Examples with MZTolerance net.sf.mzmine.parameters.parametertypes.tolerances.MZTolerance used on opensource projects

Example 1 with MZTolerance

use of net.sf.mzmine.parameters.parametertypes.tolerances.MZTolerance in project mzmine2 by mzmine.

the class MsMsSpectraMergeModule method mergeConsecutiveScans.

/**
 * Internal method for merging a list of consecutive MS/MS scans.
 *
 * @param scans MS/MS scans with their precursor information
 * @param massList name of the mass list to use when extracting peaks
 * @param scoreModel scoring model to use when removing low quality MS/MS and selecting the best
 *        quality MS/MS
 * @return merged spectrum
 */
protected MergedSpectrum mergeConsecutiveScans(ParameterSet parameters, FragmentScan scans, String massList, Ms2QualityScoreModel scoreModel) {
    int totalNumberOfScans = scans.ms2ScanNumbers.length;
    /*
     * find scan with best quality
     */
    final double[] scores = scoreModel.calculateQualityScore(scans);
    int best = 0;
    for (int k = 1; k < scores.length; ++k) {
        if (scores[k] > scores[best]) {
            best = k;
        }
    }
    if (scores[best] <= 0)
        return MergedSpectrum.empty(totalNumberOfScans);
    final List<Scan> scansToMerge = new ArrayList<>();
    scansToMerge.add(scans.origin.getScan(scans.ms2ScanNumbers[best]));
    final Scan firstScan = scansToMerge.get(0);
    final MassList firstML = firstScan.getMassList(massList);
    if (firstML == null)
        throw new RuntimeException("Scan " + firstScan.getDataFile().getName() + "#" + firstScan.getScanNumber() + " does not have a mass list " + massList);
    if (firstML.getDataPoints().length <= 1)
        return MergedSpectrum.empty(totalNumberOfScans);
    /*
     * remove scans which are considerably worse than the best scan
     */
    final double scoreThreshold = best / 5d;
    for (int i = 1; i < scores.length; ++i) {
        int k = best - i;
        if (k >= 0 && scores[k] > scoreThreshold) {
            scansToMerge.add(scans.origin.getScan(scans.ms2ScanNumbers[k]));
        }
        k = best + i;
        if (k < scores.length && scores[k] > scoreThreshold) {
            scansToMerge.add(scans.origin.getScan(scans.ms2ScanNumbers[k]));
        }
    }
    if (scansToMerge.size() == 1) {
        final MergedSpectrum single = new MergedSpectrum(scansToMerge.get(0), massList);
        single.bestFragmentScanScore = scores[best];
        single.removedScansByLowQuality = scores.length - 1;
        return single;
    }
    /*
     * merge every scan if its cosine is above the cosine threshold
     */
    final double cosineThreshold = parameters.getParameter(MsMsSpectraMergeParameters.COSINE_PARAMETER).getValue();
    final MZTolerance mzTolerance = parameters.getParameter(MsMsSpectraMergeParameters.MASS_ACCURACY).getValue();
    final MzMergeMode mzMergeMode = parameters.getParameter(MsMsSpectraMergeParameters.MZ_MERGE_MODE).getValue();
    final IntensityMergeMode intensityMergeMode = parameters.getParameter(MsMsSpectraMergeParameters.INTENSITY_MERGE_MODE).getValue();
    MergedSpectrum initial = new MergedSpectrum(scansToMerge.get(0), massList);
    initial.bestFragmentScanScore = best;
    final double lowestMassToConsider = Math.min(50d, scans.feature.getMZ() - 50d);
    final DataPoint[] initialMostIntense = ScanUtils.extractMostIntensePeaksAcrossMassRange(initial.data, Range.closed(lowestMassToConsider, 150d), 6);
    double lowestIntensityToConsider;
    final int mostIntensPeakWithin = ScanUtils.findMostIntensePeakWithin(initialMostIntense, Range.closed(lowestMassToConsider, scans.feature.getMZ()));
    if (mostIntensPeakWithin >= 0)
        lowestIntensityToConsider = 0.005d * initialMostIntense[mostIntensPeakWithin].getIntensity();
    else
        lowestIntensityToConsider = 0d;
    Range<Double> cosineRange = Range.closed(lowestMassToConsider, scans.feature.getMZ() - 20);
    final double initialCosine = ScanUtils.probabilityProductUnnormalized(initialMostIntense, initialMostIntense, mzTolerance, lowestIntensityToConsider, cosineRange);
    for (int k = 1; k < scansToMerge.size(); ++k) {
        Scan scan = scansToMerge.get(k);
        if (!(scan.getPolarity().equals(initial.polarity) && scan.getPrecursorCharge() == initial.precursorCharge && mzTolerance.checkWithinTolerance(scan.getPrecursorMZ(), initial.precursorMz))) {
            LoggerFactory.getLogger(MsMsSpectraMergeModule.class).warn("Scan " + scan.getScanNumber() + " cannot be merged: it seems to belong to a different feature.");
            continue;
        }
        DataPoint[] dataPoints = scan.getMassList(massList).getDataPoints();
        final DataPoint[] mostIntense = ScanUtils.extractMostIntensePeaksAcrossMassRange(dataPoints, cosineRange, 6);
        final double norm = ScanUtils.probabilityProductUnnormalized(mostIntense, mostIntense, mzTolerance, lowestIntensityToConsider, cosineRange);
        final double cosine = ScanUtils.probabilityProductUnnormalized(initialMostIntense, mostIntense, mzTolerance, lowestIntensityToConsider, cosineRange) / Math.sqrt(norm * initialCosine);
        if (cosine >= cosineThreshold) {
            initial = merge(initial, scan, dataPoints, mzMergeMode, intensityMergeMode, mzTolerance);
        } else {
            initial.removedScansByLowCosine++;
        }
    }
    initial.removedScansByLowQuality += (totalNumberOfScans - scansToMerge.size());
    return initial;
}

Example 2 with MZTolerance

use of net.sf.mzmine.parameters.parametertypes.tolerances.MZTolerance in project mzmine2 by mzmine.

the class MsMsSpectraMergeModule method mergeConsecutiveScans.

/**
 * Merge all consecutive MS/MS scans of the same feature within the same sample. Two scans are
 * consecutive, if there is no other MS/MS or MS in between. It is recommended to use
 * #merge(PeakListRow,String) instead. Note, that this method will not remove noise peaks from the
 * merged spectra.
 *
 * @param feature the feature which MS/MS should be merged
 * @param massList name of the mass list to use when extracting peaks
 * @return all merged spectra of consecutive MS/MS scans of the given feature
 */
public List<MergedSpectrum> mergeConsecutiveScans(ParameterSet parameters, Feature feature, String massList) {
    MZTolerance ppm = parameters.getParameter(MsMsSpectraMergeParameters.MASS_ACCURACY).getValue();
    final double isolationWindowOffset = parameters.getParameter(MsMsSpectraMergeParameters.ISOLATION_WINDOW_OFFSET).getValue();
    final double isolationWindowWidth = parameters.getParameter(MsMsSpectraMergeParameters.ISOLATION_WINDOW_WIDTH).getValue();
    FragmentScan[] allFragmentScans = FragmentScan.getAllFragmentScansFor(feature, massList, Range.closed(isolationWindowOffset - isolationWindowWidth, isolationWindowOffset + isolationWindowWidth), ppm);
    final List<MergedSpectrum> mergedSpec = new ArrayList<>();
    for (FragmentScan scan : allFragmentScans) {
        MergedSpectrum e = mergeConsecutiveScans(parameters, scan, massList, Ms2QualityScoreModel.SelectByLowChimericIntensityRelativeToMs1Intensity);
        if (e.data.length > 0)
            mergedSpec.add(e);
    }
    return mergedSpec;
}

Example 3 with MZTolerance

use of net.sf.mzmine.parameters.parametertypes.tolerances.MZTolerance in project mzmine2 by mzmine.

the class MzRangeFormulaCalculatorModule method getMzRangeFromFormula.

@Nullable
public static Range<Double> getMzRangeFromFormula(ParameterSet myParameters) {
    String formula = myParameters.getParameter(MzRangeFormulaCalculatorParameters.formula).getValue().trim();
    IonizationType ionType = myParameters.getParameter(MzRangeFormulaCalculatorParameters.ionType).getValue();
    MZTolerance mzTolerance = myParameters.getParameter(MzRangeFormulaCalculatorParameters.mzTolerance).getValue();
    Integer charge = myParameters.getParameter(MzRangeFormulaCalculatorParameters.charge).getValue();
    return getMzRangeFromFormula(formula, ionType, mzTolerance, charge);
}

Example 4 with MZTolerance

use of net.sf.mzmine.parameters.parametertypes.tolerances.MZTolerance in project mzmine2 by mzmine.

the class MzRangeMassCalculatorModule method showRangeCalculationDialog.

/**
 * Shows the calculation dialog and returns the calculated m/z range. May return null in case user
 * clicked Cancel.
 */
@Nullable
public static Range<Double> showRangeCalculationDialog() {
    ParameterSet myParameters = MZmineCore.getConfiguration().getModuleParameters(MzRangeMassCalculatorModule.class);
    if (myParameters == null)
        return null;
    ExitCode exitCode = myParameters.showSetupDialog(null, true);
    if (exitCode != ExitCode.OK)
        return null;
    Double mz = myParameters.getParameter(MzRangeMassCalculatorParameters.mz).getValue();
    MZTolerance mzTolerance = myParameters.getParameter(MzRangeMassCalculatorParameters.mzTolerance).getValue();
    if ((mz == null) || (mzTolerance == null))
        return null;
    Range<Double> mzRange = mzTolerance.getToleranceRange(mz);
    return mzRange;
}

Example 5 with MZTolerance

use of net.sf.mzmine.parameters.parametertypes.tolerances.MZTolerance in project mzmine2 by mzmine.

the class RansacAlignerSetupDialog method getVectorAlignment.

/**
 * Create the vector which contains all the possible aligned peaks.
 *
 * @return vector which contains all the possible aligned peaks.
 */
private Vector<AlignStructMol> getVectorAlignment(PeakList peakListX, PeakList peakListY, RawDataFile file, RawDataFile file2) {
    Vector<AlignStructMol> alignMol = new Vector<AlignStructMol>();
    for (PeakListRow row : peakListX.getRows()) {
        // Calculate limits for a row with which the row can be aligned
        MZTolerance mzTolerance = super.parameterSet.getParameter(RansacAlignerParameters.MZTolerance).getValue();
        RTTolerance rtTolerance = super.parameterSet.getParameter(RansacAlignerParameters.RTToleranceBefore).getValue();
        Range<Double> mzRange = mzTolerance.getToleranceRange(row.getAverageMZ());
        Range<Double> rtRange = rtTolerance.getToleranceRange(row.getAverageRT());
        // Get all rows of the aligned peaklist within parameter limits
        PeakListRow[] candidateRows = peakListY.getRowsInsideScanAndMZRange(rtRange, mzRange);
        for (PeakListRow candidateRow : candidateRows) {
            if (file == null || file2 == null) {
                alignMol.addElement(new AlignStructMol(row, candidateRow));
            } else {
                if (candidateRow.getPeak(file2) != null) {
                    alignMol.addElement(new AlignStructMol(row, candidateRow, file, file2));
                }
            }
        }
    }
    return alignMol;
}