/// <summary>
/// calculates the fit score between the theoretical distribution stored and the observed data. Normalizes the observed
/// intensity by specified intensity.
/// </summary>
/// <param name="peakData"> variable which stores the data itself</param>
/// <param name="chargeState"> charge state at which we want to compute the peak.</param>
/// <param name="peak"> peak for which we want to compute the fit function.</param>
/// <param name="mzDelta">specifies the mass delta between theoretical and observed m/z with the best fit so far.</param>
/// <param name="minIntensityForScore">minimum intensity for score</param>
/// <param name="pointsUsed">number of points used</param>
/// <param name="debug">debug output flag</param>
public override double FitScore(PeakData peakData, int chargeState, ThrashV1Peak peak, double mzDelta,
double minIntensityForScore, out int pointsUsed, bool debug = false)
{
pointsUsed = 0;
var numPoints = TheoreticalDistMzs.Count;
if (numPoints < 3)
{
return(1);
}
if (peak.Intensity <= 0)
{
return(1);
}
var maxObservedIntensity = peak.Intensity;
if (maxObservedIntensity <= 0)
{
Console.Error.WriteLine("Peak intensity was <=0 during FitScore. mz = " + peak.Mz +
" , intensity = " + peak.Intensity);
Environment.Exit(1);
}
double fit = 0;
double sum = 0;
for (var pointNum = 0; pointNum < numPoints; pointNum++)
{
var mz = TheoreticalDistMzs[pointNum] + mzDelta;
var theoreticalIntensity = (float)TheoreticalDistIntensities[pointNum];
if (theoreticalIntensity >= minIntensityForScore)
{
// observed intensities have to be normalized so that the maximum intensity is 100,
// like that for theoretical intensities.
var observedIntensity = 100 *
GetPointIntensity(mz, peakData.MzList, peakData.IntensityList) /
maxObservedIntensity;
var intensityDiff = observedIntensity - theoreticalIntensity;
fit += intensityDiff * intensityDiff;
sum += theoreticalIntensity * theoreticalIntensity;
pointsUsed++;
}
}
return(fit / (sum + 0.001));
}
/// <summary>
/// calculates the fit score for a peak against a molecular formula.
/// </summary>
/// <param name="peakData"> variable which stores the data itself</param>
/// <param name="chargeState"> charge state at which we want to compute the peak.</param>
/// <param name="peak"> peak for which we want to compute the fit function.</param>
/// <param name="formula">stores the formula we want to fit.</param>
/// <param name="deleteIntensityThreshold">intensity of least isotope to delete.</param>
/// <param name="minTheoreticalIntensityForScore">minimum intensity of point to consider for scoring purposes.</param>
/// <param name="debug">if debugging output is enabled</param>
public double GetFitScore(PeakData peakData, int chargeState, ThrashV1Peak peak, MolecularFormula formula,
double deleteIntensityThreshold, double minTheoreticalIntensityForScore, bool debug = false)
{
if (chargeState <= 0)
{
Console.WriteLine("Negative value for charge state. " + chargeState);
Environment.Exit(1);
}
if (debug)
{
Console.WriteLine("Getting isotope distribution for formula = " + formula + " mz = " + peak.Mz +
" charge = " + chargeState);
}
var resolution = peak.Mz / peak.FWHM;
IsotopeDistribution.ChargeCarrierMass = ChargeCarrierMass;
IsotopeDistribution.ApType = ApodizationType.Gaussian;
TheoreticalDistIntensities.Clear();
TheoreticalDistMzs.Clear();
IsotopeDistribution.CalculateDistribution(chargeState, resolution, formula, out TheoreticalDistMzs,
out TheoreticalDistIntensities, deleteIntensityThreshold, out IsotopeMzs, out IsotopeIntensities, debug);
var delta = peak.Mz - IsotopeDistribution.MaxPeakMz;
if (debug)
{
Console.WriteLine("Going for first fit");
}
int pointsUsed;
return(FitScore(peakData, chargeState, peak, delta, minTheoreticalIntensityForScore, out pointsUsed,
debug));
}
/// <summary>
/// calculates the fit score between the theoretical distribution stored and the observed data. Normalizes the observed
/// intensity by specified intensity.
/// </summary>
/// <param name="peakData"> variable which stores the data itself</param>
/// <param name="chargeState"> charge state at which we want to compute the peak.</param>
/// <param name="peak"> peak for which we want to compute the fit function.</param>
/// <param name="mzDelta">specifies the mass delta between theoretical and observed m/z with the best fit so far.</param>
/// <param name="minIntensityForScore">minimum intensity for score</param>
/// <param name="pointsUsed">number of points used</param>
/// <param name="debug">debug output flag</param>
public override double FitScore(PeakData peakData, int chargeState, ThrashV1Peak peak, double mzDelta,
double minIntensityForScore, out int pointsUsed, bool debug = false)
{
pointsUsed = 0;
var numPoints = TheoreticalDistMzs.Count;
if (numPoints < 3)
{
return(1);
}
double fit = 0;
double sum = 0;
for (var pointNum = 0; pointNum < numPoints; pointNum++)
{
var mz = TheoreticalDistMzs[pointNum] + mzDelta;
var theoreticalIntensity = TheoreticalDistIntensities[pointNum];
if (theoreticalIntensity >= minIntensityForScore)
{
// observed intensities have to be normalized so that the maximum intensity is 100,
// like that for theoretical intensities.
var observedIntensity = 100 *
GetPointIntensity(mz, peakData.MzList, peakData.IntensityList) /
peak.Intensity;
var intensityDiff = observedIntensity - theoreticalIntensity;
var intensitySum = observedIntensity + theoreticalIntensity;
fit += intensityDiff * intensityDiff / intensitySum;
sum += theoreticalIntensity * observedIntensity;
pointsUsed++;
}
}
return(fit / (sum + 0.001));
}
/// <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);
}
/// <summary>
/// calculates the fit score for a peak.
/// </summary>
/// <param name="peakData"> variable which stores the data itself</param>
/// <param name="chargeState"> charge state at which we want to compute the peak.</param>
/// <param name="peak"> peak for which we want to compute the fit function.</param>
/// <param name="isoRecord">stores the result of the fit.</param>
/// <param name="deleteIntensityThreshold">intensity of least isotope to delete.</param>
/// <param name="minTheoreticalIntensityForScore">minimum intensity of point to consider for scoring purposes.</param>
/// <param name="leftFitStringencyFactor"></param>
/// <param name="rightFitStringencyFactor"></param>
/// <param name="pointsUsed">Number of points used</param>
/// <param name="debug">enable debugging output</param>
/// <remarks>
/// This fitter is used by MassTransform.cpp. It does more than just get a fit score. It first
/// gets a fit score and then slides to the left until the fit score does not improve and then resets
/// to the center point and then slides to the right until the fit score does not improve. Returns the
/// best fit score and fills the isotopic profile (isotopeFitRecord)
/// </remarks>
public double GetFitScore(PeakData peakData, int chargeState, ref ThrashV1Peak peak,
out HornTransformResults isoRecord, double deleteIntensityThreshold, double minTheoreticalIntensityForScore,
double leftFitStringencyFactor, double rightFitStringencyFactor, out int pointsUsed, bool debug = false)
{
isoRecord = new HornTransformResults();
if (chargeState <= 0)
{
Console.WriteLine("Negative value for charge state. " + chargeState);
Environment.Exit(1);
}
//initialize
var peakMass = (peak.Mz - ChargeCarrierMass) * chargeState;
// by now the cc_mass, tag formula and media options in Mercury(Isotope generation)
// should be set.
if (debug)
{
Console.WriteLine("\n\n-------------------- BEGIN TRANSFORM ---------------------------" + chargeState);
Console.WriteLine("Getting isotope distribution for mass = " + peakMass + " mz = " + peak.Mz +
" charge = " + chargeState);
}
var resolution = peak.Mz / peak.FWHM;
// DJ Jan 07 2007: Need to get all peaks down to delete interval so that range of deletion is correct.
//GetIsotopeDistribution(peakMass, chargeState, resolution, TheoreticalDistMzs, TheoreticalDistIntensities,
// deleteIntensityThreshold, debug);
GetIsotopeDistribution(peakMass, chargeState, resolution, out TheoreticalDistMzs,
out TheoreticalDistIntensities, deleteIntensityThreshold, debug);
var theorPeakData = GetTheoreticalIsotopicDistributionPeakList(TheoreticalDistMzs,
TheoreticalDistIntensities);
var numpeaks = theorPeakData.GetNumPeaks();
if (debug)
{
Console.WriteLine("---------------------------------------- THEORETICAL PEAKS ------------------");
Console.WriteLine("Theoretical peak\t" + "Index\t" + "MZ\t" + "Intensity\t" + "FWHM\t" + "SigNoise");
for (var i = 0; i < numpeaks; i++)
{
ThrashV1Peak theorpeak;
theorPeakData.GetPeak(i, out theorpeak);
Console.WriteLine("Theoretical peak\t" + i + "\t" + theorpeak.Mz + "\t" +
theorpeak.Intensity + "\t" + theorpeak.FWHM + "\t" + theorpeak.SignalToNoiseDbl);
}
Console.WriteLine("----------------------------------- END THEORETICAL PEAKS ------------------");
}
// Anoop April 9 2007: For checking if the distribution does not overlap/link with any other distribution
// Beginnings of deisotoping correction
//bool is_linked = false;
//is_linked = IsIsotopeLinkedDistribution(deleteIntensityThreshold);
var delta = peak.Mz - IsotopeDistribution.MaxPeakMz;
//if(debug)
// System.Console.WriteLine("Going for first fit");
var fit = FitScore(peakData, chargeState, peak, delta, minTheoreticalIntensityForScore, out pointsUsed,
debug);
if (debug)
{
Console.WriteLine("Peak\tPeakIdx\tmz\tintens\tSN\tFWHM\tfit\tdelta");
Console.WriteLine("CENTER\t" + peak.PeakIndex + "\t" + peak.Mz + "\t" + peak.Intensity +
"\t" + peak.SignalToNoiseDbl + "\t" + peak.FWHM + "\t" + fit + "\t" + delta + "\t");
}
if (!UseThrash)
{
isoRecord.Fit = fit;
isoRecord.FitCountBasis = pointsUsed;
isoRecord.Mz = peak.Mz;
isoRecord.AverageMw = IsotopeDistribution.AverageMw + delta * chargeState;
isoRecord.MonoMw = IsotopeDistribution.MonoMw + delta * chargeState;
isoRecord.MostIntenseMw = IsotopeDistribution.MostIntenseMw + delta * chargeState;
isoRecord.DeltaMz = delta;
return(fit);
}
double p1Fit = -1, m1Fit = -1; // [gord]: this seems unused
var mPeak = IsotopeDistribution.MaxPeakMz;
var nextPeak = new ThrashV1Peak();
var bestFit = fit;
var bestFitCountBasis = pointsUsed;
var bestDelta = delta;
//double maxY = peak.mdbl_intensity;
var fitCountBasis = 0;
//------------- Slide to the LEFT --------------------------------------------------
for (var dd = 1.003 / chargeState; dd <= 10.03 / chargeState; dd += 1.003 / chargeState)
{
double mzLeft;
double intensityLeft;
//check for theoretical peak to the right of TheoreticalMaxPeak; store mz and intensity
var foundPeak = FindPeak(mPeak + dd - 0.2 / chargeState, mPeak + dd + 0.2 / chargeState, out mzLeft,
out intensityLeft,
debug);
// if the above theoretical peak was found, look one peak to the LEFT in the Experimental peaklist
if (foundPeak)
{
peakData.FindPeak(peak.Mz - dd - peak.FWHM, peak.Mz - dd + peak.FWHM,
out nextPeak);
}
if (mzLeft > 0 && nextPeak.Mz > 0)
//if there is a theoreticalPeak to the RIGHT of theoreticalMaxPeak AND there is an experimentalPeak to the LEFT of experimentalMaxPeak...
{
delta = peak.Mz - mzLeft;
// essentially, this shifts the theoretical over to the left and gets the delta; then check the fit
var currentPeakCopy = new ThrashV1Peak(peak); // in c++ this copy is created by value;
currentPeakCopy.Intensity = nextPeak.Intensity;
fit = FitScore(peakData, chargeState, currentPeakCopy, delta, minTheoreticalIntensityForScore,
out fitCountBasis, debug);
if (debug)
{
//System.Console.WriteLine(" isotopes. Fit =" + fit + " Charge = " + cs + " Intensity = " + nxt_peak.mdbl_intensity + " delta = " + delta);
Console.WriteLine("LEFT\t" + nextPeak.PeakIndex + "\t" + nextPeak.Mz + "\t" +
nextPeak.Intensity + "\t" + nextPeak.SignalToNoiseDbl + "\t" + nextPeak.FWHM +
"\t" + fit + "\t" + delta);
}
}
else
{
if (debug)
{
Console.WriteLine("LEFT\t" + -1 + "\t" + -1 + "\t" + -1 + "\t" + -1 + "\t" + -1 + "\t" + -1 +
"\t" + -1);
}
fit = bestFit + 1000; // make the fit terrible
}
// TODO: Currently, if fit score is less than best_fit, iteration stops. Future versions should continue attempted fitting if fit was within a specified range of the best fit
// 26th February 2007 Deep Jaitly
/*if (fit <= bestFit)
* {
* if (nextPeak.mdbl_intensity > peak.mdbl_intensity)
* peak.mdbl_intensity = nextPeak.mdbl_intensity;
* maxY = peak.mdbl_intensity;
* bestFit = fit;
* bestDelta = delta;
* }*/
var leftFitFactor = fit / bestFit;
if (leftFitFactor <= leftFitStringencyFactor)
{
if (nextPeak.Intensity > peak.Intensity)
{
peak.Intensity = nextPeak.Intensity;
}
//maxY = peak.mdbl_intensity;
bestFit = fit;
bestFitCountBasis = fitCountBasis;
bestDelta = delta;
}
else
{
if (p1Fit.Equals(-1)) //[gord] what is this doing? Peak1 fit??
{
p1Fit = fit;
}
if (!CompleteFitThrash)
{
break;
}
}
}
//if (debug)
// System.Console.WriteLine("\n---------------- Sliding to the RIGHT -------------------------";
for (var dd = 1.003 / chargeState; dd <= 10.03 / chargeState; dd += 1.003 / chargeState)
{
double mzRight;
double intensityRight;
////check for theoretical peak to the LEFT of TheoreticalMaxPeak; store mz and intensity
var foundPeak = FindPeak(mPeak - dd - 0.2 / chargeState, mPeak - dd + 0.2 / chargeState, out mzRight,
out intensityRight,
debug);
// if the above theoretical peak was found, look one peak to the RIGHT in the Experimental peaklist
if (foundPeak)
{
peakData.FindPeak(peak.Mz + dd - peak.FWHM, peak.Mz + dd + peak.FWHM,
out nextPeak);
}
if (mzRight > 0 && nextPeak.Mz > 0)
{
delta = peak.Mz - mzRight;
var currentPeakCopy = new ThrashV1Peak(peak);
currentPeakCopy.Intensity = nextPeak.Intensity;
fit = FitScore(peakData, chargeState, currentPeakCopy, delta, minTheoreticalIntensityForScore,
out fitCountBasis, debug);
//fit = FitScore(pk_data, cs, nxt_peak.mdbl_intensity, delta);
if (debug)
{
//System.Console.WriteLine(" isotopes. Fit =" + fit + " Charge = " + chargeState + " Intensity = " + nextPeak.mdbl_intensity + " delta = " + delta);
Console.WriteLine("RIGHT\t" + nextPeak.PeakIndex + "\t" + nextPeak.Mz + "\t" +
nextPeak.Intensity + "\t" + nextPeak.SignalToNoiseDbl + "\t" + nextPeak.FWHM +
"\t" + fit + "\t" + delta);
}
}
else
{
fit = bestFit + 1000; //force it to be a bad fit
if (debug)
{
// System.Console.WriteLine("No peak found");
Console.WriteLine("RIGHT\t" + -1 + "\t" + -1 + "\t" + -1 + "\t" + -1 + "\t" + -1 + "\t" + -1 +
"\t" + -1);
}
}
/*if (fit <= bestFit)
* {
* if (nextPeak.mdbl_intensity > peak.mdbl_intensity)
* peak.mdbl_intensity = nextPeak.mdbl_intensity;
* MaxY = peak.mdbl_intensity;
* bestFit = fit;
* bestDelta = delta;
* }*/
var rightFitFactor = fit / bestFit;
if (rightFitFactor <= rightFitStringencyFactor)
{
if (nextPeak.Intensity > peak.Intensity)
{
peak.Intensity = nextPeak.Intensity;
}
//maxY = peak.mdbl_intensity;
bestFit = fit;
bestFitCountBasis = fitCountBasis;
bestDelta = delta;
}
else
{
if (m1Fit.Equals(-1))
{
m1Fit = fit;
}
if (!CompleteFitThrash)
{
break;
}
}
}
//double theorIntensityCutoff = 30; //
//double peakWidth = peak.mdbl_FWHM;
if (debug)
{
Console.WriteLine("Std delta = \t" + bestDelta);
}
//best_delta = CalculateDeltaFromSeveralObservedPeaks(best_delta, peakWidth, pk_data, theorPeakData, theorIntensityCutoff);
if (debug)
{
Console.WriteLine("Weighted delta = \t" + bestDelta);
}
isoRecord.Fit = bestFit;
isoRecord.FitCountBasis = bestFitCountBasis;
isoRecord.ChargeState = chargeState;
isoRecord.Mz = peak.Mz;
isoRecord.DeltaMz = bestDelta;
isoRecord.AverageMw = IsotopeDistribution.AverageMw + bestDelta * chargeState;
isoRecord.MonoMw = IsotopeDistribution.MonoMw + bestDelta * chargeState;
isoRecord.MostIntenseMw = IsotopeDistribution.MostIntenseMw + bestDelta * chargeState;
//iso_record.mbln_flag_isotope_link = is_linked;
pointsUsed = bestFitCountBasis;
return(bestFit);
}
/// <summary>
/// calculates the fit score between the theoretical distribution stored and the observed data. Normalizes the observed
/// intensity by specified intensity.
/// </summary>
/// <param name="peakData"> variable which stores the data itself</param>
/// <param name="chargeState"> charge state at which we want to compute the peak.</param>
/// <param name="peak"> peak for which we want to compute the fit function.</param>
/// <param name="mzDelta">specifies the mass delta between theoretical and observed m/z with the best fit so far.</param>
/// <param name="minIntensityForScore">minimum intensity for score</param>
/// <param name="pointsUsed">number of points used</param>
/// <param name="debug">debug output flag</param>
public abstract double FitScore(PeakData peakData, int chargeState, ThrashV1Peak peak, double mzDelta,
double minIntensityForScore, out int pointsUsed, bool debug = false);
private void SetIsotopeDistributionToZero(PeakData peakData, ThrashV1Peak peak, double zeroingStartMz,
double zeroingStopMz, double monoMw, int chargeState, bool clearSpectrum, HornTransformResults record,
bool debug = false)
{
var peakIndices = new List <int>();
peakIndices.Add(peak.PeakIndex);
var mzDelta = record.DeltaMz;
if (debug)
{
Console.Error.WriteLine("Clearing peak data for " + peak.Mz + " Delta = " + mzDelta);
Console.Error.WriteLine("Zeroing range = " + zeroingStartMz + " to " + zeroingStopMz);
}
double maxMz = 0;
if (IsO16O18Data)
{
maxMz = (monoMw + 3.5) / chargeState + ChargeCarrierMass;
}
var numUnprocessedPeaks = peakData.GetNumUnprocessedPeaks();
if (numUnprocessedPeaks == 0)
{
record.IsotopePeakIndices.Add(peak.PeakIndex);
return;
}
if (clearSpectrum)
{
if (debug)
{
Console.Error.WriteLine("Deleting main peak :" + peak.Mz);
}
SetPeakToZero(peak.DataIndex, ref peakData.IntensityList, ref peakData.MzList, debug);
}
peakData.RemovePeaks(peak.Mz - peak.FWHM, peak.Mz + peak.FWHM, debug);
if (1 / (peak.FWHM * chargeState) < 3) // gord: ??
{
record.IsotopePeakIndices.Add(peak.PeakIndex);
peakData.RemovePeaks(zeroingStartMz, zeroingStopMz, debug);
return;
}
// Delete isotopes of mzs higher than mz of starting isotope
for (var peakMz = peak.Mz + 1.003 / chargeState;
(!IsO16O18Data || peakMz <= maxMz) && peakMz <= zeroingStopMz + 2 * peak.FWHM;
peakMz += 1.003 / chargeState)
{
if (debug)
{
Console.Error.WriteLine("\tFinding next peak top from " + (peakMz - 2 * peak.FWHM) + " to " +
(peakMz + 2 * peak.FWHM) + " pk = " + peakMz + " FWHM = " + peak.FWHM);
}
ThrashV1Peak nextPeak;
peakData.GetPeakFromAll(peakMz - 2 * peak.FWHM, peakMz + 2 * peak.FWHM, out nextPeak);
if (nextPeak.Mz.Equals(0))
{
if (debug)
{
Console.Error.WriteLine("\t\tNo peak found.");
}
break;
}
if (debug)
{
Console.Error.WriteLine("\t\tFound peak to delete =" + nextPeak.Mz);
}
// Before assuming that the next peak is indeed an isotope, we must check for the height of this
// isotope. If the height is greater than expected by a factor of 3, lets not delete it.
peakIndices.Add(nextPeak.PeakIndex);
SetPeakToZero(nextPeak.DataIndex, ref peakData.IntensityList, ref peakData.MzList, debug);
peakData.RemovePeaks(nextPeak.Mz - peak.FWHM, nextPeak.Mz + peak.FWHM, debug);
peakMz = nextPeak.Mz;
}
// Delete isotopes of mzs lower than mz of starting isotope
// TODO: Use the delta m/z to make sure to remove 1- peaks from the unprocessed list, but not from the list of peaks?
for (var peakMz = peak.Mz - 1.003 / chargeState;
peakMz > zeroingStartMz - 2 * peak.FWHM;
peakMz -= 1.003 / chargeState)
{
if (debug)
{
Console.Error.WriteLine("\tFinding previous peak top from " + (peakMz - 2 * peak.FWHM) + " to " +
(peakMz + 2 * peak.FWHM) + " pk = " + peakMz + " FWHM = " + peak.FWHM);
}
ThrashV1Peak nextPeak;
peakData.GetPeakFromAll(peakMz - 2 * peak.FWHM, peakMz + 2 * peak.FWHM, out nextPeak);
if (nextPeak.Mz.Equals(0))
{
if (debug)
{
Console.Error.WriteLine("\t\tNo peak found.");
}
break;
}
if (debug)
{
Console.Error.WriteLine("\t\tFound peak to delete =" + nextPeak.Mz);
}
peakIndices.Add(nextPeak.PeakIndex);
SetPeakToZero(nextPeak.DataIndex, ref peakData.IntensityList, ref peakData.MzList, debug);
peakData.RemovePeaks(nextPeak.Mz - peak.FWHM, nextPeak.Mz + peak.FWHM, debug);
peakMz = nextPeak.Mz;
}
if (debug)
{
Console.Error.WriteLine("Done Clearing peak data for " + peak.Mz);
}
peakIndices.Sort();
// now insert into array.
var numPeaksObserved = peakIndices.Count;
var numIsotopesObserved = 0;
var lastIsotopeNumObserved = int.MinValue;
for (var i = 0; i < numPeaksObserved; i++)
{
var currentIndex = peakIndices[i];
var currentPeak = new ThrashV1Peak(peakData.PeakTops[currentIndex]);
var isotopeNum = (int)(Math.Abs((currentPeak.Mz - peak.Mz) * chargeState / 1.003) + 0.5);
if (currentPeak.Mz < peak.Mz)
{
isotopeNum = -1 * isotopeNum;
}
if (isotopeNum > lastIsotopeNumObserved)
{
lastIsotopeNumObserved = isotopeNum;
numIsotopesObserved++;
if (numIsotopesObserved > MaxIsotopes)
{
break;
}
record.IsotopePeakIndices.Add(peakIndices[i]);
}
else
{
record.IsotopePeakIndices[numIsotopesObserved - 1] = peakIndices[i];
}
}
if (debug)
{
Console.Error.WriteLine("Copied " + record.NumIsotopesObserved + " isotope peak indices into record ");
}
}
protected virtual bool FindTransform(PeakData peakData, ref ThrashV1Peak peak, out HornTransformResults record,
double backgroundIntensity = 0)
{
SetIsotopeFitScorerOptions();
record = new HornTransformResults();
if (peak.SignalToNoiseDbl < MinSignalToNoise || peak.FWHM.Equals(0))
{
return(false);
}
//var resolution = peak.Mz / peak.FWHM;
/**/
var chargeState = AutoCorrelationChargeDetermination.GetChargeState(peak, peakData, ShowTraceMessages);
/*/
* // This chunk of code tries to use the DeconTools Patterson Algorithm Charge State Calculator, but it gets vastly different results.
* var xyData = new XYData();
* var mzArray = peakData.MzList.ToArray();
* var intensityArray = peakData.IntensityList.ToArray();
* xyData.SetXYValues(ref mzArray, ref intensityArray);
* var peakList = new List<Peak>();
* for (int i = 0; i < peakData.MzList.Count; i++)
* {
* peakList.Add(new Peak(peakData.MzList[i], (float)peakData.IntensityList[i], 1));
* }
* var chargeState = DeconTools.Backend.Algorithms.ChargeStateDetermination.PattersonAlgorithm.PattersonChargeStateCalculator.GetChargeState(xyData, peakList, convertDeconPeakToMSPeak(peak));
* /**/
if (chargeState == -1 && CheckPatternsAgainstChargeOne)
{
chargeState = 1;
}
if (ShowTraceMessages)
{
Console.Error.WriteLine("Deisotoping :" + peak.Mz);
Console.Error.WriteLine("Charge = " + chargeState);
}
if (chargeState == -1)
{
return(false);
}
if ((peak.Mz + ChargeCarrierMass) * chargeState > MaxMWAllowed)
{
return(false);
}
if (IsO16O18Data)
{
if (peak.FWHM < 1.0 / chargeState)
{
// move back by 4 Da and see if there is a peak.
var minMz = peak.Mz - 4.0 / chargeState - peak.FWHM;
var maxMz = peak.Mz - 4.0 / chargeState + peak.FWHM;
ThrashV1Peak o16Peak;
var found = peakData.GetPeak(minMz, maxMz, out o16Peak);
if (found && !o16Peak.Mz.Equals(peak.Mz))
{
// put back the current into the to be processed list of peaks.
peakData.AddPeakToProcessingList(peak);
// reset peak to the right peak so that the calling function may
// know that the peak might have changed in the O16/O18 business
peak = o16Peak;
peakData.RemovePeak(peak);
return(FindTransform(peakData, ref peak, out record, backgroundIntensity));
}
}
}
var peakCharge1 = new ThrashV1Peak(peak);
// Until now, we have been using constant theoretical delete intensity threshold..
// instead, from now, we should use one that is proportional to intensity, for more intense peaks.
// However this will not solve all problems. If thrashing occurs, then the peak intensity will
// change when the function returns and we may not delete far enough.
//double deleteThreshold = backgroundIntensity / peak.Intensity * 100;
//if (backgroundIntensity ==0 || deleteThreshold > _deleteIntensityThreshold)
// deleteThreshold = _deleteIntensityThreshold;
var deleteThreshold = DeleteIntensityThreshold;
int fitCountBasis;
var bestFit = _isotopeFitScorer.GetFitScore(peakData, chargeState, ref peak, out record, deleteThreshold,
MinIntensityForScore, LeftFitStringencyFactor, RightFitStringencyFactor, out fitCountBasis,
ShowTraceMessages);
// When deleting an isotopic profile, this value is set to the first m/z to perform deletion at.
double zeroingStartMz;
// When deleting an isotopic profile, this value is set to the last m/z to perform deletion at.
double zeroingStopMz;
_isotopeFitScorer.GetZeroingMassRange(out zeroingStartMz, out zeroingStopMz, record.DeltaMz, deleteThreshold,
ShowTraceMessages);
//bestFit = _isotopeFitter.GetFitScore(peakData, chargeState, peak, record, _deleteIntensityThreshold, _minTheoreticalIntensityForScore, DebugFlag);
//_isotopeFitter.GetZeroingMassRange(_zeroingStartMz, _zeroingStopMz, record.DeltaMz, _deleteIntensityThreshold, DebugFlag);
if (CheckPatternsAgainstChargeOne && chargeState != 1)
{
HornTransformResults recordCharge1;
int fitCountBasisCharge1;
var bestFitCharge1 = _isotopeFitScorer.GetFitScore(peakData, 1, ref peakCharge1, out recordCharge1,
deleteThreshold, MinIntensityForScore, LeftFitStringencyFactor,
RightFitStringencyFactor, out fitCountBasisCharge1, ShowTraceMessages);
//double bestFitCharge1 = _isotopeFitter.GetFitScore(peakData, 1, peakCharge1, recordCharge1, _deleteIntensityThreshold, _minTheoreticalIntensityForScore, DebugFlag);
//_isotopeFitter.GetZeroingMassRange(_zeroingStartMz, _zeroingStopMz, record.DeltaMz, _deleteIntensityThreshold, DebugFlag);
double startMz1 = 0;
double stopMz1 = 0;
_isotopeFitScorer.GetZeroingMassRange(out startMz1, out stopMz1, record.DeltaMz, deleteThreshold,
ShowTraceMessages);
if (bestFit > MaxFitAllowed && bestFitCharge1 < MaxFitAllowed)
{
bestFit = bestFitCharge1;
fitCountBasis = fitCountBasisCharge1;
peak = peakCharge1;
record = new HornTransformResults(recordCharge1);
zeroingStartMz = startMz1;
zeroingStopMz = stopMz1;
chargeState = 1;
}
}
if (bestFit > MaxFitAllowed) // check if fit is good enough
{
return(false);
}
if (ShowTraceMessages)
{
Console.Error.WriteLine("\tBack with fit = " + record.Fit);
}
// Applications using this DLL should use Abundance instead of AbundanceInt
record.Abundance = peak.Intensity;
record.ChargeState = chargeState;
ThrashV1Peak monoPeak;
var monoMz = record.MonoMw / record.ChargeState + ChargeCarrierMass;
// used when _reportO18Plus2Da is true.
ThrashV1Peak m3Peak;
var monoPlus2Mz = record.MonoMw / record.ChargeState + 2.0 / record.ChargeState + ChargeCarrierMass;
peakData.FindPeak(monoMz - peak.FWHM, monoMz + peak.FWHM, out monoPeak);
peakData.FindPeak(monoPlus2Mz - peak.FWHM, monoPlus2Mz + peak.FWHM, out m3Peak);
record.MonoIntensity = (int)monoPeak.Intensity;
record.MonoPlus2Intensity = (int)m3Peak.Intensity;
record.SignalToNoise = peak.SignalToNoiseDbl;
record.FWHM = peak.FWHM;
record.PeakIndex = peak.PeakIndex;
SetIsotopeDistributionToZero(peakData, peak, zeroingStartMz, zeroingStopMz, record.MonoMw, chargeState, true,
record, ShowTraceMessages);
if (ShowTraceMessages)
{
Console.Error.WriteLine("Performed deisotoping of " + peak.Mz);
}
return(true);
}
/// <summary>
/// calculates the fit score between the theoretical distribution stored and the observed data. Normalizes the observed
/// intensity by specified intensity.
/// </summary>
/// <param name="peakData"> variable which stores the data itself</param>
/// <param name="chargeState"> charge state at which we want to compute the peak.</param>
/// <param name="peak"> peak for which we want to compute the fit function.</param>
/// <param name="mzDelta">specifies the mass delta between theoretical and observed m/z with the best fit so far.</param>
/// <param name="minIntensityForScore">minimum intensity for score</param>
/// <param name="pointsUsed">number of points used</param>
/// <param name="debug">debug output flag</param>
public override double FitScore(PeakData peakData, int chargeState, ThrashV1Peak peak, double mzDelta,
double minIntensityForScore, out int pointsUsed, bool debug = false)
{
pointsUsed = 0;
var numPoints = TheoreticalDistMzs.Count;
if (numPoints < 3)
{
return(1);
}
double fit = 0;
double sum = 0;
double lastYVal = 0;
double diff = 0;
for (var pointNum = 0; pointNum < numPoints; pointNum++)
{
var mz = TheoreticalDistMzs[pointNum] + mzDelta;
var theoreticalIntensity = TheoreticalDistIntensities[pointNum];
// observed intensities have to be normalized so that the maximum intensity is 100,
if (theoreticalIntensity >= minIntensityForScore && diff >= 0 && theoreticalIntensity < lastYVal)
{
var found = false;
ThrashV1Peak foundPeak;
// remember you might be searching for the current peak (which has already been
// taken out of the list of peaks. So first check it.
if (Math.Abs(peak.Mz - mz) < 2 * peak.FWHM)
{
found = true;
foundPeak = peak;
}
else
{
peakData.FindPeak(mz - peak.FWHM, mz + peak.FWHM, out foundPeak);
if (foundPeak.Mz > 0)
{
found = true;
}
}
if (found)
{
var observedIntensity = 100 * foundPeak.Intensity / peak.Intensity;
var intensityDiff = observedIntensity - theoreticalIntensity;
var intensityAvg = (observedIntensity + theoreticalIntensity) / 2;
fit += intensityDiff * intensityDiff;
sum += intensityAvg * intensityAvg;
}
else
{
fit += theoreticalIntensity * theoreticalIntensity;
sum += theoreticalIntensity * theoreticalIntensity;
}
pointsUsed++;
}
diff = theoreticalIntensity - lastYVal;
lastYVal = theoreticalIntensity;
}
return(fit / (sum + 0.001));
}
