Examples with Peak dulab.adap.datamodel.Peak used on opensource projects

Example 6 with Peak

use of dulab.adap.datamodel.Peak in project mzmine2 by mzmine.

the class ADAP3DecompositionV1_5SetupDialog method retTimeCluster.

/**
 * Cluster all peaks in PeakList based on retention time
 *
 * @param peaks list od ADAP peaks
 * @param retTimeValues output of retention times
 * @param mzValues output of m/z-values
 * @param colorValues output of colors
 */
private void retTimeCluster(List<Peak> peaks, List<Double> retTimeValues, List<Double> mzValues, List<Double> colorValues) {
    Double minDistance = parameterSet.getParameter(ADAP3DecompositionV1_5Parameters.MIN_CLUSTER_DISTANCE).getValue();
    Integer minSize = parameterSet.getParameter(ADAP3DecompositionV1_5Parameters.MIN_CLUSTER_SIZE).getValue();
    Double minIntensity = parameterSet.getParameter(ADAP3DecompositionV1_5Parameters.MIN_CLUSTER_INTENSITY).getValue();
    if (minDistance == null || minSize == null || minIntensity == null)
        return;
    List<List<Peak>> retTimeClusters = TwoStepDecomposition.getRetTimeClusters(peaks, minDistance, minSize, minIntensity);
    int colorIndex = 0;
    final int numColors = 7;
    final double[] colors = new double[numColors];
    for (int i = 0; i < numColors; ++i) colors[i] = (double) i / numColors;
    comboClustersModel.removeAllElements();
    // Disable action listeners
    ActionListener[] comboListeners = comboClusters.getActionListeners();
    for (ActionListener l : comboListeners) comboClusters.removeActionListener(l);
    for (List<Peak> cluster : retTimeClusters) {
        for (Peak peak : cluster) {
            retTimeValues.add(peak.getRetTime());
            mzValues.add(peak.getMZ());
            colorValues.add(colors[colorIndex % numColors]);
        }
        ++colorIndex;
        ComboClustersItem newItem = new ComboClustersItem(cluster);
        int i;
        for (i = 0; i < comboClustersModel.getSize(); ++i) {
            double retTime = comboClustersModel.getElementAt(i).aveRetTime;
            if (newItem.aveRetTime < retTime) {
                comboClustersModel.insertElementAt(newItem, i);
                break;
            }
        }
        if (i == comboClustersModel.getSize())
            comboClustersModel.addElement(newItem);
    }
    // Enable action listeners
    for (ActionListener l : comboListeners) comboClusters.addActionListener(l);
}

Example 7 with Peak

use of dulab.adap.datamodel.Peak in project mzmine2 by mzmine.

the class ADAPInterface method getComponent.

public static Component getComponent(final PeakListRow row) {
    if (row.getNumberOfPeaks() == 0)
        throw new IllegalArgumentException("No peaks found");
    NavigableMap<Double, Double> spectrum = new TreeMap<>();
    // Read Spectrum information
    IsotopePattern ip = row.getBestIsotopePattern();
    if (ip != null) {
        for (DataPoint dataPoint : ip.getDataPoints()) spectrum.put(dataPoint.getMZ(), dataPoint.getIntensity());
    }
    // Read Chromatogram
    final Feature peak = row.getBestPeak();
    final RawDataFile dataFile = peak.getDataFile();
    NavigableMap<Double, Double> chromatogram = new TreeMap<>();
    for (final int scan : peak.getScanNumbers()) {
        final DataPoint dataPoint = peak.getDataPoint(scan);
        if (dataPoint != null)
            chromatogram.put(dataFile.getScan(scan).getRetentionTime(), dataPoint.getIntensity());
    }
    return new Component(null, new Peak(chromatogram, new PeakInfo().mzValue(peak.getMZ()).peakID(row.getID())), spectrum, null);
}