public ThermoSpectrum(ThermoSpectrum thermoSpectrum) : this(thermoSpectrum.xArray, thermoSpectrum.yArray, thermoSpectrum._noises, thermoSpectrum._charges, thermoSpectrum._resolutions) { }
protected static IThermoScan GetMsDataOneBasedScanFromThermoFile( int nScanNumber, IXRawfile5 theConnection, 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; theConnection.GetNoiseData(ref pvarNoisePacket, nScanNumber); 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; } ThermoSpectrum 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(intensityArray, 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 ThermoSpectrum(mzArray, intensityArray, false); } else { thermoSpectrum = new ThermoSpectrum(data); } MZAnalyzerType mzAnalyzerType; switch ((ThermoMzAnalyzer)pnMassAnalyzerType) { case ThermoMzAnalyzer.FTMS: mzAnalyzerType = MZAnalyzerType.Orbitrap; break; default: mzAnalyzerType = MZAnalyzerType.Unknown; break; } 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; if (precursorInfo.nScanNumber > 0) { oneBasedPrecursorScanNumber = precursorInfo.nScanNumber; } else if (masterScanfromTrailierExtra.HasValue) { oneBasedPrecursorScanNumber = masterScanfromTrailierExtra.Value; } else { oneBasedPrecursorScanNumber = nScanNumber - 1; // Use info from ScanEvent! Loop back until scan event is equal to 1 while (true) { if (globalParams.scanEvent[oneBasedPrecursorScanNumber - 1] == 0) { object pvarValuesHere = null; object pvarLablesHere = null; int pnArraySizeHere = 0; theConnection.GetTrailerExtraForScanNum(oneBasedPrecursorScanNumber, ref pvarLablesHere, ref pvarValuesHere, ref pnArraySizeHere); string[] labelsHere = (string[])pvarLablesHere; string[] valuesHere = (string[])pvarValuesHere; for (int i = labelsHere.GetLowerBound(0); i <= labelsHere.GetUpperBound(0); i++) { if (labelsHere[i].StartsWith("Scan Event", StringComparison.Ordinal)) { globalParams.scanEvent[oneBasedPrecursorScanNumber - 1] = int.Parse(valuesHere[i], CultureInfo.InvariantCulture); } } } if (globalParams.scanEvent[oneBasedPrecursorScanNumber - 1] == 1) { break; } oneBasedPrecursorScanNumber--; } } 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); return(new ThermoScanWithPrecursor( nScanNumber, thermoSpectrum, pnMSOrder, PolarityRegex.IsMatch(pbstrFilter) ? Polarity.Positive : Polarity.Negative, pdStartTime, new MzRange(pdLowMass, pdHighMass), pbstrFilter, mzAnalyzerType, pdTIC, selectedIonGuessMZ, selectedIonGuessChargeStateGuess, ms2isolationWidthFromTrailerExtra, (DissociationType)pnActivationType, oneBasedPrecursorScanNumber, selectedIonGuessMonoisotopicMz, injectionTimeFromTrailerExtra, noiseData, nativeId)); } else { return(new ThermoScan(nScanNumber, thermoSpectrum, 1, PolarityRegex.IsMatch(pbstrFilter) ? Polarity.Positive : Polarity.Negative, pdStartTime, new MzRange(pdLowMass, pdHighMass), pbstrFilter, mzAnalyzerType, pdTIC, injectionTimeFromTrailerExtra, noiseData, nativeId)); } }
public ThermoSpectrum(ThermoSpectrum thermoSpectrum) : this(thermoSpectrum.XArray, thermoSpectrum.YArray, true) { }