Examples with MZmineModule net.sf.mzmine.modules.MZmineModule used on opensource projects

Example 6 with MZmineModule

use of net.sf.mzmine.modules.MZmineModule in project mzmine2 by mzmine.

the class MZmineCore method main.

/**
 * Main method
 */
@SuppressWarnings("unchecked")
public static void main(String[] args) {
    // In the beginning, set the default locale to English, to avoid
    // problems with conversion of numbers etc. (e.g. decimal separator may
    // be . or , depending on the locale)
    Locale.setDefault(new Locale("en", "US"));
    logger.info("Starting MZmine " + getMZmineVersion());
    // Remove old temporary files, if we find any
    TmpFileCleanup.removeOldTemporaryFiles();
    logger.fine("Loading core classes..");
    // create instance of configuration
    configuration = new MZmineConfigurationImpl();
    // create instances of core modules
    projectManager = new ProjectManagerImpl();
    taskController = new TaskControllerImpl();
    logger.fine("Initializing core classes..");
    projectManager.initModule();
    taskController.initModule();
    logger.fine("Loading modules");
    for (Class<?> moduleClass : MZmineModulesList.MODULES) {
        try {
            logger.finest("Loading module " + moduleClass.getName());
            // Create instance and init module
            MZmineModule moduleInstance = (MZmineModule) moduleClass.newInstance();
            // Add to the module list
            initializedModules.put(moduleClass, moduleInstance);
            // Create an instance of parameter set
            Class<? extends ParameterSet> parameterSetClass = moduleInstance.getParameterSetClass();
            ParameterSet parameterSetInstance = parameterSetClass.newInstance();
            // Add the parameter set to the configuration
            configuration.setModuleParameters((Class<MZmineModule>) moduleClass, parameterSetInstance);
        } catch (Throwable e) {
            logger.log(Level.SEVERE, "Could not load module " + moduleClass, e);
            e.printStackTrace();
            continue;
        }
    }
    // If we have no arguments, run in GUI mode, otherwise run in batch mode
    if (args.length == 0) {
        // Create the Swing GUI in the event-dispatching thread, as is
        // generally recommended
        Runnable desktopInit = new Runnable() {

            @Override
            public void run() {
                logger.fine("Initializing GUI");
                MainWindow mainWindow = new MainWindow();
                desktop = mainWindow;
                mainWindow.initModule();
                // Activate project - bind it to the desktop's project tree
                MZmineProjectImpl currentProject = (MZmineProjectImpl) projectManager.getCurrentProject();
                currentProject.activateProject();
                // add desktop menu icon
                for (Class<?> moduleClass : MZmineModulesList.MODULES) {
                    MZmineModule module = initializedModules.get(moduleClass);
                    if (module instanceof MZmineRunnableModule) {
                        mainWindow.getMainMenu().addMenuItemForModule((MZmineRunnableModule) module);
                    }
                }
            }
        };
        try {
            SwingUtilities.invokeAndWait(desktopInit);
        } catch (Exception e) {
            logger.log(Level.SEVERE, "Could not initialize GUI", e);
            e.printStackTrace();
            System.exit(1);
        }
    } else {
        desktop = new HeadLessDesktop();
    }
    // load configuration
    if (MZmineConfiguration.CONFIG_FILE.exists() && MZmineConfiguration.CONFIG_FILE.canRead()) {
        try {
            configuration.loadConfiguration(MZmineConfiguration.CONFIG_FILE);
        } catch (Exception e) {
            e.printStackTrace();
        }
    }
    // if we have GUI, show it now
    if (desktop.getMainWindow() != null && !(desktop instanceof HeadLessDesktop)) {
        // update the size and position of the main window
        ParameterSet paramSet = configuration.getPreferences();
        WindowSettingsParameter settings = paramSet.getParameter(MZminePreferences.windowSetttings);
        settings.applySettingsToWindow(desktop.getMainWindow());
        // add last project menu items
        if (desktop instanceof MainWindow) {
            ((MainWindow) desktop).createLastUsedProjectsMenu(configuration.getLastProjects());
            // listen for changes
            configuration.getLastProjectsParameter().addFileListChangedListener(list -> {
                // new list of last used projects
                Desktop desk = getDesktop();
                if (desk instanceof MainWindow) {
                    ((MainWindow) desk).createLastUsedProjectsMenu(list);
                }
            });
        }
        // show the GUI
        logger.info("Showing main window");
        desktop.getMainWindow().setVisible(true);
        // show the welcome message
        desktop.setStatusBarText("Welcome to MZmine 2!");
        // Check for updated version
        NewVersionCheck NVC = new NewVersionCheck(CheckType.DESKTOP);
        Thread nvcThread = new Thread(NVC);
        nvcThread.setPriority(Thread.MIN_PRIORITY);
        nvcThread.start();
        // Tracker
        GoogleAnalyticsTracker GAT = new GoogleAnalyticsTracker("MZmine Loaded (GUI mode)", "/JAVA/Main/GUI");
        Thread gatThread = new Thread(GAT);
        gatThread.setPriority(Thread.MIN_PRIORITY);
        gatThread.start();
        // register shutdown hook only if we have GUI - we don't want to
        // save configuration on exit if we only run a batch
        ShutDownHook shutDownHook = new ShutDownHook();
        Runtime.getRuntime().addShutdownHook(shutDownHook);
    }
    // mode
    if (args.length > 0 && desktop instanceof HeadLessDesktop) {
        // Tracker
        GoogleAnalyticsTracker GAT = new GoogleAnalyticsTracker("MZmine Loaded (Headless mode)", "/JAVA/Main/GUI");
        Thread gatThread = new Thread(GAT);
        gatThread.setPriority(Thread.MIN_PRIORITY);
        gatThread.start();
        File batchFile = new File(args[0]);
        if ((!batchFile.exists()) || (!batchFile.canRead())) {
            logger.severe("Cannot read batch file " + batchFile);
            System.exit(1);
        }
        ExitCode exitCode = BatchModeModule.runBatch(projectManager.getCurrentProject(), batchFile);
        if (exitCode == ExitCode.OK)
            System.exit(0);
        else
            System.exit(1);
    }
}

Example 7 with MZmineModule

use of net.sf.mzmine.modules.MZmineModule in project mzmine2 by mzmine.

the class MZmineConfigurationImpl method saveConfiguration.

@Override
public void saveConfiguration(File file) throws IOException {
    try {
        // write sensitive parameters only to the local config file
        final boolean skipSensitive = !file.equals(MZmineConfiguration.CONFIG_FILE);
        DocumentBuilderFactory dbFactory = DocumentBuilderFactory.newInstance();
        DocumentBuilder dBuilder = dbFactory.newDocumentBuilder();
        Document configuration = dBuilder.newDocument();
        Element configRoot = configuration.createElement("configuration");
        configuration.appendChild(configRoot);
        Element prefElement = configuration.createElement("preferences");
        configRoot.appendChild(prefElement);
        preferences.setSkipSensitiveParameters(skipSensitive);
        preferences.saveValuesToXML(prefElement);
        Element lastFilesElement = configuration.createElement("lastprojects");
        configRoot.appendChild(lastFilesElement);
        lastProjects.saveValueToXML(lastFilesElement);
        Element modulesElement = configuration.createElement("modules");
        configRoot.appendChild(modulesElement);
        // traverse modules
        for (MZmineModule module : MZmineCore.getAllModules()) {
            String className = module.getClass().getName();
            Element moduleElement = configuration.createElement("module");
            moduleElement.setAttribute("class", className);
            modulesElement.appendChild(moduleElement);
            Element paramElement = configuration.createElement("parameters");
            moduleElement.appendChild(paramElement);
            ParameterSet moduleParameters = getModuleParameters(module.getClass());
            moduleParameters.setSkipSensitiveParameters(skipSensitive);
            moduleParameters.saveValuesToXML(paramElement);
        }
        // save encryption key to local config only
        // ATTENTION: this should to be written after all other configs
        final SimpleParameterSet encSet = new SimpleParameterSet(new Parameter[] { globalEncrypter });
        encSet.setSkipSensitiveParameters(skipSensitive);
        encSet.saveValuesToXML(prefElement);
        TransformerFactory transfac = TransformerFactory.newInstance();
        Transformer transformer = transfac.newTransformer();
        transformer.setOutputProperty(OutputKeys.METHOD, "xml");
        transformer.setOutputProperty(OutputKeys.INDENT, "yes");
        transformer.setOutputProperty(OutputKeys.ENCODING, "UTF-8");
        transformer.setOutputProperty("{http://xml.apache.org/xslt}indent-amount", "4");
        // Create parent folder if it does not exist
        File confParent = file.getParentFile();
        if ((confParent != null) && (!confParent.exists())) {
            confParent.mkdirs();
        }
        StreamResult result = new StreamResult(new FileOutputStream(file));
        DOMSource source = new DOMSource(configuration);
        transformer.transform(source, result);
        // make user home config file invisible on windows
        if ((!skipSensitive) && (System.getProperty("os.name").toLowerCase().contains("windows"))) {
            Files.setAttribute(file.toPath(), "dos:hidden", Boolean.TRUE, LinkOption.NOFOLLOW_LINKS);
        }
        logger.info("Saved configuration to file " + file);
    } catch (Exception e) {
        throw new IOException(e);
    }
}