public Peak(LCTrace Trace, int ApexIndex, int LeftIndex, int RightIndex)
{
this.Trace = Trace;
this.Apex = ApexIndex;
this.LeftIndex = Math.Min(LeftIndex, RightIndex);
this.RightIndex = Math.Max(LeftIndex, RightIndex);
Left = Trace.Group.Points[LeftIndex].RT;
Right = Trace.Group.Points[RightIndex].RT;
Apex = Trace.Group.Points[ApexIndex].RT;
ApexMass = Trace.Group.Points[ApexIndex].Mass;
ApexIntensity = Trace.Group.Points[ApexIndex].Intensity;
}
public void ApplyPeak(Peak P, LCTrace Trace)
{
MZData thisPoint = null;
MZData TracePoint = null;
double MSum = 0.0;
double ISum = 0.0;
double aSum = 0.0;
double bSum = 0.0;
for (int i = Trace.Group.Points[P.LeftIndex].Scan; i <= Trace.Group.Points[P.RightIndex].Scan; i++)
{
thisPoint = PointForScan(i);
TracePoint = Trace.PointForScan(i);
MSum += thisPoint == null ? 0.0 : thisPoint.Mass * thisPoint.Intensity * thisPoint.TimeCoeff;
ISum += thisPoint == null ? 0.0 : thisPoint.Intensity;
aSum += (thisPoint != null && TracePoint != null)?thisPoint.Intensity:0.0;
bSum += (thisPoint != null && TracePoint != null)?TracePoint.Intensity:0.0;
}
PeakTotal = ISum;
PeakMeanMass = ISum != 0.0 ? MSum / ISum : 0.0;
PeakRatio = bSum != 0.0 ? aSum / bSum : 0.0;
}
/**
* Wavelet-based peak detection.
* Returns a list of peaks in this chromatogram satisfying the given criteria
* Here min and max peak width are given in the units of scan time.
* (Note that this assumes scans are even in time.)
*/
public TracePeaks(LCTrace Trace)
{
this.Trace = Trace;
}
static Feature FeatureForTarget(Target T, MZData P)
{
Feature F = new Feature();
T.Feature = F;
F.Target = T;
//Monoisotopic trace
MZData Apex = null;
Apex = P;
if (Apex == null)
{
return(null);
}
F.MainTrace = LCTrace.CreateTrace(RawFileService.GroupFromPoint(Apex), Apex);//main for untargeted analysis
//? gapped for main trace
if (F.MainTrace == null)
{
return(null);
}
F.MainTrace.Attribution = "C0N0";
double RTStart = F.MainTrace.Group.Points[0].RT;
double RTEnd = F.MainTrace.Group.Points[F.MainTrace.Group.Points.Count - 1].RT;
//Check if Apex outside of RT Window
if (F.MainTrace.Apex.RT < T.RTMin || F.MainTrace.Apex.RT > T.RTMax)
{
F.MainApexOutsideRtWindow = true;
}
F.TPeaks = new TracePeaks(F.MainTrace);
F.TPeaks.waveletPeakDetection(PeakMinWidth, PeakMaxWidth, PeakMinIntensity, PeakbaselineRatio);
F.TPeaks.SelectClosestAsTarget(F.Target);
//End of monotrace
F.HasPrevIsotope = false;
//End of preisotopes
//Checks for isotopic peaks
F.Isotopes = new LCTrace[T.C13toCheck + 1];
F.Isotopes[0] = F.MainTrace;
//Pure isotopes
for (int C13 = 1; C13 <= T.C13toCheck; C13++)
{
double TargetMass = Apex.Mass + (C13Shift * (double)(C13)) / T.Charge;
MZData D = RawFileService.RawFile.RawSpectra[Apex.Scan].FindNearestPeak(TargetMass, MassError);
if (D.Mass > 0.0)
{
F.Isotopes[C13] = LCTrace.CreateTrace(RawFileService.GroupFromPoint(D), D);
}
else
{
F.Isotopes[C13] = null;
}
//Gapped trace (it was only actual if low signals is turned on - may provide some non-obvious errors)
if (F.Isotopes[C13] == null ||
(F.Isotopes[C13].Group.Points[0].RT > T.RTMin &&
F.Isotopes[C13].Group.Points[F.Isotopes[C13].Group.Points.Count - 1].RT < T.RTMax))
{
F.Isotopes[C13] = LCTrace.CreateTrace(RawFileService.GroupFromArea(T.RTMin, T.RTMax, TargetMass), D.Mass == 0.0?null:D);
}
if (F.Isotopes[C13] != null)
{
F.Isotopes[C13].Attribution = String.Format("C{0}N{1}", C13, 0);
}
}
//Apply peaks
if (F.TPeaks.TargetPeak != null)
{
F.ApplyPeak(F.TPeaks.TargetPeak);
}
return(F);
}
