private MSScan GetScanFromFile(int argScanNo, float argMinSN = 2)
{
int isProfile = 0;
_rawConnection.IsProfileScanForScanNum(argScanNo, ref isProfile);
object labels = null;
object flags = null;
_rawConnection.GetLabelData(ref labels, ref flags, ref argScanNo);
double[,] LabeledPeaks = (double[, ])labels;
//Start Read Scan
MSScan scan = new MSScan(argScanNo);
List <ThermoLabeledPeak> FullLabeledPeak = new List <ThermoLabeledPeak>();
float[] mz = new float[LabeledPeaks.GetLength(1)];
float[] intensity = new float[LabeledPeaks.GetLength(1)];
int j = 0;
for (int i = 0; i < LabeledPeaks.GetLength(1); i++)
{
double sn = LabeledPeaks[1, i] / LabeledPeaks[4, i];
if (sn >= argMinSN)
{
mz[j] = Convert.ToSingle(LabeledPeaks[0, i]);
intensity[j] = Convert.ToSingle(LabeledPeaks[1, i]);
j++;
FullLabeledPeak.Add(new ThermoLabeledPeak(
Convert.ToSingle(LabeledPeaks[0, i]),
Convert.ToSingle(LabeledPeaks[1, i]),
Convert.ToInt32(LabeledPeaks[5, i]),
Convert.ToSingle(LabeledPeaks[4, i])));
}
}
Array.Resize(ref mz, j);
Array.Resize(ref intensity, j);
//scan.MZs = ConvertDoubleArrayToFloatArray(CSMSLScan.MassSpectrum.GetMasses());
scan.MZs = mz;
//scan.Intensities = ConvertDoubleArrayToFloatArray(CSMSLScan.MassSpectrum.GetIntensities());
scan.Intensities = intensity;
scan.MsLevel = GetMsLevel(argScanNo);
double retentionTime = 0;
_rawConnection.RTFromScanNum(argScanNo, ref retentionTime);
scan.Time = retentionTime;
scan.ScanHeader = GetScanDescription(argScanNo);
if (scan.MsLevel != 1)
{
for (int chNum = 0; chNum < scan.MZs.Length; chNum++)
{
scan.MSPeaks.Add(new MSPeak(
Convert.ToSingle(scan.MZs[chNum]),
Convert.ToSingle(scan.Intensities[chNum])));
}
// Get parent information
object value = null;
_rawConnection.GetTrailerExtraValueForScanNum(argScanNo, "Master Scan Number:", ref value);
scan.ParentScanNo = Convert.ToInt32(value);
string ParentDesc = GetScanDescription(scan.ParentScanNo);
//_rawConnection.GetPrecursorInfoFromScanNum(argScanNo, ref PrecursorInfo, ref PrecursorInfoSize);
//scan.ParentMonoMW = Convert.ToSingle(PrecurorArray.);
//scan.ParentMZ = Convert.ToSingle(PrecurorArray[1,0]);
//scan.ParentCharge = Convert.ToInt32(PrecurorArray.nChargeState);
scan.IsCIDScan = IsCIDScan(argScanNo);
scan.IsFTScan = IsFTScan(argScanNo);
//Array.Clear(_transformResult, 0, _transformResult.Length);
//Array.Clear(_cidPeaks, 0, _cidPeaks.Length);
//Array.Clear(_cidMzs, 0, _cidMzs.Length);
//Array.Clear(_cidIntensities, 0, _cidIntensities.Length);
//Array.Clear(_parentRawMzs, 0, _parentRawMzs.Length);
//Array.Clear(_parentRawIntensitys, 0, _parentRawIntensitys.Length);
}
else //MS Scan
{
do
{
ThermoLabeledPeak BasePeak = FullLabeledPeak[0];
List <ThermoLabeledPeak> clusterPeaks = new List <ThermoLabeledPeak>();
List <int> RemoveIdx = new List <int>();
RemoveIdx.Add(0);
clusterPeaks.Add(BasePeak);
double Interval = 1 / (double)BasePeak.Charge;
double FirstMZ = BasePeak.MZ;
for (int i = 1; i < FullLabeledPeak.Count; i++)
{
if (FullLabeledPeak[i].MZ - FirstMZ > Interval * 10)
{
break;
}
if ((FullLabeledPeak[i].MZ - (BasePeak.MZ + Interval)) < 0.1 && (FullLabeledPeak[i].MZ - (BasePeak.MZ + Interval)) >= 0 && clusterPeaks[0].Charge == FullLabeledPeak[i].Charge)
{
BasePeak = FullLabeledPeak[i];
clusterPeaks.Add(FullLabeledPeak[i]);
RemoveIdx.Add(i);
}
}
if (clusterPeaks.Count < 3)
{
FullLabeledPeak.RemoveAt(RemoveIdx[0]);
}
else
{
float MostIntenseMZ = 0.0f;
double MostIntenseIntneisty = 0;
double ClusterIntensity = 0;
RemoveIdx.Reverse();
for (int i = 0; i < RemoveIdx.Count; i++)
{
if (FullLabeledPeak[RemoveIdx[i]].Intensity > MostIntenseIntneisty)
{
MostIntenseIntneisty = FullLabeledPeak[RemoveIdx[i]].Intensity;
MostIntenseMZ = FullLabeledPeak[RemoveIdx[i]].MZ;
}
ClusterIntensity = ClusterIntensity + FullLabeledPeak[RemoveIdx[i]].Intensity;
FullLabeledPeak.RemoveAt(RemoveIdx[i]);
}
scan.MSPeaks.Add(new MSPeak(clusterPeaks[0].Mass, clusterPeaks[0].Intensity, clusterPeaks[0].Charge, clusterPeaks[0].MZ, clusterPeaks[0].SN, MostIntenseMZ, MostIntenseIntneisty, ClusterIntensity));
}
} while (FullLabeledPeak.Count != 0);
//Array.Clear(_transformResult, 0, _transformResult.Length);
//Array.Clear(_cidPeaks, 0, _cidPeaks.Length);
//Array.Clear(_cidMzs, 0, _cidMzs.Length);
//Array.Clear(_cidIntensities, 0, _cidIntensities.Length);
}
return(scan);
}
//private MSScan GetScanFromFile(int argScanNo)
//{
// return GetScanFromFile(argScanNo);
//}
private MSScan GetScanFromFile(int argScanNo, float argMinSN = 2)//, float argPPM = 6, int argMinPeakCount=3)
{
MSDataScan DataScan = _raw.GetMsScan(argScanNo);
tolSN = argMinSN;
//tolMinPeakCount = argMinPeakCount;
//tolPPM = argPPM;
MZPeak[] peaks;
List <ThermoLabeledPeak> TPeaks = new List <ThermoLabeledPeak>();
peaks = DataScan.MassSpectrum.GetPeaks();
//Start Read Scan
MSScan scan = new MSScan(argScanNo);
scan.MsLevel = GetMsLevel(argScanNo);
scan.Time = _raw.GetRetentionTime(argScanNo);
scan.ScanHeader = _raw.GetScanFilter(argScanNo);
List <MSPeak> MSPsks = new List <MSPeak>();
#region MSScan
if (scan.MsLevel == 1)
{
float[] RawMz = new float[peaks.Length];
float[] RawIntensity = new float[peaks.Length];
for (int i = 0; i < peaks.Length; i++)
{
RawMz[i] = Convert.ToSingle(peaks[i].MZ);
RawIntensity[i] = Convert.ToSingle(peaks[i].Intensity);
ThermoLabeledPeak TPeak = (ThermoLabeledPeak)peaks[i];
if (TPeak.SN >= tolSN)
{
TPeaks.Add(TPeak);
}
}
float[] Mz = new float[TPeaks.Count];
float[] Intensity = new float[TPeaks.Count];
for (int i = 0; i < TPeaks.Count; i++)
{
Mz[i] = Convert.ToSingle(TPeaks[i].MZ);
Intensity[i] = Convert.ToSingle(TPeaks[i].Intensity);
}
scan.RawMZs = RawMz;
scan.RawIntensities = RawIntensity;
scan.MZs = Mz;
scan.Intensities = Intensity;
//************************Peak Picking
//scan.MSPeaks = MSPsks;
//List<float> TPeaksMZ = new List<float>();
//for (int i = 0; i < TPeaks.Count; i++)
//{
// TPeaksMZ.Add(Convert.ToSingle(TPeaks[i].MZ));
//}
//do
//{
// ThermoLabeledPeak BasePeak = TPeaks[0];
// List<ThermoLabeledPeak> clusterPeaks = new List<ThermoLabeledPeak>();
// List<int> RemoveIdx = new List<int>();
// RemoveIdx.Add(0);
// clusterPeaks.Add(BasePeak);
// double Interval = 1 / (double)BasePeak.Charge;
// double FirstMZ = BasePeak.MZ;
// for (int i = 1; i < TPeaks.Count; i++)
// {
// if (TPeaks[i].MZ - FirstMZ > Interval * 10)
// {
// break;
// }
// List<int> ClosePeaks = MassUtility.GetClosestMassIdxsWithinPPM(TPeaksMZ.ToArray(), Convert.ToSingle(BasePeak.MZ + Interval), argPPM);
// if (ClosePeaks.Count == 1 && TPeaks[ClosePeaks[0]].Charge == BasePeak.Charge)
// {
// BasePeak = TPeaks[i];
// clusterPeaks.Add(TPeaks[i]);
// RemoveIdx.Add(i);
// }
// else if (ClosePeaks.Count > 1)
// {
// double minPPM = 100;
// int minPPMIdx = 0;
// float maxIntensity = 0;
// int maxIntensityIdx = 0;
// for (int j = 0; j < ClosePeaks.Count; j++)
// {
// if (MassUtility.GetMassPPM(BasePeak.MZ + Interval, mz[ClosePeaks[j]]) < minPPM)
// {
// minPPMIdx = ClosePeaks[j];
// minPPM = MassUtility.GetMassPPM(BasePeak.MZ + Interval, mz[ClosePeaks[j]]);
// }
// if (intensity[ClosePeaks[j]] > maxIntensity)
// {
// maxIntensity = intensity[ClosePeaks[j]];
// maxIntensityIdx = ClosePeaks[j];
// }
// }
// BasePeak = TPeaks[minPPMIdx];
// clusterPeaks.Add(TPeaks[minPPMIdx]);
// RemoveIdx.Add(minPPMIdx);
// }
// }
// if (clusterPeaks.Count < argMinPeakCount)
// {
// TPeaks.RemoveAt(RemoveIdx[0]);
// TPeaksMZ.RemoveAt(RemoveIdx[0]);
// }
// else
// {
// float MostIntenseMZ = 0.0f;
// double MostIntenseIntneisty = 0;
// double ClusterIntensity = 0;
// RemoveIdx.Reverse();
// for (int i = 0; i < RemoveIdx.Count; i++)
// {
// if (TPeaks[RemoveIdx[i]].Intensity > MostIntenseIntneisty)
// {
// MostIntenseIntneisty = TPeaks[RemoveIdx[i]].Intensity;
// MostIntenseMZ = Convert.ToSingle(TPeaks[RemoveIdx[i]].MZ);
// }
// ClusterIntensity = ClusterIntensity + TPeaks[RemoveIdx[i]].Intensity;
// TPeaks.RemoveAt(RemoveIdx[i]);
// TPeaksMZ.RemoveAt(RemoveIdx[i]);
// }
// scan.MSPeaks.Add(new MSPeak(
// Convert.ToSingle(clusterPeaks[0].MZ),
// Convert.ToSingle(clusterPeaks[0].Intensity),
// clusterPeaks[0].Charge,
// Convert.ToSingle(clusterPeaks[0].MZ),
// Convert.ToSingle(clusterPeaks[0].SN),
// MostIntenseMZ,
// MostIntenseIntneisty,
// ClusterIntensity));
// }
//} while (TPeaks.Count != 0);
}
#endregion
#region MS/MS Scan
else
{
float[] mz = new float[peaks.Length];
float[] intensity = new float[peaks.Length];
for (int i = 0; i < peaks.Length; i++)
{
mz[i] = Convert.ToSingle(peaks[i].MZ);
intensity[i] = Convert.ToSingle(peaks[i].Intensity);
//MSPsks.Add(new MSPeak(mz[i], intensity[i]));
}
scan.MZs = mz;
scan.Intensities = intensity;
//scan.MSPeaks = MSPsks;
// Get parent information
scan.ParentScanNo = _raw.GetParentSpectrumNumber(argScanNo);
scan.ParentMZ = Convert.ToSingle(_raw.GetPrecusorMz(argScanNo));
scan.ParentCharge = _raw.GetPrecusorCharge(argScanNo);
//Parent Mono
if (scan.ParentScanNo != 0)
{
MSScan ParentScan = GetScanFromFile(scan.ParentScanNo);
int ClosedIdx = MassUtility.GetClosestMassIdx(ParentScan.MZs, scan.ParentMZ);
List <int> Peaks = FindPeakIdx(ParentScan.MZs, ClosedIdx, scan.ParentCharge, 10);
scan.ParentMonoMz = ParentScan.MZs[Peaks[0]];
}
}
#endregion
scan.IsCIDScan = IsCIDScan(argScanNo);
scan.IsHCDScan = IsHCDScan(argScanNo);
scan.IsFTScan = IsFTScan(argScanNo);
return(scan);
}