel.getSelectedStructureName();
// chosenSimContext = applnStructInputPanel.getSelectedSimContext();
// hashTable.put("selectedSimContext", chosenSimContext);
// 
// GeometryContext geoContext = chosenSimContext.getGeometryContext();
// if (!fileFilter.getDescription().equals(FileFilters.FILE_FILTER_SBML_31_SPATIAL.getDescription())) {
// // 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 '" + chosenSimContext.getName() + "' and setting structure sizes in the 'StructureMapping' tab.");
// throw UserCancelException.CANCEL_XML_TRANSLATION;
// }
// if (!geoContext.isAllSizeSpecifiedPositive() && geoContext.isAllVolFracAndSurfVolSpecified()) {
// Structure chosenStructure = chosenSimContext.getModel().getStructure(strucName);
// StructureMapping chosenStructMapping = chosenSimContext.getGeometryContext().getStructureMapping(chosenStructure);
// StructureSizeSolver.updateAbsoluteStructureSizes(chosenSimContext, chosenStructure, structSize, chosenStructMapping.getSizeParameter().getUnitDefinition());
// }
// } 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 '" + chosenSimContext.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(chosenSimContext);
// // 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 = (Simulation[])BeanUtils.getArray(orSims, Simulation.class);
// 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) {
// chosenSimulation = simSelectionPanel.getSelectedSimulation();
// if (chosenSimulation != null) {
// hashTable.put("selectedSimulation", chosenSimulation);
// }
// } else if (simOption == JOptionPane.CANCEL_OPTION || simOption == JOptionPane.CLOSED_OPTION) {
// // User did not choose a simulation whose overrides are required to be exported.
// // Without that information, cannot export successfully into SBML,
// // Hence canceling the entire export to SBML operation.
// throw UserCancelException.CANCEL_XML_TRANSLATION;
// }
// }
// } else if (option == JOptionPane.CANCEL_OPTION || option == JOptionPane.CLOSED_OPTION) {
// // User did not choose to set size for any structure.
// // Without that information, cannot export successfully into SBML,
// // Hence canceling the entire export to SBML operation.
// throw UserCancelException.CANCEL_XML_TRANSLATION;
// }
// 
// if (chosenSimulation != null) {
// // rename file to contain exported simulation.
// String ext = FilenameUtils.getExtension(selectedFileName);
// String base = FilenameUtils.getBaseName(selectedFileName);
// String path = FilenameUtils.getPath(selectedFileName);
// base += "_"  + TokenMangler.mangleToSName(chosenSimulation.getName());
// selectedFileName = path + base + ext;
// selectedFile.renameTo(new File(selectedFileName));
// }
// resetPreferredFilePath(selectedFile, userPreferences);
// return selectedFile;
// }
/**
 * Export to Geometry
 * Creation date: (5/31/2004 6:04:14 PM)
 * @param hashTable java.util.Hashtable
 * @param clientWorker cbit.vcell.desktop.controls.ClientWorker
 */
private File showGeometryModelXMLFileChooser(Hashtable<String, Object> hashTable) throws java.lang.Exception {
    Geometry geom = (Geometry) hashTable.get("documentToExport");
    JFrame currentWindow = (JFrame) hashTable.get("currentWindow");
    UserPreferences userPreferences = (UserPreferences) hashTable.get("userPreferences");
    TopLevelWindowManager topLevelWindowManager = (TopLevelWindowManager) hashTable.get("topLevelWindowManager");
    Component comp = (Component) hashTable.get("component");
    comp = (comp == null ? (currentWindow == null ? (topLevelWindowManager == null ? null : topLevelWindowManager.getComponent()) : currentWindow) : comp);
    File defaultPath = userPreferences.getCurrentDialogPath();
    VCFileChooser fileChooser = new VCFileChooser(defaultPath);
    fileChooser.setFileSelectionMode(JFileChooser.FILES_ONLY);
    fileChooser.setMultiSelectionEnabled(false);
    // fileChooser.addChoosableFileFilter(FileFilters.FILE_FILTER_VCML);
    fileChooser.addChoosableFileFilter(FileFilters.FILE_FILTER_PDF);
    if (geom.getDimension() > 0) {
        fileChooser.addChoosableFileFilter(FileFilters.FILE_FILTER_AVS);
        fileChooser.addChoosableFileFilter(FileFilters.FILE_FILTER_STL);
        fileChooser.addChoosableFileFilter(FileFilters.FILE_FILTER_PLY);
    }
    // remove all selector
    fileChooser.removeChoosableFileFilter(fileChooser.getAcceptAllFileFilter());
    // set the default file filter...
    fileChooser.setFileFilter(FileFilters.FILE_FILTER_VCML);
    fileChooser.setSelectedFile(new java.io.File(TokenMangler.fixTokenStrict(geom.getName())));
    fileChooser.setDialogTitle("Export Virtual Cell Geometry As...");
    if (fileChooser.showSaveDialog(comp) != JFileChooser.APPROVE_OPTION) {
        // user didn't choose save
        throw UserCancelException.CANCEL_FILE_SELECTION;
    } else {
        File selectedFile = fileChooser.getSelectedFile();
        javax.swing.filechooser.FileFilter fileFilter = fileChooser.getFileFilter();
        if (selectedFile == null) {
            // no file selected (no name given)
            throw UserCancelException.CANCEL_FILE_SELECTION;
        } else {
            // /
            String selectedFileName = recordAndRemoveExtension(selectedFile.getPath());
            String n = selectedFile.getPath().toLowerCase();
            if (fileFilter == FileFilters.FILE_FILTER_VCML && !n.endsWith(".vcml")) {
                selectedFile = new File(selectedFileName + ".vcml");
            } else if (fileFilter == FileFilters.FILE_FILTER_PDF && !n.endsWith(".pdf")) {
                selectedFile = new File(selectedFileName + ".pdf");
            }
            if (fileFilter == null) {
                throw new Exception("No file save type was selected.");
            }
            checkForOverwrites(selectedFile, comp, userPreferences);
            // put the filter in the hash so the export task knows what to do...
            hashTable.put("fileFilter", fileFilter);
            resetPreferredFilePath(selectedFile, userPreferences);
            return selectedFile;
        }
    }
}

Example 12 with VCFileChooser

use of org.vcell.util.gui.VCFileChooser in project vcell by virtualcell.

the class ChooseFile method showMathModelXMLFileChooser.

/**
 * Insert the method's description here.
 * Creation date: (5/31/2004 6:04:14 PM)
 * @param hashTable java.util.Hashtable
 * @param clientWorker cbit.vcell.desktop.controls.ClientWorker
 */
private File showMathModelXMLFileChooser(Hashtable<String, Object> hashTable) throws java.lang.Exception {
    // for mathmodels:
    MathModel mathModel = (MathModel) hashTable.get("documentToExport");
    JFrame currentWindow = (JFrame) hashTable.get("currentWindow");
    UserPreferences userPreferences = (UserPreferences) hashTable.get("userPreferences");
    TopLevelWindowManager topLevelWindowManager = (TopLevelWindowManager) hashTable.get("topLevelWindowManager");
    if (topLevelWindowManager == null) {
        throw new RuntimeException("toplLevelWindowManager required");
    }
    File defaultPath = userPreferences.getCurrentDialogPath();
    VCFileChooser fileChooser = new VCFileChooser(defaultPath);
    fileChooser.setFileSelectionMode(JFileChooser.FILES_ONLY);
    fileChooser.setMultiSelectionEnabled(false);
    // fileChooser.addChoosableFileFilter(FileFilters.FILE_FILTER_SBML_21);		// Can export Mathmodel to L2V1 ??
    fileChooser.addChoosableFileFilter(FileFilters.FILE_FILTER_SBML_23);
    fileChooser.addChoosableFileFilter(FileFilters.FILE_FILTER_SBML_24);
    // fileChooser.addChoosableFileFilter(FileFilters.FILE_FILTER_CELLML);
    fileChooser.addChoosableFileFilter(FileFilters.FILE_FILTER_MATLABV6);
    fileChooser.addChoosableFileFilter(FileFilters.FILE_FILTER_PDF);
    fileChooser.addChoosableFileFilter(FileFilters.FILE_FILTER_SMOLDYN_INPUT);
    // remove all selector
    fileChooser.removeChoosableFileFilter(fileChooser.getAcceptAllFileFilter());
    // set the default file filter...
    fileChooser.setFileFilter(FileFilters.FILE_FILTER_VCML);
    fileChooser.setSelectedFile(new java.io.File(TokenMangler.fixTokenStrict(mathModel.getName())));
    fileChooser.setDialogTitle("Export Virtual Cell MathModel As...");
    if (fileChooser.showSaveDialog(currentWindow) != JFileChooser.APPROVE_OPTION) {
        // user didn't choose save
        throw UserCancelException.CANCEL_FILE_SELECTION;
    } else {
        File selectedFile = fileChooser.getSelectedFile();
        javax.swing.filechooser.FileFilter fileFilter = fileChooser.getFileFilter();
        if (selectedFile == null) {
            // no file selected (no name given)
            throw UserCancelException.CANCEL_FILE_SELECTION;
        } else {
            // /
            String selectedFileName = recordAndRemoveExtension(selectedFile.getPath());
            String n = selectedFile.getPath().toLowerCase();
            if (fileFilter == FileFilters.FILE_FILTER_CELLML && !n.endsWith(".xml")) {
                selectedFile = new File(selectedFileName + ".xml");
            } else if (fileFilter == FileFilters.FILE_FILTER_VCML && !n.endsWith(".vcml")) {
                selectedFile = new File(selectedFileName + ".vcml");
            } else if ((fileFilter == FileFilters.FILE_FILTER_SBML_23 || (fileFilter == FileFilters.FILE_FILTER_SBML_24)) && !n.endsWith(".xml")) {
                selectedFile = new File(selectedFileName + ".xml");
            } else if (fileFilter == FileFilters.FILE_FILTER_MATLABV6 && !n.endsWith(".m")) {
                selectedFile = new File(selectedFileName + ".m");
            } else if (fileFilter == FileFilters.FILE_FILTER_PDF && !n.endsWith(".pdf")) {
                selectedFile = new File(selectedFileName + ".pdf");
            } else if (fileFilter == FileFilters.FILE_FILTER_SMOLDYN_INPUT && !(n.endsWith(SMOLDYN_INPUT_FILE_EXTENSION) || (n.endsWith(".txt")))) {
                selectedFile = new File(selectedFileName + SMOLDYN_INPUT_FILE_EXTENSION);
            }
            checkForOverwrites(selectedFile, topLevelWindowManager.getComponent(), userPreferences);
            // put the filter in the hash so the export task knows what to do...
            hashTable.put("fileFilter", fileFilter);
            // only non-spatial math models can be exported to CellML.
            if (fileFilter == FileFilters.FILE_FILTER_CELLML && mathModel.getMathDescription().getGeometry().getDimension() != 0) {
                throw new Exception("No non-spatial applications, can only export to this format the math from a non-spatial application");
            } else // Select a spatial stochastic simulation to export
            if (fileFilter.getDescription().equals(FileFilters.FILE_FILTER_SMOLDYN_INPUT.getDescription())) {
                Simulation[] sims = mathModel.getSimulations();
                if (sims == null || sims.length == 0) {
                    DialogUtils.showWarningDialog(topLevelWindowManager.getComponent(), "MathModel '" + mathModel.getName() + "' has no simulations to export");
                    throw UserCancelException.CANCEL_GENERIC;
                }
                String[][] rowData = new String[sims.length][2];
                for (int i = 0; i < sims.length; i++) {
                    rowData[i][0] = sims[i].getName();
                    rowData[i][1] = sims[i].getSolverTaskDescription().getSolverDescription().getDisplayLabel();
                }
                int[] selectedRow = PopupGenerator.showComponentOKCancelTableList(topLevelWindowManager.getComponent(), "Select a simulation to export", new String[] { "Simulation Name", "Solver" }, rowData, ListSelectionModel.SINGLE_SELECTION);
                if (selectedRow == null) {
                    throw UserCancelException.CANCEL_GENERIC;
                }
                String chosenSimulationName = rowData[selectedRow[0]][0];
                Simulation chosenSimulation = mathModel.getSimulation(chosenSimulationName);
                if (chosenSimulation != null) {
                    hashTable.put("selectedSimulation", chosenSimulation);
                } else {
                    throw new Exception("Couldn't match selection '" + chosenSimulationName + "' with simulation");
                }
            }
            resetPreferredFilePath(selectedFile, userPreferences);
            return selectedFile;
        }
    }
}

Example 13 with VCFileChooser

use of org.vcell.util.gui.VCFileChooser in project vcell by virtualcell.

the class BNGWindowManager method saveOutput.

/**
 * Comment
 */
public void saveOutput(String bngOutputStr) {
    // Ask user for save location
    File defaultPath = getUserPreferences().getCurrentDialogPath();
    VCFileChooser fileChooser = new VCFileChooser(defaultPath);
    fileChooser.setFileSelectionMode(javax.swing.JFileChooser.FILES_ONLY);
    fileChooser.setMultiSelectionEnabled(false);
    // remove all selector
    fileChooser.removeChoosableFileFilter(fileChooser.getAcceptAllFileFilter());
    fileChooser.setSelectedFile(new java.io.File(getBngOutputPanel().getSelectedOutputFileName()));
    fileChooser.setDialogTitle("Save Selected BNG Output Format ...");
    if (fileChooser.showSaveDialog(getBngOutputPanel()) != JFileChooser.APPROVE_OPTION) {
        // user didn't choose save
        throw UserCancelException.CANCEL_FILE_SELECTION;
    } else {
        File selectedFile = fileChooser.getSelectedFile();
        if (selectedFile == null) {
            // no file selected (no name given)
            throw UserCancelException.CANCEL_FILE_SELECTION;
        } else {
            // we have a file selection, check for overwrites
            if (selectedFile.exists()) {
                String answer = PopupGenerator.showWarningDialog(this, getUserPreferences(), UserMessage.warn_OverwriteFile, selectedFile.getAbsolutePath());
                if (answer.equals(UserMessage.OPTION_CANCEL)) {
                    throw UserCancelException.CANCEL_FILE_SELECTION;
                }
            }
            // write out text into file using FileOutputStream and PrintWriter
            java.io.FileOutputStream outputStream = null;
            String selectedFileName = selectedFile.getPath();
            try {
                outputStream = new java.io.FileOutputStream(selectedFileName);
            } catch (java.io.IOException e) {
                e.printStackTrace(System.out);
                throw new RuntimeException("Error opening file '" + selectedFileName + " to write BioNetGen output" + ": " + e.getMessage());
            }
            PrintWriter bngOutputFile = new PrintWriter(outputStream);
            bngOutputFile.print(bngOutputStr);
            bngOutputFile.close();
        }
    }
}

Example 14 with VCFileChooser

use of org.vcell.util.gui.VCFileChooser in project vcell by virtualcell.

the class BNGWindowManager method uploadBNGLFile.

/**
 * Comment
 */
public String uploadBNGLFile() throws java.io.FileNotFoundException, java.io.IOException {
    // BNG input file (.bngl) contents
    String bngInputStr = null;
    // Ask user for upload location
    File defaultPath = getUserPreferences().getCurrentDialogPath();
    VCFileChooser fileChooser = new VCFileChooser(defaultPath);
    fileChooser.setFileSelectionMode(javax.swing.JFileChooser.FILES_ONLY);
    fileChooser.setMultiSelectionEnabled(false);
    // remove all selector
    fileChooser.removeChoosableFileFilter(fileChooser.getAcceptAllFileFilter());
    // set default file filter
    fileChooser.addChoosableFileFilter(org.vcell.util.gui.exporter.FileFilters.FILE_FILTER_BNGL);
    fileChooser.setFileFilter(org.vcell.util.gui.exporter.FileFilters.FILE_FILTER_BNGL);
    // Set file chooser dialog title
    fileChooser.setDialogTitle("Upload Selected BNG file ...");
    if (fileChooser.showOpenDialog(getBngOutputPanel()) != JFileChooser.APPROVE_OPTION) {
        // user didn't choose Open
        throw UserCancelException.CANCEL_FILE_SELECTION;
    } else {
        File selectedFile = fileChooser.getSelectedFile();
        if (selectedFile == null) {
            // no file selected (no name given)
            throw UserCancelException.CANCEL_FILE_SELECTION;
        } else {
            long selectedFileLength = selectedFile.length();
            // Check if file exists
            if (!selectedFile.exists()) {
                throw new RuntimeException("File " + selectedFile.getPath() + " not found");
            }
            // Check if file has .bngl extension
            if (!selectedFile.getPath().endsWith(".bngl")) {
                DialogUtils.showErrorDialog(getComponent(), "File " + selectedFile.getPath() + " is not a .bngl file");
                throw new RuntimeException("File " + selectedFile.getPath() + " is not a .bngl file");
            }
            // Read characters from file into character array and transfer into string buffer.
            StringBuffer stringBuffer = new StringBuffer();
            FileInputStream fis = null;
            fis = new FileInputStream(selectedFile);
            InputStreamReader reader = new InputStreamReader(fis);
            try (BufferedReader br = new BufferedReader(reader)) {
                char[] charArray = new char[10000];
                while (true) {
                    int numRead = br.read(charArray, 0, charArray.length);
                    if (numRead > 0) {
                        stringBuffer.append(charArray, 0, numRead);
                    } else if (numRead == -1) {
                        break;
                    }
                }
            }
            if (stringBuffer.length() != selectedFileLength) {
                System.out.println("<<<SYSOUT ALERT>>> Reading from bng file: read " + stringBuffer.length() + " of " + selectedFileLength + " bytes of input file");
            }
            bngInputStr = stringBuffer.toString();
        }
        return bngInputStr;
    }
}

Example 15 with VCFileChooser

use of org.vcell.util.gui.VCFileChooser in project vcell by virtualcell.

the class BNGWindowManager method saveBNGLFile.

/**
 * prompt user for filename, then write String to it
 * @param bngl String to write out
 * @throws IOException
 */
public void saveBNGLFile(String bngl) throws IOException {
    File defaultPath = getUserPreferences().getCurrentDialogPath();
    VCFileChooser fileChooser = new VCFileChooser(defaultPath);
    fileChooser.setFileSelectionMode(javax.swing.JFileChooser.FILES_ONLY);
    fileChooser.setMultiSelectionEnabled(false);
    // remove all selector
    fileChooser.removeChoosableFileFilter(fileChooser.getAcceptAllFileFilter());
    // set default file filter
    fileChooser.addChoosableFileFilter(org.vcell.util.gui.exporter.FileFilters.FILE_FILTER_BNGL);
    fileChooser.setFileFilter(org.vcell.util.gui.exporter.FileFilters.FILE_FILTER_BNGL);
    // Set file chooser dialog title
    fileChooser.setDialogTitle("Save BNG file ...");
    if (fileChooser.showSaveDialog(getBngOutputPanel()) != JFileChooser.APPROVE_OPTION) {
        throw UserCancelException.CANCEL_FILE_SELECTION;
    } else {
        File selectedFile = fileChooser.getSelectedFile();
        String path = selectedFile.getAbsolutePath();
        if (path.indexOf('.') == -1) {
            path += org.vcell.util.gui.exporter.FileFilters.FILE_FILTER_BNGL.getPrimaryExtension();
            selectedFile = new File(path);
        }
        if (selectedFile.exists()) {
            final int answer = JOptionPane.showConfirmDialog(getComponent(), selectedFile + " exists. Overwrite?", "Confirm Replace", JOptionPane.YES_NO_OPTION);
            if (answer != JOptionPane.YES_OPTION) {
                return;
            }
        }
        try (FileWriter fw = new FileWriter(path)) {
            fw.write(bngl);
        }
    }
}