public override MsDataScan GetOneBasedScan(int oneBasedScanNumber)
{
if (Scans[oneBasedScanNumber - 1] == null)
{
Scans[oneBasedScanNumber - 1] = ThermoStaticData.GetMsDataOneBasedScanFromThermoFile(_rawConnection, oneBasedScanNumber, ThermoGlobalParams, filterParams);
}
return(Scans[oneBasedScanNumber - 1]);
}
public static ThermoDynamicData InitiateDynamicConnection(string filePath, IFilteringParams filterParams = null)
{
if (!File.Exists(filePath))
{
throw new FileNotFoundException();
}
if (!ThermoStaticData.CheckForMsFileReader())
{
throw new MzLibException("MsFileReader Not Installed");
}
IXRawfile5 _rawConnection = (IXRawfile5) new MSFileReader_XRawfile();
_rawConnection.Open(filePath);
_rawConnection.SetCurrentController(0, 1);
int lastspectrumNumber = -1;
_rawConnection.GetLastSpectrumNumber(ref lastspectrumNumber);
int firstspectrumNumber = -1;
_rawConnection.GetFirstSpectrumNumber(ref firstspectrumNumber);
var precursorInfoArray = new ManagedThermoHelperLayer.PrecursorInfo[lastspectrumNumber - firstspectrumNumber + 1];
string sendCheckSum;
using (FileStream stream = File.OpenRead(filePath))
{
using (SHA1Managed sha = new SHA1Managed())
{
byte[] checksum = sha.ComputeHash(stream);
sendCheckSum = BitConverter.ToString(checksum)
.Replace("-", string.Empty);
}
}
SourceFile sourceFile = new SourceFile(
@"Thermo nativeID format",
@"Thermo RAW format",
sendCheckSum,
@"SHA-1",
filePath,
Path.GetFileNameWithoutExtension(filePath));
var thermoGlobalParams = ThermoStaticData.GetAllGlobalStuff(_rawConnection, precursorInfoArray, filePath);
// if the spectra file only contains 1 scan and its MS order is 0, this indicates an errored read result
if (thermoGlobalParams.MsOrderByScan.Length == 1 && thermoGlobalParams.MsOrderByScan[0] == 0)
{
throw new MzLibException("Could not read data from file " + Path.GetFileName(filePath));
}
return(new ThermoDynamicData(_rawConnection, filterParams, lastspectrumNumber - firstspectrumNumber + 1, sourceFile, thermoGlobalParams));
}
