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

Example 1 with RawDataFile

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

the class ProjectTreeMouseHandler method handleDoubleClickEvent.

private void handleDoubleClickEvent(MouseEvent e) {
    TreePath clickedPath = tree.getPathForLocation(e.getX(), e.getY());
    if (clickedPath == null)
        return;
    DefaultMutableTreeNode node = (DefaultMutableTreeNode) clickedPath.getLastPathComponent();
    Object clickedObject = node.getUserObject();
    if (clickedObject instanceof RawDataFile) {
        RawDataFile clickedFile = (RawDataFile) clickedObject;
        TICVisualizerModule.setupNewTICVisualizer(clickedFile);
    }
    if (clickedObject instanceof PeakList) {
        PeakList clickedPeakList = (PeakList) clickedObject;
        PeakListTableModule.showNewPeakListVisualizerWindow(clickedPeakList);
    }
    if (clickedObject instanceof Scan) {
        Scan clickedScan = (Scan) clickedObject;
        SpectraVisualizerModule.showNewSpectrumWindow(clickedScan.getDataFile(), clickedScan.getScanNumber());
    }
    if (clickedObject instanceof MassList) {
        MassList clickedMassList = (MassList) clickedObject;
        Scan clickedScan = clickedMassList.getScan();
        SpectraVisualizerWindow window = SpectraVisualizerModule.showNewSpectrumWindow(clickedScan.getDataFile(), clickedScan.getScanNumber());
        MassListDataSet dataset = new MassListDataSet(clickedMassList);
        window.addDataSet(dataset, Color.green);
    }
    if (clickedObject instanceof PeakListRow) {
        PeakListRow clickedPeak = (PeakListRow) clickedObject;
        PeakSummaryVisualizerModule.showNewPeakSummaryWindow(clickedPeak);
    }
}

Example 2 with RawDataFile

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

the class RawDataTreeModel method valueForPathChanged.

public void valueForPathChanged(TreePath path, Object value) {
    DefaultMutableTreeNode node = (DefaultMutableTreeNode) path.getLastPathComponent();
    Object object = node.getUserObject();
    String newName = (String) value;
    if (object instanceof RawDataFile) {
        RawDataFile df = (RawDataFile) object;
        df.setName(newName);
    }
    if (object instanceof PeakList) {
        PeakList pl = (PeakList) object;
        pl.setName(newName);
    }
}

Example 3 with RawDataFile

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

the class SimplePeakList method addRow.

@Override
public void addRow(PeakListRow row) {
    List<RawDataFile> myFiles = Arrays.asList(this.getRawDataFiles());
    for (RawDataFile testFile : row.getRawDataFiles()) {
        if (!myFiles.contains(testFile))
            throw (new IllegalArgumentException("Data file " + testFile + " is not in this feature list"));
    }
    peakListRows.add(row);
    if (row.getDataPointMaxIntensity() > maxDataPointIntensity) {
        maxDataPointIntensity = row.getDataPointMaxIntensity();
    }
    if (mzRange == null) {
        mzRange = Range.singleton(row.getAverageMZ());
        rtRange = Range.singleton(row.getAverageRT());
    } else {
        mzRange = mzRange.span(Range.singleton(row.getAverageMZ()));
        rtRange = rtRange.span(Range.singleton(row.getAverageRT()));
    }
}

Example 4 with RawDataFile

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

the class ADAP3DecompositionV1_5Task method getPeaks.

/**
 * Convert MZmine PeakList to a list of ADAP Peaks
 *
 * @param peakList MZmine PeakList object
 * @param edgeToHeightThreshold edge-to-height threshold to determine peaks that can be merged
 * @param deltaToHeightThreshold delta-to-height threshold to determine peaks that can be merged
 * @return list of ADAP Peaks
 */
@Nonnull
public static List<Peak> getPeaks(final PeakList peakList, final double edgeToHeightThreshold, final double deltaToHeightThreshold) {
    RawDataFile dataFile = peakList.getRawDataFile(0);
    List<Peak> peaks = new ArrayList<>();
    for (PeakListRow row : peakList.getRows()) {
        Feature peak = row.getBestPeak();
        int[] scanNumbers = peak.getScanNumbers();
        // Build chromatogram
        NavigableMap<Double, Double> chromatogram = new TreeMap<>();
        for (int scanNumber : scanNumbers) {
            DataPoint dataPoint = peak.getDataPoint(scanNumber);
            if (dataPoint != null)
                chromatogram.put(dataFile.getScan(scanNumber).getRetentionTime(), dataPoint.getIntensity());
        }
        if (chromatogram.size() <= 1)
            continue;
        // Fill out PeakInfo
        PeakInfo info = new PeakInfo();
        try {
            // Note: info.peakID is the index of PeakListRow in PeakList.peakListRows (starts from 0)
            // row.getID is row.myID (starts from 1)
            info.peakID = row.getID() - 1;
            double height = -Double.MIN_VALUE;
            for (int scan : scanNumbers) {
                double intensity = peak.getDataPoint(scan).getIntensity();
                if (intensity > height) {
                    height = intensity;
                    info.peakIndex = scan;
                }
            }
            info.leftApexIndex = scanNumbers[0];
            info.rightApexIndex = scanNumbers[scanNumbers.length - 1];
            info.retTime = peak.getRT();
            info.mzValue = peak.getMZ();
            info.intensity = peak.getHeight();
            info.leftPeakIndex = info.leftApexIndex;
            info.rightPeakIndex = info.rightApexIndex;
        } catch (Exception e) {
            LOG.info("Skipping " + row + ": " + e.getMessage());
            continue;
        }
        peaks.add(new Peak(chromatogram, info));
    }
    FeatureTools.correctPeakBoundaries(peaks, edgeToHeightThreshold, deltaToHeightThreshold);
    return peaks;
}

Example 5 with RawDataFile

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

the class ADAP3DecompositionV1_5Task method decomposePeaks.

private PeakList decomposePeaks(PeakList peakList) throws CloneNotSupportedException, IOException {
    RawDataFile dataFile = peakList.getRawDataFile(0);
    // Create new feature list.
    final PeakList resolvedPeakList = new SimplePeakList(peakList + " " + parameters.getParameter(ADAP3DecompositionV1_5Parameters.SUFFIX).getValue(), dataFile);
    // Load previous applied methods.
    for (final PeakList.PeakListAppliedMethod method : peakList.getAppliedMethods()) {
        resolvedPeakList.addDescriptionOfAppliedTask(method);
    }
    // Add task description to feature list.
    resolvedPeakList.addDescriptionOfAppliedTask(new SimplePeakListAppliedMethod("Peak deconvolution by ADAP-3", parameters));
    // Collect peak information
    List<Peak> peaks = getPeaks(peakList, this.parameters.getParameter(ADAP3DecompositionV1_5Parameters.EDGE_TO_HEIGHT_RATIO).getValue(), this.parameters.getParameter(ADAP3DecompositionV1_5Parameters.DELTA_TO_HEIGHT_RATIO).getValue());
    // Find components (a.k.a. clusters of peaks with fragmentation spectra)
    List<Component> components = getComponents(peaks);
    // Create PeakListRow for each components
    List<PeakListRow> newPeakListRows = new ArrayList<>();
    int rowID = 0;
    for (final Component component : components) {
        if (component.getSpectrum().isEmpty())
            continue;
        PeakListRow row = new SimplePeakListRow(++rowID);
        // Add the reference peak
        PeakListRow refPeakRow = originalPeakList.getRow(component.getBestPeak().getInfo().peakID);
        Feature refPeak = new SimpleFeature(refPeakRow.getBestPeak());
        // Add spectrum
        List<DataPoint> dataPoints = new ArrayList<>();
        for (Map.Entry<Double, Double> entry : component.getSpectrum().entrySet()) {
            dataPoints.add(new SimpleDataPoint(entry.getKey(), entry.getValue()));
        }
        refPeak.setIsotopePattern(new SimpleIsotopePattern(dataPoints.toArray(new DataPoint[dataPoints.size()]), IsotopePattern.IsotopePatternStatus.PREDICTED, "Spectrum"));
        row.addPeak(dataFile, refPeak);
        // Add PeakInformation
        if (refPeakRow.getPeakInformation() == null) {
            SimplePeakInformation information = new SimplePeakInformation(new HashMap<>(refPeakRow.getPeakInformation().getAllProperties()));
            row.setPeakInformation(information);
        }
        // Set row properties
        row.setAverageMZ(refPeakRow.getAverageMZ());
        row.setAverageRT(refPeakRow.getAverageRT());
        // resolvedPeakList.addRow(row);
        newPeakListRows.add(row);
    }
    // ------------------------------------
    // Sort new peak rows by retention time
    // ------------------------------------
    Collections.sort(newPeakListRows, new Comparator<PeakListRow>() {

        @Override
        public int compare(PeakListRow row1, PeakListRow row2) {
            double retTime1 = row1.getAverageRT();
            double retTime2 = row2.getAverageRT();
            return Double.compare(retTime1, retTime2);
        }
    });
    for (PeakListRow row : newPeakListRows) resolvedPeakList.addRow(row);
    return resolvedPeakList;
}