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));
}
private static IMzmlScan GetMsDataOneBasedScanFromConnection(Generated.mzMLType _mzMLConnection, int oneBasedSpectrumNumber, 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[oneBasedSpectrumNumber - 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[oneBasedSpectrumNumber - 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[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))
{
throw new MzLibException("Reading profile mode mzmls not supported");
}
if (cv.accession.Equals(_totalIonCurrent))
{
tic = double.Parse(cv.value);
}
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[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;
}
}
if (filterParams != null && intensities.Length > 0 && (filterParams.MinimumAllowedIntensityRatioToBasePeakM.HasValue || filterParams.NumberOfPeaksToKeepPerWindow.HasValue) &&
((filterParams.ApplyTrimmingToMs1 && msOrder.Value == 1) || (filterParams.ApplyTrimmingToMsMs && msOrder.Value > 1)))
{
if (filterParams.NumberOfWindows == null)
{
int numPeaks = TopNpeakHelper(intensities, masses, filterParams);
Array.Resize(ref intensities, numPeaks);
Array.Resize(ref masses, numPeaks);
}
else
{
WindowModeHelper(ref intensities, ref masses, filterParams);
}
}
Array.Sort(masses, intensities);
var mzmlMzSpectrum = new MzmlMzSpectrum(masses, intensities, false);
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,
mzmlMzSpectrum,
msOrder.Value,
isCentroid.Value,
polarity,
rtInMinutes,
new MzRange(low, high),
scanFilter,
analyzer,
tic,
injectionTime,
nativeId));
}
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;
if (_mzMLConnection.run.spectrumList.spectrum[oneBasedSpectrumNumber - 1].precursorList.precursor[0].isolationWindow != null)
{
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;
if (_mzMLConnection.run.spectrumList.spectrum[oneBasedSpectrumNumber - 1].precursorList.precursor[0].activation.cvParam != null)
{
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);
}
}
}
int?precursorScanNumber;
if (_mzMLConnection.run.spectrumList.spectrum[oneBasedSpectrumNumber - 1].precursorList.precursor[0].spectrumRef == null)
{
precursorScanNumber = null;
}
else
{
precursorScanNumber = GetOneBasedPrecursorScanNumber(_mzMLConnection, oneBasedSpectrumNumber);
}
return(new MzmlScanWithPrecursor(
oneBasedSpectrumNumber,
mzmlMzSpectrum,
msOrder.Value,
isCentroid.Value,
polarity,
rtInMinutes,
new MzRange(low, high),
scanFilter,
analyzer,
tic,
selectedIonMz,
selectedIonCharge,
selectedIonIntensity,
isolationMz,
lowIsolation + highIsolation,
dissociationType,
precursorScanNumber,
monoisotopicMz,
injectionTime,
nativeId));
}
