/// <summary>
/// will calculate the delta mz (referenced to the theor) based on several of the observed peaks
/// </summary>
/// <param name="startingDelta"></param>
/// <param name="peakWidth"></param>
/// <param name="obsPeakData"></param>
/// <param name="theorPeakData"></param>
/// <param name="theorIntensityCutOff"></param>
/// <returns></returns>
public double CalculateDeltaFromSeveralObservedPeaks(double startingDelta, double peakWidth,
PeakData obsPeakData, PeakData theorPeakData, double theorIntensityCutOff)
{
//the idea is to use a selected number of theor peaks
//and for each theor peak, use the delta (mz offset) info
//to find the obs peak data and determine the delta value for that peak.
//accumulate delta values in an array and then calculate a weighted average
var numTheorPeaks = theorPeakData.GetNumPeaks();
var filteredTheorPeakData = new PeakData();
//filter the theor list
var numFilteredTheorPeaks = 0;
for (var i = 0; i < numTheorPeaks; i++)
{
ThrashV1Peak peak;
theorPeakData.GetPeak(i, out peak);
if (peak.Intensity >= theorIntensityCutOff)
{
filteredTheorPeakData.AddPeak(peak);
numFilteredTheorPeaks++;
}
}
if (numFilteredTheorPeaks == 0)
{
return(startingDelta);
}
var deltaArray = new double[numFilteredTheorPeaks];
var intensityArray = new double[numFilteredTheorPeaks];
double intensitySum = 0;
//double weightedSumOfDeltas = 0;
for (var i = 0; i < numFilteredTheorPeaks; i++)
{
ThrashV1Peak theorPeak;
filteredTheorPeakData.GetPeak(i, out theorPeak);
var targetMzLower = theorPeak.Mz + startingDelta - peakWidth;
var targetMzUpper = theorPeak.Mz + startingDelta + peakWidth;
ThrashV1Peak foundPeak;
obsPeakData.FindPeak(targetMzLower, targetMzUpper, out foundPeak);
if (foundPeak.Mz > 0)
{
deltaArray[i] = foundPeak.Mz - theorPeak.Mz;
intensityArray[i] = foundPeak.Intensity;
intensitySum += foundPeak.Intensity;
}
else
{
deltaArray[i] = startingDelta;
intensityArray[i] = 0;
//obs peak was not found; therefore assign 0 intensity (will have no effect on delta calc)
}
}
if (intensitySum.Equals(0))
{
return(startingDelta); // no obs peaks found at all; return default
}
//now perform a weighted average
double weightedDelta = 0;
for (var i = 0; i < numFilteredTheorPeaks; i++)
{
weightedDelta += intensityArray[i] / intensitySum * deltaArray[i];
}
return(weightedDelta);
}
/// <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 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));
}
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);
}
public virtual bool FindTransform(PeakData peakData, ref clsPeak peak, out clsHornTransformResults record,
double backgroundIntensity = 0)
{
record = new clsHornTransformResults();
if (peak.SignalToNoise < TransformParameters.MinS2N || peak.FWHM.Equals(0))
{
return(false);
}
//var resolution = peak.Mz / peak.FWHM;
var chargeState = AutoCorrelationChargeDetermination.GetChargeState(peak, peakData, DebugFlag);
if (chargeState == -1 && TransformParameters.CheckAllPatternsAgainstCharge1)
{
chargeState = 1;
}
if (DebugFlag)
{
Console.Error.WriteLine("Deisotoping :" + peak.Mz);
Console.Error.WriteLine("Charge = " + chargeState);
}
if (chargeState == -1)
{
return(false);
}
if ((peak.Mz + TransformParameters.CCMass) * chargeState > TransformParameters.MaxMW)
{
return(false);
}
if (TransformParameters.O16O18Media)
{
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;
clsPeak 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 clsPeak(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 = TransformParameters.DeleteIntensityThreshold;
int fitCountBasis;
var bestFit = TransformParameters.IsotopeFitScorer.GetFitScore(peakData, chargeState, ref peak, out record, deleteThreshold,
TransformParameters.MinIntensityForScore, TransformParameters.LeftFitStringencyFactor, TransformParameters.RightFitStringencyFactor, out fitCountBasis,
DebugFlag);
// 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;
TransformParameters.IsotopeFitScorer.GetZeroingMassRange(out zeroingStartMz, out zeroingStopMz, record.DeltaMz, deleteThreshold,
DebugFlag);
//bestFit = _isotopeFitter.GetFitScore(peakData, chargeState, peak, record, _deleteIntensityThreshold, _minTheoreticalIntensityForScore, DebugFlag);
//_isotopeFitter.GetZeroingMassRange(_zeroingStartMz, _zeroingStopMz, record.DeltaMz, _deleteIntensityThreshold, DebugFlag);
if (TransformParameters.CheckAllPatternsAgainstCharge1 && chargeState != 1)
{
clsHornTransformResults recordCharge1;
int fitCountBasisCharge1;
var bestFitCharge1 = TransformParameters.IsotopeFitScorer.GetFitScore(peakData, 1, ref peakCharge1, out recordCharge1,
deleteThreshold, TransformParameters.MinIntensityForScore, TransformParameters.LeftFitStringencyFactor,
TransformParameters.RightFitStringencyFactor, out fitCountBasisCharge1, DebugFlag);
//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;
TransformParameters.IsotopeFitScorer.GetZeroingMassRange(out startMz1, out stopMz1, record.DeltaMz, deleteThreshold, DebugFlag);
if (bestFit > TransformParameters.MaxFit && bestFitCharge1 < TransformParameters.MaxFit)
{
bestFit = bestFitCharge1;
fitCountBasis = fitCountBasisCharge1;
peak = peakCharge1;
record = new clsHornTransformResults(recordCharge1);
zeroingStartMz = startMz1;
zeroingStopMz = stopMz1;
chargeState = 1;
}
}
if (bestFit > TransformParameters.MaxFit) // check if fit is good enough
{
return(false);
}
if (DebugFlag)
{
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;
clsPeak monoPeak;
var monoMz = record.MonoMw / record.ChargeState + TransformParameters.CCMass;
// used when _reportO18Plus2Da is true.
clsPeak m3Peak;
var monoPlus2Mz = record.MonoMw / record.ChargeState + 2.0 / record.ChargeState + TransformParameters.CCMass;
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.SignalToNoise;
record.FWHM = peak.FWHM;
record.PeakIndex = peak.PeakIndex;
SetIsotopeDistributionToZero(peakData, peak, zeroingStartMz, zeroingStopMz, record.MonoMw, chargeState, true,
record, DebugFlag);
if (DebugFlag)
{
Console.Error.WriteLine("Performed deisotoping of " + peak.Mz);
}
return(true);
}
