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

Example 51 with SimpleDataPoint

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

the class WaveletMassDetector method getMzPeaks.

/**
 * This function searches for maximums from wavelet data points
 */
private DataPoint[] getMzPeaks(double noiseLevel, DataPoint[] originalDataPoints, DataPoint[] waveletDataPoints) {
    TreeSet<DataPoint> mzPeaks = new TreeSet<DataPoint>(new DataPointSorter(SortingProperty.MZ, SortingDirection.Ascending));
    Vector<DataPoint> rawDataPoints = new Vector<DataPoint>();
    int peakMaxInd = 0;
    int stopInd = waveletDataPoints.length - 1;
    for (int ind = 0; ind <= stopInd; ind++) {
        while ((ind <= stopInd) && (waveletDataPoints[ind].getIntensity() == 0)) {
            ind++;
        }
        peakMaxInd = ind;
        if (ind >= stopInd) {
            break;
        }
        // While peak is on
        while ((ind <= stopInd) && (waveletDataPoints[ind].getIntensity() > 0)) {
            // Check if this is the maximum point of the peak
            if (waveletDataPoints[ind].getIntensity() > waveletDataPoints[peakMaxInd].getIntensity()) {
                peakMaxInd = ind;
            }
            rawDataPoints.add(originalDataPoints[ind]);
            ind++;
        }
        if (ind >= stopInd) {
            break;
        }
        rawDataPoints.add(originalDataPoints[ind]);
        if (originalDataPoints[peakMaxInd].getIntensity() > noiseLevel) {
            SimpleDataPoint peakDataPoint = new SimpleDataPoint(originalDataPoints[peakMaxInd].getMZ(), calcAproxIntensity(rawDataPoints));
            mzPeaks.add(peakDataPoint);
        }
        rawDataPoints.clear();
    }
    return mzPeaks.toArray(new DataPoint[0]);
}

Example 52 with SimpleDataPoint

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

the class GridMassTask method addMaxDatumFromScans.

int addMaxDatumFromScans(SpotByProbes s, Chromatogram peak) {
    int i, j;
    int adds = 0;
    for (i = s.minScan; i <= s.maxScan; i++) {
        Datum[] di = roi[i];
        if (di != null && di.length > 0) {
            Datum max = new Datum(new SimpleDataPoint(0, -1), 0, new SimpleDataPoint(0, -1));
            int idx = findFirstMass(s.minMZ, di);
            for (j = idx; j < di.length && di[j].mz <= s.maxMZ; j++) {
                Datum d = di[j];
                if (d.spotId == s.spotId) {
                    if (d.intensity > max.intensity && d.mz >= s.minMZ && d.intensity > minimumHeight) {
                        max = d;
                    }
                }
            }
            if (max.intensity > 0) {
                adds++;
                peak.addMzPeak(scans[i].getScanNumber(), new SimpleDataPoint(max.mzOriginal, max.intensityOriginal));
            }
        }
    }
    return adds;
}

Example 53 with SimpleDataPoint

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

the class TwoDDataSet method getCentroidedDataPointsInRTMZRange.

// Sets the private list to contain the rt values for each data point scan of scans that fall in
// the user
// range. returns an array of the data points but not the rt.
ArrayList getCentroidedDataPointsInRTMZRange(Range<Double> rtRange, Range<Double> mzRange) {
    ArrayList<DataPoint> dataPointsInRanges = new ArrayList<DataPoint>();
    ArrayList rtInRange = new ArrayList();
    curMaxIntensity = 0.0;
    double[] searchRetentionTimes = retentionTimes;
    if (processedScans < totalScans) {
        searchRetentionTimes = new double[processedScans];
        System.arraycopy(retentionTimes, 0, searchRetentionTimes, 0, searchRetentionTimes.length);
    }
    // Find the rt of the scan at the bottom of our rtRange
    int startScanIndex = Arrays.binarySearch(searchRetentionTimes, rtRange.lowerEndpoint());
    // a couple of checks
    if (startScanIndex < 0) {
        startScanIndex = (startScanIndex * -1) - 1;
    }
    if (startScanIndex >= searchRetentionTimes.length) {
        startScanIndex = 0;
    }
    for (int scanIndex = startScanIndex; ((scanIndex < searchRetentionTimes.length) && (searchRetentionTimes[scanIndex] <= rtRange.upperEndpoint())); scanIndex++) {
        // get the list of data points
        DataPoint[] dataPoints = dataPointMatrix[scanIndex].get();
        // Binary search for the mz values in the range you want
        DataPoint searchMZ = new SimpleDataPoint(mzRange.lowerEndpoint(), 0);
        int startMZIndex = Arrays.binarySearch(dataPoints, searchMZ, new DataPointSorter(SortingProperty.MZ, SortingDirection.Ascending));
        if (startMZIndex < 0)
            startMZIndex = (startMZIndex * -1) - 1;
        if (startMZIndex >= dataPoints.length)
            startMZIndex = 0;
        for (int mzIndex = startMZIndex; ((mzIndex < dataPoints.length) && (dataPoints[mzIndex].getMZ() <= mzRange.upperEndpoint())); mzIndex++) {
            DataPoint curFoundDataPoint;
            curFoundDataPoint = dataPoints[mzIndex];
            // System.out.println("curFoundDataPoint.getMZ()");
            // System.out.println(curFoundDataPoint.getMZ());
            dataPointsInRanges.add(curFoundDataPoint);
            Double toAddRt = new Double(searchRetentionTimes[scanIndex]);
            rtInRange.add(toAddRt);
            double curIntensity = curFoundDataPoint.getIntensity();
            if (curIntensity > curMaxIntensity)
                curMaxIntensity = curIntensity;
        }
    }
    rtValuesInUserRange = rtInRange;
    return dataPointsInRanges;
}

Example 54 with SimpleDataPoint

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

the class TwoDDataSet method upperEndpointIntensity.

private double upperEndpointIntensity(DataPoint[] dataPoints, Range<Double> mzRange, PlotMode plotMode) {
    double maxIntensity = 0;
    DataPoint searchMZ = new SimpleDataPoint(mzRange.lowerEndpoint(), 0);
    int startMZIndex = Arrays.binarySearch(dataPoints, searchMZ, new DataPointSorter(SortingProperty.MZ, SortingDirection.Ascending));
    if (startMZIndex < 0)
        startMZIndex = (startMZIndex * -1) - 1;
    if (startMZIndex >= dataPoints.length)
        return 0;
    if (dataPoints[startMZIndex].getMZ() > mzRange.upperEndpoint()) {
        if (plotMode != PlotMode.CENTROID) {
            if (startMZIndex == 0)
                return 0;
            if (startMZIndex == dataPoints.length - 1)
                return dataPoints[startMZIndex - 1].getIntensity();
            // find which data point is closer
            double diffNext = dataPoints[startMZIndex].getMZ() - mzRange.upperEndpoint();
            double diffPrev = mzRange.lowerEndpoint() - dataPoints[startMZIndex - 1].getMZ();
            if (diffPrev < diffNext)
                return dataPoints[startMZIndex - 1].getIntensity();
            else
                return dataPoints[startMZIndex].getIntensity();
        } else {
            return 0;
        }
    }
    for (int mzIndex = startMZIndex; ((mzIndex < dataPoints.length) && (dataPoints[mzIndex].getMZ() <= mzRange.upperEndpoint())); mzIndex++) {
        if (dataPoints[mzIndex].getIntensity() > maxIntensity)
            maxIntensity = dataPoints[mzIndex].getIntensity();
    }
    return maxIntensity;
}

Example 55 with SimpleDataPoint

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

the class PeakSummaryComponent method actionPerformed.

public void actionPerformed(ActionEvent e) {
    String command = e.getActionCommand();
    if (command.equals("SHOW")) {
        String visualizerType = (String) comboShow.getSelectedItem();
        int[] indexesRow = peaksInfoList.getSelectedRows();
        Feature[] selectedPeaks = new Feature[indexesRow.length];
        RawDataFile[] dataFiles = new RawDataFile[indexesRow.length];
        Range<Double> rtRange = null, mzRange = null;
        for (int i = 0; i < indexesRow.length; i++) {
            selectedPeaks[i] = listElementModel.getElementAt(indexesRow[i]);
            dataFiles[i] = selectedPeaks[i].getDataFile();
            if ((rtRange == null) || (mzRange == null)) {
                rtRange = dataFiles[i].getDataRTRange(1);
                mzRange = selectedPeaks[i].getRawDataPointsMZRange();
            } else {
                rtRange = rtRange.span(dataFiles[i].getDataRTRange(1));
                mzRange = mzRange.span(selectedPeaks[i].getRawDataPointsMZRange());
            }
        }
        if (dataFiles.length == 0) {
            return;
        }
        if (visualizerType.equals("Chromatogram")) {
            // Label best peak with preferred identity.
            final Feature bestPeak = row.getBestPeak();
            final PeakIdentity peakIdentity = row.getPreferredPeakIdentity();
            final Map<Feature, String> labelMap = new HashMap<Feature, String>(1);
            if (bestPeak != null && peakIdentity != null) {
                labelMap.put(bestPeak, peakIdentity.getName());
            }
            ScanSelection scanSelection = new ScanSelection(rtRange, 1);
            TICVisualizerModule.showNewTICVisualizerWindow(dataFiles, selectedPeaks, labelMap, scanSelection, TICPlotType.BASEPEAK, mzRange);
            return;
        } else if (visualizerType.equals("Mass spectrum")) {
            for (int i = 0; i < selectedPeaks.length; ++i) {
                final Feature peak = selectedPeaks[i];
                final IsotopePattern ip = peak.getIsotopePattern();
                if (ip != null) {
                    // ------------------------------
                    // Multiply isotope pattern by -1
                    // ------------------------------
                    DataPoint[] newDataPoints = Arrays.stream(ip.getDataPoints()).map(p -> new SimpleDataPoint(p.getMZ(), -p.getIntensity())).toArray(DataPoint[]::new);
                    // ---------------------------
                    // Construct identity spectrum
                    // ---------------------------
                    List<DataPoint> identityDataPoints = new ArrayList<>();
                    PeakIdentity identity = row.getPreferredPeakIdentity();
                    if (identity != null) {
                        String spectrum = identity.getPropertyValue(PeakIdentity.PROPERTY_SPECTRUM);
                        if (spectrum != null && spectrum.length() > 2) {
                            spectrum = spectrum.substring(1, spectrum.length() - 1);
                            for (String strPair : spectrum.split(",")) {
                                String[] pair = strPair.split("=", 2);
                                if (pair.length == 2)
                                    identityDataPoints.add(new SimpleDataPoint(Double.parseDouble(pair[0]), Double.parseDouble(pair[1])));
                            }
                        }
                    }
                    if (// Plot raw spectrum and isotope pattern
                    identityDataPoints.isEmpty())
                        SpectraVisualizerModule.showNewSpectrumWindow(dataFiles[i], peak.getRepresentativeScanNumber(), null, null, null, new SimpleIsotopePattern(newDataPoints, ip.getStatus(), ip.getDescription()));
                    else
                        // Plot raw spectrum, isotope pattern, and identity spectrum
                        SpectraVisualizerModule.showNewSpectrumWindow(dataFiles[i], peak.getRepresentativeScanNumber(), null, new SimpleIsotopePattern(identityDataPoints.toArray(new DataPoint[identityDataPoints.size()]), IsotopePatternStatus.DETECTED, identity.getPropertyValue(PeakIdentity.PROPERTY_FORMULA)), null, new SimpleIsotopePattern(newDataPoints, ip.getStatus(), ip.getDescription()));
                } else
                    // Plot raw spectrum without isotope pattern
                    SpectraVisualizerModule.showNewSpectrumWindow(dataFiles[i], peak.getRepresentativeScanNumber());
            }
        } else if (visualizerType.equals("Peak in 2D")) {
            for (int i = 0; i < selectedPeaks.length; i++) {
                Range<Double> peakRTRange = selectedPeaks[i].getRawDataPointsRTRange();
                Range<Double> peakMZRange = selectedPeaks[i].getRawDataPointsMZRange();
                final double rtLen = peakRTRange.upperEndpoint() - peakRTRange.lowerEndpoint();
                Range<Double> localRTRange = Range.closed(Math.max(0, peakRTRange.lowerEndpoint() - rtLen), peakRTRange.upperEndpoint() + rtLen);
                final double mzLen = peakMZRange.upperEndpoint() - peakMZRange.lowerEndpoint();
                Range<Double> localMZRange = Range.closed(Math.max(0, peakMZRange.lowerEndpoint() - mzLen), peakMZRange.upperEndpoint() + mzLen);
                TwoDVisualizerModule.show2DVisualizerSetupDialog(dataFiles[i], localMZRange, localRTRange);
            }
        } else if (visualizerType.equals("Peak in 3D")) {
            for (int i = 0; i < selectedPeaks.length; i++) {
                Range<Double> peakRTRange = selectedPeaks[i].getRawDataPointsRTRange();
                Range<Double> peakMZRange = selectedPeaks[i].getRawDataPointsMZRange();
                final double rtLen = peakRTRange.upperEndpoint() - peakRTRange.lowerEndpoint();
                Range<Double> localRTRange = Range.closed(Math.max(0, peakRTRange.lowerEndpoint() - rtLen), peakRTRange.upperEndpoint() + rtLen);
                final double mzLen = peakMZRange.upperEndpoint() - peakMZRange.lowerEndpoint();
                Range<Double> localMZRange = Range.closed(Math.max(0, peakMZRange.lowerEndpoint() - mzLen), peakMZRange.upperEndpoint() + mzLen);
                Fx3DVisualizerModule.setupNew3DVisualizer(dataFiles[i], localMZRange, localRTRange);
            }
        } else if (visualizerType.equals("MS/MS")) {
            for (int i = 0; i < selectedPeaks.length; i++) {
                int scanNumber = selectedPeaks[i].getMostIntenseFragmentScanNumber();
                if (scanNumber > 0) {
                    SpectraVisualizerModule.showNewSpectrumWindow(dataFiles[i], scanNumber);
                } else {
                    JFrame frame = (JFrame) SwingUtilities.getAncestorOfClass(JFrame.class, this);
                    MZmineCore.getDesktop().displayMessage(frame, "There is no fragment for the mass " + MZmineCore.getConfiguration().getMZFormat().format(selectedPeaks[i].getMZ()) + "m/z in the current raw data.");
                    return;
                }
            }
        } else if (visualizerType.equals("Isotope pattern")) {
            for (int i = 0; i < selectedPeaks.length; i++) {
                IsotopePattern ip = selectedPeaks[i].getIsotopePattern();
                if (ip == null) {
                    return;
                }
                SpectraVisualizerModule.showNewSpectrumWindow(dataFiles[i], selectedPeaks[i].getMostIntenseFragmentScanNumber(), ip);
            }
        }
        return;
    }
    if (command.equals("CHANGE")) {
        int indexRow = peaksInfoList.getSelectedRow();
        if (indexRow == -1) {
            return;
        }
        Feature selectedPeak = listElementModel.getElementAt(indexRow);
        ManualPeakPickerModule.runManualDetection(selectedPeak.getDataFile(), row, null, null);
        return;
    }
}