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

Example 11 with MZTolerance

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

the class MSMSScoreCalculator method evaluateMSMS.

/**
 * Returns a calculated similarity score of
 */
public static MSMSScore evaluateMSMS(IMolecularFormula parentFormula, Scan msmsScan, ParameterSet parameters) {
    MZTolerance msmsTolerance = parameters.getParameter(MSMSScoreParameters.msmsTolerance).getValue();
    String massListName = parameters.getParameter(MSMSScoreParameters.massList).getValue();
    MassList massList = msmsScan.getMassList(massListName);
    if (massList == null) {
        throw new IllegalArgumentException("Scan #" + msmsScan.getScanNumber() + " does not have a mass list called '" + massListName + "'");
    }
    DataPoint[] msmsIons = massList.getDataPoints();
    if (msmsIons == null) {
        throw new IllegalArgumentException("Mass list " + massList + " does not contain data for scan #" + msmsScan.getScanNumber());
    }
    MolecularFormulaRange msmsElementRange = new MolecularFormulaRange();
    for (IIsotope isotope : parentFormula.isotopes()) {
        msmsElementRange.addIsotope(isotope, 0, parentFormula.getIsotopeCount(isotope));
    }
    int totalMSMSpeaks = 0, interpretedMSMSpeaks = 0;
    Map<DataPoint, String> msmsAnnotations = new Hashtable<DataPoint, String>();
    msmsCycle: for (DataPoint dp : msmsIons) {
        // Check if this is an isotope
        Range<Double> isotopeCheckRange = Range.closed(dp.getMZ() - 1.4, dp.getMZ() - 0.6);
        for (DataPoint dpCheck : msmsIons) {
            // isotope and we should ignore it
            if (isotopeCheckRange.contains(dpCheck.getMZ()) && (dpCheck.getIntensity() > dp.getIntensity())) {
                continue msmsCycle;
            }
        }
        // If getPrecursorCharge() returns 0, it means charge is unknown. In
        // that case let's assume charge 1
        int precursorCharge = msmsScan.getPrecursorCharge();
        if (precursorCharge == 0)
            precursorCharge = 1;
        // We don't know the charge of the fragment, so we will simply
        // assume 1
        double neutralLoss = msmsScan.getPrecursorMZ() * precursorCharge - dp.getMZ();
        // good threshold
        if (neutralLoss < 5) {
            continue;
        }
        Range<Double> msmsTargetRange = msmsTolerance.getToleranceRange(neutralLoss);
        IChemObjectBuilder builder = SilentChemObjectBuilder.getInstance();
        MolecularFormulaGenerator msmsEngine = new MolecularFormulaGenerator(builder, msmsTargetRange.lowerEndpoint(), msmsTargetRange.upperEndpoint(), msmsElementRange);
        IMolecularFormula formula = msmsEngine.getNextFormula();
        if (formula != null) {
            String formulaString = MolecularFormulaManipulator.getString(formula);
            msmsAnnotations.put(dp, formulaString);
            interpretedMSMSpeaks++;
        }
        totalMSMSpeaks++;
    }
    // If we did not evaluate any MS/MS peaks, we cannot calculate a score
    if (totalMSMSpeaks == 0) {
        return null;
    }
    double msmsScore = (double) interpretedMSMSpeaks / totalMSMSpeaks;
    MSMSScore result = new MSMSScore(msmsScore, msmsAnnotations);
    return result;
}

Example 12 with MZTolerance

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

the class MassListDeisotoper method filterIsotopes.

public static DataPoint[] filterIsotopes(DataPoint[] dataPoints, ParameterSet parameterSet) {
    if (dataPoints == null || dataPoints.length == 0) {
        return dataPoints;
    }
    MZTolerance mzTolerance = parameterSet.getParameter(MassListDeisotoperParameters.mzTolerance).getValue();
    boolean monotonicShape = parameterSet.getParameter(MassListDeisotoperParameters.monotonicShape).getValue();
    int maximumCharge = parameterSet.getParameter(MassListDeisotoperParameters.maximumCharge).getValue();
    int[] charges = new int[maximumCharge];
    for (int i = 0; i < maximumCharge; i++) charges[i] = i + 1;
    // sort by intensity
    dataPoints = dataPoints.clone();
    Arrays.sort(dataPoints, new DataPointSorter(SortingProperty.Intensity, SortingDirection.Descending));
    List<DataPoint> deisotopedDataPoints = new ArrayList<>();
    for (int i = 0; i < dataPoints.length; i++) {
        DataPoint aPeak = dataPoints[i];
        if (aPeak == null) {
            continue;
        }
        // Check which charge state fits best around this peak
        int bestFitCharge = 0;
        int bestFitScore = -1;
        List<DataPoint> bestFitPeaks = null;
        for (int charge : charges) {
            List<DataPoint> fittedPeaks = new ArrayList<>();
            fittedPeaks.add(aPeak);
            fitPattern(fittedPeaks, aPeak, charge, dataPoints, DELTA, monotonicShape, mzTolerance);
            int score = fittedPeaks.size();
            if ((score > bestFitScore) || ((score == bestFitScore) && (bestFitCharge > charge))) {
                bestFitScore = score;
                bestFitCharge = charge;
                bestFitPeaks = fittedPeaks;
            }
        }
        assert bestFitPeaks != null;
        // add to deisotoped
        deisotopedDataPoints.add(dataPoints[i]);
        // remove all
        for (int j = 0; j < dataPoints.length; j++) {
            if (bestFitPeaks.contains(dataPoints[j]))
                dataPoints[j] = null;
        }
    }
    return deisotopedDataPoints.toArray(new DataPoint[deisotopedDataPoints.size()]);
}