Examples with SimpleIsotopePattern net.sf.mzmine.datamodel.impl.SimpleIsotopePattern used on opensource projects

Example 16 with SimpleIsotopePattern

use of net.sf.mzmine.datamodel.impl.SimpleIsotopePattern in project mzmine2 by mzmine.

the class IsotopePatternCalculator method removeDataPointsBelowIntensity.

public static IsotopePattern removeDataPointsBelowIntensity(IsotopePattern pattern, double minIntensity) {
    DataPoint[] dp = pattern.getDataPoints();
    for (int i = 0; i < pattern.getNumberOfDataPoints(); i++) {
        if (dp[i].getIntensity() < minIntensity) {
            dp[i] = null;
        }
    }
    ArrayList<DataPoint> newDP = new ArrayList<DataPoint>();
    ArrayList<String> newComp = new ArrayList<String>();
    for (int i = 0; i < dp.length; i++) {
        DataPoint p = dp[i];
        if (dp[i] != null) {
            newDP.add(p);
            if (pattern instanceof ExtendedIsotopePattern) {
                newComp.add(((ExtendedIsotopePattern) pattern).getIsotopeComposition(i));
            }
        }
    }
    if (pattern instanceof ExtendedIsotopePattern)
        return new ExtendedIsotopePattern(newDP.toArray(new DataPoint[0]), pattern.getStatus(), pattern.getDescription(), newComp.toArray(new String[0]));
    else
        return new SimpleIsotopePattern(newDP.toArray(new DataPoint[0]), pattern.getStatus(), pattern.getDescription());
}

Example 17 with SimpleIsotopePattern

use of net.sf.mzmine.datamodel.impl.SimpleIsotopePattern in project mzmine2 by mzmine.

the class DPPIsotopeGrouperTask method run.

@Override
public void run() {
    if (!checkParameterSet() || !checkValues()) {
        setStatus(TaskStatus.ERROR);
        return;
    }
    if (!FormulaUtils.checkMolecularFormula(element)) {
        setStatus(TaskStatus.ERROR);
        logger.warning("Data point/Spectra processing: Invalid element parameter in " + getTaskDescription());
    }
    if (getDataPoints().length == 0) {
        logger.info("Data point/Spectra processing: 0 data points were passed to " + getTaskDescription() + " Please check the parameters.");
        setStatus(TaskStatus.CANCELED);
        return;
    }
    if (!(getDataPoints() instanceof ProcessedDataPoint[])) {
        logger.warning("Data point/Spectra processing: The data points passed to Isotope Grouper were not an instance of processed data points." + " Make sure to run mass detection first.");
        setStatus(TaskStatus.CANCELED);
        return;
    }
    setStatus(TaskStatus.PROCESSING);
    ProcessedDataPoint[] dataPoints = (ProcessedDataPoint[]) getDataPoints();
    int[] charges = new int[maximumCharge];
    for (int i = 0; i < maximumCharge; i++) charges[i] = i + 1;
    IsotopePattern pattern = IsotopePatternCalculator.calculateIsotopePattern(element, 0.01, 1, PolarityType.POSITIVE);
    double isotopeDistance = pattern.getDataPoints()[1].getMZ() - pattern.getDataPoints()[0].getMZ();
    ProcessedDataPoint[] sortedDataPoints = dataPoints.clone();
    Arrays.sort(sortedDataPoints, (d1, d2) -> {
        // *-1 to sort descending
        return -1 * Double.compare(d1.getIntensity(), d2.getIntensity());
    });
    List<ProcessedDataPoint> deisotopedDataPoints = new ArrayList<>();
    for (int i = 0; i < sortedDataPoints.length; i++) {
        if (isCanceled())
            return;
        DataPoint aPeak = sortedDataPoints[i];
        if (aPeak == null) {
            processedPeaks++;
            continue;
        }
        // Check which charge state fits best around this peak
        int bestFitCharge = 0;
        int bestFitScore = -1;
        Vector<DataPoint> bestFitPeaks = null;
        for (int charge : charges) {
            Vector<DataPoint> fittedPeaks = new Vector<DataPoint>();
            fittedPeaks.add(aPeak);
            fitPattern(fittedPeaks, aPeak, charge, sortedDataPoints, isotopeDistance);
            int score = fittedPeaks.size();
            if ((score > bestFitScore) || ((score == bestFitScore) && (bestFitCharge > charge))) {
                bestFitScore = score;
                bestFitCharge = charge;
                bestFitPeaks = fittedPeaks;
            }
        }
        assert bestFitPeaks != null;
        // isotope, we skip this left the original peak in the feature list.
        if (bestFitPeaks.size() == 1) {
            if (!autoRemove)
                deisotopedDataPoints.add(sortedDataPoints[i]);
            processedPeaks++;
            continue;
        }
        DataPoint[] originalPeaks = bestFitPeaks.toArray(new DataPoint[0]);
        SimpleIsotopePattern newPattern = new SimpleIsotopePattern(originalPeaks, IsotopePatternStatus.DETECTED, aPeak.toString());
        sortedDataPoints[i].addResult(new DPPIsotopePatternResult(newPattern, bestFitCharge));
        deisotopedDataPoints.add(sortedDataPoints[i]);
        for (int j = 0; j < sortedDataPoints.length; j++) {
            if (bestFitPeaks.contains(sortedDataPoints[j]))
                sortedDataPoints[j] = null;
        }
        // Update completion rate
        processedPeaks++;
    }
    deisotopedDataPoints.sort((d1, d2) -> {
        return Double.compare(d1.getMZ(), d2.getMZ());
    });
    setResults(deisotopedDataPoints.toArray(new ProcessedDataPoint[0]));
    setStatus(TaskStatus.FINISHED);
}