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

Example 11 with MassList

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

the class ChromatogramBuilderTask method run.

/**
 * @see Runnable#run()
 */
public void run() {
    setStatus(TaskStatus.PROCESSING);
    logger.info("Started chromatogram builder on " + dataFile);
    scans = scanSelection.getMatchingScans(dataFile);
    int[] allScanNumbers = scanSelection.getMatchingScanNumbers(dataFile);
    totalScans = scans.length;
    // Check if the scans are properly ordered by RT
    double prevRT = Double.NEGATIVE_INFINITY;
    for (Scan s : scans) {
        if (s.getRetentionTime() < prevRT) {
            setStatus(TaskStatus.ERROR);
            final String msg = "Retention time of scan #" + s.getScanNumber() + " is smaller then the retention time of the previous scan." + " Please make sure you only use scans with increasing retention times." + " You can restrict the scan numbers in the parameters, or you can use the Crop filter module";
            setErrorMessage(msg);
            return;
        }
        prevRT = s.getRetentionTime();
    }
    // Create new feature list
    newPeakList = new SimplePeakList(dataFile + " " + suffix, dataFile);
    Chromatogram[] chromatograms;
    HighestDataPointConnector massConnector = new HighestDataPointConnector(dataFile, allScanNumbers, minimumTimeSpan, minimumHeight, mzTolerance);
    for (Scan scan : scans) {
        if (isCanceled())
            return;
        MassList massList = scan.getMassList(massListName);
        if (massList == null) {
            setStatus(TaskStatus.ERROR);
            setErrorMessage("Scan " + dataFile + " #" + scan.getScanNumber() + " does not have a mass list " + massListName);
            return;
        }
        DataPoint[] mzValues = massList.getDataPoints();
        if (mzValues == null) {
            setStatus(TaskStatus.ERROR);
            setErrorMessage("Mass list " + massListName + " does not contain m/z values for scan #" + scan.getScanNumber() + " of file " + dataFile);
            return;
        }
        massConnector.addScan(scan.getScanNumber(), mzValues);
        processedScans++;
    }
    chromatograms = massConnector.finishChromatograms();
    // Sort the final chromatograms by m/z
    Arrays.sort(chromatograms, new PeakSorter(SortingProperty.MZ, SortingDirection.Ascending));
    // Add the chromatograms to the new feature list
    for (Feature finishedPeak : chromatograms) {
        SimplePeakListRow newRow = new SimplePeakListRow(newPeakID);
        newPeakID++;
        newRow.addPeak(dataFile, finishedPeak);
        newPeakList.addRow(newRow);
    }
    // Add new peaklist to the project
    project.addPeakList(newPeakList);
    // Add quality parameters to peaks
    QualityParameters.calculateQualityParameters(newPeakList);
    setStatus(TaskStatus.FINISHED);
    logger.info("Finished chromatogram builder on " + dataFile);
}

Example 12 with MassList

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

the class ShoulderPeaksFilterTask method run.

/**
 * @see Runnable#run()
 */
public void run() {
    setStatus(TaskStatus.PROCESSING);
    logger.info("Started mass filter on " + dataFile);
    scanNumbers = dataFile.getScanNumbers();
    totalScans = scanNumbers.length;
    // Check if we have at least one scan with a mass list of given name
    boolean haveMassList = false;
    for (int i = 0; i < totalScans; i++) {
        Scan scan = dataFile.getScan(scanNumbers[i]);
        MassList massList = scan.getMassList(massListName);
        if (massList != null) {
            haveMassList = true;
            break;
        }
    }
    if (!haveMassList) {
        setStatus(TaskStatus.ERROR);
        setErrorMessage(dataFile.getName() + " has no mass list called '" + massListName + "'");
        return;
    }
    // Process all scans
    for (int i = 0; i < totalScans; i++) {
        if (isCanceled())
            return;
        Scan scan = dataFile.getScan(scanNumbers[i]);
        MassList massList = scan.getMassList(massListName);
        // Skip those scans which do not have a mass list of given name
        if (massList == null) {
            processedScans++;
            continue;
        }
        DataPoint[] mzPeaks = massList.getDataPoints();
        DataPoint[] newMzPeaks = ShoulderPeaksFilter.filterMassValues(mzPeaks, parameters);
        SimpleMassList newMassList = new SimpleMassList(massListName + " " + suffix, scan, newMzPeaks);
        scan.addMassList(newMassList);
        // Remove old mass list
        if (autoRemove)
            scan.removeMassList(massList);
        processedScans++;
    }
    setStatus(TaskStatus.FINISHED);
    logger.info("Finished shoulder peaks filter on " + dataFile);
}

Example 13 with MassList

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

the class MsMsSpectraMergeModule method mergeConsecutiveScans.

/**
 * Internal method for merging a list of consecutive MS/MS scans.
 *
 * @param scans MS/MS scans with their precursor information
 * @param massList name of the mass list to use when extracting peaks
 * @param scoreModel scoring model to use when removing low quality MS/MS and selecting the best
 *        quality MS/MS
 * @return merged spectrum
 */
protected MergedSpectrum mergeConsecutiveScans(ParameterSet parameters, FragmentScan scans, String massList, Ms2QualityScoreModel scoreModel) {
    int totalNumberOfScans = scans.ms2ScanNumbers.length;
    /*
     * find scan with best quality
     */
    final double[] scores = scoreModel.calculateQualityScore(scans);
    int best = 0;
    for (int k = 1; k < scores.length; ++k) {
        if (scores[k] > scores[best]) {
            best = k;
        }
    }
    if (scores[best] <= 0)
        return MergedSpectrum.empty(totalNumberOfScans);
    final List<Scan> scansToMerge = new ArrayList<>();
    scansToMerge.add(scans.origin.getScan(scans.ms2ScanNumbers[best]));
    final Scan firstScan = scansToMerge.get(0);
    final MassList firstML = firstScan.getMassList(massList);
    if (firstML == null)
        throw new RuntimeException("Scan " + firstScan.getDataFile().getName() + "#" + firstScan.getScanNumber() + " does not have a mass list " + massList);
    if (firstML.getDataPoints().length <= 1)
        return MergedSpectrum.empty(totalNumberOfScans);
    /*
     * remove scans which are considerably worse than the best scan
     */
    final double scoreThreshold = best / 5d;
    for (int i = 1; i < scores.length; ++i) {
        int k = best - i;
        if (k >= 0 && scores[k] > scoreThreshold) {
            scansToMerge.add(scans.origin.getScan(scans.ms2ScanNumbers[k]));
        }
        k = best + i;
        if (k < scores.length && scores[k] > scoreThreshold) {
            scansToMerge.add(scans.origin.getScan(scans.ms2ScanNumbers[k]));
        }
    }
    if (scansToMerge.size() == 1) {
        final MergedSpectrum single = new MergedSpectrum(scansToMerge.get(0), massList);
        single.bestFragmentScanScore = scores[best];
        single.removedScansByLowQuality = scores.length - 1;
        return single;
    }
    /*
     * merge every scan if its cosine is above the cosine threshold
     */
    final double cosineThreshold = parameters.getParameter(MsMsSpectraMergeParameters.COSINE_PARAMETER).getValue();
    final MZTolerance mzTolerance = parameters.getParameter(MsMsSpectraMergeParameters.MASS_ACCURACY).getValue();
    final MzMergeMode mzMergeMode = parameters.getParameter(MsMsSpectraMergeParameters.MZ_MERGE_MODE).getValue();
    final IntensityMergeMode intensityMergeMode = parameters.getParameter(MsMsSpectraMergeParameters.INTENSITY_MERGE_MODE).getValue();
    MergedSpectrum initial = new MergedSpectrum(scansToMerge.get(0), massList);
    initial.bestFragmentScanScore = best;
    final double lowestMassToConsider = Math.min(50d, scans.feature.getMZ() - 50d);
    final DataPoint[] initialMostIntense = ScanUtils.extractMostIntensePeaksAcrossMassRange(initial.data, Range.closed(lowestMassToConsider, 150d), 6);
    double lowestIntensityToConsider;
    final int mostIntensPeakWithin = ScanUtils.findMostIntensePeakWithin(initialMostIntense, Range.closed(lowestMassToConsider, scans.feature.getMZ()));
    if (mostIntensPeakWithin >= 0)
        lowestIntensityToConsider = 0.005d * initialMostIntense[mostIntensPeakWithin].getIntensity();
    else
        lowestIntensityToConsider = 0d;
    Range<Double> cosineRange = Range.closed(lowestMassToConsider, scans.feature.getMZ() - 20);
    final double initialCosine = ScanUtils.probabilityProductUnnormalized(initialMostIntense, initialMostIntense, mzTolerance, lowestIntensityToConsider, cosineRange);
    for (int k = 1; k < scansToMerge.size(); ++k) {
        Scan scan = scansToMerge.get(k);
        if (!(scan.getPolarity().equals(initial.polarity) && scan.getPrecursorCharge() == initial.precursorCharge && mzTolerance.checkWithinTolerance(scan.getPrecursorMZ(), initial.precursorMz))) {
            LoggerFactory.getLogger(MsMsSpectraMergeModule.class).warn("Scan " + scan.getScanNumber() + " cannot be merged: it seems to belong to a different feature.");
            continue;
        }
        DataPoint[] dataPoints = scan.getMassList(massList).getDataPoints();
        final DataPoint[] mostIntense = ScanUtils.extractMostIntensePeaksAcrossMassRange(dataPoints, cosineRange, 6);
        final double norm = ScanUtils.probabilityProductUnnormalized(mostIntense, mostIntense, mzTolerance, lowestIntensityToConsider, cosineRange);
        final double cosine = ScanUtils.probabilityProductUnnormalized(initialMostIntense, mostIntense, mzTolerance, lowestIntensityToConsider, cosineRange) / Math.sqrt(norm * initialCosine);
        if (cosine >= cosineThreshold) {
            initial = merge(initial, scan, dataPoints, mzMergeMode, intensityMergeMode, mzTolerance);
        } else {
            initial.removedScansByLowCosine++;
        }
    }
    initial.removedScansByLowQuality += (totalNumberOfScans - scansToMerge.size());
    return initial;
}

Example 14 with MassList

use of net.sf.mzmine.datamodel.MassList 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 15 with MassList

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

the class RowsSpectralMatchTask method getDataPoints.

/**
 * Thresholded masslist
 *
 * @param row
 * @return
 * @throws MissingMassListException
 */
private DataPoint[] getDataPoints(Scan scan, boolean noiseFilter) throws MissingMassListException {
    if (scan == null || scan.getMassList(massListName) == null) {
        return new DataPoint[0];
    }
    MassList masses = scan.getMassList(massListName);
    DataPoint[] dps = masses.getDataPoints();
    return noiseFilter ? ScanUtils.getFiltered(dps, noiseLevel) : dps;
}