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]);
}
/**
* 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;
}