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

Example 6 with PeakListRow

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

the class IsotopePeakScannerTask method copyPeakRow.

/**
 * Create a copy of a feature list row.
 *
 * @param row the row to copy.
 * @return the newly created copy.
 */
private static PeakListRow copyPeakRow(final PeakListRow row) {
    // Copy the feature list row.
    final PeakListRow newRow = new SimplePeakListRow(row.getID());
    PeakUtils.copyPeakListRowProperties(row, newRow);
    // Copy the peaks.
    for (final Feature peak : row.getPeaks()) {
        final Feature newPeak = new SimpleFeature(peak);
        PeakUtils.copyPeakProperties(peak, newPeak);
        newRow.addPeak(peak.getDataFile(), newPeak);
    }
    return newRow;
}

Example 7 with PeakListRow

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

the class IsotopePeakScannerTask method getRowFromCandidate.

/**
 * Extracts a feature list row from a Candidates array.
 * @param candidates
 * @param bestPatternIndex The index of the isotope pattern that was found to be the best fit for the detected pattern
 * @param peakIndex the index of the candidate peak, the feature list row should be extracted for.
 * @param plh
 * @return null if no peak with the given parameters exists, the specified feature list row otherwise.
 */
@Nullable
private PeakListRow getRowFromCandidate(@Nonnull Candidates[] candidates, int bestPatternIndex, int peakIndex, @Nonnull PeakListHandler plh) {
    if (bestPatternIndex >= candidates.length)
        return null;
    if (peakIndex >= candidates[bestPatternIndex].size())
        return null;
    Candidate cand = candidates[bestPatternIndex].get(peakIndex);
    if (cand != null) {
        int id = cand.getCandID();
        PeakListRow original = plh.getRowByID(id);
        return original;
    }
    return null;
}

Example 8 with PeakListRow

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

the class IsotopePeakScannerTask method groupPeaks.

/**
 * @param pL
 * @param parentIndex index of possible parent peak
 * @param maxMass
 * @return will return ArrayList<PeakListRow> of all peaks within the range of pL[parentIndex].mz
 *         -> pL[parentIndex].mz+maxMass
 */
private ArrayList<PeakListRow> groupPeaks(PeakListRow[] pL, int parentIndex, double maxDiff) {
    ArrayList<PeakListRow> buf = new ArrayList<PeakListRow>();
    // this means the result will contain row(parentIndex) itself
    buf.add(pL[parentIndex]);
    double mz = pL[parentIndex].getAverageMZ();
    double rt = pL[parentIndex].getAverageRT();
    for (// will not add the parent peak itself
    int i = parentIndex + 1; // will not add the parent peak itself
    i < pL.length; // will not add the parent peak itself
    i++) {
        PeakListRow r = pL[i];
        if (r.getAverageHeight() < minHeight)
            continue;
        if (!(pL[i].getAverageMZ() > mz && pL[i].getAverageMZ() <= (mz + maxDiff + mzTolerance.getMzTolerance()))) {
            if (// since pL is sorted by ascending mass, we can
            pL[i].getAverageMZ() > (mz + maxDiff))
                // stop now
                return buf;
            continue;
        }
        if (checkRT && !rtTolerance.checkWithinTolerance(rt, r.getAverageRT()))
            continue;
        buf.add(pL[i]);
    }
    return buf;
}

Example 9 with PeakListRow

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

the class SQLExportTask method run.

public void run() {
    setStatus(TaskStatus.PROCESSING);
    // Get number of rows
    totalRows = peakList.getNumberOfRows();
    try {
        this.dbConnection = DriverManager.getConnection(connectionString);
    } catch (SQLException e) {
        setStatus(TaskStatus.ERROR);
        setErrorMessage("Error connecting to the SQL database: " + e.toString());
        return;
    }
    PeakListRow[] rows = peakList.getRows();
    try {
        dbConnection.setAutoCommit(false);
        // information will be exported
        if (rows.length < 1 && emptyExport) {
            exportPeakListRow(null);
        } else {
            for (PeakListRow row : rows) {
                if (getStatus() != TaskStatus.PROCESSING)
                    break;
                exportPeakListRow(row);
                processedRows++;
            }
        }
        dbConnection.commit();
        dbConnection.close();
    } catch (SQLException e) {
        setStatus(TaskStatus.ERROR);
        setErrorMessage("Error running SQL query: " + e.toString());
        return;
    }
    if (getStatus() == TaskStatus.PROCESSING)
        setStatus(TaskStatus.FINISHED);
}

Example 10 with PeakListRow

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

the class IsotopeGrouperTask method run.

/**
 * @see Runnable#run()
 */
public void run() {
    setStatus(TaskStatus.PROCESSING);
    logger.info("Running isotopic peak grouper on " + peakList);
    // We assume source peakList contains one datafile
    RawDataFile dataFile = peakList.getRawDataFile(0);
    // Create a new deisotoped peakList
    deisotopedPeakList = new SimplePeakList(peakList + " " + suffix, peakList.getRawDataFiles());
    // Collect all selected charge states
    int[] charges = new int[maximumCharge];
    for (int i = 0; i < maximumCharge; i++) charges[i] = i + 1;
    // Sort peaks by descending height
    Feature[] sortedPeaks = peakList.getPeaks(dataFile);
    Arrays.sort(sortedPeaks, new PeakSorter(SortingProperty.Height, SortingDirection.Descending));
    // Loop through all peaks
    totalPeaks = sortedPeaks.length;
    for (int ind = 0; ind < totalPeaks; ind++) {
        if (isCanceled())
            return;
        Feature aPeak = sortedPeaks[ind];
        // Check if peak was already deleted
        if (aPeak == null) {
            processedPeaks++;
            continue;
        }
        // Check which charge state fits best around this peak
        int bestFitCharge = 0;
        int bestFitScore = -1;
        Vector<Feature> bestFitPeaks = null;
        for (int charge : charges) {
            Vector<Feature> fittedPeaks = new Vector<Feature>();
            fittedPeaks.add(aPeak);
            fitPattern(fittedPeaks, aPeak, charge, sortedPeaks);
            int score = fittedPeaks.size();
            if ((score > bestFitScore) || ((score == bestFitScore) && (bestFitCharge > charge))) {
                bestFitScore = score;
                bestFitCharge = charge;
                bestFitPeaks = fittedPeaks;
            }
        }
        PeakListRow oldRow = peakList.getPeakRow(aPeak);
        assert bestFitPeaks != null;
        // isotope, we skip this left the original peak in the feature list.
        if (bestFitPeaks.size() == 1) {
            deisotopedPeakList.addRow(oldRow);
            processedPeaks++;
            continue;
        }
        // Convert the peak pattern to array
        Feature[] originalPeaks = bestFitPeaks.toArray(new Feature[0]);
        // Create a new SimpleIsotopePattern
        DataPoint[] isotopes = new DataPoint[bestFitPeaks.size()];
        for (int i = 0; i < isotopes.length; i++) {
            Feature p = originalPeaks[i];
            isotopes[i] = new SimpleDataPoint(p.getMZ(), p.getHeight());
        }
        SimpleIsotopePattern newPattern = new SimpleIsotopePattern(isotopes, IsotopePatternStatus.DETECTED, aPeak.toString());
        // the lowest m/z peak
        if (chooseMostIntense) {
            Arrays.sort(originalPeaks, new PeakSorter(SortingProperty.Height, SortingDirection.Descending));
        } else {
            Arrays.sort(originalPeaks, new PeakSorter(SortingProperty.MZ, SortingDirection.Ascending));
        }
        Feature newPeak = new SimpleFeature(originalPeaks[0]);
        newPeak.setIsotopePattern(newPattern);
        newPeak.setCharge(bestFitCharge);
        // Keep old ID
        int oldID = oldRow.getID();
        SimplePeakListRow newRow = new SimplePeakListRow(oldID);
        PeakUtils.copyPeakListRowProperties(oldRow, newRow);
        newRow.addPeak(dataFile, newPeak);
        deisotopedPeakList.addRow(newRow);
        // Remove all peaks already assigned to isotope pattern
        for (int i = 0; i < sortedPeaks.length; i++) {
            if (bestFitPeaks.contains(sortedPeaks[i]))
                sortedPeaks[i] = null;
        }
        // Update completion rate
        processedPeaks++;
    }
    // Add new peakList to the project
    project.addPeakList(deisotopedPeakList);
    // Load previous applied methods
    for (PeakListAppliedMethod proc : peakList.getAppliedMethods()) {
        deisotopedPeakList.addDescriptionOfAppliedTask(proc);
    }
    // Add task description to peakList
    deisotopedPeakList.addDescriptionOfAppliedTask(new SimplePeakListAppliedMethod("Isotopic peaks grouper", parameters));
    // Remove the original peakList if requested
    if (removeOriginal)
        project.removePeakList(peakList);
    logger.info("Finished isotopic peak grouper on " + peakList);
    setStatus(TaskStatus.FINISHED);
}