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 ");
}
}
public void PerformTransform(
float backgroundIntensity, float minPeptideIntensity, int maxProcessingTimeMinutes,
ref float[] mzs, ref float[] intensities,
ref ThrashV1Peak[] peaks, ref HornTransformResults[] transformResults,
out bool processingAborted)
{
PercentDone = 0;
processingAborted = false;
var numPoints = mzs.Length;
if (mzs.Length == 0)
{
return;
}
// mzs should be in sorted order
double minMz = mzs[0];
double maxMz = mzs[numPoints - 1];
var mzList = new List <double>(mzs.Select(x => (double)x));
var intensityList = new List <double>(intensities.Select(x => (double)x));
var peakData = new PeakData();
peakData.SetPeaks(peaks);
peakData.MzList = mzList;
peakData.IntensityList = intensityList;
if (IsMZRangeUsed)
{
minMz = MinMZ;
maxMz = MaxMZ;
}
//loads 'currentPeak' with the most intense peak within minMZ and maxMZ
ThrashV1Peak currentPeak;
var found = peakData.GetNextPeak(minMz, maxMz, out currentPeak);
//var fwhm_SN = currentPeak.FWHM;
var transformRecords = new List <HornTransformResults>();
var numTotalPeaks = peakData.GetNumPeaks();
StatusMessage = "Performing Horn Transform on peaks";
var startTime = DateTime.UtcNow;
while (found)
{
var numPeaksLeft = peakData.GetNumUnprocessedPeaks();
PercentDone = 100 * (numTotalPeaks - numPeaksLeft) / numTotalPeaks;
if (PercentDone % 5 == 0)
{
StatusMessage = string.Concat("Done with ", Convert.ToString(numTotalPeaks - numPeaksLeft), " of ",
Convert.ToString(numTotalPeaks), " peaks.");
}
if (currentPeak.Intensity < minPeptideIntensity)
{
break;
}
//--------------------- Transform performed ------------------------------
HornTransformResults transformRecord;
var foundTransform = FindTransform(peakData, ref currentPeak, out transformRecord, backgroundIntensity);
if (foundTransform && transformRecord.ChargeState <= MaxChargeAllowed)
{
if (IsActualMonoMZUsed)
{
//retrieve experimental monoisotopic peak
var monoPeakIndex = transformRecord.IsotopePeakIndices[0];
ThrashV1Peak monoPeak;
peakData.GetPeak(monoPeakIndex, out monoPeak);
//set threshold at 20% less than the expected 'distance' to the next peak
var errorThreshold = 1.003 / transformRecord.ChargeState;
errorThreshold = errorThreshold - errorThreshold * 0.2;
var calcMonoMz = transformRecord.MonoMw / transformRecord.ChargeState + 1.00727638;
if (Math.Abs(calcMonoMz - monoPeak.Mz) < errorThreshold)
{
transformRecord.MonoMw = monoPeak.Mz * transformRecord.ChargeState -
1.00727638 * transformRecord.ChargeState;
}
}
transformRecords.Add(transformRecord);
}
if (DateTime.UtcNow.Subtract(startTime).TotalMinutes > maxProcessingTimeMinutes)
{
processingAborted = true;
found = false;
}
else
{
found = peakData.GetNextPeak(minMz, maxMz, out currentPeak);
}
}
PercentDone = 100;
// Done with the transform. Lets copy them all to the given memory structure.
//Console.WriteLine("Done with Mass Transform. Found " + transformRecords.Count + " features");
transformResults = transformRecords.ToArray();
PercentDone = 100;
}
