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

Example 16 with DataPoint

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

the class IsotopePeakScannerTask method setUpDiffAutoCarbon.

/**
 * This calculates the isotope pattern using ExtendedIsotopePattern and creates an
 * ArrayList<Double> that will contain the mass shift for every expected isotope peak relative to
 * the one with the lowest mass.
 *
 * @return
 */
private double[][] setUpDiffAutoCarbon() {
    // ArrayList<Double> diff = new ArrayList<Double>(2);
    double[][] diff;
    if (scanType == ScanType.AUTOCARBON) {
        String[] strPattern = new String[carbonRange];
        ExtendedIsotopePattern[] patternBuffer = new ExtendedIsotopePattern[carbonRange];
        // in the following for we calculate up the patterns
        for (int p = 0; p < carbonRange; p++) {
            if (p + autoCarbonMin != 0)
                strPattern[p] = "C" + (p + autoCarbonMin) + element;
            else
                strPattern[p] = element;
            try {
                patternBuffer[p] = (ExtendedIsotopePattern) IsotopePatternCalculator.calculateIsotopePattern(strPattern[p], 0.001, mergeWidth, charge, polarityType, true);
                patternBuffer[p] = (ExtendedIsotopePattern) IsotopePatternCalculator.removeDataPointsBelowIntensity(patternBuffer[p], minPatternIntensity);
            } catch (Exception e) {
                logger.warning("The entered Sum formula is invalid.");
                return null;
            }
        }
        int sizeCounter = 0;
        // if they dont fit we null them
        for (int p = 0; p < carbonRange; p++) {
            if (patternBuffer[p].getNumberOfDataPoints() >= autoCarbonMinPatternSize) {
                sizeCounter++;
            } else {
                patternBuffer[p] = null;
            }
        }
        if (sizeCounter == 0)
            throw new MSDKRuntimeException("Min pattern size excludes every calculated isotope pattern.\nPlease increase min pattern intensity for more data points or decrease the minimum pattern size.");
        logger.info("about to add " + sizeCounter + " patterns to the scan.");
        diff = new double[sizeCounter][];
        int addCounter = 0;
        pattern = new ExtendedIsotopePattern[sizeCounter];
        for (int p = 0; p < carbonRange; p++) {
            if (patternBuffer[p] == null)
                continue;
            pattern[addCounter] = patternBuffer[p];
            DataPoint[] points = patternBuffer[p].getDataPoints();
            diff[addCounter] = new double[points.length];
            if (maxPatternSize < diff[addCounter].length) {
                maxPatternSize = diff[addCounter].length;
                maxPatternIndex = addCounter;
            }
            for (int i = 0; i < pattern[addCounter].getNumberOfDataPoints(); i++) {
                diff[addCounter][i] = points[i].getMZ() - points[0].getMZ();
            }
            addCounter++;
        }
    } else /* if(scanType == ScanType.SPECIFIC) */
    {
        diff = new double[1][];
        pattern = new ExtendedIsotopePattern[1];
        pattern[0] = (ExtendedIsotopePattern) IsotopePatternCalculator.calculateIsotopePattern(element, 0.001, mergeWidth, charge, polarityType, true);
        pattern[0] = (ExtendedIsotopePattern) IsotopePatternCalculator.removeDataPointsBelowIntensity(pattern[0], minPatternIntensity);
        DataPoint[] points = pattern[0].getDataPoints();
        diff[0] = new double[points.length];
        if (maxPatternSize < diff[0].length) {
            maxPatternSize = diff[0].length;
            maxPatternIndex = 0;
        }
        for (int i = 0; i < pattern[0].getNumberOfDataPoints(); i++) {
            diff[0][i] = points[i].getMZ() - points[0].getMZ();
        }
    }
    logger.info("diff set up...");
    return diff;
}

Example 17 with DataPoint

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

the class RawDataFileImpl method addScan.

@Override
public synchronized void addScan(Scan newScan) throws IOException {
    // and we just need store the reference
    if (newScan instanceof StorableScan) {
        scans.put(newScan.getScanNumber(), (StorableScan) newScan);
        return;
    }
    DataPoint[] dataPoints = newScan.getDataPoints();
    final int storageID = storeDataPoints(dataPoints);
    StorableScan storedScan = new StorableScan(newScan, this, dataPoints.length, storageID);
    scans.put(newScan.getScanNumber(), storedScan);
}

Example 18 with DataPoint

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

the class RawDataFileImpl method getDataMaxBasePeakIntensity.

/**
 * @see net.sf.mzmine.datamodel.RawDataFile#getDataMaxBasePeakIntensity()
 */
@Override
public double getDataMaxBasePeakIntensity(int msLevel) {
    // check if we have this value already cached
    Double maxBasePeak = dataMaxBasePeakIntensity.get(msLevel);
    if (maxBasePeak != null)
        return maxBasePeak;
    // find the value
    Enumeration<StorableScan> scansEnum = scans.elements();
    while (scansEnum.hasMoreElements()) {
        Scan scan = scansEnum.nextElement();
        // ignore scans of other ms levels
        if (scan.getMSLevel() != msLevel)
            continue;
        DataPoint scanBasePeak = scan.getHighestDataPoint();
        if (scanBasePeak == null)
            continue;
        if ((maxBasePeak == null) || (scanBasePeak.getIntensity() > maxBasePeak))
            maxBasePeak = scanBasePeak.getIntensity();
    }
    // return -1 if no scan at this MS level
    if (maxBasePeak == null)
        maxBasePeak = -1d;
    // cache the value
    dataMaxBasePeakIntensity.put(msLevel, maxBasePeak);
    return maxBasePeak;
}

Example 19 with DataPoint

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

the class RawDataFileImpl method readDataPoints.

public synchronized DataPoint[] readDataPoints(int ID) throws IOException {
    final Long currentOffset = dataPointsOffsets.get(ID);
    final Integer numOfDataPoints = dataPointsLengths.get(ID);
    if ((currentOffset == null) || (numOfDataPoints == null)) {
        throw new IllegalArgumentException("Unknown storage ID " + ID);
    }
    final int numOfBytes = numOfDataPoints * 2 * 4;
    if (buffer.capacity() < numOfBytes) {
        buffer = ByteBuffer.allocate(numOfBytes * 2);
    } else {
        // JDK 9 breaks compatibility with JRE8: need to cast
        // https://stackoverflow.com/questions/48693695/java-nio-buffer-not-loading-clear-method-on-runtime
        ((Buffer) buffer).clear();
    }
    dataPointsFile.seek(currentOffset);
    dataPointsFile.read(buffer.array(), 0, numOfBytes);
    FloatBuffer floatBuffer = buffer.asFloatBuffer();
    DataPoint[] dataPoints = new DataPoint[numOfDataPoints];
    for (int i = 0; i < numOfDataPoints; i++) {
        float mz = floatBuffer.get();
        float intensity = floatBuffer.get();
        dataPoints[i] = new SimpleDataPoint(mz, intensity);
    }
    return dataPoints;
}

Example 20 with DataPoint

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

the class StorableScan method updateValues.

void updateValues() {
    DataPoint[] dataPoints = getDataPoints();
    // find m/z range and base peak
    if (dataPoints.length > 0) {
        basePeak = dataPoints[0];
        mzRange = Range.singleton(dataPoints[0].getMZ());
        double tic = 0;
        for (DataPoint dp : dataPoints) {
            if (dp.getIntensity() > basePeak.getIntensity())
                basePeak = dp;
            mzRange = mzRange.span(Range.singleton(dp.getMZ()));
            tic += dp.getIntensity();
        }
        totalIonCurrent = new Double(tic);
    } else {
        mzRange = Range.singleton(0.0);
        totalIonCurrent = new Double(0);
    }
}