Examples with RetTimeClusterer dulab.adap.workflow.decomposition.RetTimeClusterer used on opensource projects

Example 1 with RetTimeClusterer

use of dulab.adap.workflow.decomposition.RetTimeClusterer in project mzmine2 by mzmine.

the class ADAP3DecompositionV2SetupDialog method retTimeCluster.

/**
 * Cluster all peaks in PeakList based on retention time
 */
private void retTimeCluster() {
    ChromatogramPeakPair chromatogramPeakPair = cboPeakLists.getItemAt(cboPeakLists.getSelectedIndex());
    if (chromatogramPeakPair == null)
        return;
    PeakList chromatogramList = chromatogramPeakPair.chromatograms;
    PeakList peakList = chromatogramPeakPair.peaks;
    if (chromatogramList == null || peakList == null)
        return;
    Double minDistance = parameterSet.getParameter(ADAP3DecompositionV2Parameters.PREF_WINDOW_WIDTH).getValue();
    if (minDistance == null || minDistance <= 0.0)
        return;
    // Convert peakList into ranges
    List<RetTimeClusterer.Interval> ranges = Arrays.stream(peakList.getRows()).map(PeakListRow::getBestPeak).map(p -> new RetTimeClusterer.Interval(p.getRawDataPointsRTRange(), p.getMZ())).collect(Collectors.toList());
    List<BetterPeak> peaks = new ADAP3DecompositionV2Utils().getPeaks(peakList);
    // Form clusters of ranges
    List<RetTimeClusterer.Cluster> retTimeClusters = new RetTimeClusterer(minDistance).execute(peaks);
    cboClusters.removeAllItems();
    cboClusters.removeActionListener(this);
    for (RetTimeClusterer.Cluster cluster : retTimeClusters) {
        int i;
        for (i = 0; i < cboClusters.getItemCount(); ++i) {
            double retTime = cboClusters.getItemAt(i).retTime;
            if (cluster.retTime < retTime) {
                cboClusters.insertItemAt(cluster, i);
                break;
            }
        }
        if (i == cboClusters.getItemCount())
            cboClusters.addItem(cluster);
    }
    cboClusters.addActionListener(this);
    retTimeMZPlot.updateData(retTimeClusters);
    shapeCluster();
}