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

Example 1 with Desktop

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

the class FragmentSearchTask method run.

/**
 * @see java.lang.Runnable#run()
 */
public void run() {
    setStatus(TaskStatus.PROCESSING);
    logger.info("Starting fragments search in " + peakList);
    PeakListRow[] rows = peakList.getRows();
    totalRows = rows.length;
    // Start with the highest peaks
    Arrays.sort(rows, new PeakListRowSorter(SortingProperty.Height, SortingDirection.Descending));
    // Compare each two rows against each other
    for (int i = 0; i < totalRows; i++) {
        for (int j = i + 1; j < rows.length; j++) {
            // Task canceled?
            if (isCanceled())
                return;
            // smaller one may be a fragment
            if (rows[i].getAverageMZ() > rows[j].getAverageMZ()) {
                if (checkFragment(rows[i], rows[j]))
                    addFragmentInfo(rows[i], rows[j]);
            } else {
                if (checkFragment(rows[j], rows[i]))
                    addFragmentInfo(rows[j], rows[i]);
            }
        }
        finishedRows++;
    }
    // Add task description to peakList
    ((SimplePeakList) peakList).addDescriptionOfAppliedTask(new SimplePeakListAppliedMethod("Identification of fragments", 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);
    logger.info("Finished fragments search in " + peakList);
}

Example 2 with Desktop

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

the class PeakListIdentificationTask method retrieveIdentification.

/**
 * Search the database for the peak's identity.
 *
 * @param row the feature list row.
 * @throws IOException if there are i/o problems.
 */
private void retrieveIdentification(final PeakListRow row) throws IOException {
    currentRow = row;
    // Determine peak charge.
    final Feature bestPeak = row.getBestPeak();
    int charge = bestPeak.getCharge();
    if (charge <= 0) {
        charge = 1;
    }
    // Calculate mass value.
    final double massValue = row.getAverageMZ() * (double) charge - ionType.getAddedMass();
    // Isotope pattern.
    final IsotopePattern rowIsotopePattern = bestPeak.getIsotopePattern();
    // Process each one of the result ID's.
    final String[] findCompounds = gateway.findCompounds(massValue, mzTolerance, numOfResults, db.getParameterSet());
    for (int i = 0; !isCanceled() && i < findCompounds.length; i++) {
        final DBCompound compound = gateway.getCompound(findCompounds[i], db.getParameterSet());
        // In case we failed to retrieve data, skip this compound
        if (compound == null)
            continue;
        final String formula = compound.getPropertyValue(PeakIdentity.PROPERTY_FORMULA);
        // If required, check isotope score.
        if (isotopeFilter && rowIsotopePattern != null && formula != null) {
            // First modify the formula according to ionization.
            final String adjustedFormula = FormulaUtils.ionizeFormula(formula, ionType, charge);
            LOG.finest("Calculating isotope pattern for compound formula " + formula + " adjusted to " + adjustedFormula);
            // Generate IsotopePattern for this compound
            final IsotopePattern compoundIsotopePattern = IsotopePatternCalculator.calculateIsotopePattern(adjustedFormula, MIN_ABUNDANCE, charge, ionType.getPolarity());
            // Check isotope pattern match
            boolean check = IsotopePatternScoreCalculator.checkMatch(rowIsotopePattern, compoundIsotopePattern, isotopeFilterParameters);
            if (!check)
                continue;
        }
        // Add the retrieved identity to the feature list row
        row.addPeakIdentity(compound, false);
        // Notify the GUI about the change in the project
        MZmineCore.getProjectManager().getCurrentProject().notifyObjectChanged(row, false);
        // Repaint the window to reflect the change in the feature list
        Desktop desktop = MZmineCore.getDesktop();
        if (!(desktop instanceof HeadLessDesktop))
            desktop.getMainWindow().repaint();
    }
}

Example 3 with Desktop

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

the class Ms2SearchTask method run.

/**
 * @see java.lang.Runnable#run()
 */
public void run() {
    setStatus(TaskStatus.PROCESSING);
    logger.info("Starting MS2 similarity search between " + peakList1 + " and " + peakList2 + " with mz tolerance:" + mzTolerance.getPpmTolerance());
    Ms2SearchResult searchResult;
    PeakListRow[] rows1 = peakList1.getRows();
    PeakListRow[] rows2 = peakList2.getRows();
    int rows1Length = rows1.length;
    int rows2Length = rows2.length;
    totalRows = rows1Length;
    for (int i = 0; i < rows1Length; i++) {
        for (int j = 0; j < rows2Length; j++) {
            Feature featureA = rows1[i].getBestPeak();
            Feature featureB = rows2[j].getBestPeak();
            // Complication. The "best" peak, may not have the "best" fragmentation
            Scan scanA = rows1[i].getBestFragmentation();
            Scan scanB = rows2[j].getBestFragmentation();
            searchResult = simpleMS2similarity(scanA, scanB, intensityThreshold, mzTolerance, massListName);
            // Report the final score to the peaklist identity
            if (searchResult != null && searchResult.getScore() > scoreThreshold && searchResult.getNumIonsMatched() >= minimumIonsMatched)
                this.addMS2Identity(rows1[i], featureA, featureB, searchResult);
            if (isCanceled())
                return;
        }
        // Update progress bar
        finishedRows++;
    }
    // Add task description to peakList
    ((SimplePeakList) peakList1).addDescriptionOfAppliedTask(new SimplePeakListAppliedMethod("Identification of similar MS2s", 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);
    logger.info("Finished MS2 similarity search for " + peakList1 + "against" + peakList2);
}

Example 4 with Desktop

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

the class CustomDBSearchTask method run.

/**
 * @see java.lang.Runnable#run()
 */
@Override
public void run() {
    setStatus(TaskStatus.PROCESSING);
    try {
        // read database contents in memory
        FileReader dbFileReader = new FileReader(dataBaseFile);
        databaseValues = CSVParser.parse(dbFileReader, fieldSeparator.charAt(0));
        if (ignoreFirstLine)
            finishedLines++;
        for (; finishedLines < databaseValues.length; finishedLines++) {
            if (isCanceled()) {
                dbFileReader.close();
                return;
            }
            try {
                processOneLine(databaseValues[finishedLines]);
            } catch (Exception e) {
            // ignore incorrect lines
            }
        }
        dbFileReader.close();
    } catch (Exception e) {
        logger.log(Level.WARNING, "Could not read file " + dataBaseFile, e);
        setStatus(TaskStatus.ERROR);
        setErrorMessage(e.toString());
        return;
    }
    // Add task description to peakList
    peakList.addDescriptionOfAppliedTask(new SimplePeakListAppliedMethod("Peak identification using 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 5 with Desktop

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

the class AdductSearchTask method run.

@Override
public void run() {
    setStatus(TaskStatus.PROCESSING);
    LOG.info("Starting adducts search in " + peakList);
    try {
        // Search the feature list for adducts.
        searchAdducts();
        if (!isCanceled()) {
            // Add task description to peakList.
            peakList.addDescriptionOfAppliedTask(new SimplePeakListAppliedMethod("Identification of adducts", parameters));
            // Repaint the window to reflect the change in the feature list
            Desktop desktop = MZmineCore.getDesktop();
            if (!(desktop instanceof HeadLessDesktop))
                desktop.getMainWindow().repaint();
            // Done.
            setStatus(TaskStatus.FINISHED);
            LOG.info("Finished adducts search in " + peakList);
        }
    } catch (Throwable t) {
        LOG.log(Level.SEVERE, "Adduct search error", t);
        setStatus(TaskStatus.ERROR);
        setErrorMessage(t.getMessage());
    }
}