public override string ToString()
{
string result = string.Empty;
if (double.IsNaN(Score) && !double.IsNaN(Confidence))
{
result = string.Format("{0},{1}", Polarity, Confidence.ToString("F"));
}
else
{
result = string.Format("{0},{1}", Polarity, Score.ToString("F"));
}
if (!string.IsNullOrEmpty(ReferencePolarity))
{
result += string.Format(",{0}", (Polarity.Equals(ReferencePolarity) ? "agrees" : "disagrees"));
}
return(result);
}
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
));
}