private List <int> FindPeakIdx(float[] argMZAry, int argTargetIdx, int argCharge, float argPPM)
{
List <int> Peak = new List <int>();
float Interval = 1 / (float)argCharge;
float FirstMZ = argMZAry[argTargetIdx];
int CurrentIdx = argTargetIdx;
Peak.Add(argTargetIdx);
//Forward Peak
for (int i = argTargetIdx - 1; i >= 0; i--)
{
if (argMZAry[argTargetIdx] - argMZAry[i] >= Interval * 10)
{
break;
}
List <int> ClosedPeaks = MassUtility.GetClosestMassIdxsWithinPPM(argMZAry, argMZAry[CurrentIdx] - Interval, argPPM);
if (ClosedPeaks.Count == 1)
{
CurrentIdx = ClosedPeaks[0];
Peak.Insert(0, ClosedPeaks[0]);
}
else if (ClosedPeaks.Count > 1)
{
double minPPM = 100;
int minPPMIdx = 0;
for (int j = 0; j < ClosedPeaks.Count; j++)
{
if (MassUtility.GetMassPPM(argMZAry[ClosedPeaks[j]], argMZAry[CurrentIdx] - Interval) < minPPM)
{
minPPMIdx = ClosedPeaks[j];
minPPM = MassUtility.GetMassPPM(argMZAry[ClosedPeaks[j]], argMZAry[CurrentIdx] + Interval);
}
}
CurrentIdx = minPPMIdx;
Peak.Insert(0, CurrentIdx);
}
}
//Backward Peak
CurrentIdx = argTargetIdx;
for (int i = argTargetIdx + 1; i < argMZAry.Length; i++)
{
if (argMZAry[i] - argMZAry[argTargetIdx] >= Interval * 10)
{
break;
}
List <int> ClosedPeaks = MassUtility.GetClosestMassIdxsWithinPPM(argMZAry, argMZAry[CurrentIdx] + Interval, argPPM);
if (ClosedPeaks.Count == 1)
{
CurrentIdx = ClosedPeaks[0];
Peak.Add(ClosedPeaks[0]);
}
else if (ClosedPeaks.Count > 1)
{
double minPPM = 100;
int minPPMIdx = 0;
for (int j = 0; j < ClosedPeaks.Count; j++)
{
if (MassUtility.GetMassPPM(argMZAry[ClosedPeaks[j]], argMZAry[CurrentIdx] + Interval) < minPPM)
{
minPPMIdx = ClosedPeaks[j];
minPPM = MassUtility.GetMassPPM(argMZAry[ClosedPeaks[j]], argMZAry[CurrentIdx] + Interval);
}
}
CurrentIdx = minPPMIdx;
Peak.Add(CurrentIdx);
}
}
return(Peak);
}
private MSScan GetScanFromFile(int argScanNo, float argMinSN = 2)//, float argPPM = 6, int argMinPeakCount=3)
{
int mslevel = GetMsLevel(argScanNo);
tolSN = argMinSN;
MSScan scan = new MSScan(argScanNo);
scan.MsLevel = GetMsLevel(argScanNo);
scan.Time = GetRetentionTime(argScanNo);
scan.ScanHeader = GetScanDescription(argScanNo);
double[,] peakData;
if (GetMzAnalyzer(argScanNo) == ThermoMzAnalyzer.ITMS) //Low Res
{
object massList = null;
object peakFlags = null;
int arraySize = -1;
double centroidPeakWidth = double.NaN;
_rawConnection.GetMassListFromScanNum(ref argScanNo, null, 0, 0, 0, 0, ref centroidPeakWidth, ref massList, ref peakFlags, ref arraySize);
peakData = (double[, ])massList;
}
else
{
object labels = null;
object flags = null;
_rawConnection.GetLabelData(ref labels, ref flags, ref argScanNo);
peakData = (double[, ])labels;
}
scan.RawMZs = new float[peakData.GetLength(1)];
scan.RawIntensities = new float[peakData.GetLength(1)];
if (mslevel == 1)
{
List <float> MzsAboveSN = new List <float>();
List <float> IntensitysAboveSN = new List <float>();
for (int i = 0; i < peakData.GetLength(1); i++)
{
scan.RawMZs[i] = Convert.ToSingle(peakData[(int)RawLabelDataColumn.MZ, i]);
scan.RawIntensities[i] = Convert.ToSingle(peakData[(int)RawLabelDataColumn.Intensity, i]);
if (peakData.GetLength(0) >= 4) //Data contain SN
{
double Noise = peakData[(int)RawLabelDataColumn.NoiseLevel, i];
double SN = 0;
if (Noise.Equals(0))
{
SN = float.NaN;
}
else
{
SN = scan.RawIntensities[i] / Noise;
}
if (SN >= tolSN)
{
MzsAboveSN.Add(scan.RawMZs[i]);
IntensitysAboveSN.Add(scan.RawIntensities[i]);
}
}
else
{
MzsAboveSN.Add(scan.RawMZs[i]);
IntensitysAboveSN.Add(scan.RawIntensities[i]);
}
}
scan.MZs = MzsAboveSN.ToArray();
scan.Intensities = IntensitysAboveSN.ToArray();
}
else // MS/MS
{
scan.MZs = new float[peakData.GetLength(1)];
scan.Intensities = new float[peakData.GetLength(1)];
for (int i = 0; i < peakData.GetLength(1); i++)
{
scan.MZs[i] = Convert.ToSingle(peakData[(int)RawLabelDataColumn.MZ, i]);
scan.Intensities[i] = Convert.ToSingle(peakData[(int)RawLabelDataColumn.Intensity, i]);
}
scan.ParentScanNo = GetParentScanNumber(argScanNo);
scan.ParentMZ = GetPrecusorMz(argScanNo);
scan.ParentCharge = GetPrecusorCharge(argScanNo);
//Sometime get wrong value
//scan.ParentMonoMz = Convert.ToSingle(GetExtraValue(argScanNo, "Monoisotopic M/Z:"));
//Find in raw data
scan.ParentMonoMz = GetPrecusorMz(argScanNo);
MSScan parentScan = GetScanFromFile(scan.ParentScanNo);
float peakBefore = scan.ParentMZ - (1 / (float)scan.ParentCharge);
float foundPeak = parentScan.RawMZs.OrderBy(x => Math.Abs(x - peakBefore)).ToList()[0];
while (MassUtility.GetMassPPM(foundPeak, peakBefore) <= 10) //10PPM
{
//Find another
scan.ParentMonoMz = foundPeak;
peakBefore = foundPeak - (1 / (float)scan.ParentCharge);
foundPeak = parentScan.MZs.OrderBy(x => Math.Abs(x - peakBefore)).ToList()[0];
}
scan.ParentBasePeak = parentScan.MaxIntensity;
scan.ParentIntensity = parentScan.RawIntensities[parentScan.RawMZs.ToList().IndexOf(scan.ParentMonoMz)];
}
scan.IsCIDScan = IsCIDScan(argScanNo);
scan.IsHCDScan = IsHCDScan(argScanNo);
scan.IsFTScan = IsFTScan(argScanNo);
return(scan);
}