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

Example 66 with PeakList

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

the class DuplicateFilterModule method runModule.

@Override
@Nonnull
public ExitCode runModule(@Nonnull MZmineProject project, @Nonnull ParameterSet parameters, @Nonnull Collection<Task> tasks) {
    PeakList[] peakLists = parameters.getParameter(DuplicateFilterParameters.peakLists).getValue().getMatchingPeakLists();
    for (PeakList peakList : peakLists) {
        Task newTask = new DuplicateFilterTask(project, peakList, parameters);
        tasks.add(newTask);
    }
    return ExitCode.OK;
}

Example 67 with PeakList

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

the class LogratioPlotModule method runModule.

@Override
@Nonnull
public ExitCode runModule(@Nonnull MZmineProject project, @Nonnull ParameterSet parameters, @Nonnull Collection<Task> tasks) {
    PeakList[] peakLists = parameters.getParameter(CVParameters.peakLists).getValue().getMatchingPeakLists();
    for (PeakList pl : peakLists) {
        // Create dataset & paint scale
        AbstractXYZDataset dataset = new LogratioDataset(pl, parameters);
        InterpolatingLookupPaintScale paintScale = new InterpolatingLookupPaintScale();
        paintScale.add(-1.00, new Color(0, 255, 0));
        paintScale.add(0.00, new Color(0, 0, 0));
        paintScale.add(1.00, new Color(255, 0, 0));
        // Create & show window
        RTMZAnalyzerWindow window = new RTMZAnalyzerWindow(dataset, pl, paintScale);
        window.setVisible(true);
    }
    return ExitCode.OK;
}

Example 68 with PeakList

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

the class CVPlotModule method runModule.

@Override
@Nonnull
public ExitCode runModule(@Nonnull MZmineProject project, @Nonnull ParameterSet parameters, @Nonnull Collection<Task> tasks) {
    PeakList[] peakLists = parameters.getParameter(CVParameters.peakLists).getValue().getMatchingPeakLists();
    for (PeakList pl : peakLists) {
        // Create dataset & paint scale
        AbstractXYZDataset dataset = new CVDataset(pl, parameters);
        InterpolatingLookupPaintScale paintScale = new InterpolatingLookupPaintScale();
        paintScale.add(0.00, new Color(0, 0, 0));
        paintScale.add(0.15, new Color(102, 255, 102));
        paintScale.add(0.30, new Color(51, 102, 255));
        paintScale.add(0.45, new Color(255, 0, 0));
        // Create & show window
        RTMZAnalyzerWindow window = new RTMZAnalyzerWindow(dataset, pl, paintScale);
        window.setVisible(true);
    }
    return ExitCode.OK;
}

Example 69 with PeakList

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

the class CameraSearchTask method run.

@Override
public void run() {
    try {
        setStatus(TaskStatus.PROCESSING);
        // Check number of raw data files.
        if (peakList.getNumberOfRawDataFiles() != 1) {
            throw new IllegalStateException("CAMERA can only process feature lists for a single raw data file, i.e. non-aligned feature lists.");
        }
        // Run the search.
        cameraSearch(peakList.getRawDataFile(0));
        // Create new list with IsotopePattern information
        PeakList newPeakList = null;
        if (parameters.getParameter(CameraSearchParameters.CREATE_NEW_LIST).getValue()) {
            switch(groupBy) {
                case CameraSearchParameters.GROUP_BY_PCGROUP:
                    newPeakList = groupPeaksByPCGroup(peakList);
                    break;
                default:
                    newPeakList = groupPeaksByIsotope(peakList);
            }
        }
        if (!isCanceled()) {
            if (newPeakList != null) {
                project.addPeakList(newPeakList);
                QualityParameters.calculateQualityParameters(newPeakList);
            }
            // Finished.
            setStatus(TaskStatus.FINISHED);
            LOG.info("CAMERA Search completed");
        }
        // Repaint the window to reflect the change in the feature list
        Desktop desktop = MZmineCore.getDesktop();
        if (!(desktop instanceof HeadLessDesktop))
            desktop.getMainWindow().repaint();
    } catch (Throwable t) {
        LOG.log(Level.SEVERE, "CAMERA Search error", t);
        setErrorMessage(t.getMessage());
        setStatus(TaskStatus.ERROR);
    }
}

Example 70 with PeakList

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

the class CameraSearchTask method groupPeaksByPCGroup.

/**
 * Uses PCGroup-field in PeakIdentity to group peaks and build spectrum
 *
 * @param peakList a PeakList object
 * @return a new PeakList object
 */
private PeakList groupPeaksByPCGroup(PeakList peakList) {
    // Create new feature list.
    final PeakList combinedPeakList = new SimplePeakList(peakList + " " + parameters.getParameter(CameraSearchParameters.SUFFIX).getValue(), peakList.getRawDataFiles());
    // Load previous applied methods.
    for (final PeakList.PeakListAppliedMethod method : peakList.getAppliedMethods()) {
        combinedPeakList.addDescriptionOfAppliedTask(method);
    }
    // Add task description to feature list.
    combinedPeakList.addDescriptionOfAppliedTask(new SimplePeakListAppliedMethod("Bioconductor CAMERA", parameters));
    // --------------------
    // Find unique PCGroups
    // --------------------
    Set<String> pcGroups = new HashSet<>();
    for (PeakListRow row : peakList.getRows()) {
        PeakIdentity identity = row.getPreferredPeakIdentity();
        if (identity == null)
            continue;
        String groupName = identity.getName();
        if (groupName == null || groupName.length() == 0)
            continue;
        pcGroups.add(groupName);
    }
    List<PeakListRow> groupRows = new ArrayList<>();
    // Set <String> groupNames = new HashSet <> ();
    Map<Double, Double> spectrum = new HashMap<>();
    List<PeakListRow> newPeakListRows = new ArrayList<>();
    for (String groupName : pcGroups) {
        // -----------------------------------------
        // Find all peaks belonging to isotopeGroups
        // -----------------------------------------
        groupRows.clear();
        // groupNames.clear();
        spectrum.clear();
        double maxIntensity = 0.0;
        PeakListRow groupRow = null;
        for (PeakListRow row : peakList.getRows()) {
            PeakIdentity identity = row.getPreferredPeakIdentity();
            if (identity == null)
                continue;
            String name = identity.getName();
            if (name.equals(groupName)) {
                double intensity = row.getAverageHeight();
                groupRows.add(row);
                // groupNames.add(name);
                spectrum.put(row.getAverageMZ(), intensity);
                if (intensity > maxIntensity) {
                    maxIntensity = intensity;
                    groupRow = row;
                }
            }
        }
        if (groupRow == null || spectrum.size() <= 1)
            continue;
        PeakIdentity identity = groupRow.getPreferredPeakIdentity();
        if (identity == null)
            continue;
        DataPoint[] dataPoints = new DataPoint[spectrum.size()];
        int count = 0;
        for (Entry<Double, Double> e : spectrum.entrySet()) dataPoints[count++] = new SimpleDataPoint(e.getKey(), e.getValue());
        IsotopePattern pattern = new SimpleIsotopePattern(dataPoints, IsotopePatternStatus.PREDICTED, "Spectrum");
        groupRow.getBestPeak().setIsotopePattern(pattern);
        // combinedPeakList.addRow(groupRow);
        newPeakListRows.add(groupRow);
    }
    // ------------------------------------
    // 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) combinedPeakList.addRow(row);
    return combinedPeakList;
}