/// <summary>
/// Gets the charge state (determined by AutoCorrelation algorithm) for a peak in some data.
/// </summary>
/// <param name="peak">is the peak whose charge we want to detect.</param>
/// <param name="peakData">is the PeakData object containing raw data, peaks, etc which are used in the process.</param>
/// <param name="debug"></param>
/// <returns>Returns the charge of the feature.</returns>
public static int GetChargeState(ThrashV1Peak peak, PeakData peakData, bool debug)
{
var minus = 0.1;
var plus = 1.1; // right direction to look
var startIndex = PeakIndex.GetNearest(peakData.MzList, peak.Mz - peak.FWHM - minus, peak.DataIndex);
var stopIndex = PeakIndex.GetNearest(peakData.MzList, peak.Mz + peak.FWHM + plus, peak.DataIndex);
var numPts = stopIndex - startIndex;
var numL = numPts;
if (numPts < 5)
{
return(-1);
}
if (numPts < 256)
{
numL = 10 * numPts;
}
// TODO: PattersonChargeStateCalculator does a lot of funny stuff around here.
// variable to help us perform spline interpolation.
// count is stopIndex - startIndex + 1 because we need to include the values at stopIndex as well
// NOTE: This output is different from what the DeconEngineV2 code outputs; there are notes in that code
// wondering if there was a bug in the previous implementation imported from VB, of starting at startIndex + 1.
// That code performed interpolation on the range from startIndex + 1 to stopIndex, inclusive, and minMz set to PeakData.MzList[startIndex + 1].
// This code can produce output that more closely matches the DeconEngineV2 output by using
// "startIndex, stopIndex - startIndex + 2" as the parameters to "GetRange()", and setting minMz to PeakData.MzList[startIndex + 1].
// Since using startIndex and stopIndex directly produces output that mostly differs on fit score by a small amount,
// we are changing this code to use them.
var interpolator = CubicSpline.InterpolateNaturalSorted(
peakData.MzList.GetRange(startIndex, stopIndex - startIndex + 1).ToArray(),
peakData.IntensityList.GetRange(startIndex, stopIndex - startIndex + 1).ToArray());
var minMz = peakData.MzList[startIndex];
var maxMz = peakData.MzList[stopIndex];
// List to store the interpolated intensities of the region on which we performed the cubic spline interpolation.
var iv = new List <double>(numL);
for (var i = 0; i < numL; i++)
{
var xVal = minMz + (maxMz - minMz) * i / numL;
var fVal = interpolator.Interpolate(xVal);
iv.Add(fVal);
}
if (debug)
{
Console.Error.WriteLine("mz,intensity");
for (var i = 0; i < numL; i++)
{
var xVal = minMz + (maxMz - minMz) * i / numL;
Console.Error.WriteLine(xVal + "," + iv[i]);
}
}
// List to store the auto correlation values at the points in the region.
var autoCorrelationScores = ACss(iv.ToArray());
if (debug)
{
Console.Error.WriteLine("AutoCorrelation values");
for (var i = 0; i < autoCorrelationScores.Count; i++)
{
var score = autoCorrelationScores[i];
Console.Error.WriteLine((maxMz - minMz) * i / numL + "," + score);
}
}
var minN = 0;
while (minN < numL - 1 && autoCorrelationScores[minN] > autoCorrelationScores[minN + 1])
{
minN++;
}
var success = HighestChargeStatePeak(minMz, maxMz, minN, autoCorrelationScores, MaxCharge, out var bestAcScore, out _);
if (!success)
{
return(-1); // Didn't find anything
}
// List to temporarily store charge list. These charges are calculated at peak values of auto correlation.
// Now go back through the CS peaks and make a list of all CS that are at least 10% of the highest
var charges = GenerateChargeStates(minMz, maxMz, minN, autoCorrelationScores, MaxCharge, bestAcScore);
// Get the final CS value to be returned
var returnChargeStateVal = -1;
// TODO: PattersonChargeStateCalculator really doesn't match the following code.
var fwhm = peak.FWHM; // Store a copy of the FWHM to avoid modifying the actual value
if (fwhm > 0.1)
{
fwhm = 0.1;
}
for (var i = 0; i < charges.Count; i++)
{
// no point retesting previous charge.
var tempChargeState = charges[i];
var skip = false;
for (var j = 0; j < i; j++)
{
if (charges[j] == tempChargeState)
{
skip = true;
break;
}
}
if (skip)
{
continue;
}
if (tempChargeState > 0)
{
var peakA = peak.Mz + 1.0 / tempChargeState;
var found = peakData.GetPeakFromAllOriginalIntensity(peakA - fwhm, peakA + fwhm, out var isoPeak);
if (found)
{
returnChargeStateVal = tempChargeState;
if (isoPeak.Mz * tempChargeState < 3000)
{
break;
}
// if the mass is greater than 3000, lets make sure that multiple isotopes exist.
peakA = peak.Mz - 1.03 / tempChargeState;
found = peakData.GetPeakFromAllOriginalIntensity(peakA - fwhm, peakA + fwhm, out isoPeak);
if (found)
{
return(tempChargeState);
}
}
else
{
peakA = peak.Mz - 1.0 / tempChargeState;
found = peakData.GetPeakFromAllOriginalIntensity(peakA - fwhm, peakA + fwhm, out isoPeak);
if (found && isoPeak.Mz * tempChargeState < 3000)
{
return(tempChargeState);
}
}
}
}
return(returnChargeStateVal);
}