public override int LoadIndex(string FileName)
{
this.RawFileName = FileName;
RawFile = new MassSpecDataReader();
MSReader = RawFile;
MSReader.OpenDataFile(FileName);
Spectra = (int)(MSReader.MSScanFileInformation.TotalScansPresent);
bool PosMode = false, NegMode = false;
if (Spectra <= 0)
{
return(0);
}
int i, LastFull = 0, Total = 0;
//there will be fake [0] spectra with no data and fake last spectra with no data
//it is made to make any chromatogram start and end with zero
IndexDir = new int[Spectra + 2];
IndexRev = new int[Spectra + 2];
RawSpectra = new RawSpectrum[Spectra + 2];
for (int j = 0; j <= Spectra + 1; j++)
{
RawSpectra[j] = new RawSpectrum();
}
TimeStamps = new double[Spectra + 2];
TimeCoefs = new double[Spectra + 2];
LowRT = 0.0;
HighRT = 0.0;
int Progress = 0;
for (i = 1; i <= Spectra; i++)
{
if ((int)(100.0 * ((double)i / (double)Spectra)) > Progress)//report progress
{
Progress = (int)(100.0 * ((double)i / (double)Spectra));
RepProgress?.Invoke(Progress);
}
IMSScanRecord ScanRecord = MSReader.GetScanRecord(i - 1);
if (ScanRecord.MSScanType == MSScanType.Scan && ScanRecord.MSLevel == MSLevel.MS && ScanRecord.CollisionEnergy == 0.0) //if spectra is a FULL MS
{
PosMode |= ScanRecord.IonPolarity == IonPolarity.Positive;
NegMode |= ScanRecord.IonPolarity == IonPolarity.Negative;
RawSpectra[i].RT = ScanRecord.RetentionTime;
TimeStamps[i] = RawSpectra[i].RT - RawSpectra[LastFull].RT;
RawSpectra[i].Scan = i;
IndexDir[LastFull] = i;
IndexRev[i] = LastFull;
LastFull = i;
Total++;
}
}
IndexDir[LastFull] = Spectra + 1;
IndexDir[Spectra + 1] = -1;
IndexRev[Spectra + 1] = LastFull;
TotalRT = RawSpectra[LastFull].RT;
AverageTimeStamp = TotalRT / Total;
//time interval bias coefficients
for (i = IndexDir[0]; IndexDir[i] != -1; i = IndexDir[i])
{
TimeCoefs[i] = (TimeStamps[i] + TimeStamps[IndexDir[i]]) / (2.0 * AverageTimeStamp);
}
TimeCoefs[i] = 1.0;
//Fake spectra number 0 has to have reasonable RT
double FRT = RawSpectra[IndexDir[0]].RT;
double SRT = RawSpectra[IndexDir[IndexDir[0]]].RT;
RawSpectra[0].RT = Math.Max(0, FRT - (SRT - FRT));
//Last spectra also has to have reasonable RT
FRT = RawSpectra[LastFull].RT;
SRT = RawSpectra[IndexRev[LastFull]].RT;
RawSpectra[Spectra + 1].RT = FRT + (FRT - SRT);
RawSpectra[0].Data = new MZData[0];
RawSpectra[Spectra + 1].Data = new MZData[0];
PeakFilter = new MsdrPeakFilter();
PeakFilter.AbsoluteThreshold = 5.0;
if (PosMode && !NegMode)
{
Mode = 1;
}
if (!PosMode && NegMode)
{
Mode = -1;
}
return(Spectra);
}
public static PeakList <Peak> GetPeakList(this IMsdrDataReader reader, double retentionTime, IMsdrPeakFilter peakFilter)
{
PeakList <Peak> result = new PeakList <Peak>();
IBDASpecData s = reader.GetSpectrum(retentionTime, MSScanType.All, IonPolarity.Mixed, IonizationMode.Unspecified, peakFilter, true);
for (int i = 0; i < s.XArray.Length; i++)
{
result.Add(new Peak(s.XArray[i], s.YArray[i]));
}
if (s.MZOfInterest.Length > 0)
{
result.PrecursorMZ = s.MZOfInterest[0].Start;
}
result.ScanTimes.Add(new ScanTime(0, retentionTime));
return(result);
}
