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

Example 1 with MassSpectrumType

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

the class ScanSelectionParameter method loadValueFromXML.

@Override
public void loadValueFromXML(Element xmlElement) {
    Range<Integer> scanNumberRange = null;
    Integer baseFilteringInteger = null;
    Range<Double> scanRTRange = null;
    PolarityType polarity = null;
    MassSpectrumType spectrumType = null;
    Integer msLevel = null;
    String scanDefinition = null;
    scanNumberRange = XMLUtils.parseIntegerRange(xmlElement, "scan_numbers");
    scanRTRange = XMLUtils.parseDoubleRange(xmlElement, "retention_time");
    NodeList items = xmlElement.getElementsByTagName("ms_level");
    for (int i = 0; i < items.getLength(); i++) {
        msLevel = Integer.valueOf(items.item(i).getTextContent());
    }
    items = xmlElement.getElementsByTagName("polarity");
    for (int i = 0; i < items.getLength(); i++) {
        try {
            polarity = PolarityType.valueOf(items.item(i).getTextContent());
        } catch (Exception e) {
            polarity = PolarityType.fromSingleChar(items.item(i).getTextContent());
        }
    }
    items = xmlElement.getElementsByTagName("spectrum_type");
    for (int i = 0; i < items.getLength(); i++) {
        spectrumType = MassSpectrumType.valueOf(items.item(i).getTextContent());
    }
    items = xmlElement.getElementsByTagName("scan_definition");
    for (int i = 0; i < items.getLength(); i++) {
        scanDefinition = items.item(i).getTextContent();
    }
    this.value = new ScanSelection(scanNumberRange, baseFilteringInteger, scanRTRange, polarity, spectrumType, msLevel, scanDefinition);
}

Example 2 with MassSpectrumType

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

the class ScanSelectionParameter method saveValueToXML.

@Override
public void saveValueToXML(Element xmlElement) {
    if (value == null)
        return;
    Document parentDocument = xmlElement.getOwnerDocument();
    final Range<Integer> scanNumberRange = value.getScanNumberRange();
    final Range<Double> scanRetentionTimeRange = value.getScanRTRange();
    final Integer baseFilteringInteger = value.getBaseFilteringInteger();
    final PolarityType polarity = value.getPolarity();
    final MassSpectrumType spectrumType = value.getSpectrumType();
    final Integer msLevel = value.getMsLevel();
    final String scanDefinition = value.getScanDefinition();
    XMLUtils.appendRange(xmlElement, "scan_numbers", scanNumberRange);
    XMLUtils.appendRange(xmlElement, "retention_time", scanRetentionTimeRange);
    if (baseFilteringInteger != null) {
        Element newElement = parentDocument.createElement("baseFilteringInteger");
        newElement.setTextContent(baseFilteringInteger.toString());
        xmlElement.appendChild(newElement);
    }
    if (polarity != null) {
        Element newElement = parentDocument.createElement("polarity");
        newElement.setTextContent(polarity.toString());
        xmlElement.appendChild(newElement);
    }
    if (spectrumType != null) {
        Element newElement = parentDocument.createElement("spectrum_type");
        newElement.setTextContent(spectrumType.toString());
        xmlElement.appendChild(newElement);
    }
    if (msLevel != null) {
        Element newElement = parentDocument.createElement("ms_level");
        newElement.setTextContent(String.valueOf(msLevel));
        xmlElement.appendChild(newElement);
    }
    if (scanDefinition != null) {
        Element newElement = parentDocument.createElement("scan_definition");
        newElement.setTextContent(scanDefinition);
        xmlElement.appendChild(newElement);
    }
}

Example 3 with MassSpectrumType

use of net.sf.mzmine.datamodel.MassSpectrumType 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 4 with MassSpectrumType

use of net.sf.mzmine.datamodel.MassSpectrumType 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;
}

Example 5 with MassSpectrumType

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

the class MzMLReadTask method run.

/**
 * @see java.lang.Runnable#run()
 */
public void run() {
    setStatus(TaskStatus.PROCESSING);
    logger.info("Started parsing file " + file);
    MzMLUnmarshaller unmarshaller = new MzMLUnmarshaller(file);
    totalScans = unmarshaller.getObjectCountForXpath("/run/spectrumList/spectrum");
    fillScanIdTable(unmarshaller.unmarshalCollectionFromXpath("/run/spectrumList/spectrum", Spectrum.class), totalScans);
    MzMLObjectIterator<Spectrum> spectrumIterator = unmarshaller.unmarshalCollectionFromXpath("/run/spectrumList/spectrum", Spectrum.class);
    try {
        while (spectrumIterator.hasNext()) {
            if (isCanceled())
                return;
            Spectrum spectrum = spectrumIterator.next();
            // Ignore scans that are not MS, e.g. UV
            if (!isMsSpectrum(spectrum)) {
                parsedScans++;
                continue;
            }
            String scanId = spectrum.getId();
            Integer scanNumber = scanIdTable.get(scanId);
            if (scanNumber == null)
                throw new IllegalStateException("Cannot determine scan number: " + scanId);
            // Extract scan data
            int msLevel = extractMSLevel(spectrum);
            double retentionTime = extractRetentionTime(spectrum);
            PolarityType polarity = extractPolarity(spectrum);
            int parentScan = extractParentScanNumber(spectrum);
            double precursorMz = extractPrecursorMz(spectrum);
            int precursorCharge = extractPrecursorCharge(spectrum);
            String scanDefinition = extractScanDefinition(spectrum);
            DataPoint[] dataPoints = extractDataPoints(spectrum);
            // Auto-detect whether this scan is centroided
            MassSpectrumType spectrumType = ScanUtils.detectSpectrumType(dataPoints);
            SimpleScan scan = new SimpleScan(null, scanNumber, msLevel, retentionTime, precursorMz, precursorCharge, null, dataPoints, spectrumType, polarity, scanDefinition, null);
            for (SimpleScan s : parentStack) {
                if (s.getScanNumber() == parentScan) {
                    s.addFragmentScan(scanNumber);
                }
            }
            /*
         * Verify the size of parentStack. The actual size of the window to cover possible
         * candidates is defined by limitSize.
         */
            if (parentStack.size() > PARENT_STACK_SIZE) {
                SimpleScan firstScan = parentStack.removeLast();
                newMZmineFile.addScan(firstScan);
            }
            parentStack.addFirst(scan);
            parsedScans++;
        }
        while (!parentStack.isEmpty()) {
            SimpleScan scan = parentStack.removeLast();
            newMZmineFile.addScan(scan);
        }
        finalRawDataFile = newMZmineFile.finishWriting();
        project.addFile(finalRawDataFile);
    } catch (Throwable e) {
        e.printStackTrace();
        setStatus(TaskStatus.ERROR);
        setErrorMessage("Error parsing mzML: " + ExceptionUtils.exceptionToString(e));
        e.printStackTrace();
        return;
    }
    if (parsedScans == 0) {
        setStatus(TaskStatus.ERROR);
        setErrorMessage("No scans found");
        return;
    }
    logger.info("Finished parsing " + file + ", parsed " + parsedScans + " scans");
    setStatus(TaskStatus.FINISHED);
}