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

Example 61 with RawDataFile

use of net.sf.mzmine.datamodel.RawDataFile 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 62 with RawDataFile

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

the class PeakExtenderTask method getExtendedPeak.

private Feature getExtendedPeak(Feature oldPeak) {
    double maxHeight = oldPeak.getHeight();
    int originScanNumber = oldPeak.getRepresentativeScanNumber();
    RawDataFile rawFile = oldPeak.getDataFile();
    ExtendedPeak newPeak = new ExtendedPeak(rawFile);
    int totalScanNumber = rawFile.getNumOfScans();
    Range<Double> mzRange = mzTolerance.getToleranceRange(oldPeak.getMZ());
    Scan scan;
    DataPoint dataPoint;
    // Look for dataPoint related to this peak to the left
    int scanNumber = originScanNumber;
    scanNumber--;
    while (scanNumber > 0) {
        scan = rawFile.getScan(scanNumber);
        if (scan == null) {
            scanNumber--;
            continue;
        }
        if (scan.getMSLevel() != 1) {
            scanNumber--;
            continue;
        }
        dataPoint = ScanUtils.findBasePeak(scan, mzRange);
        if (dataPoint == null)
            break;
        if (dataPoint.getIntensity() < minimumHeight)
            break;
        newPeak.addMzPeak(scanNumber, dataPoint);
        if (dataPoint.getIntensity() > maxHeight)
            maxHeight = dataPoint.getIntensity();
        scanNumber--;
    }
    // Add original dataPoint
    newPeak.addMzPeak(originScanNumber, oldPeak.getDataPoint(originScanNumber));
    // Look to the right
    scanNumber = originScanNumber;
    scanNumber++;
    while (scanNumber <= totalScanNumber) {
        scan = rawFile.getScan(scanNumber);
        if (scan == null) {
            scanNumber++;
            continue;
        }
        if (scan.getMSLevel() != 1) {
            scanNumber++;
            continue;
        }
        dataPoint = ScanUtils.findBasePeak(scan, mzRange);
        if (dataPoint == null)
            break;
        if (dataPoint.getIntensity() < minimumHeight)
            break;
        newPeak.addMzPeak(scanNumber, dataPoint);
        if (dataPoint.getIntensity() > maxHeight)
            maxHeight = dataPoint.getIntensity();
        scanNumber++;
    }
    newPeak.finishExtendedPeak();
    newPeak.setMostIntenseFragmentScanNumber(oldPeak.getMostIntenseFragmentScanNumber());
    int[] scanNumbers = newPeak.getScanNumbers();
    logger.finest("Extended peak original " + originScanNumber + " from " + scanNumbers[0] + " - " + scanNumbers[scanNumbers.length - 1] + " height " + maxHeight);
    return newPeak;
}

Example 63 with RawDataFile

use of net.sf.mzmine.datamodel.RawDataFile 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 64 with RawDataFile

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

the class ShapeModelerSetupDialog method loadPreviewPeak.

private void loadPreviewPeak() {
    PeakListRow previewRow = (PeakListRow) comboPeak.getSelectedItem();
    if (previewRow == null)
        return;
    logger.finest("Loading new preview peak " + previewRow);
    Feature previewPeak = previewRow.getPeaks()[0];
    ticPlot.removeAllTICDataSets();
    // Load the intensities into array
    RawDataFile dataFile = previewPeak.getDataFile();
    int[] scanNumbers = previewPeak.getScanNumbers();
    double[] retentionTimes = new double[scanNumbers.length];
    for (int i = 0; i < scanNumbers.length; i++) retentionTimes[i] = dataFile.getScan(scanNumbers[i]).getRetentionTime();
    double[] intensities = new double[scanNumbers.length];
    for (int i = 0; i < scanNumbers.length; i++) {
        DataPoint dp = previewPeak.getDataPoint(scanNumbers[i]);
        if (dp != null)
            intensities[i] = dp.getIntensity();
        else
            intensities[i] = 0;
    }
    // Create shape model
    updateParameterSetFromComponents();
    JComboBox<?> component = (JComboBox<?>) getComponentForParameter(ShapeModelerParameters.shapeModelerType);
    ShapeModel model = (ShapeModel) component.getSelectedItem();
    JFormattedTextField resolutionField = (JFormattedTextField) getComponentForParameter(ShapeModelerParameters.massResolution);
    double resolution = ((Number) resolutionField.getValue()).doubleValue();
    try {
        Class<?> shapeModelClass = model.getModelClass();
        Constructor<?> shapeModelConstruct = shapeModelClass.getConstructors()[0];
        // shapePeakModel(ChromatographicPeak originalDetectedShape, int[]
        // scanNumbers,
        // double[] intensities, double[] retentionTimes, double resolution)
        Feature shapePeak = (Feature) shapeModelConstruct.newInstance(previewPeak, scanNumbers, intensities, retentionTimes, resolution);
        PeakDataSet peakDataSet = new PeakDataSet(shapePeak);
        ticPlot.addPeakDataset(peakDataSet);
        ticDataset = new ChromatogramTICDataSet(previewRow.getPeaks()[0]);
        ticPlot.addTICDataset(ticDataset);
        // Set auto range to axes
        ticPlot.getXYPlot().getDomainAxis().setAutoRange(true);
        ticPlot.getXYPlot().getDomainAxis().setAutoTickUnitSelection(true);
        ticPlot.getXYPlot().getRangeAxis().setAutoRange(true);
        ticPlot.getXYPlot().getRangeAxis().setAutoTickUnitSelection(true);
    } catch (Exception e) {
        String message = "Error trying to make an instance of Peak Builder " + model;
        MZmineCore.getDesktop().displayErrorMessage(this, message);
        logger.severe(message);
        e.printStackTrace();
        return;
    }
}

Example 65 with RawDataFile

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

the class MinimumSearchPeakDetector method resolvePeaks.

@Override
public ResolvedPeak[] resolvePeaks(final Feature chromatogram, ParameterSet parameters, RSessionWrapper rSession, CenterFunction mzCenterFunction, double msmsRange, double rTRangeMSMS) {
    int[] scanNumbers = chromatogram.getScanNumbers();
    final int scanCount = scanNumbers.length;
    double[] retentionTimes = new double[scanCount];
    double[] intensities = new double[scanCount];
    RawDataFile dataFile = chromatogram.getDataFile();
    for (int i = 0; i < scanCount; i++) {
        final int scanNum = scanNumbers[i];
        retentionTimes[i] = dataFile.getScan(scanNum).getRetentionTime();
        DataPoint dp = chromatogram.getDataPoint(scanNum);
        if (dp != null)
            intensities[i] = dp.getIntensity();
        else
            intensities[i] = 0.0;
    }
    final int lastScan = scanCount - 1;
    assert scanCount > 0;
    final Range<Double> peakDuration = parameters.getParameter(PEAK_DURATION).getValue();
    final double searchRTRange = parameters.getParameter(SEARCH_RT_RANGE).getValue();
    final double minRatio = parameters.getParameter(MIN_RATIO).getValue();
    final double minHeight = Math.max(parameters.getParameter(MIN_ABSOLUTE_HEIGHT).getValue(), parameters.getParameter(MIN_RELATIVE_HEIGHT).getValue() * chromatogram.getHeight());
    final List<ResolvedPeak> resolvedPeaks = new ArrayList<ResolvedPeak>();
    // First, remove all data points below chromatographic threshold.
    final double chromatographicThresholdLevel = MathUtils.calcQuantile(intensities, parameters.getParameter(CHROMATOGRAPHIC_THRESHOLD_LEVEL).getValue());
    for (int i = 0; i < intensities.length; i++) {
        if (intensities[i] < chromatographicThresholdLevel) {
            intensities[i] = 0.0;
        }
    }
    // candidate for a resolved peak.
    startSearch: for (int currentRegionStart = 0; currentRegionStart < lastScan - 2; currentRegionStart++) {
        // Find at least two consecutive non-zero data points
        if (intensities[currentRegionStart] == 0.0 || intensities[currentRegionStart + 1] == 0.0)
            continue;
        double currentRegionHeight = intensities[currentRegionStart];
        endSearch: for (int currentRegionEnd = currentRegionStart + 1; currentRegionEnd < scanCount; currentRegionEnd++) {
            // Update height of current region.
            currentRegionHeight = Math.max(currentRegionHeight, intensities[currentRegionEnd]);
            // have to stop here.
            if (currentRegionEnd == lastScan || intensities[currentRegionEnd + 1] == 0.0) {
                // Find the intensity at the sides (lowest data points).
                final double peakMinLeft = intensities[currentRegionStart];
                final double peakMinRight = intensities[currentRegionEnd];
                // Check the shape of the peak.
                if (currentRegionHeight >= minHeight && currentRegionHeight >= peakMinLeft * minRatio && currentRegionHeight >= peakMinRight * minRatio && peakDuration.contains(retentionTimes[currentRegionEnd] - retentionTimes[currentRegionStart])) {
                    resolvedPeaks.add(new ResolvedPeak(chromatogram, currentRegionStart, currentRegionEnd, mzCenterFunction, msmsRange, rTRangeMSMS));
                }
                // Set the next region start to current region end - 1
                // because it will be immediately
                // increased +1 as we continue the for-cycle.
                currentRegionStart = currentRegionEnd - 1;
                continue startSearch;
            }
            // Minimum duration of peak must be at least searchRTRange.
            if (retentionTimes[currentRegionEnd] - retentionTimes[currentRegionStart] >= searchRTRange) {
                // Set the RT range to check
                final Range<Double> checkRange = Range.closed(retentionTimes[currentRegionEnd] - searchRTRange, retentionTimes[currentRegionEnd] + searchRTRange);
                // current peak i.
                for (int i = currentRegionEnd - 1; i > 0; i--) {
                    if (!checkRange.contains(retentionTimes[i]))
                        break;
                    if (intensities[i] < intensities[currentRegionEnd]) {
                        continue endSearch;
                    }
                }
                // Search on the right from current peak i.
                for (int i = currentRegionEnd + 1; i < scanCount; i++) {
                    if (!checkRange.contains(retentionTimes[i]))
                        break;
                    if (intensities[i] < intensities[currentRegionEnd]) {
                        continue endSearch;
                    }
                }
                // Find the intensity at the sides (lowest data points).
                final double peakMinLeft = intensities[currentRegionStart];
                final double peakMinRight = intensities[currentRegionEnd];
                // ratio condition, continue searching for next minimum.
                if (currentRegionHeight >= peakMinRight * minRatio) {
                    // Check the shape of the peak.
                    if (currentRegionHeight >= minHeight && currentRegionHeight >= peakMinLeft * minRatio && currentRegionHeight >= peakMinRight * minRatio && peakDuration.contains(retentionTimes[currentRegionEnd] - retentionTimes[currentRegionStart])) {
                        resolvedPeaks.add(new ResolvedPeak(chromatogram, currentRegionStart, currentRegionEnd, mzCenterFunction, msmsRange, rTRangeMSMS));
                    }
                    // Set the next region start to current region end-1
                    // because it will be immediately
                    // increased +1 as we continue the for-cycle.
                    currentRegionStart = currentRegionEnd - 1;
                    continue startSearch;
                }
            }
        }
    }
    return resolvedPeaks.toArray(new ResolvedPeak[resolvedPeaks.size()]);
}