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

Example 66 with DataPoint

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

the class SameRangeTask method fillGap.

private Feature fillGap(PeakListRow row, RawDataFile column) {
    SameRangePeak newPeak = new SameRangePeak(column);
    Range<Double> mzRange = null, rtRange = null;
    // Check the peaks for selected data files
    for (RawDataFile dataFile : row.getRawDataFiles()) {
        Feature peak = row.getPeak(dataFile);
        if (peak == null)
            continue;
        if ((mzRange == null) || (rtRange == null)) {
            mzRange = peak.getRawDataPointsMZRange();
            rtRange = peak.getRawDataPointsRTRange();
        } else {
            mzRange = mzRange.span(peak.getRawDataPointsMZRange());
            rtRange = rtRange.span(peak.getRawDataPointsRTRange());
        }
    }
    assert mzRange != null;
    assert rtRange != null;
    Range<Double> mzRangeWithTol = mzTolerance.getToleranceRange(mzRange);
    // Get scan numbers
    int[] scanNumbers = column.getScanNumbers(1, rtRange);
    boolean dataPointFound = false;
    for (int scanNumber : scanNumbers) {
        if (isCanceled())
            return null;
        // Get next scan
        Scan scan = column.getScan(scanNumber);
        // Find most intense m/z peak
        DataPoint basePeak = ScanUtils.findBasePeak(scan, mzRangeWithTol);
        if (basePeak != null) {
            if (basePeak.getIntensity() > 0)
                dataPointFound = true;
            newPeak.addDatapoint(scan.getScanNumber(), basePeak);
        } else {
            DataPoint fakeDataPoint = new SimpleDataPoint(RangeUtils.rangeCenter(mzRangeWithTol), 0);
            newPeak.addDatapoint(scan.getScanNumber(), fakeDataPoint);
        }
    }
    if (dataPointFound) {
        newPeak.finalizePeak();
        if (newPeak.getArea() == 0)
            return null;
        return newPeak;
    }
    return null;
}

Example 67 with DataPoint

use of net.sf.mzmine.datamodel.DataPoint 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 68 with DataPoint

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

the class IsotopePatternPreviewDialog method updateTable.

/**
 * this is being called by the calculation task to update the table
 * @param pattern
 */
protected void updateTable(ExtendedIsotopePattern pattern) {
    DataPoint[] dp = pattern.getDataPoints();
    Object[][] data = new Object[dp.length][];
    for (int i = 0; i < pattern.getNumberOfDataPoints(); i++) {
        data[i] = new Object[3];
        data[i][0] = mzFormat.format(dp[i].getMZ());
        data[i][1] = relFormat.format(dp[i].getIntensity());
        data[i][2] = pattern.getIsotopeComposition(i);
    }
    if (pol == PolarityType.NEUTRAL)
        // column 1 = "Exact mass / Da"
        table = new JTable(data, columns[0]);
    else
        // column 2 = "m/z"
        table = new JTable(data, columns[1]);
    pnText.setViewportView(table);
    // make editing impossible
    table.setDefaultEditor(Object.class, null);
}

Example 69 with DataPoint

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

the class NativeFileReadTask method readRAWDump.

/**
 * This method reads the dump of the RAW data file produced by RAWdump.exe utility (see
 * RAWdump.cpp source for details).
 */
private void readRAWDump(InputStream dumpStream) throws IOException {
    String line;
    byte[] byteBuffer = new byte[100000];
    double[] mzValuesBuffer = new double[10000];
    double[] intensityValuesBuffer = new double[10000];
    while ((line = TextUtils.readLineFromStream(dumpStream)) != null) {
        if (isCanceled()) {
            return;
        }
        if (line.startsWith("ERROR: ")) {
            throw (new IOException(line.substring("ERROR: ".length())));
        }
        if (line.startsWith("NUMBER OF SCANS: ")) {
            totalScans = Integer.parseInt(line.substring("NUMBER OF SCANS: ".length()));
        }
        if (line.startsWith("SCAN NUMBER: ")) {
            scanNumber = Integer.parseInt(line.substring("SCAN NUMBER: ".length()));
        }
        if (line.startsWith("SCAN ID: ")) {
            scanId = line.substring("SCAN ID: ".length());
        }
        if (line.startsWith("MS LEVEL: ")) {
            msLevel = Integer.parseInt(line.substring("MS LEVEL: ".length()));
        }
        if (line.startsWith("POLARITY: ")) {
            if (line.contains("-"))
                polarity = PolarityType.NEGATIVE;
            else if (line.contains("+"))
                polarity = PolarityType.POSITIVE;
            else
                polarity = PolarityType.UNKNOWN;
            // In such case, we can parse it from the scan filter line (scanId).
            if ((polarity == PolarityType.UNKNOWN) && (fileType == RawDataFileType.THERMO_RAW) && (!Strings.isNullOrEmpty(scanId))) {
                if (scanId.startsWith("-"))
                    polarity = PolarityType.NEGATIVE;
                else if (scanId.startsWith("+"))
                    polarity = PolarityType.POSITIVE;
            }
        }
        if (line.startsWith("RETENTION TIME: ")) {
            // Retention time is reported in minutes.
            retentionTime = Double.parseDouble(line.substring("RETENTION TIME: ".length()));
        }
        if (line.startsWith("PRECURSOR: ")) {
            String[] tokens = line.split(" ");
            double token2 = Double.parseDouble(tokens[1]);
            int token3 = Integer.parseInt(tokens[2]);
            precursorMZ = token2;
            precursorCharge = token3;
            // FTMS + p ESI d Full ms2 279.16@hcd25.00 [50.00-305.00]
            if (precursorMZ == 0.0 && fileType == RawDataFileType.THERMO_RAW && (!Strings.isNullOrEmpty(scanId))) {
                Pattern precursorPattern = Pattern.compile(".* ms\\d+ (\\d+\\.\\d+)[@ ]");
                Matcher m = precursorPattern.matcher(scanId);
                if (m.find()) {
                    String precursorMzString = m.group(1);
                    try {
                        precursorMZ = Double.parseDouble(precursorMzString);
                    } catch (Exception e) {
                        e.printStackTrace();
                    // ignore
                    }
                }
            }
        }
        if (line.startsWith("MASS VALUES: ")) {
            Pattern p = Pattern.compile("MASS VALUES: (\\d+) x (\\d+) BYTES");
            Matcher m = p.matcher(line);
            if (!m.matches())
                throw new IOException("Could not parse line " + line);
            numOfDataPoints = Integer.parseInt(m.group(1));
            final int byteSize = Integer.parseInt(m.group(2));
            final int numOfBytes = numOfDataPoints * byteSize;
            if (byteBuffer.length < numOfBytes)
                byteBuffer = new byte[numOfBytes * 2];
            dumpStream.read(byteBuffer, 0, numOfBytes);
            ByteBuffer mzByteBuffer = ByteBuffer.wrap(byteBuffer, 0, numOfBytes).order(ByteOrder.LITTLE_ENDIAN);
            if (mzValuesBuffer.length < numOfDataPoints)
                mzValuesBuffer = new double[numOfDataPoints * 2];
            for (int i = 0; i < numOfDataPoints; i++) {
                double newValue;
                if (byteSize == 8)
                    newValue = mzByteBuffer.getDouble();
                else
                    newValue = mzByteBuffer.getFloat();
                mzValuesBuffer[i] = newValue;
            }
        }
        if (line.startsWith("INTENSITY VALUES: ")) {
            Pattern p = Pattern.compile("INTENSITY VALUES: (\\d+) x (\\d+) BYTES");
            Matcher m = p.matcher(line);
            if (!m.matches())
                throw new IOException("Could not parse line " + line);
            // VALUES
            if (numOfDataPoints != Integer.parseInt(m.group(1))) {
                throw new IOException("Scan " + scanNumber + " contained " + numOfDataPoints + " mass values, but " + m.group(1) + " intensity values");
            }
            final int byteSize = Integer.parseInt(m.group(2));
            final int numOfBytes = numOfDataPoints * byteSize;
            if (byteBuffer.length < numOfBytes)
                byteBuffer = new byte[numOfBytes * 2];
            dumpStream.read(byteBuffer, 0, numOfBytes);
            ByteBuffer intensityByteBuffer = ByteBuffer.wrap(byteBuffer, 0, numOfBytes).order(ByteOrder.LITTLE_ENDIAN);
            if (intensityValuesBuffer.length < numOfDataPoints)
                intensityValuesBuffer = new double[numOfDataPoints * 2];
            for (int i = 0; i < numOfDataPoints; i++) {
                double newValue;
                if (byteSize == 8)
                    newValue = intensityByteBuffer.getDouble();
                else
                    newValue = intensityByteBuffer.getFloat();
                intensityValuesBuffer[i] = newValue;
            }
            // INTENSITY VALUES was the last item of the scan, so now we can
            // convert the data to DataPoint[] array and create a new scan
            DataPoint[] dataPoints = new DataPoint[numOfDataPoints];
            for (int i = 0; i < numOfDataPoints; i++) {
                dataPoints[i] = new SimpleDataPoint(mzValuesBuffer[i], intensityValuesBuffer[i]);
            }
            // Auto-detect whether this scan is centroided
            MassSpectrumType spectrumType = ScanUtils.detectSpectrumType(dataPoints);
            SimpleScan newScan = new SimpleScan(null, scanNumber, msLevel, retentionTime, precursorMZ, precursorCharge, null, dataPoints, spectrumType, polarity, scanId, mzRange);
            newMZmineFile.addScan(newScan);
            parsedScans++;
            // Clean the variables for next scan
            scanNumber = 0;
            scanId = null;
            polarity = null;
            mzRange = null;
            msLevel = 0;
            retentionTime = 0;
            precursorMZ = 0;
            precursorCharge = 0;
            numOfDataPoints = 0;
        }
    }
}

Example 70 with DataPoint

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

the class NetCDFReadTask method readNextScan.

/**
 * Reads one scan from the file. Requires that general information has already been read.
 */
private Scan readNextScan() throws IOException {
    // Get scan starting position and length
    int[] scanStartPosition = new int[1];
    int[] scanLength = new int[1];
    Integer[] startAndLength = scansIndex.get(scanNum);
    // End of file
    if (startAndLength == null) {
        return null;
    }
    scanStartPosition[0] = startAndLength[0];
    scanLength[0] = startAndLength[1];
    // Get retention time of the scan
    Double retentionTime = scansRetentionTimes.get(scanNum);
    if (retentionTime == null) {
        logger.severe("Could not find retention time for scan " + scanNum);
        throw (new IOException("Could not find retention time for scan " + scanNum));
    }
    // An empty scan needs special attention..
    if (scanLength[0] == 0) {
        scanNum++;
        return new SimpleScan(null, scanNum, 1, retentionTime.doubleValue(), 0, 0, null, new DataPoint[0], MassSpectrumType.CENTROIDED, PolarityType.UNKNOWN, "", null);
    }
    // Is there any way how to extract polarity from netcdf?
    PolarityType polarity = PolarityType.UNKNOWN;
    // Is there any way how to extract scan definition from netcdf?
    String scanDefinition = "";
    // Read mass and intensity values
    Array massValueArray;
    Array intensityValueArray;
    try {
        massValueArray = massValueVariable.read(scanStartPosition, scanLength);
        intensityValueArray = intensityValueVariable.read(scanStartPosition, scanLength);
    } catch (Exception e) {
        logger.log(Level.SEVERE, "Could not read from variables mass_values and/or intensity_values.", e);
        throw (new IOException("Could not read from variables mass_values and/or intensity_values."));
    }
    Index massValuesIndex = massValueArray.getIndex();
    Index intensityValuesIndex = intensityValueArray.getIndex();
    int arrayLength = massValueArray.getShape()[0];
    DataPoint[] dataPoints = new DataPoint[arrayLength];
    for (int j = 0; j < arrayLength; j++) {
        Index massIndex0 = massValuesIndex.set0(j);
        Index intensityIndex0 = intensityValuesIndex.set0(j);
        double mz = massValueArray.getDouble(massIndex0) * massValueScaleFactor;
        double intensity = intensityValueArray.getDouble(intensityIndex0) * intensityValueScaleFactor;
        dataPoints[j] = new SimpleDataPoint(mz, intensity);
    }
    scanNum++;
    // Auto-detect whether this scan is centroided
    MassSpectrumType spectrumType = ScanUtils.detectSpectrumType(dataPoints);
    SimpleScan buildingScan = new SimpleScan(null, scanNum, 1, retentionTime.doubleValue(), 0, 0, null, dataPoints, spectrumType, polarity, scanDefinition, null);
    return buildingScan;
}