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

Example 41 with PeakListRow

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

the class CameraSearchTask method groupPeaksByIsotope.

/**
 * Uses Isotope-field in PeakIdentity to group isotopes and build spectrum
 *
 * @param peakList PeakList object
 * @return new PeakList object
 */
private PeakList groupPeaksByIsotope(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 isotopes belonging to the same group
    // ------------------------------------------------
    Set<String> isotopeGroups = new HashSet<>();
    for (PeakListRow row : peakList.getRows()) {
        PeakIdentity identity = row.getPreferredPeakIdentity();
        if (identity == null)
            continue;
        String isotope = identity.getPropertyValue("Isotope");
        if (isotope == null)
            continue;
        String isotopeGroup = isotope.substring(1, isotope.indexOf("]"));
        if (isotopeGroup == null || isotopeGroup.length() == 0)
            continue;
        isotopeGroups.add(isotopeGroup);
    }
    List<PeakListRow> groupRows = new ArrayList<>();
    Set<String> groupNames = new HashSet<>();
    Map<Double, Double> spectrum = new HashMap<>();
    List<PeakListRow> newPeakListRows = new ArrayList<>();
    for (String isotopeGroup : isotopeGroups) {
        // -----------------------------------------
        // Find all peaks belonging to isotopeGroups
        // -----------------------------------------
        groupRows.clear();
        groupNames.clear();
        spectrum.clear();
        int minLength = Integer.MAX_VALUE;
        PeakListRow groupRow = null;
        for (PeakListRow row : peakList.getRows()) {
            PeakIdentity identity = row.getPreferredPeakIdentity();
            if (identity == null)
                continue;
            String isotope = identity.getPropertyValue("Isotope");
            if (isotope == null)
                continue;
            String isoGroup = isotope.substring(1, isotope.indexOf("]"));
            if (isoGroup == null)
                continue;
            if (isoGroup.equals(isotopeGroup)) {
                groupRows.add(row);
                groupNames.add(identity.getName());
                spectrum.put(row.getAverageMZ(), row.getAverageHeight());
                if (isoGroup.length() < minLength) {
                    minLength = isoGroup.length();
                    groupRow = row;
                }
            }
        }
        // Skip peaks that have different identity names (belong to different pcgroup)
        if (groupRow == null || groupNames.size() != 1)
            continue;
        if (groupRow == null)
            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);
    }
    if (includeSingletons) {
        for (PeakListRow row : peakList.getRows()) {
            PeakIdentity identity = row.getPreferredPeakIdentity();
            if (identity == null)
                continue;
            String isotope = identity.getPropertyValue("Isotope");
            if (isotope == null || isotope.length() == 0) {
                DataPoint[] dataPoints = new DataPoint[1];
                dataPoints[0] = new SimpleDataPoint(row.getAverageMZ(), row.getAverageHeight());
                IsotopePattern pattern = new SimpleIsotopePattern(dataPoints, IsotopePatternStatus.PREDICTED, "Spectrum");
                row.getBestPeak().setIsotopePattern(pattern);
                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) combinedPeakList.addRow(row);
    return combinedPeakList;
}

Example 42 with PeakListRow

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

the class AdductSearchTask method searchAdducts.

/**
 * Search peak-list for adducts.
 */
private void searchAdducts() {
    // Get rows.
    final PeakListRow[] rows = peakList.getRows();
    totalRows = rows.length;
    // Start with the highest peaks.
    Arrays.sort(rows, new PeakListRowSorter(SortingProperty.Height, SortingDirection.Descending));
    // Compare each pair of rows against each other.
    for (int i = 0; !isCanceled() && i < totalRows; i++) {
        for (int j = 0; !isCanceled() && j < totalRows; j++) {
            if (i == j)
                continue;
            findAdducts(rows[i], rows[j]);
        }
        finishedRows++;
    }
}

Example 43 with PeakListRow

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

the class TargetedPeakDetectionModuleTask method run.

public void run() {
    setStatus(TaskStatus.PROCESSING);
    // Calculate total number of scans in all files
    totalScans = dataFile.getNumOfScans(1);
    // Create new feature list
    processedPeakList = new SimplePeakList(dataFile.getName() + " " + suffix, dataFile);
    List<PeakInformation> peaks = this.readFile();
    if (peaks == null || peaks.isEmpty()) {
        setStatus(TaskStatus.ERROR);
        setErrorMessage("Could not read file or the file is empty ");
        return;
    }
    // Fill new feature list with empty rows
    for (int row = 0; row < peaks.size(); row++) {
        PeakListRow newRow = new SimplePeakListRow(ID++);
        processedPeakList.addRow(newRow);
    }
    // Canceled?
    if (isCanceled()) {
        return;
    }
    List<Gap> gaps = new ArrayList<Gap>();
    // gaps if necessary
    for (int row = 0; row < peaks.size(); row++) {
        PeakListRow newRow = processedPeakList.getRow(row);
        // Create a new gap
        Range<Double> mzRange = mzTolerance.getToleranceRange(peaks.get(row).getMZ());
        Range<Double> rtRange = rtTolerance.getToleranceRange(peaks.get(row).getRT());
        newRow.addPeakIdentity(new SimplePeakIdentity(peaks.get(row).getName()), true);
        Gap newGap = new Gap(newRow, dataFile, mzRange, rtRange, intTolerance, noiseLevel);
        gaps.add(newGap);
    }
    // Stop processing this file if there are no gaps
    if (gaps.isEmpty()) {
        processedScans += dataFile.getNumOfScans();
    }
    // Get all scans of this data file
    int[] scanNumbers = dataFile.getScanNumbers(msLevel);
    if (scanNumbers == null) {
        logger.log(Level.WARNING, "Could not read file with the MS level of " + msLevel);
        setStatus(TaskStatus.ERROR);
        return;
    }
    // Process each scan
    for (int scanNumber : scanNumbers) {
        // Canceled?
        if (isCanceled()) {
            return;
        }
        // Get the scan
        Scan scan = dataFile.getScan(scanNumber);
        // Feed this scan to all gaps
        for (Gap gap : gaps) {
            gap.offerNextScan(scan);
        }
        processedScans++;
    }
    // Finalize gaps
    for (Gap gap : gaps) {
        gap.noMoreOffers();
    }
    // Append processed feature list to the project
    project.addPeakList(processedPeakList);
    // Add quality parameters to peaks
    QualityParameters.calculateQualityParameters(processedPeakList);
    // Add task description to peakList
    processedPeakList.addDescriptionOfAppliedTask(new SimplePeakListAppliedMethod("Targeted feature detection ", parameters));
    logger.log(Level.INFO, "Finished targeted feature detection on {0}", this.dataFile);
    setStatus(TaskStatus.FINISHED);
}

Example 44 with PeakListRow

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

the class CSVExportTask method exportPeakList.

private void exportPeakList(PeakList peakList, FileWriter writer, File fileName) {
    NumberFormat mzForm = MZmineCore.getConfiguration().getMZFormat();
    RawDataFile[] rawDataFiles = peakList.getRawDataFiles();
    // Buffer for writing
    StringBuffer line = new StringBuffer();
    // Write column headers
    // Common elements
    int length = commonElements.length;
    String name;
    for (int i = 0; i < length; i++) {
        name = commonElements[i].toString();
        name = name.replace("Export ", "");
        name = escapeStringForCSV(name);
        line.append(name + fieldSeparator);
    }
    // peak Information
    Set<String> peakInformationFields = new HashSet<>();
    for (PeakListRow row : peakList.getRows()) {
        if (!filter.filter(row))
            continue;
        if (row.getPeakInformation() != null) {
            for (String key : row.getPeakInformation().getAllProperties().keySet()) {
                peakInformationFields.add(key);
            }
        }
    }
    if (exportAllPeakInfo)
        for (String field : peakInformationFields) line.append(field + fieldSeparator);
    // Data file elements
    length = dataFileElements.length;
    for (int df = 0; df < peakList.getNumberOfRawDataFiles(); df++) {
        for (int i = 0; i < length; i++) {
            name = rawDataFiles[df].getName();
            name = name + " " + dataFileElements[i].toString();
            name = escapeStringForCSV(name);
            line.append(name + fieldSeparator);
        }
    }
    line.append("\n");
    try {
        writer.write(line.toString());
    } catch (Exception e) {
        setStatus(TaskStatus.ERROR);
        setErrorMessage("Could not write to file " + fileName);
        return;
    }
    // Write data rows
    for (PeakListRow peakListRow : peakList.getRows()) {
        if (!filter.filter(peakListRow)) {
            processedRows++;
            continue;
        }
        // Cancel?
        if (isCanceled()) {
            return;
        }
        // Reset the buffer
        line.setLength(0);
        // Common elements
        length = commonElements.length;
        for (int i = 0; i < length; i++) {
            switch(commonElements[i]) {
                case ROW_ID:
                    line.append(peakListRow.getID() + fieldSeparator);
                    break;
                case ROW_MZ:
                    line.append(peakListRow.getAverageMZ() + fieldSeparator);
                    break;
                case ROW_RT:
                    line.append(peakListRow.getAverageRT() + fieldSeparator);
                    break;
                case ROW_IDENTITY:
                    // Identity elements
                    PeakIdentity peakId = peakListRow.getPreferredPeakIdentity();
                    if (peakId == null) {
                        line.append(fieldSeparator);
                        break;
                    }
                    String propertyValue = peakId.toString();
                    propertyValue = escapeStringForCSV(propertyValue);
                    line.append(propertyValue + fieldSeparator);
                    break;
                case ROW_IDENTITY_ALL:
                    // Identity elements
                    PeakIdentity[] peakIdentities = peakListRow.getPeakIdentities();
                    propertyValue = "";
                    for (int x = 0; x < peakIdentities.length; x++) {
                        if (x > 0)
                            propertyValue += idSeparator;
                        propertyValue += peakIdentities[x].toString();
                    }
                    propertyValue = escapeStringForCSV(propertyValue);
                    line.append(propertyValue + fieldSeparator);
                    break;
                case ROW_IDENTITY_DETAILS:
                    peakId = peakListRow.getPreferredPeakIdentity();
                    if (peakId == null) {
                        line.append(fieldSeparator);
                        break;
                    }
                    propertyValue = peakId.getDescription();
                    if (propertyValue != null)
                        propertyValue = propertyValue.replaceAll("\\n", ";");
                    propertyValue = escapeStringForCSV(propertyValue);
                    line.append(propertyValue + fieldSeparator);
                    break;
                case ROW_COMMENT:
                    String comment = escapeStringForCSV(peakListRow.getComment());
                    line.append(comment + fieldSeparator);
                    break;
                case ROW_PEAK_NUMBER:
                    int numDetected = 0;
                    for (Feature p : peakListRow.getPeaks()) {
                        if (p.getFeatureStatus() == FeatureStatus.DETECTED) {
                            numDetected++;
                        }
                    }
                    line.append(numDetected + fieldSeparator);
                    break;
            }
        }
        // peak Information
        if (exportAllPeakInfo) {
            if (peakListRow.getPeakInformation() != null) {
                Map<String, String> allPropertiesMap = peakListRow.getPeakInformation().getAllProperties();
                for (String key : peakInformationFields) {
                    String value = allPropertiesMap.get(key);
                    if (value == null)
                        value = "";
                    line.append(value + fieldSeparator);
                }
            }
        }
        // Data file elements
        length = dataFileElements.length;
        for (RawDataFile dataFile : rawDataFiles) {
            for (int i = 0; i < length; i++) {
                Feature peak = peakListRow.getPeak(dataFile);
                if (peak != null) {
                    switch(dataFileElements[i]) {
                        case PEAK_STATUS:
                            line.append(peak.getFeatureStatus() + fieldSeparator);
                            break;
                        case PEAK_NAME:
                            line.append(PeakUtils.peakToString(peak) + fieldSeparator);
                            break;
                        case PEAK_MZ:
                            line.append(peak.getMZ() + fieldSeparator);
                            break;
                        case PEAK_RT:
                            line.append(peak.getRT() + fieldSeparator);
                            break;
                        case PEAK_RT_START:
                            line.append(peak.getRawDataPointsRTRange().lowerEndpoint() + fieldSeparator);
                            break;
                        case PEAK_RT_END:
                            line.append(peak.getRawDataPointsRTRange().upperEndpoint() + fieldSeparator);
                            break;
                        case PEAK_DURATION:
                            line.append(RangeUtils.rangeLength(peak.getRawDataPointsRTRange()) + fieldSeparator);
                            break;
                        case PEAK_HEIGHT:
                            line.append(peak.getHeight() + fieldSeparator);
                            break;
                        case PEAK_AREA:
                            line.append(peak.getArea() + fieldSeparator);
                            break;
                        case PEAK_CHARGE:
                            line.append(peak.getCharge() + fieldSeparator);
                            break;
                        case PEAK_DATAPOINTS:
                            line.append(peak.getScanNumbers().length + fieldSeparator);
                            break;
                        case PEAK_FWHM:
                            line.append(peak.getFWHM() + fieldSeparator);
                            break;
                        case PEAK_TAILINGFACTOR:
                            line.append(peak.getTailingFactor() + fieldSeparator);
                            break;
                        case PEAK_ASYMMETRYFACTOR:
                            line.append(peak.getAsymmetryFactor() + fieldSeparator);
                            break;
                        case PEAK_MZMIN:
                            line.append(peak.getRawDataPointsMZRange().lowerEndpoint() + fieldSeparator);
                            break;
                        case PEAK_MZMAX:
                            line.append(peak.getRawDataPointsMZRange().upperEndpoint() + fieldSeparator);
                            break;
                    }
                } else {
                    switch(dataFileElements[i]) {
                        case PEAK_STATUS:
                            line.append(FeatureStatus.UNKNOWN + fieldSeparator);
                            break;
                        default:
                            line.append("0" + fieldSeparator);
                            break;
                    }
                }
            }
        }
        line.append("\n");
        try {
            writer.write(line.toString());
        } catch (Exception e) {
            setStatus(TaskStatus.ERROR);
            setErrorMessage("Could not write to file " + fileName);
            return;
        }
        processedRows++;
    }
}

Example 45 with PeakListRow

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

the class GnpsFbmnExportTask method copyPeakRow.

/**
 * Create a copy of a feature list row.
 */
private static PeakListRow copyPeakRow(final PeakListRow row) {
    // Copy the feature list row.
    final PeakListRow newRow = new SimplePeakListRow(row.getID());
    PeakUtils.copyPeakListRowProperties(row, newRow);
    // Copy the peaks.
    for (final Feature peak : row.getPeaks()) {
        final Feature newPeak = new SimpleFeature(peak);
        PeakUtils.copyPeakProperties(peak, newPeak);
        newRow.addPeak(peak.getDataFile(), newPeak);
    }
    return newRow;
}