public bool IndexMassSpectralPeaks(SpectraFileInfo fileInfo, bool silent, Dictionary <SpectraFileInfo, Ms1ScanInfo[]> _ms1Scans)
{
if (!silent)
{
Console.WriteLine("Reading spectra file");
}
MsDataScan[] msDataScans = null;
// read spectra file
var ext = Path.GetExtension(fileInfo.FullFilePathWithExtension).ToUpperInvariant();
if (ext == ".MZML")
{
try
{
msDataScans = Mzml.LoadAllStaticData(fileInfo.FullFilePathWithExtension).GetAllScansList()
.OrderBy(p => p.OneBasedScanNumber).ToArray();
}
catch (FileNotFoundException)
{
if (!silent)
{
Console.WriteLine("\nCan't find .mzML file" + fileInfo.FullFilePathWithExtension + "\n");
}
return(false);
}
catch (Exception e)
{
if (!silent)
{
Console.WriteLine("Problem opening .mzML file " + fileInfo.FullFilePathWithExtension + "; " +
e.Message);
}
return(false);
}
for (int i = 0; i < msDataScans.Length; i++)
{
if (msDataScans[i].MsnOrder > 1)
{
msDataScans[i] = null;
}
}
}
else if (ext == ".RAW")
{
var tempList = new List <MsDataScan>();
ThermoDynamicData dynamicConnection = null;
try
{
dynamicConnection = new ThermoDynamicData(fileInfo.FullFilePathWithExtension);
// use thermo dynamic connection to get the ms1 scans and then dispose of the connection
for (int i = 0; i < dynamicConnection.MsOrdersByScan.Length; i++)
{
if (dynamicConnection.MsOrdersByScan[i] == 1)
{
tempList.Add(dynamicConnection.GetOneBasedScanFromDynamicConnection(i + 1));
}
else
{
tempList.Add(null);
}
}
dynamicConnection.CloseDynamicConnection();
}
catch (FileNotFoundException)
{
if (dynamicConnection != null)
{
dynamicConnection.CloseDynamicConnection();
}
if (!silent)
{
Console.WriteLine("\nCan't find .raw file" + fileInfo.FullFilePathWithExtension + "\n");
}
return(false);
}
catch (Exception e)
{
if (dynamicConnection != null)
{
dynamicConnection.CloseDynamicConnection();
}
if (!silent)
{
throw new MzLibException("FlashLFQ Error: Problem opening .raw file " + fileInfo.FullFilePathWithExtension + "; " + e.Message);
}
}
msDataScans = tempList.ToArray();
}
else
{
if (!silent)
{
Console.WriteLine("Unsupported file type " + ext);
return(false);
}
}
if (!silent)
{
Console.WriteLine("Indexing MS1 peaks");
}
if (!msDataScans.Any(p => p != null))
{
_indexedPeaks = new List <IndexedMassSpectralPeak> [0];
return(false);
}
_indexedPeaks = new List <IndexedMassSpectralPeak> [(int)Math.Ceiling(msDataScans.Where(p => p != null &&
p.MassSpectrum.LastX != null).Max(p => p.MassSpectrum.LastX.Value) * BinsPerDalton) + 1];
int scanIndex = 0;
List <Ms1ScanInfo> scanInfo = new List <Ms1ScanInfo>();
for (int i = 0; i < msDataScans.Length; i++)
{
if (msDataScans[i] == null)
{
continue;
}
scanInfo.Add(new Ms1ScanInfo(msDataScans[i].OneBasedScanNumber, scanIndex, msDataScans[i].RetentionTime));
for (int j = 0; j < msDataScans[i].MassSpectrum.XArray.Length; j++)
{
int roundedMz = (int)Math.Round(msDataScans[i].MassSpectrum.XArray[j] * BinsPerDalton, 0);
if (_indexedPeaks[roundedMz] == null)
{
_indexedPeaks[roundedMz] = new List <IndexedMassSpectralPeak>();
}
_indexedPeaks[roundedMz].Add(new IndexedMassSpectralPeak(msDataScans[i].MassSpectrum.XArray[j],
msDataScans[i].MassSpectrum.YArray[j], scanIndex, msDataScans[i].RetentionTime));
}
scanIndex++;
}
_ms1Scans.Add(fileInfo, scanInfo.ToArray());
if (_indexedPeaks == null || _indexedPeaks.Length == 0)
{
if (!silent)
{
Console.WriteLine("FlashLFQ Error: The file " + fileInfo.FilenameWithoutExtension + " contained no MS1 peaks!");
}
return(false);
}
return(true);
}
