public XCaliburRun2()
{
_msfileReader = new MSFileReaderLib.MSFileReader_XRawfile();
IsDataThresholded = true;
IsMsAbundanceReportedAsAverage = true;
MSFileType = Globals.MSFileType.Finnigan;
ContainsMSMSData = true;
XYData = new XYData();
ParentScanList = new Dictionary <int, int>();
}
internal List <Ion> GetSpectrum(string rawFile, int scanNo)
{
List <Ion> returnIons = new List <Ion>();
MSFileReaderLib.MSFileReader_XRawfile m2 = new MSFileReaderLib.MSFileReader_XRawfile();
m2.Open(rawFile);
m2.SetCurrentController(0, 1);
string filter = null;
m2.GetFilterForScanNum(scanNo, ref filter);
double scanCentroidPeakWidth = 0.005;
int arraySize = maxNoPeaks;
object massList = null;
object peakFlags = null;
m2.GetMassListFromScanNum(
ref scanNo,
filter,
scanIntensityCutoffType,
scanIntensityCutoffValue,
maxNoPeaks,
scanCentroidResult,
ref scanCentroidPeakWidth,
ref massList,
ref peakFlags,
ref arraySize);
double[,] thisMassList = (double[, ])massList;
int l = thisMassList.GetLength(1);
for (int counter = 0; counter < thisMassList.GetLength(1); counter++)
{
double intensity = Math.Round(thisMassList[1, counter], 1);
if (intensity > 0)
{
Ion ion = new Ion(Math.Round(thisMassList[0, counter], 5), intensity, 0, 0);
returnIons.Add(ion);
}
}
return(returnIons);
}
/// <summary>
///
/// </summary>
/// <param name="rawFile">The Thermo RAW File</param>
/// <param name="scanNumbers">If no scan numbers are in the array the filter will search for all scan numbers</param>
/// <returns></returns>
public List <MSLight> GetSpectra(string rawFile, List <int> scanNumbers, bool onlyMS1)
{
Console.WriteLine("Parsing " + rawFile);
MSFileReaderLib.MSFileReader_XRawfile m2 = new MSFileReaderLib.MSFileReader_XRawfile();
m2.Open(rawFile);
m2.SetCurrentController(0, 1);
//string filter2 = "";
//m2.GetFilterForScanNum(50, ref filter2);
int noSpectra = 0;
m2.GetNumSpectra(ref noSpectra);
MSLight lastMS1 = new MSLight();
List <MSLight> mySpectra = new List <MSLight>(noSpectra);
for (int i = 1; i <= noSpectra; i++)
{
string filter = null;
if (scanNumbers.Count == 0 || scanNumbers.Contains(i))
{
m2.GetFilterForScanNum(i, ref filter);
MSLight thisMS = new MSLight();
Ion precursor = new Ion(-1, -1, -1, -1);
if (isMS1.IsMatch(filter))
{
lastMS1 = thisMS;
}
else
{
if (onlyMS1)
{
continue;
}
if (!MyParams.UseThermoMonoIsotopicPrediction)
{
precursor = GetPrecursor(filter, lastMS1);
}
}
//-------------
double retentionTime = 0;
m2.RTFromScanNum(i, ref retentionTime);
string thisFilter = null;
m2.GetFilterForScanNum(i, ref thisFilter);
string flags = null;
m2.GetFlags(ref flags);
//------------
double scanCentroidPeakWidth = 0.005;
int arraySize = maxNoPeaks;
object massList = null;
object peakFlags = null;
m2.GetMassListFromScanNum(
ref i,
filter,
scanIntensityCutoffType,
scanIntensityCutoffValue,
maxNoPeaks,
scanCentroidResult,
ref scanCentroidPeakWidth,
ref massList,
ref peakFlags,
ref arraySize);
thisMS.ScanNumber = i;
object trailerLabels = null;
object trailerValues = null;
int cc = 0;
m2.GetTrailerExtraForScanNum(i, ref trailerLabels, ref trailerValues, ref cc);
object chargeStateObject = null;
m2.GetTrailerExtraValueForScanNum(i, "Charge State:", ref chargeStateObject);
double chargeState = double.Parse(chargeStateObject.ToString());
string[] theStringValues = (string[])trailerValues;
if (theStringValues[1].Contains("="))
{
string [] split = Regex.Split(theStringValues[1], "=");
string [] correction = Regex.Split(split[1], ";");
thisMS.IonInjectionTime = double.Parse(correction[0]);
}
else
{
thisMS.IonInjectionTime = double.Parse(theStringValues[2]);
}
Match instrument = captureInstrumentType.Match(filter);
thisMS.InstrumentType = instrument.Groups[1].ToString();
thisMS.ILines.Add("I\tFilter\t" + filter);
Match activationType = captureActivationType.Match(filter);
thisMS.ActivationType = activationType.Groups[1].ToString().ToUpper();
if (!thisMS.ActivationType.Equals(""))
{
if (MyParams.UseThermoMonoIsotopicPrediction)
{
object monoisotopicObject = null;
m2.GetTrailerExtraValueForScanNum(i, "Monoisotopic M/Z:", ref monoisotopicObject);
double objectValue = Math.Round(double.Parse(monoisotopicObject.ToString()), 4);
if (objectValue == 0)
{
//Thermo was unable to determine precursor so we will try to get it.
precursor = GetPrecursor(filter, lastMS1);
thisMS.ChargedPrecursor = precursor.MZ;
}
else
{
precursor = new Ion(objectValue, 1, 1, i);
//Console.WriteLine("Monoisotopic Thermo: " + precursor.MZ);
thisMS.ChargedPrecursor = precursor.MZ;
}
}
else
{
thisMS.ChargedPrecursor = precursor.MZ;
}
if (chargeState == 0)
{
thisMS.ZLines.Add("Z\t2\t" + Math.Round(PatternTools.pTools.DechargeMSPeakToPlus1(precursor.MZ, 2), 4));
thisMS.ZLines.Add("Z\t3\t" + Math.Round(PatternTools.pTools.DechargeMSPeakToPlus1(precursor.MZ, 3), 4));
}
else
{
thisMS.ZLines.Add("Z\t" + int.Parse(chargeState.ToString()).ToString() + "\t" + Math.Round(PatternTools.pTools.DechargeMSPeakToPlus1(precursor.MZ, chargeState), 4));
}
thisMS.ILines.Add("I\tPrecursorScan\t" + lastMS1.ScanNumber);
thisMS.ILines.Add("I\tPrecursorInt\t" + precursor.Intensity);
}
double[,] thisMassList = (double[, ])massList;
int l = thisMassList.GetLength(1);
double[] mz = new double[thisMassList.GetLength(1)];
double[] intensity = new double[thisMassList.GetLength(1)];
for (int counter = 0; counter < thisMassList.GetLength(1); counter++)
{
if (thisMassList[1, counter] > 0.5) //check if we have a minimum intensity
{
mz[counter] = Math.Round(thisMassList[0, counter], 5);
intensity[counter] = Math.Round(thisMassList[1, counter], 1);
//thisMS.MZ.Add(Math.Round(thisMassList[0, counter], 5));
//thisMS.Intensity.Add(Math.Round(thisMassList[1, counter], 1));
}
}
if (mz.Length == 0) //There is no use in saving an empty MS
{
continue;
}
thisMS.MZ = mz.ToList();
thisMS.Intensity = intensity.ToList();
thisMS.CromatographyRetentionTime = Math.Round(retentionTime, 3);
//----------------------------
mySpectra.Add(thisMS);
}
}
Console.WriteLine(".");
m2.Close();
//Some final cleanup
mySpectra.RemoveAll(a => a.MZ.Count < 5);
if (MyParams.ActivateSpectraCleaner)
{
CleanSpectra(mySpectra);
}
return(mySpectra);
}
