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

Example 6 with SimplePeakListRow

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

the class StreamPeakListRowLearnerTask 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 SimplePeakListRow

use of net.sf.mzmine.datamodel.impl.SimplePeakListRow 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 8 with SimplePeakListRow

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

the class ShapeModelerTask method run.

public void run() {
    setStatus(TaskStatus.PROCESSING);
    Class<?> shapeModelClass = shapeModelerType.getModelClass();
    Constructor<?> shapeModelConstruct;
    shapeModelConstruct = shapeModelClass.getConstructors()[0];
    // Get data file information
    RawDataFile dataFile = originalPeakList.getRawDataFile(0);
    // Create new feature list
    newPeakList = new SimplePeakList(originalPeakList + " " + suffix, dataFile);
    totalRows = originalPeakList.getNumberOfRows();
    int[] scanNumbers;
    double[] retentionTimes, intensities;
    SimplePeakListRow newRow;
    for (PeakListRow row : originalPeakList.getRows()) {
        if (isCanceled())
            return;
        newRow = new SimplePeakListRow(newPeakID);
        try {
            for (Feature peak : row.getPeaks()) {
                // Load the intensities into array
                dataFile = peak.getDataFile();
                scanNumbers = peak.getScanNumbers();
                retentionTimes = new double[scanNumbers.length];
                for (int i = 0; i < scanNumbers.length; i++) retentionTimes[i] = dataFile.getScan(scanNumbers[i]).getRetentionTime();
                intensities = new double[scanNumbers.length];
                for (int i = 0; i < scanNumbers.length; i++) {
                    DataPoint dp = peak.getDataPoint(scanNumbers[i]);
                    if (dp != null)
                        intensities[i] = dp.getIntensity();
                    else
                        intensities[i] = 0;
                }
                Feature shapePeak = (Feature) shapeModelConstruct.newInstance(peak, scanNumbers, intensities, retentionTimes, resolution);
                newRow.addPeak(shapePeak.getDataFile(), shapePeak);
            }
        } catch (Exception e) {
            String message = "Error trying to make an instance of shape model class " + shapeModelClass;
            MZmineCore.getDesktop().displayErrorMessage(MZmineCore.getDesktop().getMainWindow(), message);
            logger.severe(message);
            return;
        }
        newPeakList.addRow(newRow);
        newPeakID++;
        processedRows++;
    }
    // Add new peaklist to the project
    project.addPeakList(newPeakList);
    // Add quality parameters to peaks
    QualityParameters.calculateQualityParameters(newPeakList);
    // Remove the original peaklist if requested
    if (removeOriginal)
        project.removePeakList(originalPeakList);
    // Load previous applied methods
    for (PeakListAppliedMethod proc : originalPeakList.getAppliedMethods()) {
        newPeakList.addDescriptionOfAppliedTask(proc);
    }
    // Add task description to peakList
    newPeakList.addDescriptionOfAppliedTask(new SimplePeakListAppliedMethod("Peaks shaped by " + shapeModelerType + " function", parameters));
    logger.finest("Finished peak shape modeler " + processedRows + " rows processed");
    setStatus(TaskStatus.FINISHED);
}

Example 9 with SimplePeakListRow

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

the class PeakExtenderTask method run.

/**
 * @see Runnable#run()
 */
public void run() {
    setStatus(TaskStatus.PROCESSING);
    logger.info("Running peak extender on " + peakList);
    // We assume source peakList contains one datafile
    RawDataFile dataFile = peakList.getRawDataFile(0);
    // Create a new deisotoped peakList
    extendedPeakList = new SimplePeakList(peakList + " " + suffix, peakList.getRawDataFiles());
    // 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;
    Feature oldPeak;
    for (int ind = 0; ind < totalPeaks; ind++) {
        if (isCanceled())
            return;
        oldPeak = sortedPeaks[ind];
        if (oldPeak.getHeight() >= minimumHeight) {
            Feature newPeak = this.getExtendedPeak(oldPeak);
            // Get previous pekaListRow
            PeakListRow oldRow = peakList.getPeakRow(oldPeak);
            // keep old ID
            int oldID = oldRow.getID();
            SimplePeakListRow newRow = new SimplePeakListRow(oldID);
            PeakUtils.copyPeakListRowProperties(oldRow, newRow);
            newRow.addPeak(dataFile, newPeak);
            extendedPeakList.addRow(newRow);
        }
        // Update completion rate
        processedPeaks++;
    }
    // Add new peakList to the project
    project.addPeakList(extendedPeakList);
    // Add quality parameters to peaks
    QualityParameters.calculateQualityParameters(extendedPeakList);
    // Load previous applied methods
    for (PeakListAppliedMethod proc : peakList.getAppliedMethods()) {
        extendedPeakList.addDescriptionOfAppliedTask(proc);
    }
    // Add task description to peakList
    extendedPeakList.addDescriptionOfAppliedTask(new SimplePeakListAppliedMethod("Peak extender", parameters));
    // Remove the original peakList if requested
    if (removeOriginal)
        project.removePeakList(peakList);
    logger.info("Finished peak extender on " + peakList);
    setStatus(TaskStatus.FINISHED);
}

Example 10 with SimplePeakListRow

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

the class SameRangeTask method run.

public void run() {
    logger.info("Started gap-filling " + peakList);
    setStatus(TaskStatus.PROCESSING);
    // Get total number of rows
    totalRows = peakList.getNumberOfRows();
    // Get feature list columns
    RawDataFile[] columns = peakList.getRawDataFiles();
    // Create new feature list
    processedPeakList = new SimplePeakList(peakList + " " + suffix, columns);
    /**
     ***********************************************************
     * Creating a stream to process the data in parallel
     */
    processedRowsAtomic = new AtomicInteger(0);
    List<PeakListRow> outputList = Collections.synchronizedList(new ArrayList<>());
    peakList.parallelStream().forEach(sourceRow -> {
        // Canceled?
        if (isCanceled())
            return;
        PeakListRow newRow = new SimplePeakListRow(sourceRow.getID());
        // Copy comment
        newRow.setComment(sourceRow.getComment());
        // Copy identities
        for (PeakIdentity ident : sourceRow.getPeakIdentities()) newRow.addPeakIdentity(ident, false);
        if (sourceRow.getPreferredPeakIdentity() != null)
            newRow.setPreferredPeakIdentity(sourceRow.getPreferredPeakIdentity());
        // Copy each peaks and fill gaps
        for (RawDataFile column : columns) {
            // Canceled?
            if (isCanceled())
                return;
            // Get current peak
            Feature currentPeak = sourceRow.getPeak(column);
            // If there is a gap, try to fill it
            if (currentPeak == null)
                currentPeak = fillGap(sourceRow, column);
            // If a peak was found or created, add it
            if (currentPeak != null)
                newRow.addPeak(column, currentPeak);
        }
        outputList.add(newRow);
        processedRowsAtomic.getAndAdd(1);
    });
    outputList.stream().forEach(newRow -> {
        processedPeakList.addRow((PeakListRow) newRow);
    });
    // Canceled?
    if (isCanceled())
        return;
    // Append processed feature list to the project
    project.addPeakList(processedPeakList);
    // Add quality parameters to peaks
    QualityParameters.calculateQualityParameters(processedPeakList);
    // Add task description to peakList
    processedPeakList.addDescriptionOfAppliedTask(new SimplePeakListAppliedMethod("Gap filling using RT and m/z range", parameters));
    // Remove the original peaklist if requested
    if (removeOriginal)
        project.removePeakList(peakList);
    setStatus(TaskStatus.FINISHED);
    logger.info("Finished gap-filling " + peakList);
}