public static void Processing(ref MultiGlycanESI argMultiGlycan)
{
GlycanCompound processed;
try
{
List<string> identifiedGlycan =argMultiGlycan.IdentifiedGlycanCompounds.Select(x => x.GlycanKey).Distinct().ToList();
Dictionary<string,List<int>> dictGlycanKeySearchRange = new Dictionary<string, List<int>>();
int LastScan = argMultiGlycan.RawReader.NumberOfScans;
foreach (string glycanKey in identifiedGlycan)
{
List<int> identifedScans =
argMultiGlycan.MatchedPeakInScan.Where(x => x.GlycanComposition.GlycanKey == glycanKey)
.Select(y => y.ScanNum)
.ToList();
identifedScans.Sort();
int frontEdge = identifedScans[0];
double FirstIdentifiedTime = argMultiGlycan.RawReader.ReadScan(frontEdge).Time;
while (frontEdge>1)
{
frontEdge -= 1;
if (argMultiGlycan.RawReader.GetMsLevel(frontEdge) != 1)
{
continue;
}
MSScan s = argMultiGlycan.RawReader.ReadScan(frontEdge);
if (FirstIdentifiedTime - s.Time > 5)
{
break;
}
}
int backEdge = identifedScans[identifedScans.Count - 1];
double LastIdentifedTime = argMultiGlycan.RawReader.ReadScan(backEdge).Time;
while (backEdge < LastScan)
{
backEdge += 1;
if (argMultiGlycan.RawReader.GetMsLevel(backEdge) != 1)
{
continue;
}
MSScan s = argMultiGlycan.RawReader.ReadScan(backEdge);
if (s.Time - LastIdentifedTime > 5)
{
break;
}
}
dictGlycanKeySearchRange.Add(glycanKey, new List<int>(){frontEdge,backEdge});
}
List<MSScan> msScans = new List<MSScan>();
string previousGlycanKey = "";
foreach (GlycanCompound g in argMultiGlycan.GlycanList.OrderBy(x=> x.GlycanKey))
{
if (!identifiedGlycan.Contains(g.GlycanKey))
{
continue;
}
if (previousGlycanKey != g.GlycanKey)
{
msScans.Clear();
//Read Scans
int startScan = dictGlycanKeySearchRange[g.GlycanKey][0] >= 1 ? dictGlycanKeySearchRange[g.GlycanKey][0] : 1;
int endScan = dictGlycanKeySearchRange[g.GlycanKey][1] <= LastScan ? dictGlycanKeySearchRange[g.GlycanKey][1] : LastScan;
msScans.AddRange(argMultiGlycan.RawReader.ReadScanWMSLevel(startScan, endScan,1));
previousGlycanKey = g.GlycanKey;
}
//FindPeaks
int charge = g.Charge;
List<List<MSScan>> scanSectionsContainPeaks = new List<List<MSScan>>();
for (int i = 0; i < msScans.Count; i++)
{
MSScan scan = msScans[i];
int closedIdx = MassUtility.GetClosestMassIdx(scan.MZs, (float) g.MZ);
if (MassUtility.GetMassPPM(scan.MZs[closedIdx], g.MZ) <=argMultiGlycan.MassPPM)
{
List<int> peaks = FindPeakIdx(scan.MZs, closedIdx, charge, argMultiGlycan.IsotopePPM);
if (peaks.Count - peaks.IndexOf(closedIdx) < argMultiGlycan.MininumIsotopePeakCount)
{
continue;
}
//Found peaks
if (scanSectionsContainPeaks.Count > 0)
{
MSScan lastSectionLastScan = scanSectionsContainPeaks.Last().Last();
if (scan.Time - lastSectionLastScan.Time > 2.5)
{
scanSectionsContainPeaks.Add(new List<MSScan>(){scan});
}
else
{
scanSectionsContainPeaks.Last().Add(scan);
}
}
else
{
scanSectionsContainPeaks.Add(new List<MSScan>(){scan});
}
}
}
//If scans can form an elution profile add to identifed result;
foreach (List<MSScan> sectionScans in scanSectionsContainPeaks)
{
if (sectionScans.Count < 3)
{
continue;
}
else
{
//Add matched peak
foreach (MSScan s in sectionScans)
{
int PeakIdx = MassUtility.GetClosestMassIdx(s.MZs, (float)g.MZ);
MatchedGlycanPeak mPeak = new MatchedGlycanPeak(s.ScanNo, s.Time, s.MSPeaks[PeakIdx], g);
List<int> peaks = FindPeakIdx(s.MZs, PeakIdx, charge, argMultiGlycan.IsotopePPM);
int startIdx = peaks.IndexOf(PeakIdx);
List<MSPoint> lstIsotopes= new List<MSPoint>();
for (int i = startIdx; i < peaks.Count; i++)
{
lstIsotopes.Add(new MSPoint(s.MZs[peaks[i]],s.Intensities[peaks[i]]));
}
mPeak.MSPoints = lstIsotopes;
if (!argMultiGlycan.MatchedPeakInScan.Contains(mPeak))
{
argMultiGlycan.MatchedPeakInScan.Add(mPeak);
}
}
}
}
}
//foreach (GlycanCompound g in argMultiGlycan.IdentifiedGlycanCompounds)
//{
// processed = g;
// //Search Peak in front of the peak
// ThermoRawReader raw = (ThermoRawReader)argMultiGlycan.RawReader;
// List<int> identifedScans = argMultiGlycan.MatchedPeakInScan.Where(x => x.GlycanComposition == g).Select(y => y.ScanNum).ToList();
// for (int i = 0; i < identifedScans.Count; i++)
// {
// int identifiedScanNum = identifedScans[i];
// while (true)
// {
// identifiedScanNum -= 1;
// if (identifiedScanNum < 1 || raw.GetRetentionTime(identifedScans[i]) - raw.GetRetentionTime(identifiedScanNum) > argMultiGlycan.MaxLCFrontMin)
// {
// break;
// }
// if (raw.GetMsLevel((identifiedScanNum)) != 1)
// {
// continue;
// }
// MSScan scan = raw.ReadScan(identifiedScanNum);
// int PeakIdx = MassUtility.GetClosestMassIdx(scan.MZs, (float)g.MZ);
// if (MassUtility.GetMassPPM(scan.MZs[PeakIdx], g.MZ) > argMultiGlycan.MassPPM)
// {
// continue;
// }
// //Find isotope cluster
// List<MSPoint> lstIsotopes = new List<MSPoint>();
// lstIsotopes.Add(new MSPoint(scan.MZs[PeakIdx],scan.Intensities[PeakIdx]));
// float targetMZ = (float)g.MZ;
// do
// {
// targetMZ += 1.0f/g.Charge;
// PeakIdx = MassUtility.GetClosestMassIdx(scan.MZs, targetMZ);
// if (MassUtility.GetMassPPM(scan.MZs[PeakIdx], targetMZ) <= argMultiGlycan.MassPPM)
// {
// lstIsotopes.Add(new MSPoint(scan.MZs[PeakIdx],scan.Intensities[PeakIdx]));
// }
// else
// {
// break;
// }
// } while (true);
// if (lstIsotopes.Count < argMultiGlycan.MininumIsotopePeakCount)
// {
// continue;
// }
// MatchedGlycanPeak mPeak = new MatchedGlycanPeak(scan.ScanNo, scan.Time, scan.MSPeaks[PeakIdx], g);
// mPeak.MSPoints = lstIsotopes;
// if (!argMultiGlycan.MatchedPeakInScan.Contains(mPeak))
// {
// argMultiGlycan.MatchedPeakInScan.Add(mPeak);
// }
// }
// identifiedScanNum = identifedScans[i];
// while (true)
// {
// identifiedScanNum += 1;
// if (identifiedScanNum > raw.NumberOfScans || raw.GetRetentionTime(identifiedScanNum) - raw.GetRetentionTime(identifedScans[i]) > argMultiGlycan.MaxLCBackMin)
// {
// break;
// }
// if (raw.GetMsLevel((identifiedScanNum)) != 1)
// {
// continue;
// }
// MSScan scan = raw.ReadScan(identifiedScanNum);
// int PeakIdx = MassUtility.GetClosestMassIdx(scan.MZs, (float)g.MZ);
// if (MassUtility.GetMassPPM(scan.MZs[PeakIdx], g.MZ) > argMultiGlycan.MassPPM)
// {
// continue;
// }
// //Find isotope cluster
// List<MSPoint> lstIsotopes = new List<MSPoint>();
// lstIsotopes.Add(new MSPoint(scan.MZs[PeakIdx], scan.Intensities[PeakIdx]));
// float targetMZ = (float)g.MZ;
// do
// {
// targetMZ += 1.0f / g.Charge;
// PeakIdx = MassUtility.GetClosestMassIdx(scan.MZs, targetMZ);
// if (MassUtility.GetMassPPM(scan.MZs[PeakIdx], targetMZ) <= argMultiGlycan.MassPPM)
// {
// lstIsotopes.Add(new MSPoint(scan.MZs[PeakIdx], scan.Intensities[PeakIdx]));
// }
// else
// {
// break;
// }
// } while (true);
// if (lstIsotopes.Count < argMultiGlycan.MininumIsotopePeakCount)
// {
// continue;
// }
// MatchedGlycanPeak mPeak = new MatchedGlycanPeak(scan.ScanNo, scan.Time, scan.MSPeaks[PeakIdx], g);
// mPeak.MSPoints = lstIsotopes;
// if (!argMultiGlycan.MatchedPeakInScan.Contains(mPeak))
// {
// argMultiGlycan.MatchedPeakInScan.Add(mPeak);
// }
// }
// }
//}
}
catch (Exception ex)
{
throw ex;
}
}
public static void Processing(ref MultiGlycanESI argMultiGlycan)
{
try
{
List <string> identifiedGlycan = argMultiGlycan.IdentifiedGlycanCompounds.Select(x => x.GlycanKey).Distinct().ToList();
Dictionary <string, List <int> > dictGlycanKeySearchRange = new Dictionary <string, List <int> >();
int LastScan = argMultiGlycan.RawReader.NumberOfScans;
foreach (string glycanKey in identifiedGlycan)
{
List <int> identifedScans =
argMultiGlycan.MatchedPeakInScan.Where(x => x.GlycanComposition.GlycanKey == glycanKey)
.Select(y => y.ScanNum)
.ToList();
identifedScans.Sort();
int frontEdge = identifedScans[0];
double FirstIdentifiedTime = argMultiGlycan.RawReader.ReadScan(frontEdge).Time;
while (frontEdge > 1)
{
frontEdge -= 1;
if (argMultiGlycan.RawReader.GetMsLevel(frontEdge) != 1)
{
continue;
}
MSScan s = argMultiGlycan.RawReader.ReadScan(frontEdge);
if (FirstIdentifiedTime - s.Time > 5)
{
break;
}
}
int backEdge = identifedScans[identifedScans.Count - 1];
double LastIdentifedTime = argMultiGlycan.RawReader.ReadScan(backEdge).Time;
while (backEdge < LastScan)
{
backEdge += 1;
if (argMultiGlycan.RawReader.GetMsLevel(backEdge) != 1)
{
continue;
}
MSScan s = argMultiGlycan.RawReader.ReadScan(backEdge);
if (s.Time - LastIdentifedTime > 5)
{
break;
}
}
dictGlycanKeySearchRange.Add(glycanKey, new List <int>()
{
frontEdge, backEdge
});
}
List <MSScan> msScans = new List <MSScan>();
string previousGlycanKey = "";
foreach (GlycanCompound g in argMultiGlycan.GlycanList.OrderBy(x => x.GlycanKey))
{
if (!identifiedGlycan.Contains(g.GlycanKey))
{
continue;
}
if (previousGlycanKey != g.GlycanKey)
{
msScans.Clear();
//Read Scans
int startScan = dictGlycanKeySearchRange[g.GlycanKey][0] >= 1 ? dictGlycanKeySearchRange[g.GlycanKey][0] : 1;
int endScan = dictGlycanKeySearchRange[g.GlycanKey][1] <= LastScan ? dictGlycanKeySearchRange[g.GlycanKey][1] : LastScan;
msScans.AddRange(argMultiGlycan.RawReader.ReadScanWMSLevel(startScan, endScan, 1));
previousGlycanKey = g.GlycanKey;
}
//FindPeaks
int charge = g.Charge;
List <List <MSScan> > scanSectionsContainPeaks = new List <List <MSScan> >();
for (int i = 0; i < msScans.Count; i++)
{
MSScan scan = msScans[i];
int closedIdx = MassUtility.GetClosestMassIdx(scan.MZs, (float)g.MZ);
if (MassUtility.GetMassPPM(scan.MZs[closedIdx], g.MZ) <= argMultiGlycan.MassPPM)
{
List <int> peaks = FindPeakIdx(scan.MZs, closedIdx, charge, argMultiGlycan.IsotopePPM);
if (peaks.Count - peaks.IndexOf(closedIdx) < argMultiGlycan.MininumIsotopePeakCount)
{
continue;
}
//Found peaks
if (scanSectionsContainPeaks.Count > 0)
{
MSScan lastSectionLastScan = scanSectionsContainPeaks.Last().Last();
if (scan.Time - lastSectionLastScan.Time > 2.5)
{
scanSectionsContainPeaks.Add(new List <MSScan>()
{
scan
});
}
else
{
scanSectionsContainPeaks.Last().Add(scan);
}
}
else
{
scanSectionsContainPeaks.Add(new List <MSScan>()
{
scan
});
}
}
}
//If scans can form an elution profile add to identifed result;
foreach (List <MSScan> sectionScans in scanSectionsContainPeaks)
{
if (sectionScans.Count < 3)
{
continue;
}
else
{
//Add matched peak
foreach (MSScan s in sectionScans)
{
int PeakIdx = MassUtility.GetClosestMassIdx(s.MZs, (float)g.MZ);
MatchedGlycanPeak mPeak = new MatchedGlycanPeak(s.ScanNo, s.Time, s.MSPeaks[PeakIdx], g);
List <int> peaks = FindPeakIdx(s.MZs, PeakIdx, charge, argMultiGlycan.IsotopePPM);
int startIdx = peaks.IndexOf(PeakIdx);
List <MSPoint> lstIsotopes = new List <MSPoint>();
for (int i = startIdx; i < peaks.Count; i++)
{
lstIsotopes.Add(new MSPoint(s.MZs[peaks[i]], s.Intensities[peaks[i]]));
}
mPeak.MSPoints = lstIsotopes;
if (!argMultiGlycan.MatchedPeakInScan.Contains(mPeak))
{
argMultiGlycan.MatchedPeakInScan.Add(mPeak);
}
}
}
}
}
//foreach (GlycanCompound g in argMultiGlycan.IdentifiedGlycanCompounds)
//{
// processed = g;
// //Search Peak in front of the peak
// ThermoRawReader raw = (ThermoRawReader)argMultiGlycan.RawReader;
// List<int> identifedScans = argMultiGlycan.MatchedPeakInScan.Where(x => x.GlycanComposition == g).Select(y => y.ScanNum).ToList();
// for (int i = 0; i < identifedScans.Count; i++)
// {
// int identifiedScanNum = identifedScans[i];
// while (true)
// {
// identifiedScanNum -= 1;
// if (identifiedScanNum < 1 || raw.GetRetentionTime(identifedScans[i]) - raw.GetRetentionTime(identifiedScanNum) > argMultiGlycan.MaxLCFrontMin)
// {
// break;
// }
// if (raw.GetMsLevel((identifiedScanNum)) != 1)
// {
// continue;
// }
// MSScan scan = raw.ReadScan(identifiedScanNum);
// int PeakIdx = MassUtility.GetClosestMassIdx(scan.MZs, (float)g.MZ);
// if (MassUtility.GetMassPPM(scan.MZs[PeakIdx], g.MZ) > argMultiGlycan.MassPPM)
// {
// continue;
// }
// //Find isotope cluster
// List<MSPoint> lstIsotopes = new List<MSPoint>();
// lstIsotopes.Add(new MSPoint(scan.MZs[PeakIdx],scan.Intensities[PeakIdx]));
// float targetMZ = (float)g.MZ;
// do
// {
// targetMZ += 1.0f/g.Charge;
// PeakIdx = MassUtility.GetClosestMassIdx(scan.MZs, targetMZ);
// if (MassUtility.GetMassPPM(scan.MZs[PeakIdx], targetMZ) <= argMultiGlycan.MassPPM)
// {
// lstIsotopes.Add(new MSPoint(scan.MZs[PeakIdx],scan.Intensities[PeakIdx]));
// }
// else
// {
// break;
// }
// } while (true);
// if (lstIsotopes.Count < argMultiGlycan.MininumIsotopePeakCount)
// {
// continue;
// }
// MatchedGlycanPeak mPeak = new MatchedGlycanPeak(scan.ScanNo, scan.Time, scan.MSPeaks[PeakIdx], g);
// mPeak.MSPoints = lstIsotopes;
// if (!argMultiGlycan.MatchedPeakInScan.Contains(mPeak))
// {
// argMultiGlycan.MatchedPeakInScan.Add(mPeak);
// }
// }
// identifiedScanNum = identifedScans[i];
// while (true)
// {
// identifiedScanNum += 1;
// if (identifiedScanNum > raw.NumberOfScans || raw.GetRetentionTime(identifiedScanNum) - raw.GetRetentionTime(identifedScans[i]) > argMultiGlycan.MaxLCBackMin)
// {
// break;
// }
// if (raw.GetMsLevel((identifiedScanNum)) != 1)
// {
// continue;
// }
// MSScan scan = raw.ReadScan(identifiedScanNum);
// int PeakIdx = MassUtility.GetClosestMassIdx(scan.MZs, (float)g.MZ);
// if (MassUtility.GetMassPPM(scan.MZs[PeakIdx], g.MZ) > argMultiGlycan.MassPPM)
// {
// continue;
// }
// //Find isotope cluster
// List<MSPoint> lstIsotopes = new List<MSPoint>();
// lstIsotopes.Add(new MSPoint(scan.MZs[PeakIdx], scan.Intensities[PeakIdx]));
// float targetMZ = (float)g.MZ;
// do
// {
// targetMZ += 1.0f / g.Charge;
// PeakIdx = MassUtility.GetClosestMassIdx(scan.MZs, targetMZ);
// if (MassUtility.GetMassPPM(scan.MZs[PeakIdx], targetMZ) <= argMultiGlycan.MassPPM)
// {
// lstIsotopes.Add(new MSPoint(scan.MZs[PeakIdx], scan.Intensities[PeakIdx]));
// }
// else
// {
// break;
// }
// } while (true);
// if (lstIsotopes.Count < argMultiGlycan.MininumIsotopePeakCount)
// {
// continue;
// }
// MatchedGlycanPeak mPeak = new MatchedGlycanPeak(scan.ScanNo, scan.Time, scan.MSPeaks[PeakIdx], g);
// mPeak.MSPoints = lstIsotopes;
// if (!argMultiGlycan.MatchedPeakInScan.Contains(mPeak))
// {
// argMultiGlycan.MatchedPeakInScan.Add(mPeak);
// }
// }
// }
//}
}
catch (Exception ex)
{
throw ex;
}
}
public ClusteredPeak(MatchedGlycanPeak argMatchedGlycanPeak)
{
_MatchedPeaksInScan = new List<MatchedGlycanPeak>();
_MatchedPeaksInScan.Add(argMatchedGlycanPeak);
}
public ClusteredPeak(MatchedGlycanPeak argMatchedGlycanPeak)
{
_MatchedPeaksInScan = new List <MatchedGlycanPeak>();
_MatchedPeaksInScan.Add(argMatchedGlycanPeak);
}