Examples with Desktop net.sf.mzmine.desktop.Desktop used on opensource projects

Example 6 with Desktop

use of net.sf.mzmine.desktop.Desktop in project mzmine2 by mzmine.

the class PeakListIdentificationTask method notifyRow.

/**
 * Method notifies object about content update
 *
 * @param row to be notified
 */
private static void notifyRow(PeakListRow row) {
    MZmineCore.getProjectManager().getCurrentProject().notifyObjectChanged(row, false);
    Desktop desktop = MZmineCore.getDesktop();
    if (!(desktop instanceof HeadLessDesktop))
        desktop.getMainWindow().repaint();
}

Example 7 with Desktop

use of net.sf.mzmine.desktop.Desktop in project mzmine2 by mzmine.

the class PrecursorDBSearchTask method run.

/**
 * @see java.lang.Runnable#run()
 */
@Override
public void run() {
    setStatus(TaskStatus.PROCESSING);
    int count = 0;
    try {
        tasks = parseFile(dataBaseFile);
        totalTasks = tasks.size();
        if (!tasks.isEmpty()) {
            // wait for the tasks to finish
            while (!isCanceled() && !tasks.isEmpty()) {
                for (int i = 0; i < tasks.size(); i++) {
                    if (tasks.get(i).isFinished() || tasks.get(i).isCanceled()) {
                        tasks.remove(i);
                        i--;
                    }
                }
                // wait for all sub tasks to finish
                try {
                    Thread.sleep(100);
                } catch (Exception e) {
                    cancel();
                }
            }
            // cancelled
            if (isCanceled()) {
                tasks.stream().forEach(AbstractTask::cancel);
            }
        } else {
            setStatus(TaskStatus.ERROR);
            setErrorMessage("DB file was empty - or error while parsing " + dataBaseFile);
        }
    } catch (Exception e) {
        logger.log(Level.SEVERE, "Could not read file " + dataBaseFile, e);
        setStatus(TaskStatus.ERROR);
        setErrorMessage(e.toString());
    }
    logger.info("Added " + matches.get() + " matches to possible precursors in library: " + dataBaseFile.getAbsolutePath());
    // Add task description to peakList
    peakList.addDescriptionOfAppliedTask(new SimplePeakListAppliedMethod("Possible precursor identification using MS/MS spectral database " + dataBaseFile, parameters));
    // Repaint the window to reflect the change in the feature list
    Desktop desktop = MZmineCore.getDesktop();
    if (!(desktop instanceof HeadLessDesktop))
        desktop.getMainWindow().repaint();
    setStatus(TaskStatus.FINISHED);
}

Example 8 with Desktop

use of net.sf.mzmine.desktop.Desktop in project mzmine2 by mzmine.

the class SelectedRowsLocalSpectralDBSearchTask method run.

/**
 * @see java.lang.Runnable#run()
 */
@Override
public void run() {
    setStatus(TaskStatus.PROCESSING);
    int count = 0;
    if (peakListRows.length == 1) {
        // add result frame
        resultWindow = new SpectraIdentificationResultsWindow();
        resultWindow.setVisible(true);
    } else {
        resultWindow = null;
    }
    try {
        tasks = parseFile(dataBaseFile);
        totalTasks = tasks.size();
        if (!tasks.isEmpty()) {
            // wait for the tasks to finish
            while (!isCanceled() && !tasks.isEmpty()) {
                for (int i = 0; i < tasks.size(); i++) {
                    if (tasks.get(i).isFinished() || tasks.get(i).isCanceled()) {
                        count += tasks.get(i).getCount();
                        tasks.remove(i);
                        i--;
                    }
                }
                // wait for all sub tasks to finish
                try {
                    Thread.sleep(100);
                } catch (Exception e) {
                    cancel();
                }
            }
            // cancelled
            if (isCanceled()) {
                tasks.stream().forEach(AbstractTask::cancel);
            }
        } else {
            setStatus(TaskStatus.ERROR);
            setErrorMessage("DB file was empty - or error while parsing " + dataBaseFile);
        }
    } catch (Exception e) {
        logger.log(Level.SEVERE, "Could not read file " + dataBaseFile, e);
        setStatus(TaskStatus.ERROR);
        setErrorMessage(e.toString());
    }
    logger.info("Added " + count + " spectral library matches");
    if (resultWindow != null) {
        resultWindow.setTitle("Matched " + count + " compounds for feature list row: " + peakListRows[0]);
        resultWindow.setMatchingFinished();
        resultWindow.revalidate();
        resultWindow.repaint();
    }
    // Repaint the window to reflect the change in the feature list
    Desktop desktop = MZmineCore.getDesktop();
    if (!(desktop instanceof HeadLessDesktop))
        desktop.getMainWindow().repaint();
    // work around to update feature list identities
    if (table.getRowCount() > 0)
        table.setRowSelectionInterval(0, 0);
    setStatus(TaskStatus.FINISHED);
}

Example 9 with Desktop

use of net.sf.mzmine.desktop.Desktop in project mzmine2 by mzmine.

the class StatusBarHandler method publish.

/**
 * @see java.util.logging.Handler#publish(java.util.logging.LogRecord)
 */
public void publish(LogRecord record) {
    // if the event level is below INFO, ignore it
    if (record.getLevel().intValue() < infoLevel)
        return;
    // get Desktop instance
    Desktop desktop = MZmineCore.getDesktop();
    if (desktop == null)
        return;
    if (desktop.getMainWindow() == null)
        return;
    Date recordTime = new Date(record.getMillis());
    // format the message
    String formattedMessage = "[" + timeFormat.format(recordTime) + "]: " + record.getMessage();
    // default color is black
    Color messageColor = Color.black;
    // display severe errors in red
    if (record.getLevel().equals(Level.SEVERE))
        messageColor = Color.red;
    // set status bar text
    desktop.setStatusBarText(formattedMessage, messageColor);
}

Example 10 with Desktop

use of net.sf.mzmine.desktop.Desktop in project mzmine2 by mzmine.

the class LocalSpectralDBSearchTask method run.

/**
 * @see java.lang.Runnable#run()
 */
@Override
public void run() {
    setStatus(TaskStatus.PROCESSING);
    int count = 0;
    try {
        tasks = parseFile(dataBaseFile);
        totalTasks = tasks.size();
        if (!tasks.isEmpty()) {
            // wait for the tasks to finish
            while (!isCanceled() && !tasks.isEmpty()) {
                for (int i = 0; i < tasks.size(); i++) {
                    if (tasks.get(i).isFinished() || tasks.get(i).isCanceled()) {
                        count += tasks.get(i).getCount();
                        tasks.remove(i);
                        i--;
                    }
                }
                // wait for all sub tasks to finish
                try {
                    Thread.sleep(100);
                } catch (Exception e) {
                    cancel();
                }
            }
            // cancelled
            if (isCanceled()) {
                tasks.stream().forEach(AbstractTask::cancel);
            }
        } else {
            setStatus(TaskStatus.ERROR);
            setErrorMessage("DB file was empty - or error while parsing " + dataBaseFile);
        }
    } catch (Exception e) {
        logger.log(Level.SEVERE, "Could not read file " + dataBaseFile, e);
        setStatus(TaskStatus.ERROR);
        setErrorMessage(e.toString());
    }
    logger.info("Added " + count + " spectral library matches");
    // Add task description to peakList
    peakList.addDescriptionOfAppliedTask(new SimplePeakListAppliedMethod("Peak identification using MS/MS spectral database " + dataBaseFile, parameters));
    // Repaint the window to reflect the change in the feature list
    Desktop desktop = MZmineCore.getDesktop();
    if (!(desktop instanceof HeadLessDesktop))
        desktop.getMainWindow().repaint();
    setStatus(TaskStatus.FINISHED);
}