public MsScan(int scanNumber, XRawFileIO reader)
{
ScanNumber = scanNumber;
if (!reader.GetScanInfo(scanNumber, out var scanInfo))
{
ConsoleMsgUtils.ShowWarning("Scan {0} not found in {1}", scanNumber, Path.GetFileName(reader.RawFilePath));
return;
}
// Get centroided data
var dataPointCount = GetScanData(reader, scanInfo, out var mzList, out var intensityList);
MsLevel = scanInfo.MSLevel;
PeaksCount = dataPointCount;
switch (scanInfo.IonMode)
{
case IonModeConstants.Positive:
Polarity = "+";
break;
case IonModeConstants.Negative:
Polarity = "-";
break;
case IonModeConstants.Unknown:
Polarity = string.Empty;
break;
}
FilterLine = scanInfo.FilterText;
ScanType = GetScanType();
RetentionTime = "PT" + Math.Round(scanInfo.RetentionTime * 60, 8) + "S";
TotIonCurrent = scanInfo.TotalIonCurrent;
string encodedPeaks;
if (PeaksCount == 0)
{
LowMz = 0;
HighMz = 0;
BasePeakMz = 0;
BasePeakIntensity = 0;
encodedPeaks = Base64EncodeMsData(mzList, intensityList);
}
else
{
LowMz = mzList.Min();
HighMz = mzList.Max();
BasePeakMz = scanInfo.BasePeakMZ;
BasePeakIntensity = scanInfo.BasePeakIntensity;
encodedPeaks = Base64EncodeMsData(mzList, intensityList);
}
PeakData = new Peaks(32, "network", "m/z-int", "none", 0, encodedPeaks);
}
public MsScan(int scanNumber, int msLevel, int peaksCount, string polarity, string scanType, string filterLine, string retentionTime, double lowMz, double highMz,
double basePeakMz, double basePeakIntensity, double totIonCurrent, Peaks peakData)
{
ScanNumber = scanNumber;
MsLevel = msLevel;
PeaksCount = peaksCount;
Polarity = polarity;
ScanType = scanType;
FilterLine = filterLine;
RetentionTime = retentionTime;
LowMz = lowMz;
HighMz = highMz;
BasePeakMz = basePeakMz;
BasePeakIntensity = basePeakIntensity;
TotIonCurrent = totIonCurrent;
PeakData = peakData;
}
private Ms1Scan(int num, int msLevel, int peaksCount, string polarity, string scanType, string filterLine, string retentionTime, double lowMz, double highMz,
double basePeakMz, double basePeakIntensity, double totIonCurrent, Peaks peakData) : base(num, msLevel, peaksCount, polarity, scanType, filterLine,
retentionTime, lowMz, highMz, basePeakMz, basePeakIntensity, totIonCurrent, peakData)
{
ScanNumber = num;
MsLevel = msLevel;
PeaksCount = peaksCount;
Polarity = polarity;
ScanType = scanType;
FilterLine = filterLine;
RetentionTime = retentionTime;
LowMz = lowMz;
HighMz = highMz;
BasePeakMz = basePeakMz;
BasePeakIntensity = basePeakIntensity;
TotIonCurrent = totIonCurrent;
PeakData = peakData;
}