private MZAnalyzerType GetMzAnalyzer(int spectrumNumber)
{
int mzanalyzer = 0;
_rawConnection.GetMassAnalyzerTypeForScanNum(spectrumNumber, ref mzanalyzer);
switch ((ThermoMzAnalyzer)mzanalyzer)
{
case ThermoMzAnalyzer.FTMS:
return(MZAnalyzerType.Orbitrap);
default:
return(MZAnalyzerType.Unknown);
}
}
public override MZAnalyzerType GetMzAnalyzer(int spectrumNumber)
{
int mzanalyzer = 0;
_rawConnection.GetMassAnalyzerTypeForScanNum(spectrumNumber, ref mzanalyzer);
switch ((ThermoMzAnalyzer)mzanalyzer)
{
case ThermoMzAnalyzer.FTMS:
return(MZAnalyzerType.Orbitrap);
case ThermoMzAnalyzer.ITMS:
return(MZAnalyzerType.IonTrap2D);
case ThermoMzAnalyzer.Sector:
return(MZAnalyzerType.Sector);
case ThermoMzAnalyzer.TOFMS:
return(MZAnalyzerType.TOF);
default:
return(MZAnalyzerType.Unknown);
}
}
public static MsDataScan GetMsDataOneBasedScanFromThermoFile(IXRawfile5 theConnection, int nScanNumber, ThermoGlobalParams globalParams, IFilteringParams filterParams = null)
{
int pnNumPackets = 0;
double pdLowMass = 0;
double pdHighMass = 0;
double pdTIC = 0;
double pdBasePeakMass = 0;
double pdBasePeakIntensity = 0;
int pnNumChannels = 0;
int pbUniformTime = 0;
double pdFrequency = 0;
double pdStartTime = 0;
theConnection.GetScanHeaderInfoForScanNum(nScanNumber, ref pnNumPackets, ref pdStartTime, ref pdLowMass, ref pdHighMass, ref pdTIC, ref pdBasePeakMass, ref pdBasePeakIntensity, ref pnNumChannels, ref pbUniformTime, ref pdFrequency);
double?ms2isolationWidthFromTrailerExtra = null;
double?injectionTimeFromTrailerExtra = null;
double?precursorMonoisotopicMZfromTrailierExtra = null;
int? chargeStatefromTrailierExtra = null;
int? masterScanfromTrailierExtra = null;
object pvarValues = null;
object pvarLables = null;
int pnArraySize = 0;
theConnection.GetTrailerExtraForScanNum(nScanNumber, ref pvarLables, ref pvarValues, ref pnArraySize);
string[] labels = (string[])pvarLables;
string[] values = (string[])pvarValues;
for (int i = labels.GetLowerBound(0); i <= labels.GetUpperBound(0); i++)
{
if (labels[i].StartsWith("MS2 Isolation Width", StringComparison.Ordinal))
{
ms2isolationWidthFromTrailerExtra = double.Parse(values[i], CultureInfo.InvariantCulture) == 0 ?
(double?)null :
double.Parse(values[i], CultureInfo.InvariantCulture);
}
if (labels[i].StartsWith("Ion Injection Time (ms)", StringComparison.Ordinal))
{
injectionTimeFromTrailerExtra = double.Parse(values[i], CultureInfo.InvariantCulture) == 0 ?
(double?)null :
double.Parse(values[i], CultureInfo.InvariantCulture);
}
if (labels[i].StartsWith("Monoisotopic M/Z", StringComparison.Ordinal))
{
precursorMonoisotopicMZfromTrailierExtra = double.Parse(values[i], CultureInfo.InvariantCulture) == 0 ?
(double?)null :
double.Parse(values[i], CultureInfo.InvariantCulture);
}
if (labels[i].StartsWith("Charge State", StringComparison.Ordinal))
{
chargeStatefromTrailierExtra = int.Parse(values[i], CultureInfo.InvariantCulture) == 0 ?
(int?)null :
int.Parse(values[i], CultureInfo.InvariantCulture);
}
if (labels[i].StartsWith("Master Scan Number", StringComparison.Ordinal))
{
masterScanfromTrailierExtra = int.Parse(values[i], CultureInfo.InvariantCulture) == 0 ?
(int?)null :
int.Parse(values[i], CultureInfo.InvariantCulture);
}
}
string pbstrFilter = null;
theConnection.GetFilterForScanNum(nScanNumber, ref pbstrFilter);
int pnMSOrder = 0;
theConnection.GetMSOrderForScanNum(nScanNumber, ref pnMSOrder);
int pnMassAnalyzerType = 0;
theConnection.GetMassAnalyzerTypeForScanNum(nScanNumber, ref pnMassAnalyzerType);
object pvarNoisePacket = null;
try //if there is no noise data
{
theConnection.GetNoiseData(ref pvarNoisePacket, nScanNumber);
}
catch
{
//pvarNoisePAcket is already null
}
double[,] noiseData = pvarNoisePacket as double[, ];
double[,] data;
try
{
object pvarFlags = null;
object pvarLabels = null;
theConnection.GetLabelData(ref pvarLabels, ref pvarFlags, ref nScanNumber);
data = pvarLabels as double[, ];
if (data == null || data.Length == 0)
{
throw new MzLibException("For spectrum number " + nScanNumber + " the data is null!");
}
}
catch (MzLibException)
{
// Warning: the masses reported by GetMassListFromScanNum when centroiding are not properly calibrated and thus could be off by 0.3 m/z or more
double pdCentroidPeakWidth = 0;
object pvarnMassList = null;
object pvarPeakFlags = null;
theConnection.GetMassListFromScanNum(ref nScanNumber, null, 0, 0, 0, 1, ref pdCentroidPeakWidth, ref pvarnMassList, ref pvarPeakFlags, ref pnArraySize);
data = (double[, ])pvarnMassList;
}
MzSpectrum thermoSpectrum;
if (filterParams != null && data.GetLength(1) > 0 && (filterParams.MinimumAllowedIntensityRatioToBasePeakM.HasValue || filterParams.NumberOfPeaksToKeepPerWindow.HasValue) && ((filterParams.ApplyTrimmingToMs1 && pnMSOrder == 1) || (filterParams.ApplyTrimmingToMsMs && pnMSOrder > 1)))
{
var count = data.GetLength(1);
var mzArray = new double[count];
var intensityArray = new double[count];
Buffer.BlockCopy(data, 0, mzArray, 0, sizeof(double) * count);
Buffer.BlockCopy(data, sizeof(double) * count, intensityArray, 0, sizeof(double) * count);
if (filterParams.NumberOfWindows == null)
{
int numPeaks = TopNpeakHelper(ref intensityArray, ref mzArray, filterParams);
//the following arrays are modified after TopN helper
Array.Resize(ref intensityArray, numPeaks);
Array.Resize(ref mzArray, numPeaks);
}
//Array reference passed by value, array calues will be modified after calling
else
{
WindowModeHelper(ref intensityArray, ref mzArray, filterParams);
}
Array.Sort(mzArray, intensityArray);
thermoSpectrum = new MzSpectrum(mzArray, intensityArray, false);
}
else
{
thermoSpectrum = new MzSpectrum(data);
}
MZAnalyzerType mzAnalyzerType;
if ((ThermoMzAnalyzer)pnMassAnalyzerType == ThermoMzAnalyzer.FTMS)
{
mzAnalyzerType = MZAnalyzerType.Orbitrap;
}
else
{
mzAnalyzerType = MZAnalyzerType.Unknown;
}
string nativeId = "controllerType=0 controllerNumber=1 scan=" + nScanNumber;
if (pnMSOrder > 1)
{
int pnActivationType = 0;
theConnection.GetActivationTypeForScanNum(nScanNumber, pnMSOrder, ref pnActivationType);
// INITIALIZE globalParams.couldBePrecursor[nScanNumber - 1] (for dynamic connections that don't have it initialized yet)
if (globalParams.CouldBePrecursor[nScanNumber - 1].Equals(default(ManagedThermoHelperLayer.PrecursorInfo)))
{
var ok = new ManagedThermoHelperLayer.HelperClass();
globalParams.CouldBePrecursor[nScanNumber - 1] = ok.GetSingleScanPrecursorInfo(nScanNumber, globalParams.FilePath);
}
var precursorInfo = globalParams.CouldBePrecursor[nScanNumber - 1];
// THIS METHOD IS BUGGY!!! DO NOT USE
//theConnection.FindPrecursorMassInFullScan(nScanNumber, ref pnMasterScan, ref pdFoundMass, ref pdHeaderMass, ref pnChargeState);
int oneBasedPrecursorScanNumber = -1;
if (precursorInfo.nScanNumber > 0)
{
oneBasedPrecursorScanNumber = precursorInfo.nScanNumber;
}
else if (masterScanfromTrailierExtra.HasValue && masterScanfromTrailierExtra > 0)
{
oneBasedPrecursorScanNumber = masterScanfromTrailierExtra.Value;
}
else
{
// we weren't able to get the precursor scan number, so we'll have to guess;
// loop back to find precursor scan
// (assumed to be the first scan before this scan with an MS order of this scan's MS order - 1)
// e.g., if this is an MS2 scan, find the first MS1 scan before this and assume that's the precursor scan
int scanOrder = globalParams.MsOrderByScan[nScanNumber - 1];
int precursorScanOrder = scanOrder - 1;
for (int i = nScanNumber - 1; i >= 0; i--)
{
int msOrder = globalParams.MsOrderByScan[i];
if (msOrder == precursorScanOrder)
{
oneBasedPrecursorScanNumber = i + 1;
break;
}
}
}
if (oneBasedPrecursorScanNumber == -1)
{
throw new MzLibException("Could not find precursor info for scan #" + nScanNumber);
}
int?selectedIonGuessChargeStateGuess = null;
if (precursorInfo.nChargeState > 0)
{
selectedIonGuessChargeStateGuess = precursorInfo.nChargeState;
}
else if (chargeStatefromTrailierExtra.HasValue)
{
selectedIonGuessChargeStateGuess = chargeStatefromTrailierExtra;
}
double?selectedIonGuessMonoisotopicMz = null;
if (precursorMonoisotopicMZfromTrailierExtra.HasValue && precursorMonoisotopicMZfromTrailierExtra.Value > 0)
{
selectedIonGuessMonoisotopicMz = precursorMonoisotopicMZfromTrailierExtra;
}
if (precursorInfo.dMonoIsoMass > 0 && !selectedIonGuessMonoisotopicMz.HasValue)
{
selectedIonGuessMonoisotopicMz = precursorInfo.dMonoIsoMass;
}
Regex matcher;
if (pbstrFilter.ToLower().Contains("msx"))
{
matcher = mFindParentIonOnlyMsx;
}
else
{
matcher = mFindParentIonOnlyNonMsx;
}
double selectedIonGuessMZ = double.Parse(matcher.Match(pbstrFilter).Groups["ParentMZ"].Value);
// int? selectedIonChargeStateGuess, double? selectedIonIntensity, double? isolationMZ, double? isolationWidth, DissociationType dissociationType, int? oneBasedPrecursorScanNumber, double? selectedIonMonoisotopicGuessMz, double? injectionTime, double[,] noiseData, string nativeId)
// double TotalIonCurrent, double selectedIonMZ, int? selectedIonChargeStateGuess, double? selectedIonIntensity, double? isolationMZ, double? isolationWidth, DissociationType dissociationType, int? oneBasedPrecursorScanNumber, double? selectedIonMonoisotopicGuessMz, double? injectionTime, double[,] noiseData, string nativeId)
return(new MsDataScan(
thermoSpectrum,
nScanNumber,
pnMSOrder,
true,
PolarityRegex.IsMatch(pbstrFilter) ? Polarity.Positive : Polarity.Negative,
pdStartTime,
new MzRange(pdLowMass, pdHighMass),
pbstrFilter,
mzAnalyzerType,
pdTIC,
injectionTimeFromTrailerExtra,
noiseData,
nativeId,
selectedIonGuessMZ,
selectedIonGuessChargeStateGuess,
null,
selectedIonGuessMZ,
ms2isolationWidthFromTrailerExtra,
(DissociationType)pnActivationType,
oneBasedPrecursorScanNumber,
selectedIonGuessMonoisotopicMz
));
}
else
{
return(new MsDataScan(
thermoSpectrum,
nScanNumber,
1,
true,
PolarityRegex.IsMatch(pbstrFilter) ? Polarity.Positive : Polarity.Negative,
pdStartTime,
new MzRange(pdLowMass, pdHighMass),
pbstrFilter,
mzAnalyzerType,
pdTIC,
injectionTimeFromTrailerExtra,
noiseData,
nativeId));
}
}
public void Convert(TaskProgress progress)
{
// temporarily keep the previous MS1 and MS2 spectra for possible speeding up;
MassSpectrum lastMS1Spec = null;
int lastMS1ScanNum = -1;
MassSpectrum lastMS2Spec = null;
int lastMS2ScanNum = -1;
int spectrumProcessed = 0;
// get instrument method names;
int pnNumInstMethods = 0;
object pvarNames = null;
_rawReader.GetInstMethodNames(ref pnNumInstMethods, ref pvarNames);
// create instance for data preprocessing;
PrecursorPredictor pp = null;
if (expType == ExperimentType.DIA && predictPrecursors)
{
pp = new PrecursorPredictor(DEFAULT_DIA_ISO_WIN_SIZE, 1, 6, 0);
}
//Scan whole raw file to remember scan Number of MS1
if (correctPrecMz)
{
for (int scanNum = FirstScanNum; scanNum <= LastScanNum; scanNum++)
{
int MSOrder = 0;
_rawReader.GetNumberOfMSOrdersFromScanNum(scanNum, ref MSOrder);
// check the MS level;
if (MSOrder == 0)
{
MS1ScanNum.Add(scanNum);
}
}
}
for (int scanNum = FirstScanNum; scanNum <= LastScanNum; scanNum++)
{
MassSpectrum spec = GetSpectrumByScanNum(scanNum);
// Console.Write("^^^^^" + spec.Peaks.Count);
if (spec == null)
{
continue;
}
// get the mass analyzer type;
int pnMassAnalyzerType = 0;
_rawReader.GetMassAnalyzerTypeForScanNum(scanNum, ref pnMassAnalyzerType);
// get the precursors;
//if (spec.MsLevel > 1)
//{
// Object pvarPrecursorInfos = null;
// int pnArraySize = 0;
// _rawReader.GetPrecursorInfoFromScanNum(scanNum, ref pvarPrecursorInfos, ref pnArraySize);
//}
// if the spectrum has an empty peak list, abandon this spectrum;
if (spec.Peaks.Count > 0)
{
if (spec.MsLevel > 1)
{
if (spec.PrecursorScanNumber == 0)
{
if (spec.MsLevel == 2)
{
spec.PrecursorScanNumber = lastMS1Spec == null ? 0 : lastMS1ScanNum;
}
else if (spec.MsLevel == 3)
{
spec.PrecursorScanNumber = lastMS2Spec == null ? 0 : lastMS2ScanNum;
}
}
}
if (spec.MsLevel == 2)
{
if (expType == ExperimentType.DDA)
{
if (spec.PrecursorScanNumber == lastMS1ScanNum)
{
// double check the precursor m/z value in the MS1 scan;
ExtractPrecursorMz(spec, lastMS1Spec);
if (correctPrecMz)
{
spec = CalCorrectPrecursor(spec, lastMS1Spec);
}
}
else
{
// check whether the precursor scan number is available;
if (spec.PrecursorScanNumber > 0)
{
MassSpectrum precSpec = GetSpectrumByScanNum(spec.PrecursorScanNumber);
// double check the precursor m/z value in the MS1 scan;
ExtractPrecursorMz(spec, precSpec);
if (correctPrecMz)
{
spec = CalCorrectPrecursor(spec, lastMS1Spec);
}
}
}
}
else if (expType == ExperimentType.DIA && predictPrecursors)
{
if (spec.PrecursorScanNumber == lastMS1ScanNum)
{
pp.PredictPrecursors(ref spec, ref lastMS1Spec);
}
else
{
// check whether the precursor scan number is available;
if (spec.PrecursorScanNumber > 0)
{
MassSpectrum precSpec = GetSpectrumByScanNum(spec.PrecursorScanNumber);
pp.PredictPrecursors(ref spec, ref precSpec);
}
}
}
}
if (spec.MsLevel == 3)
{
if (expType == ExperimentType.DDA)
{
if (spec.PrecursorScanNumber == lastMS2ScanNum)
{
// double check the precursor m/z value in the MS2 scan;
ExtractPrecursorMz(spec, lastMS2Spec);
}
else
{
// check whether the precursor scan number is available;
if (spec.PrecursorScanNumber > 0)
{
// double check the precursor m/z value in the MS2 scan;
MassSpectrum precSpec = GetSpectrumByScanNum(spec.PrecursorScanNumber);
ExtractPrecursorMz(spec, precSpec);
}
}
}
else if (expType == ExperimentType.DIA && predictPrecursors)
{
if (spec.PrecursorScanNumber == lastMS1ScanNum)
{
pp.PredictPrecursors(ref spec, ref lastMS1Spec);
}
else
{
// check whether the precursor scan number is available;
if (spec.PrecursorScanNumber > 0)
{
MassSpectrum precSpec = GetSpectrumByScanNum(spec.PrecursorScanNumber);
pp.PredictPrecursors(ref spec, ref precSpec);
}
}
}
}
if (spec.MsLevel == 2 && exportChargeState)
{
if (expType == ExperimentType.DDA)
{
//Collection charge of MS2
if (chargeNum.ContainsKey(spec.Precursors[0].Item2))
{
chargeNum[spec.Precursors[0].Item2] += 1;
}
else
{
chargeNum.Add(spec.Precursors[0].Item2, 1);
}
}
}
// write into the output files;
WriteToOutFiles(spec);
}
if (spec.MsLevel == 1)
{
lastMS1ScanNum = spec.ScanNumber;
lastMS1Spec = spec;
}
else if (spec.MsLevel == 2)
{
lastMS2ScanNum = spec.ScanNumber;
lastMS2Spec = spec;
}
if (progress.Aborted)
{
break;
}
spectrumProcessed++;
progress.CurrentProgress = (int)((double)spectrumProcessed / (LastScanNum - FirstScanNum + 1) * 100);
if (progress.CurrentProgress > lastProgress)
{
try
{
int currentLineCursor = Console.CursorTop;
Console.SetCursorPosition(0, Console.CursorTop);
lastProgress = progress.CurrentProgress;
Console.WriteLine(" Reading RAW File: " + lastProgress + "%");
Console.SetCursorPosition(0, currentLineCursor);
}
catch (IOException ex)
{
if (progress.CurrentProgress - lastProgress >= 10 || progress.CurrentProgress == 100)
{
lastProgress = progress.CurrentProgress;
Console.WriteLine(" Reading RAW File: " + lastProgress + "%");
}
}
}
}
if (expType == ExperimentType.DDA && exportChargeState)
{
_chargeNumWriter = new StreamWriter(outFileWithoutExtentionName + "txt");
//export charge states to file
ExportChargeStatesToFile(chargeNum);
}
// complete mzXML file writing if mzXMLWriter is available;
if (_mzXMLWriter != null)
{
_mzXMLWriter.WriteIndex();
_mzXMLWriter.WriteEnd();
}
}
