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

Example 46 with PeakListRow

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

the class GnpsFbmnExportTask method export.

private void export(PeakList peakList, FileWriter writer, File curFile) throws IOException {
    final String newLine = System.lineSeparator();
    for (PeakListRow row : peakList.getRows()) {
        String rowID = Integer.toString(row.getID());
        String retTimeInSeconds = Double.toString(Math.round(row.getAverageRT() * 60 * 100) / 100.);
        // Get the MS/MS scan number
        Feature bestPeak = row.getBestPeak();
        if (bestPeak == null)
            continue;
        int msmsScanNumber = bestPeak.getMostIntenseFragmentScanNumber();
        if (rowID != null) {
            PeakListRow copyRow = copyPeakRow(row);
            // Best peak always exists, because feature list row has at least one peak
            bestPeak = copyRow.getBestPeak();
            // Get the MS/MS scan number
            msmsScanNumber = bestPeak.getMostIntenseFragmentScanNumber();
            while (msmsScanNumber < 1) {
                copyRow.removePeak(bestPeak.getDataFile());
                if (copyRow.getPeaks().length == 0)
                    break;
                bestPeak = copyRow.getBestPeak();
                msmsScanNumber = bestPeak.getMostIntenseFragmentScanNumber();
            }
        }
        if (msmsScanNumber >= 1) {
            // MS/MS scan must exist, because msmsScanNumber was > 0
            Scan msmsScan = bestPeak.getDataFile().getScan(msmsScanNumber);
            MassList massList = msmsScan.getMassList(massListName);
            if (massList == null) {
                MZmineCore.getDesktop().displayErrorMessage(MZmineCore.getDesktop().getMainWindow(), "There is no mass list called " + massListName + " for MS/MS scan #" + msmsScanNumber + " (" + bestPeak.getDataFile() + ")");
                return;
            }
            writer.write("BEGIN IONS" + newLine);
            if (rowID != null)
                writer.write("FEATURE_ID=" + rowID + newLine);
            String mass = Double.toString(Math.round(row.getAverageMZ() * 10000) / 10000.);
            if (mass != null)
                writer.write("PEPMASS=" + mass + newLine);
            if (rowID != null) {
                writer.write("SCANS=" + rowID + newLine);
                writer.write("RTINSECONDS=" + retTimeInSeconds + newLine);
            }
            int msmsCharge = msmsScan.getPrecursorCharge();
            String msmsPolarity = msmsScan.getPolarity().asSingleChar();
            if (msmsPolarity.equals("0"))
                msmsPolarity = "";
            if (msmsCharge == 0) {
                msmsCharge = 1;
                msmsPolarity = "";
            }
            writer.write("CHARGE=" + msmsCharge + msmsPolarity + newLine);
            writer.write("MSLEVEL=2" + newLine);
            DataPoint[] dataPoints = massList.getDataPoints();
            if (mergeParameters != null) {
                MsMsSpectraMergeModule merger = MZmineCore.getModuleInstance(MsMsSpectraMergeModule.class);
                MergedSpectrum spectrum = merger.getBestMergedSpectrum(mergeParameters, row, massListName);
                if (spectrum != null) {
                    dataPoints = spectrum.data;
                    writer.write("MERGED_STATS=");
                    writer.write(spectrum.getMergeStatsDescription());
                    writer.write(newLine);
                }
            }
            for (DataPoint peak : dataPoints) {
                writer.write(peak.getMZ() + " " + peak.getIntensity() + newLine);
            }
            writer.write("END IONS" + newLine);
            writer.write(newLine);
        }
    }
}

Example 47 with PeakListRow

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

the class RowsSpectralMatchTask method run.

/**
 * @see java.lang.Runnable#run()
 */
@Override
public void run() {
    setStatus(TaskStatus.PROCESSING);
    for (PeakListRow row : rows) {
        if (isCanceled()) {
            logger.info("Added " + count + " spectral library matches (before being cancelled)");
            repaintWindow();
            return;
        }
        try {
            // All MS2 or only best MS2 scan
            // best MS1 scan
            // check for MS1 or MSMS scan
            List<Scan> scans = getScans(row);
            List<DataPoint[]> rowMassLists = new ArrayList<>();
            for (Scan scan : scans) {
                // get mass list and perform deisotoping if active
                DataPoint[] rowMassList = getDataPoints(scan, true);
                if (removeIsotopes)
                    rowMassList = removeIsotopes(rowMassList);
                rowMassLists.add(rowMassList);
            }
            // match against all library entries
            for (SpectralDBEntry ident : list) {
                SpectralDBPeakIdentity best = null;
                // match all scans against this ident to find best match
                for (int i = 0; i < scans.size(); i++) {
                    SpectralSimilarity sim = spectraDBMatch(row, rowMassLists.get(i), ident);
                    if (sim != null && (!needsIsotopePattern || SpectralMatchTask.checkForIsotopePattern(sim, mzToleranceSpectra, minMatchedIsoSignals)) && (best == null || best.getSimilarity().getScore() < sim.getScore())) {
                        best = new SpectralDBPeakIdentity(scans.get(i), massListName, ident, sim, METHOD);
                    }
                }
                // has match?
                if (best != null) {
                    addIdentity(row, best);
                    count++;
                }
            }
            // sort identities based on similarity score
            SortSpectralDBIdentitiesTask.sortIdentities(row);
        } catch (MissingMassListException e) {
            logger.log(Level.WARNING, "No mass list in spectrum for rowID=" + row.getID(), e);
            errorCounter++;
        }
        // check for max error (missing masslist)
        if (errorCounter > MAX_ERROR) {
            logger.log(Level.WARNING, "Data base matching failed. To many missing mass lists ");
            setStatus(TaskStatus.ERROR);
            setErrorMessage("Data base matching failed. To many missing mass lists ");
            list = null;
            return;
        }
        // next row
        finishedRows++;
    }
    if (count > 0)
        logger.info("Added " + count + " spectral library matches");
    // Repaint the window to reflect the change in the feature list
    repaintWindow();
    list = null;
    setStatus(TaskStatus.FINISHED);
}

Example 48 with PeakListRow

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

the class SiriusExportTask method runSingleRows.

public void runSingleRows(PeakListRow[] rows) {
    setStatus(TaskStatus.PROCESSING);
    // prefill statistics
    prefillStatistics(rows);
    try (final BufferedWriter bw = new BufferedWriter(new FileWriter(fileName, true))) {
        for (PeakListRow row : rows) exportPeakListRow(row, bw);
    } catch (IOException e) {
        setStatus(TaskStatus.ERROR);
        setErrorMessage("Could not open file " + fileName + " for writing.");
    }
    if (getStatus() == TaskStatus.PROCESSING)
        setStatus(TaskStatus.FINISHED);
}

Example 49 with PeakListRow

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

the class GnpsFbmnMgfExportTask method copyPeakRow.

/**
 * Create a copy of a feature list row.
 */
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 50 with PeakListRow

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

the class VanKrevelenDiagramParameters method showSetupDialog.

@Override
public ExitCode showSetupDialog(Window parent, boolean valueCheckRequired) {
    PeakList[] selectedPeakLists = getParameter(peakList).getValue().getMatchingPeakLists();
    if (selectedPeakLists.length > 0) {
        PeakListRow[] plRows = selectedPeakLists[0].getRows();
        Arrays.sort(plRows, new PeakListRowSorter(SortingProperty.MZ, SortingDirection.Ascending));
    }
    return super.showSetupDialog(parent, valueCheckRequired);
}