use of net.sf.mzmine.project.impl.MZmineProjectImpl 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);
}
}
use of net.sf.mzmine.project.impl.MZmineProjectImpl in project mzmine2 by mzmine.
the class SortPeakListsModule method runModule.
@Override
@Nonnull
public ExitCode runModule(@Nonnull MZmineProject project, @Nonnull ParameterSet parameters, @Nonnull Collection<Task> tasks) {
List<PeakList> peakLists = Arrays.asList(parameters.getParameter(SortPeakListsParameters.peakLists).getValue().getMatchingPeakLists());
PeakListTreeModel model = null;
if (project instanceof MZmineProjectImpl) {
model = ((MZmineProjectImpl) project).getPeakListTreeModel();
} else if (MZmineCore.getDesktop() instanceof MainWindow) {
ProjectTree tree = ((MainWindow) MZmineCore.getDesktop()).getMainPanel().getPeakListTree();
model = (PeakListTreeModel) tree.getModel();
}
if (model == null)
throw new MSDKRuntimeException("Cannot find feature list tree model for sorting. Different MZmine project impl?");
final DefaultMutableTreeNode rootNode = model.getRoot();
// Get all tree nodes that represent selected feature lists, and remove
// them from
final ArrayList<DefaultMutableTreeNode> selectedNodes = new ArrayList<DefaultMutableTreeNode>();
for (int row = 0; row < rootNode.getChildCount(); row++) {
DefaultMutableTreeNode selectedNode = (DefaultMutableTreeNode) rootNode.getChildAt(row);
Object selectedObject = selectedNode.getUserObject();
if (peakLists.contains(selectedObject)) {
selectedNodes.add(selectedNode);
}
}
// Get the index of the first selected item
final ArrayList<Integer> positions = new ArrayList<Integer>();
for (DefaultMutableTreeNode node : selectedNodes) {
int nodeIndex = rootNode.getIndex(node);
if (nodeIndex != -1)
positions.add(nodeIndex);
}
if (positions.isEmpty())
return ExitCode.ERROR;
int insertPosition = Collections.min(positions);
// Sort the feature lists by name
Collections.sort(selectedNodes, new Comparator<DefaultMutableTreeNode>() {
@Override
public int compare(DefaultMutableTreeNode o1, DefaultMutableTreeNode o2) {
return o1.getUserObject().toString().compareTo(o2.getUserObject().toString());
}
});
// Reorder the nodes in the tree model
for (DefaultMutableTreeNode node : selectedNodes) {
model.removeNodeFromParent(node);
model.insertNodeInto(node, rootNode, insertPosition);
insertPosition++;
}
return ExitCode.OK;
}
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