Examples with MZmineProject net.sf.mzmine.datamodel.MZmineProject used on opensource projects

Example 11 with MZmineProject

use of net.sf.mzmine.datamodel.MZmineProject in project mzmine2 by mzmine.

the class DeconvolutionModule method runModule.

@Override
@Nonnull
public ExitCode runModule(@Nonnull MZmineProject project, @Nonnull final ParameterSet parameters, @Nonnull final Collection<Task> tasks) {
    PeakList[] peakLists = parameters.getParameter(DeconvolutionParameters.PEAK_LISTS).getValue().getMatchingPeakLists();
    // function to calculate center mz
    CenterFunction mzCenterFunction = parameters.getParameter(DeconvolutionParameters.MZ_CENTER_FUNCTION).getValue();
    // use a LOG weighted, noise corrected, maximum weight capped function
    if (mzCenterFunction.getMeasure().equals(CenterMeasure.AUTO)) {
        // data point with lowest intensity
        // weight = LOG(value) - LOG(noise) (maxed to maxWeight)
        double noise = Arrays.stream(peakLists).flatMap(pkl -> Arrays.stream(pkl.getRows())).map(r -> r.getPeaks()[0]).mapToDouble(peak -> peak.getRawDataPointsIntensityRange().lowerEndpoint()).filter(v -> v != 0).min().orElse(0);
        // maxWeight 4 corresponds to a linear range of 4 orders of magnitude
        // everything higher than this will be capped to this weight
        // do not overestimate influence of very high data points on mass accuracy
        double maxWeight = 4;
        // use a LOG weighted, noise corrected, maximum weight capped function
        mzCenterFunction = new CenterFunction(CenterMeasure.AVG, Weighting.LOG10, noise, maxWeight);
    }
    for (final PeakList peakList : peakLists) {
        tasks.add(new DeconvolutionTask(project, peakList, parameters, mzCenterFunction));
    }
    return ExitCode.OK;
}