public ThermoSpectrum GetSpectrum(int spectrumNumber, bool profileIfAvailable = false)
{
bool useProfile = false;
if (profileIfAvailable)
{
int isProfile = 0;
_rawConnection.IsProfileScanForScanNum(spectrumNumber, ref isProfile);
useProfile = isProfile == 1;
}
return(new ThermoSpectrum(GetLabeledData(spectrumNumber) ?? GetUnlabeledData(spectrumNumber, !useProfile)));
}
public MZSpectrum GetSpectrum(int spectrumNumber, bool profileIfAvailable = false)
{
bool useProfile = false;
if (profileIfAvailable)
{
int isProfile = 0;
_rawConnection.IsProfileScanForScanNum(spectrumNumber, ref isProfile);
useProfile = isProfile == 1;
}
var peakData = GetUnlabeledData(spectrumNumber, !useProfile);
return(new MZSpectrum(peakData));
}
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);
}
