Example #1
0
  public DataPoint[] getMassValues(Scan scan, String job, ParameterSet parameters) {

    double noiseLevel = parameters.getParameter(ExactMassDetectorParameters.noiseLevel).getValue();

    // Create a tree set of detected mzPeaks sorted by MZ in ascending order
    TreeSet<ExactMzDataPoint> mzPeaks =
        new TreeSet<ExactMzDataPoint>(
            new DataPointSorter(SortingProperty.MZ, SortingDirection.Ascending));

    // Create a tree set of candidate mzPeaks sorted by intensity in
    // descending order.
    TreeSet<ExactMzDataPoint> candidatePeaks =
        new TreeSet<ExactMzDataPoint>(
            new DataPointSorter(SortingProperty.Intensity, SortingDirection.Descending));

    // First get all candidate peaks (local maximum)
    getLocalMaxima(scan, candidatePeaks, noiseLevel);

    // We calculate the exact mass for each peak,
    // starting with biggest intensity peak and so on
    while (candidatePeaks.size() > 0) {

      // Always take the biggest (intensity) peak
      ExactMzDataPoint currentCandidate = candidatePeaks.first();

      // Calculate the exact mass and update value in current candidate
      // (MzPeak)
      double exactMz = calculateExactMass(currentCandidate);
      currentCandidate.setMZ(exactMz);

      // Add this candidate to the final tree set sorted by MZ and remove
      // from tree set sorted by intensity
      mzPeaks.add(currentCandidate);
      candidatePeaks.remove(currentCandidate);
    }

    // Return an array of detected MzPeaks sorted by MZ
    return mzPeaks.toArray(new ExactMzDataPoint[0]);
  }
Example #2
0
  /**
   * This method calculates the exact mass of a peak using the FWHM concept and linear equation (y =
   * mx + b).
   *
   * @param ExactMassDataPoint
   * @return double
   */
  private double calculateExactMass(ExactMzDataPoint currentCandidate) {

    /*
     * According with the FWHM concept, the exact mass of this peak is the
     * half point of FWHM. In order to get the points in the curve that
     * define the FWHM, we use the linear equation.
     *
     * First we look for, in left side of the peak, 2 data points together
     * that have an intensity less (first data point) and bigger (second
     * data point) than half of total intensity. Then we calculate the slope
     * of the line defined by this two data points. At least, we calculate
     * the point in this line that has an intensity equal to the half of
     * total intensity
     *
     * We repeat the same process in the right side.
     */

    double xRight = -1, xLeft = -1;
    double halfIntensity = currentCandidate.getIntensity() / 2;
    DataPoint[] rangeDataPoints = currentCandidate.getRawDataPoints();

    for (int i = 0; i < rangeDataPoints.length - 1; i++) {

      // Left side of the curve
      if ((rangeDataPoints[i].getIntensity() <= halfIntensity)
          && (rangeDataPoints[i].getMZ() < currentCandidate.getMZ())
          && (rangeDataPoints[i + 1].getIntensity() >= halfIntensity)) {

        // First point with intensity just less than half of total
        // intensity
        double leftY1 = rangeDataPoints[i].getIntensity();
        double leftX1 = rangeDataPoints[i].getMZ();

        // Second point with intensity just bigger than half of total
        // intensity
        double leftY2 = rangeDataPoints[i + 1].getIntensity();
        double leftX2 = rangeDataPoints[i + 1].getMZ();

        // We calculate the slope with formula m = Y1 - Y2 / X1 - X2
        double mLeft = (leftY1 - leftY2) / (leftX1 - leftX2);

        // We calculate the desired point (at half intensity) with the
        // linear equation
        // X = X1 + [(Y - Y1) / m ], where Y = half of total intensity
        xLeft = leftX1 + (((halfIntensity) - leftY1) / mLeft);
        continue;
      }

      // Right side of the curve
      if ((rangeDataPoints[i].getIntensity() >= halfIntensity)
          && (rangeDataPoints[i].getMZ() > currentCandidate.getMZ())
          && (rangeDataPoints[i + 1].getIntensity() <= halfIntensity)) {

        // First point with intensity just bigger than half of total
        // intensity
        double rightY1 = rangeDataPoints[i].getIntensity();
        double rightX1 = rangeDataPoints[i].getMZ();

        // Second point with intensity just less than half of total
        // intensity
        double rightY2 = rangeDataPoints[i + 1].getIntensity();
        double rightX2 = rangeDataPoints[i + 1].getMZ();

        // We calculate the slope with formula m = Y1 - Y2 / X1 - X2
        double mRight = (rightY1 - rightY2) / (rightX1 - rightX2);

        // We calculate the desired point (at half intensity) with the
        // linear equation
        // X = X1 + [(Y - Y1) / m ], where Y = half of total intensity
        xRight = rightX1 + (((halfIntensity) - rightY1) / mRight);
        break;
      }
    }

    // We verify the values to confirm we find the desired points. If not we
    // return the same mass value.
    if ((xRight == -1) || (xLeft == -1)) return currentCandidate.getMZ();

    // The center of left and right points is the exact mass of our peak.
    double exactMass = (xLeft + xRight) / 2;

    return exactMass;
  }