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); }