Examples with Peak dulab.adap.datamodel.Peak used on opensource projects

Example 1 with Peak

use of dulab.adap.datamodel.Peak in project mzmine2 by mzmine.

the class ADAP3DecompositionV1_5SetupDialog method shapeCluster.

/**
 * Cluster list of PeakInfo based on the chromatographic shapes
 *
 * @param peaks list of ADAP peaks
 * @param outClusters output of clusters
 * @param outText output of tooltip text
 * @param outColors output of colors
 */
private void shapeCluster(List<Peak> peaks, List<List<NavigableMap<Double, Double>>> outClusters, List<List<String>> outText, List<Double> outColors) {
    NumberFormat numberFormat = NumberFormat.getNumberInstance();
    Double edgeToHeightRatio = parameterSet.getParameter(ADAP3DecompositionV1_5Parameters.EDGE_TO_HEIGHT_RATIO).getValue();
    Double deltaToHeightRatio = parameterSet.getParameter(ADAP3DecompositionV1_5Parameters.DELTA_TO_HEIGHT_RATIO).getValue();
    Boolean useIsShared = parameterSet.getParameter(ADAP3DecompositionV1_5Parameters.USE_ISSHARED).getValue();
    Double shapeSimThreshold = parameterSet.getParameter(ADAP3DecompositionV1_5Parameters.SHAPE_SIM_THRESHOLD).getValue();
    Double minModelPeakSharpness = parameterSet.getParameter(ADAP3DecompositionV1_5Parameters.MIN_MODEL_SHARPNESS).getValue();
    List<Range<Double>> deprecatedMZValues = parameterSet.getParameter(ADAP3DecompositionV1_5Parameters.MZ_VALUES).getValue();
    if (edgeToHeightRatio == null || deltaToHeightRatio == null || useIsShared == null || shapeSimThreshold == null || minModelPeakSharpness == null || deprecatedMZValues == null)
        return;
    List<Peak> modelPeakCandidates = TwoStepDecomposition.filterPeaks(peaks, useIsShared, edgeToHeightRatio, deltaToHeightRatio, minModelPeakSharpness, deprecatedMZValues);
    if (modelPeakCandidates.isEmpty())
        return;
    List<List<Peak>> clusters = TwoStepDecomposition.getShapeClusters(modelPeakCandidates, shapeSimThreshold);
    outClusters.clear();
    outText.clear();
    outColors.clear();
    Random rand = new Random();
    rand.setSeed(0);
    int colorIndex = 0;
    final int numColors = 10;
    final double[] colors = new double[numColors];
    for (int i = 0; i < numColors; ++i) colors[i] = rand.nextDouble();
    for (List<Peak> cluster : clusters) {
        List<NavigableMap<Double, Double>> c = new ArrayList<>(cluster.size());
        List<String> texts = new ArrayList<>(cluster.size());
        for (Peak peak : cluster) {
            c.add(peak.getChromatogram());
            texts.add(peak.getInfo() + "\nSharpness: " + numberFormat.format(FeatureTools.sharpnessYang(peak.getChromatogram())));
        }
        outClusters.add(c);
        outText.add(texts);
        outColors.add(colors[colorIndex % numColors]);
        ++colorIndex;
    }
}

Example 2 with Peak

use of dulab.adap.datamodel.Peak 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 3 with Peak

use of dulab.adap.datamodel.Peak 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;
}

Example 4 with Peak

use of dulab.adap.datamodel.Peak in project mzmine2 by mzmine.

the class ADAP3AlignerTask method alignPeaks.

private PeakList alignPeaks() {
    // Collect all data files
    List<RawDataFile> allDataFiles = new ArrayList<>(peakLists.length);
    for (final PeakList peakList : peakLists) {
        RawDataFile[] dataFiles = peakList.getRawDataFiles();
        if (dataFiles.length != 1)
            throw new IllegalArgumentException("Found more then one data " + "file in some of the peaks lists");
        allDataFiles.add(dataFiles[0]);
    }
    for (int i = 0; i < peakLists.length; ++i) {
        PeakList peakList = peakLists[i];
        Sample sample = new Sample(i);
        for (final PeakListRow row : peakList.getRows()) {
            Component component = getComponent(row);
            if (component != null)
                sample.addComponent(component);
        }
        alignment.addSample(sample);
    }
    process();
    // Create new feature list
    final PeakList alignedPeakList = new SimplePeakList(peakListName, allDataFiles.toArray(new RawDataFile[0]));
    int rowID = 0;
    List<ReferenceComponent> alignedComponents = alignment.getComponents();
    Collections.sort(alignedComponents);
    for (final ReferenceComponent referenceComponent : alignedComponents) {
        SimplePeakListRow newRow = new SimplePeakListRow(++rowID);
        for (int i = 0; i < referenceComponent.size(); ++i) {
            Component component = referenceComponent.getComponent(i);
            Peak peak = component.getBestPeak();
            peak.getInfo().mzValue(component.getMZ());
            PeakListRow row = findPeakListRow(referenceComponent.getSampleID(i), peak.getInfo().peakID);
            if (row == null)
                throw new IllegalStateException(String.format("Cannot find a feature list row for fileId = %d and peakId = %d", referenceComponent.getSampleID(), peak.getInfo().peakID));
            RawDataFile file = row.getRawDataFiles()[0];
            // Create a new MZmine feature
            Feature feature = ADAPInterface.peakToFeature(file, peak);
            // Add spectrum as an isotopic pattern
            DataPoint[] spectrum = component.getSpectrum().entrySet().stream().map(e -> new SimpleDataPoint(e.getKey(), e.getValue())).toArray(DataPoint[]::new);
            feature.setIsotopePattern(new SimpleIsotopePattern(spectrum, IsotopePattern.IsotopePatternStatus.PREDICTED, "Spectrum"));
            newRow.addPeak(file, feature);
        }
        // Save alignment score
        SimplePeakInformation peakInformation = (SimplePeakInformation) newRow.getPeakInformation();
        if (peakInformation == null)
            peakInformation = new SimplePeakInformation();
        peakInformation.addProperty("Alignment score", Double.toString(referenceComponent.getScore()));
        newRow.setPeakInformation(peakInformation);
        alignedPeakList.addRow(newRow);
    }
    return alignedPeakList;
}

Example 5 with Peak

use of dulab.adap.datamodel.Peak in project mzmine2 by mzmine.

the class ADAP3AlignerTask method getComponent.

/**
 * Convert a {@link PeakListRow} with one {@link Feature} into {@link Component}.
 *
 * @param row an instance of {@link PeakListRow}. This parameter cannot be null.
 * @return an instance of {@link Component} or null if the row doesn't contain any peaks or isotope patterns.
 */
@Nullable
private Component getComponent(final PeakListRow row) {
    if (row.getNumberOfPeaks() == 0)
        return null;
    // Read Spectrum information
    NavigableMap<Double, Double> spectrum = new TreeMap<>();
    IsotopePattern pattern = row.getBestIsotopePattern();
    if (pattern == null)
        throw new IllegalArgumentException("ADAP Alignment requires mass " + "spectra (or isotopic patterns) of peaks. No spectra found.");
    for (DataPoint dataPoint : pattern.getDataPoints()) spectrum.put(dataPoint.getMZ(), dataPoint.getIntensity());
    // Read Chromatogram
    final Feature peak = row.getBestPeak();
    final RawDataFile dataFile = peak.getDataFile();
    NavigableMap<Double, Double> chromatogram = new TreeMap<>();
    for (final int scan : peak.getScanNumbers()) {
        final DataPoint dataPoint = peak.getDataPoint(scan);
        if (dataPoint != null)
            chromatogram.put(dataFile.getScan(scan).getRetentionTime(), dataPoint.getIntensity());
    }
    return new Component(null, new Peak(chromatogram, new PeakInfo().mzValue(peak.getMZ()).peakID(row.getID())), spectrum, null);
}