public virtual object Clone()
{
var result = new clsHornTransformResults
{
PeakIndex = PeakIndex,
ScanNum = ScanNum,
ChargeState = ChargeState,
Abundance = Abundance,
Mz = Mz,
Fit = Fit,
FitCountBasis = FitCountBasis,
AverageMw = AverageMw,
MonoMw = MonoMw,
MostIntenseMw = MostIntenseMw,
FWHM = FWHM,
SignalToNoise = SignalToNoise,
MonoIntensity = MonoIntensity,
MonoPlus2Intensity = MonoPlus2Intensity,
DeltaMz = DeltaMz,
IsotopePeakIndices = new List <int>(IsotopePeakIndices)
};
//result.AbundanceInt = this.AbundanceInt;
return(result);
}
public clsHornTransformResults(clsHornTransformResults a)
{
PeakIndex = a.PeakIndex;
ScanNum = a.ScanNum;
ChargeState = a.ChargeState;
Abundance = a.Abundance;
Mz = a.Mz;
Fit = a.Fit;
FitCountBasis = a.FitCountBasis;
AverageMw = a.AverageMw;
MonoMw = a.MonoMw;
MostIntenseMw = a.MostIntenseMw;
FWHM = a.FWHM;
SignalToNoise = a.SignalToNoise;
MonoIntensity = a.MonoIntensity;
MonoPlus2Intensity = a.MonoPlus2Intensity;
DeltaMz = a.DeltaMz;
IsotopePeakIndices = new List <int>(a.IsotopePeakIndices);
}
private void SetIsotopeDistributionToZero(PeakData peakData, clsPeak peak, double zeroingStartMz,
double zeroingStopMz, double monoMw, int chargeState, bool clearSpectrum, clsHornTransformResults 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 (TransformParameters.O16O18Media)
{
maxMz = (monoMw + 3.5) / chargeState + TransformParameters.CCMass;
}
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;
(!TransformParameters.O16O18Media || 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);
}
clsPeak 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);
}
clsPeak 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 clsPeak(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 ");
}
}
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);
}
