private static int GetOneBasedPrecursorScanNumber(Generated.mzMLType _mzMLConnection, int oneBasedSpectrumNumber)
{
string precursorID = _mzMLConnection.run.spectrumList.spectrum[oneBasedSpectrumNumber - 1].precursorList.precursor[0].spectrumRef;
do
{
oneBasedSpectrumNumber--;
} while (!precursorID.Equals(_mzMLConnection.run.spectrumList.spectrum[oneBasedSpectrumNumber - 1].id));
return(oneBasedSpectrumNumber);
}
private static MZAnalyzerType GetMzAnalyzer(Generated.mzMLType _mzMLConnection, string filter)
{
if (filter != null && analyzerDictionary.TryGetValue(MZAnalyzerTypeRegex.Match(filter).Captures[0].Value, out MZAnalyzerType valuee))
{
return(valuee);
}
// Maybe in the beginning of the file, there is a single analyzer?
// Gets the first analyzer used.
if (_mzMLConnection.instrumentConfigurationList.instrumentConfiguration != null)
{
return(analyzerDictionary.TryGetValue(_mzMLConnection.instrumentConfigurationList.instrumentConfiguration[0].cvParam[0].accession, out valuee) ? valuee : MZAnalyzerType.Unknown);
}
return(MZAnalyzerType.Unknown);
}
public static void CreateAndWriteMyMzmlWithCalibratedSpectra(IMsDataFile <IMsDataScan <IMzSpectrum <IMzPeak> > > myMsDataFile, string outputFile, bool writeIndexed)
{
var mzML = new Generated.mzMLType()
{
version = "1",
cvList = new Generated.CVListType()
};
mzML.cvList.count = "1";
mzML.cvList.cv = new Generated.CVType[1];
mzML.cvList.cv[0] = new Generated.CVType()
{
URI = @"https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master/psi-ms.obo",
fullName = "Proteomics Standards Initiative Mass Spectrometry Ontology",
id = "MS"
};
mzML.fileDescription = new Generated.FileDescriptionType()
{
fileContent = new Generated.ParamGroupType()
};
mzML.fileDescription.fileContent.cvParam = new Generated.CVParamType[2];
mzML.fileDescription.fileContent.cvParam[0] = new Generated.CVParamType()
{
accession = "MS:1000579" // MS1 Data
};
mzML.fileDescription.fileContent.cvParam[1] = new Generated.CVParamType()
{
accession = "MS:1000580" // MSn Data
};
mzML.softwareList = new Generated.SoftwareListType()
{
count = "1",
software = new Generated.SoftwareType[1]
};
// TODO: add the raw file fields
mzML.softwareList.software[0] = new Generated.SoftwareType()
{
id = "mzLib",
version = "1",
cvParam = new Generated.CVParamType[1]
};
mzML.softwareList.software[0].cvParam[0] = new Generated.CVParamType()
{
accession = "MS:1000799",
value = "mzLib"
};
// Leaving empty. Can't figure out the configurations.
// ToDo: read instrumentConfigurationList from mzML file
mzML.instrumentConfigurationList = new Generated.InstrumentConfigurationListType();
mzML.dataProcessingList = new Generated.DataProcessingListType()
{
count = "1",
dataProcessing = new Generated.DataProcessingType[1]
};
// Only writing mine! Might have had some other data processing (but not if it is a raw file)
// ToDo: read dataProcessingList from mzML file
mzML.dataProcessingList.dataProcessing[0] = new Generated.DataProcessingType()
{
id = "mzLibProcessing"
};
mzML.run = new Generated.RunType()
{
chromatogramList = new Generated.ChromatogramListType()
{
count = "1",
chromatogram = new Generated.ChromatogramType[1]
}
};
// ToDo: Finish the chromatogram writing!
mzML.run.chromatogramList.chromatogram[0] = new Generated.ChromatogramType();
mzML.run.spectrumList = new Generated.SpectrumListType()
{
count = (myMsDataFile.NumSpectra).ToString(CultureInfo.InvariantCulture),
defaultDataProcessingRef = "mzLibProcessing",
spectrum = new Generated.SpectrumType[myMsDataFile.NumSpectra]
};
// Loop over all spectra
for (int i = 1; i <= myMsDataFile.NumSpectra; i++)
{
mzML.run.spectrumList.spectrum[i - 1] = new Generated.SpectrumType()
{
defaultArrayLength = myMsDataFile.GetOneBasedScan(i).MassSpectrum.Size,
index = i.ToString(CultureInfo.InvariantCulture),
id = myMsDataFile.GetOneBasedScan(i).OneBasedScanNumber.ToString(),
cvParam = new Generated.CVParamType[8]
};
mzML.run.spectrumList.spectrum[i - 1].cvParam[0] = new Generated.CVParamType();
if (myMsDataFile.GetOneBasedScan(i).MsnOrder == 1)
{
mzML.run.spectrumList.spectrum[i - 1].cvParam[0].accession = "MS:1000579";
}
else if (myMsDataFile.GetOneBasedScan(i) is IMsDataScanWithPrecursor <IMzSpectrum <IMzPeak> > )
{
var scanWithPrecursor = myMsDataFile.GetOneBasedScan(i) as IMsDataScanWithPrecursor <IMzSpectrum <IMzPeak> >;
mzML.run.spectrumList.spectrum[i - 1].cvParam[0].accession = "MS:1000580";
// So needs a precursor!
mzML.run.spectrumList.spectrum[i - 1].precursorList = new Generated.PrecursorListType()
{
count = 1.ToString(),
precursor = new Generated.PrecursorType[1]
};
mzML.run.spectrumList.spectrum[i - 1].precursorList.precursor[0] = new Generated.PrecursorType();
string precursorID = scanWithPrecursor.OneBasedPrecursorScanNumber.ToString();
mzML.run.spectrumList.spectrum[i - 1].precursorList.precursor[0].spectrumRef = precursorID;
mzML.run.spectrumList.spectrum[i - 1].precursorList.precursor[0].selectedIonList = new Generated.SelectedIonListType()
{
count = 1.ToString(),
selectedIon = new Generated.ParamGroupType[1]
};
mzML.run.spectrumList.spectrum[i - 1].precursorList.precursor[0].selectedIonList.selectedIon[0] = new Generated.ParamGroupType()
{
cvParam = new Generated.CVParamType[3]
};
// Selected ion MZ
mzML.run.spectrumList.spectrum[i - 1].precursorList.precursor[0].selectedIonList.selectedIon[0].cvParam[0] = new Generated.CVParamType()
{
name = "selected ion m/z",
value = scanWithPrecursor.SelectedIonMZ.ToString(CultureInfo.InvariantCulture),
accession = "MS:1000744"
};
// Charge State
if (scanWithPrecursor.SelectedIonChargeStateGuess.HasValue)
{
mzML.run.spectrumList.spectrum[i - 1].precursorList.precursor[0].selectedIonList.selectedIon[0].cvParam[1] = new Generated.CVParamType()
{
name = "charge state",
value = scanWithPrecursor.SelectedIonChargeStateGuess.Value.ToString(CultureInfo.InvariantCulture),
accession = "MS:1000041"
};
}
// Selected ion intensity
if (scanWithPrecursor.SelectedIonIntensity.HasValue)
{
mzML.run.spectrumList.spectrum[i - 1].precursorList.precursor[0].selectedIonList.selectedIon[0].cvParam[2] = new Generated.CVParamType()
{
name = "peak intensity",
value = scanWithPrecursor.SelectedIonIntensity.Value.ToString(CultureInfo.InvariantCulture),
accession = "MS:1000042"
};
}
MzRange isolationRange = scanWithPrecursor.IsolationRange;
mzML.run.spectrumList.spectrum[i - 1].precursorList.precursor[0].isolationWindow = new Generated.ParamGroupType()
{
cvParam = new Generated.CVParamType[3]
};
mzML.run.spectrumList.spectrum[i - 1].precursorList.precursor[0].isolationWindow.cvParam[0] = new Generated.CVParamType()
{
accession = "MS:1000827",
name = "isolation window target m/z",
value = isolationRange.Mean.ToString(CultureInfo.InvariantCulture)
};
mzML.run.spectrumList.spectrum[i - 1].precursorList.precursor[0].isolationWindow.cvParam[1] = new Generated.CVParamType()
{
accession = "MS:1000828",
name = "isolation window lower offset",
value = (isolationRange.Width / 2).ToString(CultureInfo.InvariantCulture)
};
mzML.run.spectrumList.spectrum[i - 1].precursorList.precursor[0].isolationWindow.cvParam[2] = new Generated.CVParamType()
{
accession = "MS:1000829",
name = "isolation window upper offset",
value = (isolationRange.Width / 2).ToString(CultureInfo.InvariantCulture)
};
mzML.run.spectrumList.spectrum[i - 1].precursorList.precursor[0].activation = new Generated.ParamGroupType()
{
cvParam = new Generated.CVParamType[1]
};
mzML.run.spectrumList.spectrum[i - 1].precursorList.precursor[0].activation.cvParam[0] = new Generated.CVParamType();
DissociationType dissociationType = scanWithPrecursor.DissociationType;
mzML.run.spectrumList.spectrum[i - 1].precursorList.precursor[0].activation.cvParam[0].accession = DissociationTypeAccessions[dissociationType];
mzML.run.spectrumList.spectrum[i - 1].precursorList.precursor[0].activation.cvParam[0].name = DissociationTypeNames[dissociationType];
}
mzML.run.spectrumList.spectrum[i - 1].cvParam[1] = new Generated.CVParamType()
{
name = "ms level",
accession = "MS:1000511",
value = myMsDataFile.GetOneBasedScan(i).MsnOrder.ToString(CultureInfo.InvariantCulture)
};
mzML.run.spectrumList.spectrum[i - 1].cvParam[2] = new Generated.CVParamType()
{
name = CentroidNames[myMsDataFile.GetOneBasedScan(i).IsCentroid],
accession = CentroidAccessions[myMsDataFile.GetOneBasedScan(i).IsCentroid]
};
if (PolarityNames.TryGetValue(myMsDataFile.GetOneBasedScan(i).Polarity, out string polarityName) && PolarityAccessions.TryGetValue(myMsDataFile.GetOneBasedScan(i).Polarity, out string polarityAccession))
{
mzML.run.spectrumList.spectrum[i - 1].cvParam[3] = new Generated.CVParamType()
{
name = polarityName,
accession = polarityAccession
};
}
// Spectrum title
mzML.run.spectrumList.spectrum[i - 1].cvParam[4] = new Generated.CVParamType()
{
name = "spectrum title",
accession = "MS:1000796",
value = myMsDataFile.GetOneBasedScan(i).OneBasedScanNumber.ToString()
};
if ((myMsDataFile.GetOneBasedScan(i).MassSpectrum.Size) > 0)
{
// Lowest observed mz
mzML.run.spectrumList.spectrum[i - 1].cvParam[5] = new Generated.CVParamType()
{
name = "lowest observed m/z",
accession = "MS:1000528",
value = myMsDataFile.GetOneBasedScan(i).MassSpectrum.FirstX.ToString(CultureInfo.InvariantCulture)
};
// Highest observed mz
mzML.run.spectrumList.spectrum[i - 1].cvParam[6] = new Generated.CVParamType()
{
name = "highest observed m/z",
accession = "MS:1000527",
value = myMsDataFile.GetOneBasedScan(i).MassSpectrum.LastX.ToString(CultureInfo.InvariantCulture)
};
}
// Total ion current
mzML.run.spectrumList.spectrum[i - 1].cvParam[7] = new Generated.CVParamType()
{
name = "total ion current",
accession = "MS:1000285",
value = myMsDataFile.GetOneBasedScan(i).TotalIonCurrent.ToString(CultureInfo.InvariantCulture)
};
// Retention time
mzML.run.spectrumList.spectrum[i - 1].scanList = new Generated.ScanListType()
{
count = "1",
scan = new Generated.ScanType[1]
};
mzML.run.spectrumList.spectrum[i - 1].scanList.scan[0] = new Generated.ScanType()
{
cvParam = new Generated.CVParamType[3]
};
mzML.run.spectrumList.spectrum[i - 1].scanList.scan[0].cvParam[0] = new Generated.CVParamType()
{
name = "scan start time",
accession = "MS:1000016",
value = myMsDataFile.GetOneBasedScan(i).RetentionTime.ToString(CultureInfo.InvariantCulture),
unitCvRef = "UO",
unitAccession = "UO:0000031",
unitName = "minute"
};
mzML.run.spectrumList.spectrum[i - 1].scanList.scan[0].cvParam[1] = new Generated.CVParamType()
{
name = "filter string",
accession = "MS:1000512",
value = myMsDataFile.GetOneBasedScan(i).ScanFilter
};
if (myMsDataFile.GetOneBasedScan(i).InjectionTime.HasValue)
{
mzML.run.spectrumList.spectrum[i - 1].scanList.scan[0].cvParam[2] = new Generated.CVParamType()
{
name = "ion injection time",
accession = "MS:1000927",
value = myMsDataFile.GetOneBasedScan(i).InjectionTime.Value.ToString(CultureInfo.InvariantCulture)
};
}
if (myMsDataFile.GetOneBasedScan(i) is IMsDataScanWithPrecursor <IMzSpectrum <IMzPeak> > )
{
var scanWithPrecursor = myMsDataFile.GetOneBasedScan(i) as IMsDataScanWithPrecursor <IMzSpectrum <IMzPeak> >;
if (scanWithPrecursor.SelectedIonMonoisotopicGuessMz.HasValue)
{
mzML.run.spectrumList.spectrum[i - 1].scanList.scan[0].userParam = new Generated.UserParamType[1];
mzML.run.spectrumList.spectrum[i - 1].scanList.scan[0].userParam[0] = new Generated.UserParamType()
{
name = "[mzLib]Monoisotopic M/Z:",
value = scanWithPrecursor.SelectedIonMonoisotopicGuessMz.Value.ToString(CultureInfo.InvariantCulture)
};
}
}
mzML.run.spectrumList.spectrum[i - 1].scanList.scan[0].scanWindowList = new Generated.ScanWindowListType()
{
count = 1,
scanWindow = new Generated.ParamGroupType[1]
};
mzML.run.spectrumList.spectrum[i - 1].scanList.scan[0].scanWindowList.scanWindow[0] = new Generated.ParamGroupType()
{
cvParam = new Generated.CVParamType[2]
};
mzML.run.spectrumList.spectrum[i - 1].scanList.scan[0].scanWindowList.scanWindow[0].cvParam[0] = new Generated.CVParamType()
{
name = "scan window lower limit",
accession = "MS:1000501",
value = myMsDataFile.GetOneBasedScan(i).ScanWindowRange.Minimum.ToString(CultureInfo.InvariantCulture)
};
mzML.run.spectrumList.spectrum[i - 1].scanList.scan[0].scanWindowList.scanWindow[0].cvParam[1] = new Generated.CVParamType()
{
name = "scan window upper limit",
accession = "MS:1000500",
value = myMsDataFile.GetOneBasedScan(i).ScanWindowRange.Maximum.ToString(CultureInfo.InvariantCulture)
};
mzML.run.spectrumList.spectrum[i - 1].binaryDataArrayList = new Generated.BinaryDataArrayListType()
{
// ONLY WRITING M/Z AND INTENSITY DATA, NOT THE CHARGE! (but can add charge info later)
// CHARGE (and other stuff) CAN BE IMPORTANT IN ML APPLICATIONS!!!!!
count = 2.ToString(),
binaryDataArray = new Generated.BinaryDataArrayType[5]
};
// M/Z Data
mzML.run.spectrumList.spectrum[i - 1].binaryDataArrayList.binaryDataArray[0] = new Generated.BinaryDataArrayType()
{
binary = myMsDataFile.GetOneBasedScan(i).MassSpectrum.Get64BitXarray()
};
mzML.run.spectrumList.spectrum[i - 1].binaryDataArrayList.binaryDataArray[0].encodedLength = (4 * Math.Ceiling(((double)mzML.run.spectrumList.spectrum[i - 1].binaryDataArrayList.binaryDataArray[0].binary.Length / 3))).ToString(CultureInfo.InvariantCulture);
mzML.run.spectrumList.spectrum[i - 1].binaryDataArrayList.binaryDataArray[0].cvParam = new Generated.CVParamType[3];
mzML.run.spectrumList.spectrum[i - 1].binaryDataArrayList.binaryDataArray[0].cvParam[0] = new Generated.CVParamType()
{
accession = "MS:1000514",
name = "m/z array"
};
mzML.run.spectrumList.spectrum[i - 1].binaryDataArrayList.binaryDataArray[0].cvParam[1] = new Generated.CVParamType()
{
accession = "MS:1000523",
name = "64-bit float"
};
mzML.run.spectrumList.spectrum[i - 1].binaryDataArrayList.binaryDataArray[0].cvParam[2] = new Generated.CVParamType()
{
accession = "MS:1000576",
name = "no compression"
};
// Intensity Data
mzML.run.spectrumList.spectrum[i - 1].binaryDataArrayList.binaryDataArray[1] = new Generated.BinaryDataArrayType()
{
binary = myMsDataFile.GetOneBasedScan(i).MassSpectrum.Get64BitYarray()
};
mzML.run.spectrumList.spectrum[i - 1].binaryDataArrayList.binaryDataArray[1].encodedLength = (4 * Math.Ceiling(((double)mzML.run.spectrumList.spectrum[i - 1].binaryDataArrayList.binaryDataArray[1].binary.Length / 3))).ToString(CultureInfo.InvariantCulture);
mzML.run.spectrumList.spectrum[i - 1].binaryDataArrayList.binaryDataArray[1].cvParam = new Generated.CVParamType[3];
mzML.run.spectrumList.spectrum[i - 1].binaryDataArrayList.binaryDataArray[1].cvParam[0] = new Generated.CVParamType()
{
accession = "MS:1000515",
name = "intensity array"
};
mzML.run.spectrumList.spectrum[i - 1].binaryDataArrayList.binaryDataArray[1].cvParam[1] = new Generated.CVParamType()
{
accession = "MS:1000523",
name = "64-bit float"
};
mzML.run.spectrumList.spectrum[i - 1].binaryDataArrayList.binaryDataArray[1].cvParam[2] = new Generated.CVParamType()
{
accession = "MS:1000576",
name = "no compression"
};
if (myMsDataFile.GetOneBasedScan(i).NoiseData != null)
{
// mass
mzML.run.spectrumList.spectrum[i - 1].binaryDataArrayList.binaryDataArray[2] = new Generated.BinaryDataArrayType()
{
binary = myMsDataFile.GetOneBasedScan(i).Get64BitNoiseDataMass()
};
mzML.run.spectrumList.spectrum[i - 1].binaryDataArrayList.binaryDataArray[2].encodedLength = (4 * Math.Ceiling(((double)mzML.run.spectrumList.spectrum[i - 1].binaryDataArrayList.binaryDataArray[2].binary.Length / 3))).ToString(CultureInfo.InvariantCulture);
mzML.run.spectrumList.spectrum[i - 1].binaryDataArrayList.binaryDataArray[2].cvParam = new Generated.CVParamType[3];
mzML.run.spectrumList.spectrum[i - 1].binaryDataArrayList.binaryDataArray[2].cvParam[0] = new Generated.CVParamType()
{
accession = "MS:1000786",
name = "non-standard data array"
};
mzML.run.spectrumList.spectrum[i - 1].binaryDataArrayList.binaryDataArray[2].cvParam[1] = new Generated.CVParamType()
{
accession = "MS:1000523",
name = "64-bit float"
};
mzML.run.spectrumList.spectrum[i - 1].binaryDataArrayList.binaryDataArray[2].cvParam[2] = new Generated.CVParamType()
{
accession = "MS:1000576",
name = "no compression"
};
mzML.run.spectrumList.spectrum[i - 1].binaryDataArrayList.binaryDataArray[2].userParam = new Generated.UserParamType[1];
mzML.run.spectrumList.spectrum[i - 1].binaryDataArrayList.binaryDataArray[2].userParam[0] = new Generated.UserParamType()
{
name = "kelleherCustomType",
value = "noise m/z"
};
// noise
mzML.run.spectrumList.spectrum[i - 1].binaryDataArrayList.binaryDataArray[3] = new Generated.BinaryDataArrayType()
{
binary = myMsDataFile.GetOneBasedScan(i).Get64BitNoiseDataNoise()
};
mzML.run.spectrumList.spectrum[i - 1].binaryDataArrayList.binaryDataArray[3].encodedLength = (4 * Math.Ceiling(((double)mzML.run.spectrumList.spectrum[i - 1].binaryDataArrayList.binaryDataArray[3].binary.Length / 3))).ToString(CultureInfo.InvariantCulture);
mzML.run.spectrumList.spectrum[i - 1].binaryDataArrayList.binaryDataArray[3].cvParam = new Generated.CVParamType[3];
mzML.run.spectrumList.spectrum[i - 1].binaryDataArrayList.binaryDataArray[3].cvParam[0] = new Generated.CVParamType()
{
accession = "MS:1000786",
name = "non-standard data array"
};
mzML.run.spectrumList.spectrum[i - 1].binaryDataArrayList.binaryDataArray[3].cvParam[1] = new Generated.CVParamType()
{
accession = "MS:1000523",
name = "64-bit float"
};
mzML.run.spectrumList.spectrum[i - 1].binaryDataArrayList.binaryDataArray[3].cvParam[2] = new Generated.CVParamType()
{
accession = "MS:1000576",
name = "no compression"
};
mzML.run.spectrumList.spectrum[i - 1].binaryDataArrayList.binaryDataArray[3].userParam = new Generated.UserParamType[1];
mzML.run.spectrumList.spectrum[i - 1].binaryDataArrayList.binaryDataArray[3].userParam[0] = new Generated.UserParamType()
{
name = "kelleherCustomType",
value = "noise baseline"
};
// baseline
mzML.run.spectrumList.spectrum[i - 1].binaryDataArrayList.binaryDataArray[4] = new Generated.BinaryDataArrayType()
{
binary = myMsDataFile.GetOneBasedScan(i).Get64BitNoiseDataBaseline()
};
mzML.run.spectrumList.spectrum[i - 1].binaryDataArrayList.binaryDataArray[4].encodedLength = (4 * Math.Ceiling(((double)mzML.run.spectrumList.spectrum[i - 1].binaryDataArrayList.binaryDataArray[4].binary.Length / 3))).ToString(CultureInfo.InvariantCulture);
mzML.run.spectrumList.spectrum[i - 1].binaryDataArrayList.binaryDataArray[4].cvParam = new Generated.CVParamType[3];
mzML.run.spectrumList.spectrum[i - 1].binaryDataArrayList.binaryDataArray[4].cvParam[0] = new Generated.CVParamType()
{
accession = "MS:1000786",
name = "non-standard data array"
};
mzML.run.spectrumList.spectrum[i - 1].binaryDataArrayList.binaryDataArray[4].cvParam[1] = new Generated.CVParamType()
{
accession = "MS:1000523",
name = "64-bit float"
};
mzML.run.spectrumList.spectrum[i - 1].binaryDataArrayList.binaryDataArray[4].cvParam[2] = new Generated.CVParamType()
{
accession = "MS:1000576",
name = "no compression"
};
mzML.run.spectrumList.spectrum[i - 1].binaryDataArrayList.binaryDataArray[4].userParam = new Generated.UserParamType[1];
mzML.run.spectrumList.spectrum[i - 1].binaryDataArrayList.binaryDataArray[4].userParam[0] = new Generated.UserParamType()
{
name = "kelleherCustomType",
value = "noise intensity"
};
}
}
if (writeIndexed)
{
throw new NotImplementedException("Writing indexed mzMLs not yet supported");
}
else
{
using (TextWriter writer = new StreamWriter(outputFile))
{
mzmlSerializer.Serialize(writer, mzML);
}
}
}
private static MsDataScan GetMsDataOneBasedScanFromConnection(Generated.mzMLType _mzMLConnection, int oneBasedIndex, IFilteringParams filterParams)
{
// Read in the instrument configuration types from connection (in mzml it's at the start)
Generated.InstrumentConfigurationType[] configs = new Generated.InstrumentConfigurationType[_mzMLConnection.instrumentConfigurationList.instrumentConfiguration.Length];
for (int i = 0; i < _mzMLConnection.instrumentConfigurationList.instrumentConfiguration.Length; i++)
{
configs[i] = _mzMLConnection.instrumentConfigurationList.instrumentConfiguration[i];
}
var defaultInstrumentConfig = _mzMLConnection.run.defaultInstrumentConfigurationRef;
// May be null!
var scanSpecificInsturmentConfig = _mzMLConnection.run.spectrumList.spectrum[oneBasedIndex - 1].scanList.scan[0].instrumentConfigurationRef;
MZAnalyzerType analyzer = default(MZAnalyzerType);
// use default
if (scanSpecificInsturmentConfig == null || scanSpecificInsturmentConfig == defaultInstrumentConfig)
{
if (configs[0].componentList == null)
{
analyzer = default(MZAnalyzerType);
}
else if (analyzerDictionary.TryGetValue(configs[0].componentList.analyzer[0].cvParam[0].accession, out MZAnalyzerType returnVal))
{
analyzer = returnVal;
}
}
// use scan-specific
else
{
for (int i = 0; i < _mzMLConnection.instrumentConfigurationList.instrumentConfiguration.Length; i++)
{
if (configs[i].id.Equals(scanSpecificInsturmentConfig))
{
analyzerDictionary.TryGetValue(configs[i].componentList.analyzer[0].cvParam[0].accession, out MZAnalyzerType returnVal);
analyzer = returnVal;
}
}
}
string nativeId = _mzMLConnection.run.spectrumList.spectrum[oneBasedIndex - 1].id;
int? msOrder = null;
bool? isCentroid = null;
Polarity polarity = Polarity.Unknown;
double tic = double.NaN;
foreach (Generated.CVParamType cv in _mzMLConnection.run.spectrumList.spectrum[oneBasedIndex - 1].cvParam)
{
if (cv.accession.Equals(_msnOrderAccession))
{
msOrder = int.Parse(cv.value);
}
if (cv.accession.Equals(_centroidSpectrum))
{
isCentroid = true;
}
if (cv.accession.Equals(_profileSpectrum))
{
throw new MzLibException("Reading profile mode mzmls not supported");
}
if (cv.accession.Equals(_totalIonCurrent))
{
tic = double.Parse(cv.value, CultureInfo.InvariantCulture);
}
if (polarity.Equals(Polarity.Unknown))
{
polarityDictionary.TryGetValue(cv.accession, out polarity);
}
}
if (!msOrder.HasValue || !isCentroid.HasValue)
{
throw new MzLibException("!msOrder.HasValue || !isCentroid.HasValue");
}
double[] masses = new double[0];
double[] intensities = new double[0];
foreach (Generated.BinaryDataArrayType binaryData in _mzMLConnection.run.spectrumList.spectrum[oneBasedIndex - 1].binaryDataArrayList.binaryDataArray)
{
bool compressed = false;
bool mzArray = false;
bool intensityArray = false;
bool is32bit = true;
foreach (Generated.CVParamType cv in binaryData.cvParam)
{
compressed |= cv.accession.Equals(_zlibCompression);
is32bit &= !cv.accession.Equals(_64bit);
is32bit |= cv.accession.Equals(_32bit);
mzArray |= cv.accession.Equals(_mzArray);
intensityArray |= cv.accession.Equals(_intensityArray);
}
double[] data = ConvertBase64ToDoubles(binaryData.binary, compressed, is32bit);
if (mzArray)
{
masses = data;
}
if (intensityArray)
{
intensities = data;
}
}
double high = double.NaN;
double low = double.NaN;
var aScanWindowList = _mzMLConnection.run.spectrumList.spectrum[oneBasedIndex - 1].scanList.scan[0].scanWindowList;
if (aScanWindowList != null)
{
foreach (Generated.CVParamType cv in _mzMLConnection.run.spectrumList.spectrum[oneBasedIndex - 1].scanList.scan[0].scanWindowList.scanWindow[0].cvParam)
{
if (cv.accession.Equals(_scanWindowLowerLimit))
{
low = double.Parse(cv.value, CultureInfo.InvariantCulture);
}
else if (cv.accession.Equals(_scanWindowUpperLimit))
{
high = double.Parse(cv.value, CultureInfo.InvariantCulture);
}
}
}
if (filterParams != null && intensities.Length > 0 && ((filterParams.ApplyTrimmingToMs1 && msOrder.Value == 1) || (filterParams.ApplyTrimmingToMsMs && msOrder.Value > 1)))
{
WindowModeHelper(ref intensities, ref masses, filterParams, low, high);
}
Array.Sort(masses, intensities);
var mzmlMzSpectrum = new MzSpectrum(masses, intensities, false);
double rtInMinutes = double.NaN;
string scanFilter = null;
double?injectionTime = null;
int oneBasedScanNumber = oneBasedIndex;
if (_mzMLConnection.run.spectrumList.spectrum[oneBasedIndex - 1].scanList.scan[0].cvParam != null)
{
foreach (Generated.CVParamType cv in _mzMLConnection.run.spectrumList.spectrum[oneBasedIndex - 1].scanList.scan[0].cvParam)
{
if (cv.accession.Equals(_retentionTime))
{
rtInMinutes = double.Parse(cv.value, CultureInfo.InvariantCulture);
if (cv.unitName == "second")
{
rtInMinutes /= 60;
}
}
if (cv.accession.Equals(_filterString))
{
scanFilter = cv.value;
}
if (cv.accession.Equals(_ionInjectionTime))
{
injectionTime = double.Parse(cv.value, CultureInfo.InvariantCulture);
}
if (cv.accession.Equals(_oneBasedScanNumber)) //get the real one based spectrum number (if available), the other assumes they are in order. This is present in .mgf->.mzml conversions from MSConvert
{
oneBasedScanNumber = int.Parse(cv.value);
}
}
}
if (msOrder.Value == 1)
{
return(new MsDataScan(
mzmlMzSpectrum,
oneBasedScanNumber,
msOrder.Value,
isCentroid.Value,
polarity,
rtInMinutes,
new MzRange(low, high),
scanFilter,
analyzer,
tic,
injectionTime,
null,
nativeId));
}
double selectedIonMz = double.NaN;
int? selectedIonCharge = null;
double?selectedIonIntensity = null;
foreach (Generated.CVParamType cv in _mzMLConnection.run.spectrumList.spectrum[oneBasedIndex - 1].precursorList.precursor[0].selectedIonList.selectedIon[0].cvParam)
{
if (cv.accession.Equals(_selectedIonMz))
{
selectedIonMz = double.Parse(cv.value, CultureInfo.InvariantCulture);
}
if (cv.accession.Equals(_precursorCharge))
{
selectedIonCharge = int.Parse(cv.value, CultureInfo.InvariantCulture);
}
if (cv.accession.Equals(_peakIntensity))
{
selectedIonIntensity = double.Parse(cv.value, CultureInfo.InvariantCulture);
}
}
double?isolationMz = null;
double lowIsolation = double.NaN;
double highIsolation = double.NaN;
if (_mzMLConnection.run.spectrumList.spectrum[oneBasedIndex - 1].precursorList.precursor[0].isolationWindow != null)
{
foreach (Generated.CVParamType cv in _mzMLConnection.run.spectrumList.spectrum[oneBasedIndex - 1].precursorList.precursor[0].isolationWindow.cvParam)
{
if (cv.accession.Equals(_isolationWindowTargetMZ))
{
isolationMz = double.Parse(cv.value, CultureInfo.InvariantCulture);
}
if (cv.accession.Equals(_isolationWindowLowerOffset))
{
lowIsolation = double.Parse(cv.value, CultureInfo.InvariantCulture);
}
if (cv.accession.Equals(_isolationWindowUpperOffset))
{
highIsolation = double.Parse(cv.value, CultureInfo.InvariantCulture);
}
}
}
DissociationType dissociationType = DissociationType.Unknown;
if (_mzMLConnection.run.spectrumList.spectrum[oneBasedIndex - 1].precursorList.precursor[0].activation.cvParam != null)
{
foreach (Generated.CVParamType cv in _mzMLConnection.run.spectrumList.spectrum[oneBasedIndex - 1].precursorList.precursor[0].activation.cvParam)
{
dissociationDictionary.TryGetValue(cv.accession, out dissociationType);
}
}
double?monoisotopicMz = null;
if (_mzMLConnection.run.spectrumList.spectrum[oneBasedIndex - 1].scanList.scan[0].userParam != null)
{
foreach (var userParam in _mzMLConnection.run.spectrumList.spectrum[oneBasedIndex - 1].scanList.scan[0].userParam)
{
if (userParam.name.EndsWith("Monoisotopic M/Z:"))
{
monoisotopicMz = double.Parse(userParam.value, CultureInfo.InvariantCulture);
}
}
}
int?precursorScanNumber;
if (_mzMLConnection.run.spectrumList.spectrum[oneBasedIndex - 1].precursorList.precursor[0].spectrumRef == null)
{
precursorScanNumber = null;
}
else
{
precursorScanNumber = GetOneBasedPrecursorScanNumber(_mzMLConnection, oneBasedIndex);
}
return(new MsDataScan(
mzmlMzSpectrum,
oneBasedIndex,
msOrder.Value,
isCentroid.Value,
polarity,
rtInMinutes,
new MzRange(low, high),
scanFilter,
analyzer,
tic,
injectionTime,
null,
nativeId,
selectedIonMz,
selectedIonCharge,
selectedIonIntensity,
isolationMz,
lowIsolation + highIsolation,
dissociationType,
precursorScanNumber,
monoisotopicMz
));
}
private static MsDataScan GetMsDataOneBasedScanFromConnection(Generated.mzMLType _mzMLConnection, int oneBasedIndex, IFilteringParams filterParams)
{
// Read in the instrument configuration types from connection (in mzml it's at the start)
Generated.InstrumentConfigurationType[] configs = new Generated.InstrumentConfigurationType[_mzMLConnection.instrumentConfigurationList.instrumentConfiguration.Length];
for (int i = 0; i < _mzMLConnection.instrumentConfigurationList.instrumentConfiguration.Length; i++)
{
configs[i] = _mzMLConnection.instrumentConfigurationList.instrumentConfiguration[i];
}
var defaultInstrumentConfig = _mzMLConnection.run.defaultInstrumentConfigurationRef;
// May be null!
var scanSpecificInsturmentConfig = _mzMLConnection.run.spectrumList.spectrum[oneBasedIndex - 1].scanList.scan[0].instrumentConfigurationRef;
MZAnalyzerType analyzer = default(MZAnalyzerType);
// use default
if (scanSpecificInsturmentConfig == null || scanSpecificInsturmentConfig == defaultInstrumentConfig)
{
if (configs[0].componentList == null)
{
analyzer = default(MZAnalyzerType);
}
else if (AnalyzerDictionary.TryGetValue(configs[0].componentList.analyzer[0].cvParam[0].accession, out MZAnalyzerType returnVal))
{
analyzer = returnVal;
}
}
// use scan-specific
else
{
for (int i = 0; i < _mzMLConnection.instrumentConfigurationList.instrumentConfiguration.Length; i++)
{
if (configs[i].id.Equals(scanSpecificInsturmentConfig))
{
AnalyzerDictionary.TryGetValue(configs[i].componentList.analyzer[0].cvParam[0].accession, out MZAnalyzerType returnVal);
analyzer = returnVal;
}
}
}
string nativeId = _mzMLConnection.run.spectrumList.spectrum[oneBasedIndex - 1].id;
int? msOrder = null;
bool? isCentroid = null;
Polarity polarity = Polarity.Unknown;
double tic = double.NaN;
foreach (Generated.CVParamType cv in _mzMLConnection.run.spectrumList.spectrum[oneBasedIndex - 1].cvParam)
{
if (cv.accession.Equals(_msnOrderAccession))
{
msOrder = int.Parse(cv.value);
}
if (cv.accession.Equals(_centroidSpectrum))
{
isCentroid = true;
}
if (cv.accession.Equals(_profileSpectrum))
{
throw new MzLibException("Reading profile mode mzmls not supported");
}
if (cv.accession.Equals(_totalIonCurrent))
{
tic = double.Parse(cv.value, CultureInfo.InvariantCulture);
}
if (polarity.Equals(Polarity.Unknown))
{
PolarityDictionary.TryGetValue(cv.accession, out polarity);
}
}
double rtInMinutes = double.NaN;
string scanFilter = null;
double?injectionTime = null;
int oneBasedScanNumber = oneBasedIndex;
if (_mzMLConnection.run.spectrumList.spectrum[oneBasedIndex - 1].scanList.scan[0].cvParam != null)
{
foreach (Generated.CVParamType cv in _mzMLConnection.run.spectrumList.spectrum[oneBasedIndex - 1].scanList.scan[0].cvParam)
{
if (cv.accession.Equals(_retentionTime))
{
rtInMinutes = double.Parse(cv.value, CultureInfo.InvariantCulture);
if (cv.unitName == "second")
{
rtInMinutes /= 60;
}
}
if (cv.accession.Equals(_filterString))
{
scanFilter = cv.value;
}
if (cv.accession.Equals(_ionInjectionTime))
{
injectionTime = double.Parse(cv.value, CultureInfo.InvariantCulture);
}
if (cv.accession.Equals(_oneBasedScanNumber)) //get the real one based spectrum number (if available), the other assumes they are in order. This is present in .mgf->.mzml conversions from MSConvert
{
oneBasedScanNumber = int.Parse(cv.value);
}
}
}
if (!msOrder.HasValue || !isCentroid.HasValue)
{
//one instance when this if statment is true (i.e. not false) is when there is no mz/intensity data
//so, we return the MsDataScan object with a null spectrum
//scans w/ null spectra are checked later and the scan numbers associated w those scans are returned to the reader.
return(new MsDataScan(
null,
oneBasedScanNumber,
msOrder.Value,
false, //have to return a value here b/c it is not nullable
polarity,
rtInMinutes,
null,
scanFilter,
analyzer,
tic,
injectionTime,
null,
nativeId));
}
double[] masses = new double[0];
double[] intensities = new double[0];
foreach (Generated.BinaryDataArrayType binaryData in _mzMLConnection.run.spectrumList.spectrum[oneBasedIndex - 1].binaryDataArrayList.binaryDataArray)
{
bool compressed = false;
bool mzArray = false;
bool intensityArray = false;
bool is32bit = true;
foreach (Generated.CVParamType cv in binaryData.cvParam)
{
compressed |= cv.accession.Equals(_zlibCompression);
is32bit &= !cv.accession.Equals(_64bit);
is32bit |= cv.accession.Equals(_32bit);
mzArray |= cv.accession.Equals(_mzArray);
intensityArray |= cv.accession.Equals(_intensityArray);
}
//in the futurem we may see scass w/ no data and there will be a crash here. if that happens, you can retrun an MsDataScan with null as the mzSpectrum
//the scans with no spectra will be reported to the reader and left out of the scan list.
double[] data = ConvertBase64ToDoubles(binaryData.binary, compressed, is32bit);
if (mzArray)
{
masses = data;
}
if (intensityArray)
{
intensities = data;
}
}
double high = double.NaN;
double low = double.NaN;
var aScanWindowList = _mzMLConnection.run.spectrumList.spectrum[oneBasedIndex - 1].scanList.scan[0].scanWindowList;
if (aScanWindowList != null)
{
foreach (Generated.CVParamType cv in _mzMLConnection.run.spectrumList.spectrum[oneBasedIndex - 1].scanList.scan[0].scanWindowList.scanWindow[0].cvParam)
{
if (cv.accession.Equals(_scanWindowLowerLimit))
{
low = double.Parse(cv.value, CultureInfo.InvariantCulture);
}
else if (cv.accession.Equals(_scanWindowUpperLimit))
{
high = double.Parse(cv.value, CultureInfo.InvariantCulture);
}
}
}
//Remove Zero Intensity Peaks
double zeroEquivalentIntensity = 0.01;
int zeroIntensityCount = intensities.Count(i => i < zeroEquivalentIntensity);
int intensityValueCount = intensities.Count();
if (zeroIntensityCount > 0 && zeroIntensityCount < intensityValueCount)
{
Array.Sort(intensities, masses);
double[] nonZeroIntensities = new double[intensityValueCount - zeroIntensityCount];
double[] nonZeroMzs = new double[intensityValueCount - zeroIntensityCount];
intensities = intensities.SubArray(zeroIntensityCount, intensityValueCount - zeroIntensityCount);
masses = masses.SubArray(zeroIntensityCount, intensityValueCount - zeroIntensityCount);
Array.Sort(masses, intensities);
}
if (filterParams != null && intensities.Length > 0 && ((filterParams.ApplyTrimmingToMs1 && msOrder.Value == 1) || (filterParams.ApplyTrimmingToMsMs && msOrder.Value > 1)))
{
WindowModeHelper(ref intensities, ref masses, filterParams, low, high);
}
Array.Sort(masses, intensities);
var mzmlMzSpectrum = new MzSpectrum(masses, intensities, false);
if (msOrder.Value == 1)
{
return(new MsDataScan(
mzmlMzSpectrum,
oneBasedScanNumber,
msOrder.Value,
isCentroid.Value,
polarity,
rtInMinutes,
new MzRange(low, high),
scanFilter,
analyzer,
tic,
injectionTime,
null,
nativeId));
}
double selectedIonMz = double.NaN;
int? selectedIonCharge = null;
double?selectedIonIntensity = null;
foreach (Generated.CVParamType cv in _mzMLConnection.run.spectrumList.spectrum[oneBasedIndex - 1].precursorList.precursor[0].selectedIonList.selectedIon[0].cvParam)
{
if (cv.accession.Equals(_selectedIonMz))
{
selectedIonMz = double.Parse(cv.value, CultureInfo.InvariantCulture);
}
if (cv.accession.Equals(_precursorCharge))
{
selectedIonCharge = int.Parse(cv.value, CultureInfo.InvariantCulture);
}
if (cv.accession.Equals(_peakIntensity))
{
selectedIonIntensity = double.Parse(cv.value, CultureInfo.InvariantCulture);
}
}
double?isolationMz = null;
double lowIsolation = double.NaN;
double highIsolation = double.NaN;
if (_mzMLConnection.run.spectrumList.spectrum[oneBasedIndex - 1].precursorList.precursor[0].isolationWindow != null)
{
foreach (Generated.CVParamType cv in _mzMLConnection.run.spectrumList.spectrum[oneBasedIndex - 1].precursorList.precursor[0].isolationWindow.cvParam)
{
if (cv.accession.Equals(_isolationWindowTargetMZ))
{
isolationMz = double.Parse(cv.value, CultureInfo.InvariantCulture);
}
if (cv.accession.Equals(_isolationWindowLowerOffset))
{
lowIsolation = double.Parse(cv.value, CultureInfo.InvariantCulture);
}
if (cv.accession.Equals(_isolationWindowUpperOffset))
{
highIsolation = double.Parse(cv.value, CultureInfo.InvariantCulture);
}
}
}
DissociationType dissociationType = DissociationType.Unknown;
if (_mzMLConnection.run.spectrumList.spectrum[oneBasedIndex - 1].precursorList.precursor[0].activation.cvParam != null)
{
// for EThcD scans, the dissociation type will not be listed as EThcD. it will be 2 different dissociation types
// in the list, one as ETD and one with HCD. so we need to check for that case and interpret it as EThcD.
List <DissociationType> scanDissociationTypes = new List <DissociationType>();
foreach (Generated.CVParamType cv in _mzMLConnection.run.spectrumList.spectrum[oneBasedIndex - 1].precursorList.precursor[0].activation.cvParam)
{
if (DissociationDictionary.TryGetValue(cv.accession, out var scanDissociationType))
{
scanDissociationTypes.Add(scanDissociationType);
}
}
if (scanDissociationTypes.Contains(DissociationType.ETD) && scanDissociationTypes.Contains(DissociationType.HCD))
{
dissociationType = DissociationType.EThcD;
}
else if (scanDissociationTypes.Any())
{
dissociationType = scanDissociationTypes.First();
}
else
{
dissociationType = DissociationType.Unknown;
}
}
double?monoisotopicMz = null;
if (_mzMLConnection.run.spectrumList.spectrum[oneBasedIndex - 1].scanList.scan[0].userParam != null)
{
foreach (var userParam in _mzMLConnection.run.spectrumList.spectrum[oneBasedIndex - 1].scanList.scan[0].userParam)
{
if (userParam.name.EndsWith("Monoisotopic M/Z:"))
{
monoisotopicMz = double.Parse(userParam.value, CultureInfo.InvariantCulture);
}
}
}
int?precursorScanNumber;
if (_mzMLConnection.run.spectrumList.spectrum[oneBasedIndex - 1].precursorList.precursor[0].spectrumRef == null)
{
precursorScanNumber = null;
}
else
{
precursorScanNumber = GetOneBasedPrecursorScanNumber(_mzMLConnection, oneBasedIndex);
}
return(new MsDataScan(
mzmlMzSpectrum,
oneBasedIndex,
msOrder.Value,
isCentroid.Value,
polarity,
rtInMinutes,
new MzRange(low, high),
scanFilter,
analyzer,
tic,
injectionTime,
null,
nativeId,
selectedIonMz,
selectedIonCharge,
selectedIonIntensity,
isolationMz,
lowIsolation + highIsolation,
dissociationType,
precursorScanNumber,
monoisotopicMz
));
}
private static IMzmlScan GetMsDataOneBasedScanFromConnection(Generated.mzMLType _mzMLConnection, int oneBasedSpectrumNumber)
{
double[] masses = null;
double[] intensities = null;
foreach (Generated.BinaryDataArrayType binaryData in _mzMLConnection.run.spectrumList.spectrum[oneBasedSpectrumNumber - 1].binaryDataArrayList.binaryDataArray)
{
bool compressed = false;
bool mzArray = false;
bool intensityArray = false;
bool is32bit = true;
foreach (Generated.CVParamType cv in binaryData.cvParam)
{
compressed |= cv.accession.Equals(_zlibCompression);
is32bit &= !cv.accession.Equals(_64bit);
is32bit |= cv.accession.Equals(_32bit);
mzArray |= cv.accession.Equals(_mzArray);
intensityArray |= cv.accession.Equals(_intensityArray);
}
double[] data = ConvertBase64ToDoubles(binaryData.binary, compressed, is32bit);
if (mzArray)
{
masses = data;
}
if (intensityArray)
{
intensities = data;
}
}
var ok = new MzmlMzSpectrum(masses, intensities, false);
int? msOrder = null;
bool? isCentroid = null;
Polarity polarity = Polarity.Unknown;
double tic = double.NaN;
foreach (Generated.CVParamType cv in _mzMLConnection.run.spectrumList.spectrum[oneBasedSpectrumNumber - 1].cvParam)
{
if (cv.accession.Equals(_msnOrderAccession))
{
msOrder = int.Parse(cv.value);
}
if (cv.accession.Equals(_centroidSpectrum))
{
isCentroid = true;
}
if (cv.accession.Equals(_profileSpectrum))
{
isCentroid = false;
}
if (cv.accession.Equals(_totalIonCurrent))
{
tic = double.Parse(cv.value);
}
polarityDictionary.TryGetValue(cv.accession, out polarity);
}
double rtInMinutes = double.NaN;
string scanFilter = null;
double?injectionTime = null;
if (_mzMLConnection.run.spectrumList.spectrum[oneBasedSpectrumNumber - 1].scanList.scan[0].cvParam != null)
{
foreach (Generated.CVParamType cv in _mzMLConnection.run.spectrumList.spectrum[oneBasedSpectrumNumber - 1].scanList.scan[0].cvParam)
{
if (cv.accession.Equals(_retentionTime))
{
rtInMinutes = double.Parse(cv.value);
if (cv.unitName == "second")
{
rtInMinutes /= 60;
}
}
if (cv.accession.Equals(_filterString))
{
scanFilter = cv.value;
}
if (cv.accession.Equals(_ionInjectionTime))
{
injectionTime = double.Parse(cv.value);
}
}
}
double high = double.NaN;
double low = double.NaN;
if (_mzMLConnection.run.spectrumList.spectrum[oneBasedSpectrumNumber - 1].scanList.scan[0].scanWindowList != null)
{
foreach (Generated.CVParamType cv in _mzMLConnection.run.spectrumList.spectrum[oneBasedSpectrumNumber - 1].scanList.scan[0].scanWindowList.scanWindow[0].cvParam)
{
if (cv.accession.Equals(_scanWindowLowerLimit))
{
low = double.Parse(cv.value);
}
if (cv.accession.Equals(_scanWindowUpperLimit))
{
high = double.Parse(cv.value);
}
}
}
if (msOrder.Value == 1)
{
return(new MzmlScan(oneBasedSpectrumNumber, ok, msOrder.Value, isCentroid.Value, polarity, rtInMinutes, new MzRange(low, high), scanFilter, GetMzAnalyzer(_mzMLConnection, scanFilter), tic, injectionTime));
}
double selectedIonMz = double.NaN;
int? selectedIonCharge = null;
double?selectedIonIntensity = null;
foreach (Generated.CVParamType cv in _mzMLConnection.run.spectrumList.spectrum[oneBasedSpectrumNumber - 1].precursorList.precursor[0].selectedIonList.selectedIon[0].cvParam)
{
if (cv.accession.Equals(_selectedIonMz))
{
selectedIonMz = double.Parse(cv.value);
}
if (cv.accession.Equals(_precursorCharge))
{
selectedIonCharge = int.Parse(cv.value);
}
if (cv.accession.Equals(_peakIntensity))
{
selectedIonIntensity = double.Parse(cv.value);
}
}
double?isolationMz = null;
double lowIsolation = double.NaN;
double highIsolation = double.NaN;
foreach (Generated.CVParamType cv in _mzMLConnection.run.spectrumList.spectrum[oneBasedSpectrumNumber - 1].precursorList.precursor[0].isolationWindow.cvParam)
{
if (cv.accession.Equals(_isolationWindowTargetMZ))
{
isolationMz = double.Parse(cv.value);
}
if (cv.accession.Equals(_isolationWindowLowerOffset))
{
lowIsolation = double.Parse(cv.value);
}
if (cv.accession.Equals(_isolationWindowUpperOffset))
{
highIsolation = double.Parse(cv.value);
}
}
DissociationType dissociationType = DissociationType.Unknown;
foreach (Generated.CVParamType cv in _mzMLConnection.run.spectrumList.spectrum[oneBasedSpectrumNumber - 1].precursorList.precursor[0].activation.cvParam)
{
dissociationDictionary.TryGetValue(cv.accession, out dissociationType);
}
double?monoisotopicMz = null;
if (_mzMLConnection.run.spectrumList.spectrum[oneBasedSpectrumNumber - 1].scanList.scan[0].userParam != null)
{
foreach (var userParam in _mzMLConnection.run.spectrumList.spectrum[oneBasedSpectrumNumber - 1].scanList.scan[0].userParam)
{
if (userParam.name.EndsWith("Monoisotopic M/Z:"))
{
monoisotopicMz = double.Parse(userParam.value);
}
}
}
return(new MzmlScanWithPrecursor(oneBasedSpectrumNumber,
ok,
msOrder.Value,
isCentroid.Value,
polarity,
rtInMinutes,
new MzRange(low, high),
scanFilter,
GetMzAnalyzer(_mzMLConnection, scanFilter),
tic,
selectedIonMz,
selectedIonCharge,
selectedIonIntensity,
isolationMz.Value,
lowIsolation + highIsolation,
dissociationType,
GetOneBasedPrecursorScanNumber(_mzMLConnection, oneBasedSpectrumNumber),
monoisotopicMz,
injectionTime));
}
