public override MsDataScan GetOneBasedScan(int oneBasedScanNumber)
{
if (Scans[oneBasedScanNumber - 1] == null)
{
var representativeScanNumber = oneBasedScanNumber + (numScansToAverage - 1) / 2;
var representative = raw.GetOneBasedScan(representativeScanNumber);
if (representative.MsnOrder != 1)
{
throw new MzLibException("Scan " + representativeScanNumber + " is not MS1 scan");
}
int msnOrder = 1;
Polarity polarity = representative.Polarity;
if (!representative.IsCentroid)
{
throw new MzLibException("Scan " + representativeScanNumber + " is not centroid scan");
}
bool isCentroid = true;
double retentionTime = representative.RetentionTime;
MZAnalyzerType mzAnalyzer = representative.MzAnalyzer;
MzSpectrum peaks = CombinePeaks(raw.GetAllScansList().Where(b => b.OneBasedScanNumber >= oneBasedScanNumber && b.OneBasedScanNumber <= oneBasedScanNumber + numScansToAverage - 1).Select(b => b.MassSpectrum).ToList(), ppmToleranceForPeakCombination);
MzRange scanWindowRange = representative.ScanWindowRange;
double totalIonCurrent = peaks.SumOfAllY;
double injectionTime = double.NaN;
double[,] noiseData = null;
Scans[oneBasedScanNumber - 1] = new MsDataScan(peaks, oneBasedScanNumber, msnOrder, isCentroid, polarity, retentionTime, scanWindowRange, null, mzAnalyzer, totalIonCurrent, injectionTime, noiseData, "scan=" + oneBasedScanNumber);
}
return(Scans[oneBasedScanNumber - 1]);
}
public MsDataScan(MzSpectrum massSpectrum, int oneBasedScanNumber, int msnOrder, bool isCentroid, Polarity polarity, double retentionTime, MzRange scanWindowRange, string scanFilter, MZAnalyzerType mzAnalyzer,
double totalIonCurrent, double?injectionTime, double[,] noiseData, string nativeId, double?selectedIonMz = null, int?selectedIonChargeStateGuess = null, double?selectedIonIntensity = null, double?isolationMZ = null,
double?isolationWidth = null, DissociationType?dissociationType = null, int?oneBasedPrecursorScanNumber = null, double?selectedIonMonoisotopicGuessMz = null, string hcdEnergy = null)
{
OneBasedScanNumber = oneBasedScanNumber;
MsnOrder = msnOrder;
IsCentroid = isCentroid;
Polarity = polarity;
RetentionTime = retentionTime;
ScanWindowRange = scanWindowRange;
ScanFilter = scanFilter;
MzAnalyzer = mzAnalyzer;
TotalIonCurrent = totalIonCurrent;
InjectionTime = injectionTime;
NoiseData = noiseData;
MassSpectrum = massSpectrum;
NativeId = nativeId;
OneBasedPrecursorScanNumber = oneBasedPrecursorScanNumber;
IsolationMz = isolationMZ;
IsolationWidth = isolationWidth;
DissociationType = dissociationType;
SelectedIonMZ = selectedIonMz;
SelectedIonIntensity = selectedIonIntensity;
SelectedIonChargeStateGuess = selectedIonChargeStateGuess;
SelectedIonMonoisotopicGuessMz = selectedIonMonoisotopicGuessMz;
HcdEnergy = hcdEnergy;
}
protected MsDataScan(int oneBasedScanNumber, int msnOrder, bool isCentroid, Polarity polarity, double retentionTime, MzRange scanWindowRange, string scanFilter, MZAnalyzerType mzAnalyzer, double totalIonCurrent, double?injectionTime, double[,] noiseData)
{
OneBasedScanNumber = oneBasedScanNumber;
MsnOrder = msnOrder;
IsCentroid = isCentroid;
Polarity = polarity;
RetentionTime = retentionTime;
ScanWindowRange = scanWindowRange;
ScanFilter = scanFilter;
MzAnalyzer = mzAnalyzer;
TotalIonCurrent = totalIonCurrent;
InjectionTime = injectionTime;
NoiseData = noiseData;
}
public MsDataScan(TSpectrum massSpectrum, int oneBasedScanNumber, int msnOrder, bool isCentroid, Polarity polarity, double retentionTime, MzRange scanWindowRange, string scanFilter, MZAnalyzerType mzAnalyzer, double totalIonCurrent, double?injectionTime, double[,] noiseData, string nativeId)
{
OneBasedScanNumber = oneBasedScanNumber;
MsnOrder = msnOrder;
IsCentroid = isCentroid;
Polarity = polarity;
RetentionTime = retentionTime;
ScanWindowRange = scanWindowRange;
ScanFilter = scanFilter;
MzAnalyzer = mzAnalyzer;
TotalIonCurrent = totalIonCurrent;
InjectionTime = injectionTime;
NoiseData = noiseData;
MassSpectrum = massSpectrum;
NativeId = nativeId;
}
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
));
}
public override double GetResolution(int spectrumNumber)
{
int arraySize = 0;
object keys = null;
object values = null;
_rawConnection.GetTrailerExtraForScanNum(spectrumNumber, ref keys, ref values, ref arraySize);
MZAnalyzerType analyzer = GetMzAnalyzer(spectrumNumber);
double resolution = 0;
switch (analyzer)
{
case MZAnalyzerType.FTICR:
case MZAnalyzerType.Orbitrap:
string name = GetInstrumentName();
if (name == "Orbitrap Fusion" || name == "Q Exactive")
{
object obj = GetExtraValue(spectrumNumber, "Orbitrap Resolution:");
resolution = Convert.ToDouble(obj);
if (resolution <= 0)
{
// Find first peak with S/N greater than 3 to use for resolution calculation
double[,] data = GetLabeledData(spectrumNumber);
int totalPeaks = data.GetLength(1);
List <double> avgResolution = new List <double>();
for (int i = 0; i < totalPeaks; i++)
{
double signalToNoise = data[1, i] / data[4, i];
if (signalToNoise >= 5)
{
double mz = data[0, i];
double peakRes = data[2, i];
double correctedResolution = peakRes * Math.Sqrt(mz / 200);
avgResolution.Add(correctedResolution);
}
}
double meanResolution = avgResolution.Median();
if (meanResolution <= 25000)
{
return(15000);
}
if (meanResolution <= 45000)
{
return(30000);
}
if (meanResolution <= 100000)
{
return(60000);
}
if (meanResolution <= 200000)
{
return(120000);
}
if (meanResolution <= 400000)
{
return(240000);
}
return(450000);
}
return(resolution);
}
else
{
object obj = GetExtraValue(spectrumNumber, "FT Resolution:");
resolution = Convert.ToDouble(obj);
if (resolution > 300000)
{
return(480000);
}
return(resolution);
}
}
return(resolution);
}
protected MsDataScanWithPrecursor(TSpectrum massSpectrum, int ScanNumber, int MsnOrder, bool isCentroid, Polarity Polarity, double RetentionTime, MzRange MzRange, string ScanFilter, MZAnalyzerType MzAnalyzer, double TotalIonCurrent, double selectedIonMZ, int?selectedIonChargeStateGuess, double?selectedIonIntensity, double?isolationMZ, double?isolationWidth, DissociationType dissociationType, int?oneBasedPrecursorScanNumber, double?selectedIonMonoisotopicGuessMz, double?injectionTime, double[,] noiseData, string nativeId)
: base(massSpectrum, ScanNumber, MsnOrder, isCentroid, Polarity, RetentionTime, MzRange, ScanFilter, MzAnalyzer, TotalIonCurrent, injectionTime, noiseData, nativeId)
{
this.OneBasedPrecursorScanNumber = oneBasedPrecursorScanNumber;
this.IsolationMz = isolationMZ;
this.IsolationWidth = isolationWidth;
this.DissociationType = dissociationType;
this.SelectedIonMZ = selectedIonMZ;
this.SelectedIonIntensity = selectedIonIntensity;
this.SelectedIonChargeStateGuess = selectedIonChargeStateGuess;
this.SelectedIonMonoisotopicGuessMz = selectedIonMonoisotopicGuessMz;
}
public MzmlScan(int oneBasedScanNumber, MzmlMzSpectrum massSpectrum, int msnOrder, bool isCentroid, Polarity polarity, double retentionTime, MzRange scanWindowRange, string scanFilter, MZAnalyzerType mzAnalyzer, double totalIonCurrent, double?injectionTime)
: base(oneBasedScanNumber, msnOrder, isCentroid, polarity, retentionTime, scanWindowRange, scanFilter, mzAnalyzer, totalIonCurrent, injectionTime, null)
{
this.MassSpectrum = massSpectrum;
}
/// <summary>
/// Gets the scan with the specified one-based scan number.
/// </summary>
public override MsDataScan GetOneBasedScanFromDynamicConnection(int oneBasedScanNumber, IFilteringParams filterParams = null)
{
MsDataScan scan = null;
if (ScanNumberToByteOffset.TryGetValue(oneBasedScanNumber, out long byteOffset))
{
// seek to the byte of the scan
reader.BaseStream.Position = byteOffset;
reader.DiscardBufferedData();
// DO NOT USE THIS METHOD! it does not seek reliably
//stream.BaseStream.Seek(byteOffset, SeekOrigin.Begin);
// read the scan
using (XmlReader xmlReader = XmlReader.Create(reader))
{
string nativeId = null;
while (xmlReader.Read())
{
// this skips whitespace
string upperName = xmlReader.Name.ToUpper();
if (upperName == "SPECTRUM" && xmlReader.IsStartElement())
{
nativeId = xmlReader["id"];
break;
}
}
// deserializing the scan's data doesn't work well. the spectrum type is deserialized
// but sub-elements aren't. this is probably because we're trying to deserialize only
// a part of the XML file... deserialization would probably be cleaner code than
// using the current implementation but I couldn't get it to work
//var deserializedSpectrum = (IO.MzML.Generated.SpectrumType)serializer.Deserialize(xmlReader.ReadSubtree());
MzSpectrum spectrum = null;
int? msOrder = 0;
bool? isCentroid = false;
Polarity polarity = Polarity.Unknown;
double retentionTime = double.NaN;
MzRange range = null;
string scanFilter = null;
MZAnalyzerType mzAnalyzerType = MZAnalyzerType.Unknown;
double tic = 0;
double? injTime = null;
double[,] noiseData = null; // TODO: read this
double? selectedIonMz = null;
int? selectedCharge = null;
double? selectedIonIntensity = null;
double? isolationMz = null; // TODO: should this be refined? or taken from the scan header?
double? isolationWidth = null;
DissociationType?dissociationType = null;
int? oneBasedPrecursorScanNumber = null;
double? selectedIonMonoisotopicGuessMz = null;
double scanLowerLimit = double.NaN;
double scanUpperLimit = double.NaN;
double isolationWindowLowerOffset = double.NaN;
double isolationWindowUpperOffset = double.NaN;
bool compressed = false;
bool readingMzs = false;
bool readingIntensities = false;
bool is32bit = true;
double[] mzs = null;
double[] intensities = null;
while (xmlReader.Read())
{
switch (xmlReader.Name.ToUpper())
{
// controlled vocabulary parameter
case "CVPARAM":
string cvParamAccession = xmlReader["accession"];
if (Mzml.DissociationDictionary.ContainsKey(cvParamAccession))
{
dissociationType = Mzml.DissociationDictionary[cvParamAccession];
break;
}
if (Mzml.PolarityDictionary.ContainsKey(cvParamAccession))
{
polarity = Mzml.PolarityDictionary[cvParamAccession];
break;
}
switch (cvParamAccession)
{
// MS order
case "MS:1000511":
msOrder = int.Parse(xmlReader["value"]);
break;
// centroid mode
case "MS:1000127":
isCentroid = true;
break;
// profile mode
case "MS:1000128":
isCentroid = false;
throw new MzLibException("Reading profile mode mzmls not supported");
break;
// total ion current
case "MS:1000285":
tic = double.Parse(xmlReader["value"]);
break;
// retention time
case "MS:1000016":
retentionTime = double.Parse(xmlReader["value"]);
break;
// filter string
case "MS:1000512":
scanFilter = xmlReader["value"];
break;
// ion injection time
case "MS:1000927":
injTime = double.Parse(xmlReader["value"]);
break;
// scan lower limit
case "MS:1000501":
scanLowerLimit = double.Parse(xmlReader["value"]);
break;
// scan upper limit
case "MS:1000500":
scanUpperLimit = double.Parse(xmlReader["value"]);
break;
// isolation window lower offset
case "MS:1000828":
isolationWindowLowerOffset = double.Parse(xmlReader["value"]);
break;
// isolation window upper offset
case "MS:1000829":
isolationWindowUpperOffset = double.Parse(xmlReader["value"]);
break;
// isolated m/z
case "MS:1000827":
isolationMz = double.Parse(xmlReader["value"]);
break;
// selected ion m/z
case "MS:1000744":
selectedIonMz = double.Parse(xmlReader["value"]);
break;
// selected charge state
case "MS:1000041":
selectedCharge = int.Parse(xmlReader["value"]);
break;
// selected intensity
case "MS:1000042":
selectedIonIntensity = double.Parse(xmlReader["value"]);
break;
// mass analyzer types
case "MS:1000081":
mzAnalyzerType = MZAnalyzerType.Quadrupole;
break;
case "MS:1000291":
mzAnalyzerType = MZAnalyzerType.IonTrap2D;
break;
case "MS:1000082":
mzAnalyzerType = MZAnalyzerType.IonTrap3D;
break;
case "MS:1000484":
mzAnalyzerType = MZAnalyzerType.Orbitrap;
break;
case "MS:1000084":
mzAnalyzerType = MZAnalyzerType.TOF;
break;
case "MS:1000079":
mzAnalyzerType = MZAnalyzerType.FTICR;
break;
case "MS:1000080":
mzAnalyzerType = MZAnalyzerType.Sector;
break;
case "MS:1000523":
is32bit = false;
break;
case "MS:1000574":
compressed = true;
break;
case "MS:1000514":
readingMzs = true;
break;
case "MS:1000515":
readingIntensities = true;
break;
}
break;
// binary data array (e.g., m/z or intensity array)
case "BINARY":
if (!readingMzs && !readingIntensities)
{
break;
}
while (string.IsNullOrWhiteSpace(xmlReader.Value))
{
xmlReader.Read();
}
string binaryString = xmlReader.Value;
byte[] binaryData = null;
if (!is32bit)
{
binaryData = Convert.FromBase64String(binaryString);
}
else
{
// todo: check. not sure if this is right
binaryData = Encoding.UTF8.GetBytes(binaryString);
}
double[] data = Mzml.ConvertBase64ToDoubles(binaryData, compressed, is32bit);
if (readingMzs)
{
mzs = data;
readingMzs = false;
}
else if (readingIntensities)
{
intensities = data;
readingIntensities = false;
}
break;
case "PRECURSOR":
if (xmlReader.IsStartElement())
{
string precursorScanInfo = xmlReader["spectrumRef"];
if (precursorScanInfo != null)
{
oneBasedPrecursorScanNumber = NativeIdToScanNumber[precursorScanInfo];
}
}
break;
case "USERPARAM":
if (xmlReader.IsStartElement() && xmlReader["name"] != null && xmlReader["name"] == "[mzLib]Monoisotopic M/Z:")
{
selectedIonMonoisotopicGuessMz = double.Parse(xmlReader["value"]);
}
break;
// done reading spectrum
case "SPECTRUM":
if (!xmlReader.IsStartElement())
{
if (msOrder > 1)
{
isolationWidth = isolationWindowUpperOffset + isolationWindowLowerOffset;
if (dissociationType == null)
{
dissociationType = DissociationType.Unknown;
}
}
if (!msOrder.HasValue || !isCentroid.HasValue)
{
throw new MzLibException("Could not determine the MS order or centroid/profile status");
}
// peak filtering
if (filterParams != null && intensities.Length > 0 &&
((filterParams.ApplyTrimmingToMs1 && msOrder.Value == 1) || (filterParams.ApplyTrimmingToMsMs && msOrder.Value > 1)))
{
MsDataFile.WindowModeHelper(ref intensities, ref mzs, filterParams, scanLowerLimit, scanUpperLimit);
}
Array.Sort(mzs, intensities);
range = new MzRange(scanLowerLimit, scanUpperLimit);
spectrum = new MzSpectrum(mzs, intensities, false);
scan = new MsDataScan(spectrum, oneBasedScanNumber, msOrder.Value, isCentroid.Value, polarity,
retentionTime, range, scanFilter, mzAnalyzerType, tic, injTime, noiseData,
nativeId, selectedIonMz, selectedCharge, selectedIonIntensity, isolationMz, isolationWidth,
dissociationType, oneBasedPrecursorScanNumber, selectedIonMonoisotopicGuessMz);
return(scan);
}
else
{
throw new MzLibException("Spectrum data is malformed");
}
}
}
}
}
return(scan);
}
public MzmlScanWithPrecursor(int ScanNumber, MzmlMzSpectrum massSpectrum, int MsnOrder, bool isCentroid, Polarity Polarity, double RetentionTime, MzRange MzRange, string ScanFilter, MZAnalyzerType MzAnalyzer, double TotalIonCurrent, double selectedIonMz, int?selectedIonChargeStateGuess, double?selectedIonIntensity, double isolationMZ, double?isolationWidth, DissociationType dissociationType, int oneBasedPrecursorScanNumber, double?selectedIonGuessMonoisotopicMZ, double?injectionTime)
: base(ScanNumber, MsnOrder, isCentroid, Polarity, RetentionTime, MzRange, ScanFilter, MzAnalyzer, TotalIonCurrent, selectedIonMz, selectedIonChargeStateGuess, selectedIonIntensity, isolationMZ, isolationWidth, dissociationType, oneBasedPrecursorScanNumber, selectedIonGuessMonoisotopicMZ, injectionTime, null)
{
this.MassSpectrum = massSpectrum;
}
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
));
}
public ThermoScan(int oneBasedScanNumber, ThermoSpectrum massSpectrum, int msnOrder, Polarity polarity, double retentionTime, MzRange scanWindowRange, string scanFilter, MZAnalyzerType mzAnalyzer, double totalIonCurrent, double?injectionTime, double[,] noiseData, string nativeId)
: base(massSpectrum, oneBasedScanNumber, msnOrder, true, polarity, retentionTime, scanWindowRange, scanFilter, mzAnalyzer, totalIonCurrent, injectionTime, noiseData, nativeId)
{
}
public ThermoScanWithPrecursor(int ScanNumber, ThermoSpectrum massSpectrum, int MsnOrder, Polarity Polarity, double RetentionTime, MzRange MzRange, string ScanFilter, MZAnalyzerType MzAnalyzer, double TotalIonCurrent, double selectedIonGuessMZ, int?selectedIonGuessChargeStateGuess, double?isolationWidth, DissociationType dissociationType, int?oneBasedPrecursorScanNumber, double?selectedIonGuessMonoisotopicMZ, double?injectionTime, double[,] noiseData, string nativeId)
: base(massSpectrum, ScanNumber, MsnOrder, true, Polarity, RetentionTime, MzRange, ScanFilter, MzAnalyzer, TotalIonCurrent, selectedIonGuessMZ, selectedIonGuessChargeStateGuess, null, selectedIonGuessMZ, isolationWidth, dissociationType, oneBasedPrecursorScanNumber, selectedIonGuessMonoisotopicMZ, injectionTime, noiseData, nativeId)
{
}