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);
}
public override XYData GetMassSpectrum(ScanSet scanset, double minMZ, double maxMZ)
{
// Note that we're using function attribute HandleProcessCorruptedStateExceptions
// to force .NET to properly catch critical errors thrown by the XRawfile DLL
Check.Require(scanset != null, "Can't get mass spectrum; inputted set of scans is null");
if (scanset == null)
{
return(null);
}
Check.Require(scanset.IndexValues.Count > 0, "Can't get mass spectrum; no scan numbers inputted");
double[,] vals = null;
var spectraAreSummed = scanset.IndexValues.Count > 1;
var scanNumFirst = scanset.IndexValues[0];
var scanNumLast = scanset.IndexValues[scanset.IndexValues.Count - 1];
string scanDescription;
if (spectraAreSummed)
{
scanDescription = "scan " + scanset.PrimaryScanNumber + "( summing scans " + scanNumFirst + " to " + scanNumLast + ")";
}
else
{
scanDescription = "scan " + scanset.PrimaryScanNumber;
}
try
{
if (spectraAreSummed)
{
var backgroundScan1First = 0;
var backgroundScan1Last = 0;
var backgroundScan2First = 0;
var backgroundScan2Last = 0;
const string filter = "p full ms"; //only sum MS1 data
const int intensityCutoffType = 0;
const int intensityCutoffValue = 0;
const int maxNumberOfPeaks = 0;
const int centroidResult = 0;
double centVal = 0;
object massList = null;
object peakFlags = null;
var arraySize = 0;
_msfileReader.GetAverageMassList(
ref scanNumFirst,
ref scanNumLast,
ref backgroundScan1First,
ref backgroundScan1Last,
ref backgroundScan2First,
ref backgroundScan2Last,
filter,
intensityCutoffType,
intensityCutoffValue,
maxNumberOfPeaks,
centroidResult,
ref centVal,
ref massList,
ref peakFlags,
ref arraySize);
vals = (double[, ])massList;
}
else
{
var scanNum = scanset.PrimaryScanNumber;
string filter = null;
const int intensityCutoffType = 0;
const int intensityCutoffValue = 0;
const int maxNumberOfPeaks = 0;
const int centroidResult = 0;
double centVal = 0;
object massList = null;
object peakFlags = null;
var arraySize = 0;
_msfileReader.GetMassListFromScanNum(
ref scanNum,
filter,
intensityCutoffType,
intensityCutoffValue,
maxNumberOfPeaks,
centroidResult,
ref centVal,
ref massList,
ref peakFlags,
ref arraySize);
vals = (double[, ])massList;
}
}
catch (System.AccessViolationException)
{
var errorMessage = "XCaliburRun2.GetMassSpectrum: Unable to load data for " + scanDescription +
"; possibly a corrupt .Raw file";
Console.WriteLine(errorMessage);
Logger.Instance.AddEntry(errorMessage);
}
catch (Exception ex)
{
Logger.Instance.AddEntry("XCaliburRun2.GetMassSpectrum: Unable to load data for " + scanDescription +
": " + ex.Message + "; possibly a corrupt .Raw file");
}
if (vals == null)
{
return(null);
}
var length = vals.GetLength(1);
var xvals = new List <double>();
var yvals = new List <double>();
// Note from MEM (October 2013)
// GetMassListFromScanNum generally returns the data sorted by m/z ascending
// However, there are edge cases for certain spectra in certain datasets where adjacent data points are out of order and need to be swapped
// Therefore, we must validate that the data is truly sorted, and if we find a discrepancy, sort it after populating xydata.Xvalues and xydata.Yvalues
var sortRequired = false;
for (var i = 0; i < length; i++)
{
var xValue = vals[0, i];
if (xValue < minMZ || xValue > maxMZ)
{
continue;
}
var yValue = vals[1, i];
if (i > 0 && xValue < vals[0, i - 1])
{
// Points are out of order; this rarely occurs but it is possible and has been observed
sortRequired = true;
}
xvals.Add(xValue);
yvals.Add(yValue);
}
var xydata = new XYData
{
Xvalues = xvals.ToArray(),
Yvalues = yvals.ToArray()
};
if (sortRequired)
{
Array.Sort(xydata.Xvalues, xydata.Yvalues);
}
return(xydata);
}