Examples with PeakListHandler net.sf.mzmine.modules.peaklistmethods.isotopes.isotopepeakscanner.PeakListHandler used on opensource projects

Example 1 with PeakListHandler

use of net.sf.mzmine.modules.peaklistmethods.isotopes.isotopepeakscanner.PeakListHandler in project mzmine2 by mzmine.

the class NeutralLossFilterTask method run.

@Override
public void run() {
    setStatus(TaskStatus.PROCESSING);
    totalRows = peakList.getNumberOfRows();
    ArrayList<Double> diff = setUpDiff();
    if (diff == null || Double.compare(dMassLoss, 0.0d) == 0) {
        setErrorMessage("Could not set up neutral loss. Mass loss could not be calculated from the formula or is 0.0");
        setStatus(TaskStatus.ERROR);
        return;
    }
    if (suffix.equals("auto")) {
        if (molecule.equals(""))
            suffix = " NL: " + dMassLoss + " RTtol: " + rtTolerance.getTolerance() + "_results";
        else
            suffix = " NL (" + molecule + "): " + dMassLoss + " RTtol: " + rtTolerance.getTolerance() + "_results";
    }
    // get all rows and sort by m/z
    PeakListRow[] rows = peakList.getRows();
    Arrays.sort(rows, new PeakListRowSorter(SortingProperty.MZ, SortingDirection.Ascending));
    PeakListHandler plh = new PeakListHandler();
    plh.setUp(peakList);
    resultPeakList = new SimplePeakList(peakList.getName() + suffix, peakList.getRawDataFiles());
    PeakListHandler resultMap = new PeakListHandler();
    for (int i = 0; i < totalRows; i++) {
        // i will represent the index of the row in peakList
        if (rows[i].getPeakIdentities().length > 0) {
            finishedRows++;
            continue;
        }
        message = "Row " + i + "/" + totalRows;
        // now get all peaks that lie within RT and maxIsotopeMassRange: pL[index].mz ->
        // pL[index].mz+maxMass
        ArrayList<PeakListRow> groupedPeaks = groupPeaks(rows, i, diff.get(diff.size() - 1).doubleValue());
        if (groupedPeaks.size() < 2) {
            finishedRows++;
            continue;
        }
        // this will store row indexes of
        ResultBuffer[] resultBuffer = new ResultBuffer[diff.size()];
        // and mz
        for (// resultBuffer[i] index will represent Isotope[i] (if
        int a = 0; // resultBuffer[i] index will represent Isotope[i] (if
        a < diff.size(); // resultBuffer[i] index will represent Isotope[i] (if
        a++) // numAtoms = 0)
        // [0] will be the isotope with lowest mass#
        resultBuffer[a] = new ResultBuffer();
        for (// go through all possible peaks
        int j = 0; // go through all possible peaks
        j < groupedPeaks.size(); // go through all possible peaks
        j++) {
            for (// check for each peak if it is a possible feature for
            int k = 0; // check for each peak if it is a possible feature for
            k < diff.size(); // check for each peak if it is a possible feature for
            k++) // every diff[](isotope)
            {
                // k represents the isotope number the peak will be a candidate for
                if (mzTolerance.checkWithinTolerance(groupedPeaks.get(0).getAverageMZ() + diff.get(k), groupedPeaks.get(j).getAverageMZ())) {
                    // this will automatically add groupedPeaks[0] to the list -> isotope with
                    // lowest mass
                    // +1 result for isotope k
                    resultBuffer[k].addFound();
                    // row in groupedPeaks[]
                    resultBuffer[k].addRow(j);
                    resultBuffer[k].addID(groupedPeaks.get(j).getID());
                }
            }
        }
        if (// this means that for every isotope we expected to find,
        !checkIfAllTrue(resultBuffer)) // we found one or more possible features
        {
            finishedRows++;
            continue;
        }
        Candidates candidates = new Candidates(diff.size(), minHeight, mzTolerance, plh);
        for (// reminder: resultBuffer.length = diff.size()
        int k = 0; // reminder: resultBuffer.length = diff.size()
        k < resultBuffer.length; // reminder: resultBuffer.length = diff.size()
        k++) {
            for (int l = 0; l < resultBuffer[k].getFoundCount(); l++) {
                // k represents index resultBuffer[k] and thereby the isotope number
                // l represents the number of results in resultBuffer[k]
                candidates.get(k).checkForBetterRating(groupedPeaks, 0, resultBuffer[k].getRow(l), diff.get(k), minRating);
            }
        }
        if (!checkIfAllTrue(candidates.getCandidates())) {
            finishedRows++;
            // jump to next i
            continue;
        }
        String comParent = "", comChild = "";
        PeakListRow originalChild = getRowFromCandidate(candidates, 0, plh);
        if (originalChild == null) {
            finishedRows++;
            continue;
        }
        PeakListRow child = copyPeakRow(originalChild);
        if (resultMap.containsID(child.getID()))
            comChild += resultMap.getRowByID(child.getID()).getComment();
        comChild += "Parent ID: " + candidates.get(1).getCandID();
        addComment(child, comChild);
        List<PeakListRow> rowBuffer = new ArrayList<PeakListRow>();
        boolean allPeaksAddable = true;
        rowBuffer.add(child);
        for (// we skip k=0 because == groupedPeaks[0] which we
        int k = 1; // we skip k=0 because == groupedPeaks[0] which we
        k < candidates.size(); // we skip k=0 because == groupedPeaks[0] which we
        k++) // added before
        {
            PeakListRow originalParent = getRowFromCandidate(candidates, 1, plh);
            if (originalParent == null) {
                allPeaksAddable = false;
                continue;
            }
            PeakListRow parent = copyPeakRow(originalParent);
            if (resultMap.containsID(parent.getID()))
                comParent += resultMap.getRowByID(parent.getID()).getComment();
            comParent += ("[--IS PARENT-- child ID: " + child.getID() + " ] | ");
            addComment(parent, comParent);
            addComment(child, " m/z shift(ppm): " + round(((parent.getAverageMZ() - child.getAverageMZ()) - diff.get(1)) / parent.getAverageMZ() * 1E6, 2) + " ");
            rowBuffer.add(parent);
        }
        if (allPeaksAddable)
            for (PeakListRow row : rowBuffer) resultMap.addRow(row);
        if (isCanceled())
            return;
        finishedRows++;
    }
    ArrayList<Integer> keys = resultMap.getAllKeys();
    for (int j = 0; j < keys.size(); j++) resultPeakList.addRow(resultMap.getRowByID(keys.get(j)));
    if (resultPeakList.getNumberOfRows() > 1)
        addResultToProject();
    else
        message = "Element not found.";
    setStatus(TaskStatus.FINISHED);
}