/// <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); }