/// <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);
}
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;
}
