Examples with ResolvedPeak net.sf.mzmine.modules.peaklistmethods.peakpicking.deconvolution.ResolvedPeak used on opensource projects

Example 6 with ResolvedPeak

use of net.sf.mzmine.modules.peaklistmethods.peakpicking.deconvolution.ResolvedPeak in project mzmine2 by mzmine.

the class SavitzkyGolayPeakDetector method peaksSearch.

/**
 * Search for peaks.
 *
 * @param chromatogram the chromatogram to search.
 * @param scanNumbers scan number to focus search on
 * @param derivativeOfIntensities derivatives of intensity values.
 * @param noiseThreshold noise threshold.
 * @return array of peaks found.
 */
private static Feature[] peaksSearch(final Feature chromatogram, final int[] scanNumbers, final double[] derivativeOfIntensities, final double noiseThreshold, CenterFunction mzCenterFunction, final double msmsRange, final double rTRangeMSMS) {
    // Flag to identify the current and next overlapped peak.
    boolean activeFirstPeak = false;
    boolean activeSecondPeak = false;
    // Flag to indicate the value of 2nd derivative pass noise threshold
    // level.
    boolean passThreshold = false;
    // Number of times that 2nd derivative cross zero value for the current
    // feature detection.
    int crossZero = 0;
    final int totalNumberPoints = derivativeOfIntensities.length;
    // Indexes of start and ending of the current peak and beginning of the
    // next.
    int currentPeakStart = totalNumberPoints;
    int nextPeakStart = totalNumberPoints;
    int currentPeakEnd = 0;
    final List<Feature> resolvedPeaks = new ArrayList<Feature>(2);
    // 
    for (int i = 1; i < totalNumberPoints; i++) {
        // Changing sign and crossing zero
        if (derivativeOfIntensities[i - 1] < 0.0 && derivativeOfIntensities[i] > 0.0 || derivativeOfIntensities[i - 1] > 0.0 && derivativeOfIntensities[i] < 0.0) {
            if (derivativeOfIntensities[i - 1] < 0.0 && derivativeOfIntensities[i] > 0.0) {
                if (crossZero == 2) {
                    // passThreshold flag is activated.
                    if (passThreshold) {
                        activeSecondPeak = true;
                        nextPeakStart = i;
                    } else {
                        currentPeakStart = i;
                        crossZero = 0;
                        activeFirstPeak = true;
                    }
                }
            }
            // Finalize the first overlapped peak.
            if (crossZero == 3) {
                activeFirstPeak = false;
                currentPeakEnd = i;
            }
            // Increments when detect a crossing zero event
            passThreshold = false;
            if (activeFirstPeak || activeSecondPeak) {
                crossZero++;
            }
        }
        // Filter for noise threshold level.
        if (Math.abs(derivativeOfIntensities[i]) > noiseThreshold) {
            passThreshold = true;
        }
        // Start peak region.
        if (crossZero == 0 && derivativeOfIntensities[i] > 0.0 && !activeFirstPeak) {
            activeFirstPeak = true;
            currentPeakStart = i;
            crossZero++;
        }
        // Finalize the peak region in case of zero values.
        if (derivativeOfIntensities[i - 1] == 0.0 && derivativeOfIntensities[i] == 0.0 && activeFirstPeak) {
            currentPeakEnd = crossZero < 3 ? 0 : i;
            activeFirstPeak = false;
            activeSecondPeak = false;
            crossZero = 0;
        }
        // start to the first available data point.
        while (currentPeakStart < scanNumbers.length - 1) {
            if (chromatogram.getDataPoint(scanNumbers[currentPeakStart]) == null) {
                currentPeakStart++;
            } else {
                break;
            }
        }
        // peak there.
        for (int newEnd = currentPeakStart; newEnd <= currentPeakEnd; newEnd++) {
            if (chromatogram.getDataPoint(scanNumbers[newEnd]) == null) {
                currentPeakEnd = newEnd - 1;
                break;
            }
        }
        // the chromatogram.
        if (currentPeakEnd - currentPeakStart > 0 && !activeFirstPeak) {
            resolvedPeaks.add(new ResolvedPeak(chromatogram, currentPeakStart, currentPeakEnd, mzCenterFunction, msmsRange, rTRangeMSMS));
            // for this new current peak.
            if (activeSecondPeak) {
                activeSecondPeak = false;
                activeFirstPeak = true;
                crossZero = derivativeOfIntensities[i] > 0.0 ? 1 : 2;
                currentPeakStart = nextPeakStart;
            } else {
                crossZero = 0;
                currentPeakStart = totalNumberPoints;
            }
            passThreshold = false;
            nextPeakStart = totalNumberPoints;
            currentPeakEnd = 0;
        }
    }
    return resolvedPeaks.toArray(new Feature[resolvedPeaks.size()]);
}