private MsDataSpectrum GetSpectrumFromJObject(JObject jObject, int msLevel)
{
// ReSharper disable NonLocalizedString
string strMzs = jObject["mzs-base64"].ToString();
string strIntensities = jObject["intensities-base64"].ToString();
byte[] mzBytes = Convert.FromBase64String(strMzs);
byte[] intensityBytes = Convert.FromBase64String(strIntensities);
double[] mzs = PrimitiveArrays.FromBytes <double>(
PrimitiveArrays.ReverseBytesInBlocks(mzBytes, sizeof(double)));
float[] intensityFloats = PrimitiveArrays.FromBytes <float>(
PrimitiveArrays.ReverseBytesInBlocks(intensityBytes, sizeof(float)));
double[] intensities = intensityFloats.Select(f => (double)f).ToArray();
double? driftTime = null;
JToken jDriftTime;
if (jObject.TryGetValue("driftTime", out jDriftTime))
{
driftTime = jDriftTime.ToObject <double>();
}
MsDataSpectrum spectrum = new MsDataSpectrum
{
Index = jObject["index"].ToObject <int>(),
RetentionTime = jObject["rt"].ToObject <double>(),
Mzs = mzs,
Intensities = intensities,
DriftTimeMsec = driftTime,
};
return(spectrum);
// ReSharper restore NonLocalizedString
}
/// <summary>
/// Demultiplexes a real .mxML file in a case where the answer is simple, and checks the answer is correct.
/// </summary>
private static void TestSpectrumDemultiplex(AbstractDemultiplexer demultiplexer,
int spectrumIndex,
MsDataSpectrum originalSpectrum,
int[] intensityIndices,
double[] intensityValues,
int deconvIndex)
{
var deconvSpectra = demultiplexer.GetDeconvolvedSpectra(spectrumIndex, originalSpectrum);
int numberMzPoints = originalSpectrum.Intensities.Length;
double[] peakSums = new double[numberMzPoints];
for (int i = 0; i < numberMzPoints; ++i)
{
peakSums[i] = 0.0;
}
foreach (var deconvSpectrum in deconvSpectra)
{
Assert.AreEqual(deconvSpectrum.Intensities.Length, originalSpectrum.Intensities.Length);
for (int i = 0; i < numberMzPoints; ++i)
{
peakSums[i] += deconvSpectrum.Intensities[i];
}
}
for (int i = 0; i < numberMzPoints; ++i)
{
Assert.AreEqual(peakSums[i], originalSpectrum.Intensities[i], 0.01);
}
for (int i = 0; i < intensityIndices.Length; ++i)
{
Assert.AreEqual(deconvSpectra[deconvIndex].Intensities[intensityIndices[i]], intensityValues[i], 0.1);
}
}
public bool IsSimSpectrum(MsDataSpectrum dataSpectrum, MsDataSpectrum[] spectra)
{
if (!EnabledMs || _mseLevel > 0)
{
return(false);
}
bool isSimSpectrum = dataSpectrum.Level == 1 &&
IsSimIsolation(GetIsolationWindows(dataSpectrum.Precursors).FirstOrDefault());
if (isSimSpectrum && spectra.Length > 1)
{
// If this is actually a run of IMS bins, look at the aggregate isolation window
var rt = spectra[0].RetentionTime;
var win = GetIsolationWindows(spectra[0].Precursors).FirstOrDefault();
double mzLow = win.IsolationMz.Value - win.IsolationWidth.Value / 2;
double mzHigh = win.IsolationMz.Value + win.IsolationWidth.Value / 2;
for (var i = 1; i < spectra.Length; i++)
{
var spec = spectra[i];
if (!Equals(spec.RetentionTime, rt) || !IonMobilityValue.IsExpectedValueOrdering(spectra[i - 1].IonMobility, spec.IonMobility))
{
return(true); // Not a run of IMS bins, must have been actual SIM scan
}
win = GetIsolationWindows(spec.Precursors).FirstOrDefault();
mzLow = Math.Min(mzLow, win.IsolationMz.Value - win.IsolationWidth.Value / 2);
mzHigh = Math.Max(mzHigh, win.IsolationMz.Value + win.IsolationWidth.Value / 2);
}
var width = mzHigh - mzLow;
isSimSpectrum = IsSimIsolation(new IsolationWindowFilter(new SignedMz(mzLow + width / 2), width));
}
return(isSimSpectrum);
}
public bool IsSimSpectrum(MsDataSpectrum dataSpectrum)
{
if (!EnabledMs || _mseLevel > 0)
{
return(false);
}
return(dataSpectrum.Level == 1 &&
IsSimIsolation(GetIsolationWindows(dataSpectrum.Precursors).FirstOrDefault()));
}
public void GetChromatograms(List <Protein> targets, double tolerance)
{
MsDataSpectrum defaultSpectrum = new MsDataSpectrum();
MsDataSpectrum[] msDataSpectrums = new MsDataSpectrum[1];
msDataSpectrums[0] = defaultSpectrum;
_chromatograms = new List <Chromatogram>();
var Channels = (from spectrum in _msDataFileImpl.MsDataSpectrums
group spectrum by spectrum.PrecursorMZ into spectrumgroup
select new { ChannelMS1 = spectrumgroup.Key, ChannelSpectrums = spectrumgroup }).ToDictionary(di => di.ChannelMS1, di => di.ChannelSpectrums);
var Proteins = targets;
var Targets = from protein in Proteins
from peptide in protein.Peptides
from precursor in peptide.Precursors
select new
{
ProteinName = protein.Name,
PeptideName = peptide.Name,
PrecursorIsoform = precursor.IsotopeLabelType,
PrecursorMZ = precursor.PrecursorMZ,
Products = precursor.Products
};
foreach (var Target in Targets)
{
var SpectrumsForChannel = from channel in Channels
where ProcessRawDataTools.InMZTolerance(channel.Key, Target.PrecursorMZ, tolerance) == true
select channel.Value;
if (SpectrumsForChannel.Any())
{
var ExtraChromatograms = from mzspectrum in SpectrumsForChannel.Single()
select new
{
mzspectrum.PrecursorMZ,
mzspectrum.RetentionTime,
mzspectrum.IonIT,
mzspectrum.TIC,
SumOfIntensities = mzspectrum.Intensities.Sum(),
SumOfPositiveMatch = ProcessRawDataTools.AggIonCounts(mzspectrum.Mzs, mzspectrum.Intensities, Target.Products, tolerance)[0],
SumOfNegativeMatch = ProcessRawDataTools.AggIonCounts(mzspectrum.Mzs, mzspectrum.Intensities, Target.Products, tolerance)[1]
};
_chromatograms.Add(new Chromatogram()
{
Protein = Target.ProteinName,
Peptide = Target.ProteinName,
IsotopeLabelType = Target.PrecursorIsoform,
PrecursorMZ = Target.PrecursorMZ,
RetentionTimes = ExtraChromatograms.Select(ec => ec.RetentionTime.GetValueOrDefault(0)).ToArray(),
IonInjectionTimes = ExtraChromatograms.Select(ec => ec.IonIT.GetValueOrDefault(0)).ToArray(),
SumOfIntensities = ExtraChromatograms.Select(ec => ec.SumOfIntensities).ToArray(),
SumOfPositiveMatch = ExtraChromatograms.Select(ec => ec.SumOfPositiveMatch).ToArray(),
SumOfNegativeMatch = ExtraChromatograms.Select(ec => ec.SumOfNegativeMatch).ToArray()
});
}
}
}
private int Compare(MsDataSpectrum spectrum, double ionMobilityValue)
{
var sim = spectrum.IonMobility.Mobility;
if (!sim.HasValue)
{
return(0);
}
return(Compare(sim.Value, ionMobilityValue));
}
public bool IsMsMsSpectrum(MsDataSpectrum dataSpectrum)
{
if (!EnabledMsMs)
{
return(false);
}
if (_mseLevel > 0)
{
return(UpdateMseLevel(dataSpectrum) == 2);
}
return(dataSpectrum.Level == 2);
}
private static MsDataSpectrum MakeDeconvSpectrum(MsDataSpectrum originalSpectrum, List <KeyValuePair <double, double> > peaks)
{
return(new MsDataSpectrum
{
RetentionTime = originalSpectrum.RetentionTime,
Centroided = originalSpectrum.Centroided,
IonMobility = originalSpectrum.IonMobility,
Level = originalSpectrum.Level,
Mzs = peaks.Select(p => p.Key).ToArray(),
Intensities = peaks.Select(p => p.Value).ToArray(),
});
}
private double GetIntensity(MsDataSpectrum spectrum, double mz)
{
if (spectrum == null)
{
// if we're at a boundary, return minimum value. This means if the peak
// is not in the other stripe, we get it. Otherwise, they essentially
// get the intensity.
return(double.Epsilon);
}
var indices = _fragmentTolerance.GetIndices(spectrum.Mzs, mz);
return(indices.Sum(i => spectrum.Intensities[i]));
}
private int UpdateMseLevel(MsDataSpectrum dataSpectrum)
{
int returnval;
if ((_mseLastSpectrum == null) || !ReferenceEquals(dataSpectrum, _mseLastSpectrum)) // is this the same one we were just asked about?
{
// Waters MSe is enumerated in interleaved scans ("functions" in the raw data) 1==MS 2==MSMS 3=ignore
// Bruker MSe is enumerated in interleaved MS1 and MS/MS scans
// Agilent MSe is a series of MS1 scans with ramped CE (SpectrumList_Agilent returns these as MS1,MS2,MS2,...)
// but with ion mobility, as of June 2014, it's just a series of MS2 scans with a single nonzero CE, or MS1 scans with 0 CE
if (_isAgilentMse)
{
if (1 == dataSpectrum.Level)
{
_mseLevel = 1; // Expecting a series of MS2 scans to follow after this
returnval = 1; // Report as MS1
}
else if ((2 == dataSpectrum.Level) &&
(_mseLastSpectrum != null)) // Sometimes the file doesn't contain that leading MS1 scan
{
_mseLevel = 2;
returnval = 2;
}
else
{
returnval = 0; // Not useful - probably the file started off mid-cycle, with MS2 CE>0
}
}
else if (!_isWatersMse)
{
// Bruker - Alternate between 1 and 2
_mseLevel = (_mseLevel % 2) + 1;
returnval = _mseLevel;
}
else
{
// Waters - mse level 1 in raw data "function 1", mse level 2 in raw data "function 2", and "function 3" which we ignore (lockmass?)
// All are declared mslevel=1, but we can tell these apart by inspecting the Id which is formatted as <function>.<process>.<scan>
_mseLevel = int.Parse(dataSpectrum.Id.Split('.')[0]);
returnval = _mseLevel;
}
_mseLastSpectrumLevel = returnval;
}
else
{
returnval = _mseLastSpectrumLevel; // we were just asked about this spectrum, no update this time
}
_mseLastSpectrum = dataSpectrum;
return(returnval);
}
public bool IsBeyondRange(MsDataSpectrum spectrum)
{
if (!_endIonMobilityValue.HasValue)
{
return(false);
}
double im = _endIonMobilityValue.Value;
if (_endOffset != 0)
{
im += _endOffset; // For breakpoint
}
return(Compare(spectrum, im) > 0);
}
private Spectrum GenerateMSAmandaSpectrum(MsDataSpectrum spectrum, int index)
{
Spectrum amandaSpectrum = new Spectrum()
{
RT = spectrum.RetentionTime.Value, SpectrumId = index
};
amandaSpectrum.FragmentsPeaks = GetFragmentPeaks(spectrum.Mzs, spectrum.Intensities);
amandaSpectrum.ScanNumber = spectrum.Index;
if (spectrum.Precursors[0].ChargeState.HasValue && spectrum.Precursors[0].PrecursorMz.HasValue)
{
amandaSpectrum.Precursor.SetMassCharge(spectrum.Precursors[0].PrecursorMz.Value, spectrum.Precursors[0].ChargeState.Value, true);
}
//SpectTitleMap.Add(index, spectrum.Id);
return(amandaSpectrum);
}
public List <Spectrum> ParseNextSpectra(int numberOfSpectraToRead, out int nrOfParsed, CancellationToken cancellationToken = new CancellationToken())
{
List <Spectrum> spectra = new List <Spectrum>();
nrOfParsed = 0;
while (nrOfParsed < numberOfSpectraToRead && specId < spectrumFileReader.SpectrumCount)
{
MsDataSpectrum spectrum = spectrumFileReader.GetSpectrum(specId);
cancellationToken.ThrowIfCancellationRequested();
++specId;
if (spectrum.Level != 2)
{
continue;
}
Spectrum amandaSpectrum = GenerateMSAmandaSpectrum(spectrum, amandaId);
if (amandaSpectrum.Precursor.Charge == 0)
{
foreach (int charge in consideredCharges)
{
Spectrum newSpect = GenerateSpectrum(amandaSpectrum, amandaId,
spectrum.Precursors[0].PrecursorMz.Value, charge);
SpectTitleMap.Add(amandaId, spectrum.Id);
++amandaId;
spectra.Add(newSpect);
}
}
else
{
SpectTitleMap.Add(amandaId, spectrum.Id);
++amandaId;
spectra.Add(amandaSpectrum);
}
++nrOfParsed;
}
CurrentSpectrum += nrOfParsed;
return(spectra);
}
private MsDataSpectrum GetSpectrumFromJObject(JObject jObject, int msLevel)
{
// ReSharper disable NonLocalizedString
string strMzs = jObject["mzs-base64"].ToString();
string strIntensities = jObject["intensities-base64"].ToString();
byte[] mzBytes = Convert.FromBase64String(strMzs);
byte[] intensityBytes = Convert.FromBase64String(strIntensities);
double[] mzs = PrimitiveArrays.FromBytes <double>(
PrimitiveArrays.ReverseBytesInBlocks(mzBytes, sizeof(double)));
float[] intensityFloats = PrimitiveArrays.FromBytes <float>(
PrimitiveArrays.ReverseBytesInBlocks(intensityBytes, sizeof(float)));
double[] intensities = intensityFloats.Select(f => (double)f).ToArray();
IonMobilityValue ionMobility = IonMobilityValue.EMPTY;
JToken jDriftTime;
if (jObject.TryGetValue("driftTime", out jDriftTime))
{
var driftTime = jDriftTime.ToObject <double>();
if (driftTime != 0)
{
ionMobility = IonMobilityValue.GetIonMobilityValue(driftTime, MsDataFileImpl.eIonMobilityUnits.drift_time_msec);
}
}
MsDataSpectrum spectrum = new MsDataSpectrum
{
Index = jObject["index"].ToObject <int>(),
RetentionTime = jObject["rt"].ToObject <double>(),
Mzs = mzs,
Intensities = intensities,
IonMobility = ionMobility,
};
return(spectrum);
// ReSharper restore NonLocalizedString
}
/// <summary>
/// generates a fake deconvolution solution for the given test spectrum
/// in order to make sure that the deconvolution results are being applied
/// correctly to scale peaks in the test spectrum
/// </summary>
private static void TestPeakIntensityCorrection(MsDataSpectrum testSpectrum,
AbstractIsoWindowMapper isoMapper,
AbstractDemultiplexer demultiplexer)
{
// Store a reference to the old spectrum processor
var oldProcessor = demultiplexer.SpectrumProcessor;
MsxDeconvSolverHandler db = new MsxDeconvSolverHandler(100, 120, 35);
int[] isoIndices;
int[] deconvIndices;
double[] mask = new double[100];
isoMapper.GetWindowMask(testSpectrum, out isoIndices, out deconvIndices, ref mask);
db.SetDeconvIndices(deconvIndices);
Assert.IsTrue(deconvIndices.Contains(50));
Assert.IsTrue(deconvIndices.Contains(47));
Assert.IsTrue(deconvIndices.Contains(15));
Assert.IsTrue(deconvIndices.Contains(17));
Assert.IsTrue(deconvIndices.Contains(74));
Assert.AreEqual(5, deconvIndices.Length);
// Prepare the transition binner with a precursor containing transitions overlapping
// peaks in the test spectrum
List <double> precursors = new List <double>();
List <KeyValuePair <double, double> > transitions = new List <KeyValuePair <double, double> >();
var precVals = new[] { 710.57 };
var transMzs = new[] { 372.18, 373.1588, 373.1794, 375.2, 379.23, 387.19 };
var transWidths = new[] { 0.3, 0.04, 0.02, 1.0, 1.0, 1.0 };
foreach (var precMz in precVals)
{
for (int i = 0; i < isoIndices.Length; ++i)
{
var transMz = transMzs[i];
var transWidth = transWidths[i];
precursors.Add(precMz);
transitions.Add(new KeyValuePair <double, double>(transMz, transWidth));
}
}
var transBinner = new TransitionBinner(precursors, transitions, isoMapper);
var binIndicesSet = new HashSet <int>(transBinner.BinsForDeconvWindows(deconvIndices));
double[][] deconvIntensities = new double[deconvIndices.Length][];
double[][] deconvMzs = new double[deconvIndices.Length][];
for (int i = 0; i < deconvIndices.Length; ++i)
{
deconvIntensities[i] = new double[testSpectrum.Mzs.Length];
deconvMzs[i] = new double[testSpectrum.Mzs.Length];
}
List <int> binIndicesList = binIndicesSet.ToList();
binIndicesList.Sort();
// Use each transition bin index to test a different possible
// type of demultiplexed solution
int numDeMultiplexedTrans = binIndicesSet.Count;
double[] peakSums = new double[numDeMultiplexedTrans];
// Initialize the deconvBlock
db.Solution.Resize(100, binIndicesList.Count);
db.Solution.Clear();
// Transition index 0, each row is a precursor
// the values for each precursor are the relative contribution
// of that precursor to the observed (convolved) intensity of the peak
db.Solution.Matrix[2, 0] = 0.0;
db.Solution.Matrix[1, 0] = 0.0;
db.Solution.Matrix[0, 0] = 0.0;
db.Solution.Matrix[3, 0] = 0.0;
db.Solution.Matrix[4, 0] = 0.0;
peakSums[0] = 0.0;
// Transition index 1, each row is a precursor
db.Solution.Matrix[2, 1] = 1.0;
db.Solution.Matrix[1, 1] = 1.0;
db.Solution.Matrix[0, 1] = 2.0;
db.Solution.Matrix[3, 1] = 1.0;
db.Solution.Matrix[4, 1] = 1.0;
peakSums[1] = 6.0;
// Transition index 2, each row is a precursor
db.Solution.Matrix[2, 2] = 2.0;
db.Solution.Matrix[1, 2] = 1.0;
db.Solution.Matrix[0, 2] = 3.0;
db.Solution.Matrix[3, 2] = 3.0;
db.Solution.Matrix[4, 2] = 1.0;
peakSums[2] = 10.0;
// Transition index 3, each row is a precursor
db.Solution.Matrix[2, 3] = 0.0;
db.Solution.Matrix[1, 3] = 0.0;
db.Solution.Matrix[0, 3] = 1.0;
db.Solution.Matrix[3, 3] = 0.0;
db.Solution.Matrix[4, 3] = 0.0;
peakSums[3] = 1.0;
// Transition index 4, each row is a precursor
db.Solution.Matrix[2, 4] = 1.0;
db.Solution.Matrix[1, 4] = 1.0;
db.Solution.Matrix[0, 4] = 1.0;
db.Solution.Matrix[3, 4] = 1.0;
db.Solution.Matrix[4, 4] = 1.0;
peakSums[4] = 5.0;
// Transition bin index (in transBinner) -> solution transition index (0-4 above), needed for
// CorrectPeakIntensities call
Dictionary <int, int> binToDeconvIndex = new Dictionary <int, int>(numDeMultiplexedTrans);
int numBinIndices = binIndicesList.Count;
for (int i = 0; i < numBinIndices; ++i)
{
binToDeconvIndex[binIndicesList[i]] = i;
}
var queryBinEnumerator = transBinner.BinsFromValues(testSpectrum.Mzs, true);
demultiplexer.SpectrumProcessor = new SpectrumProcessor(165, isoMapper, transBinner);
// Apply the peak intensity correction
demultiplexer.CorrectPeakIntensitiesTest(testSpectrum, binIndicesSet, peakSums,
queryBinEnumerator, db, ref deconvIntensities,
ref deconvMzs);
// Check that the five solutions defined above were applied correctly
// by CorrectPeakIntensities
// If all precursors contribute 0 intensity, the peak should be zero for every
// deconvolved spectrum
for (int i = 0; i < deconvIndices.Length; ++i)
{
Assert.AreEqual(deconvIntensities[i][binToDeconvIndex[0]], 0.0);
}
// Find the index of the demultiplexed spectrum corresponding to the precursor
// at 710.57 m/z for which we generated the dummy demultiplexing solution for
int windowIndex;
isoMapper.TryGetDeconvFromMz(710.57, out windowIndex);
Assert.AreEqual(50, windowIndex);
int isoIndex = deconvIndices.IndexOf(i => i == windowIndex);
Assert.AreNotEqual(-1, isoIndex);
// This peak falls in one transition bin (transition index 1)
// 47 is the index of a peak in the test spectrum
var originalIntensity = testSpectrum.Intensities[47];
var expectedIntensity = originalIntensity * (2.0 / 6.0);
Assert.AreEqual(deconvIntensities[isoIndex][47], expectedIntensity, 0.00001);
// This peak falls in one transitions bin (transition index 2)
originalIntensity = testSpectrum.Intensities[50];
expectedIntensity = originalIntensity * (3.0 / 10.0);
Assert.AreEqual(deconvIntensities[isoIndex][50], expectedIntensity, 0.00001);
// This peak falls in both transition indices 1 and 2, the expected adjusted
// intensity should be the average of the solution from each transition bin
originalIntensity = testSpectrum.Intensities[49];
expectedIntensity = originalIntensity * (19.0 / 60.0);
Assert.AreEqual(deconvIntensities[isoIndex][49], expectedIntensity, 0.00001);
// This peak falls in transition index 3, and the demultiplexing spectra
// indicates that all of the intensity of teh original peak comes from
// the precursor window at isoIndex that's being queried. The peak intensity
// should not change
originalIntensity = testSpectrum.Intensities[108];
expectedIntensity = originalIntensity;
Assert.AreEqual(deconvIntensities[isoIndex][108], expectedIntensity, 0.00001);
// This peak falls in one transition bin (transition index 5)
originalIntensity = testSpectrum.Intensities[149];
expectedIntensity = originalIntensity * (1.0 / 5.0);
Assert.AreEqual(deconvIntensities[isoIndex][149], expectedIntensity, 0.00001);
// Undo changes to the spectrum processor in case this demultiplexer object is
// reused
demultiplexer.SpectrumProcessor = oldProcessor;
}
private static TransitionBinner TestTransitionBinnerOverlap(MsDataSpectrum spectrum,
AbstractIsoWindowMapper isoMapper, double[] binnedIntensities)
{
// Multiple transitions overlapping the same peak from the same precursor
var precursorList = new List <double>();
var transitionList = new List <KeyValuePair <double, double> >();
precursorList.Add(710.5); //transition: start - stop index
transitionList.Add(new KeyValuePair <double, double>(380.19, 1.0)); // 379.69-380.69 Bin3
precursorList.Add(710.5);
transitionList.Add(new KeyValuePair <double, double>(380.44, 1.0)); // 379.94-380.94 Bin4
precursorList.Add(710.5);
transitionList.Add(new KeyValuePair <double, double>(380.49, 0.6)); // 380.19-380.79 Bin5
// And a non-overlapping transition for good measure
precursorList.Add(710.5);
transitionList.Add(new KeyValuePair <double, double>(389.19, 0.3)); // 389.04 - 389.34 Bin7
// And a transition that won't have any peaks in the spectrum
precursorList.Add(710.5);
transitionList.Add(new KeyValuePair <double, double>(377.0, 0.7)); // 376.65-377.35 Bin0
// And now another precursor with some of the transitions overlapping the first
precursorList.Add(595.0);
transitionList.Add(new KeyValuePair <double, double>(380.0, 1.0)); // 379.5 - 380.5 Bin2
precursorList.Add(595.0);
transitionList.Add(new KeyValuePair <double, double>(379.55, 1.0)); // 379.05 - 380.05 Bin1
precursorList.Add(595.0);
transitionList.Add(new KeyValuePair <double, double>(389.15, 0.4)); // 388.95 - 389.35 Bin6
var transitionBinner = new TransitionBinner(precursorList, transitionList, isoMapper);
double[] binnedData = new double[transitionList.Count];
transitionBinner.BinData(spectrum.Mzs, spectrum.Intensities, ref binnedData);
// Test that m/z, intensity pairs were binned correctly into their transitions
for (int i = 0; i < binnedData.Length; ++i)
{
Assert.AreEqual(binnedIntensities[i], binnedData[i], 0.001);
}
// Get the precursor index for this precursor
// make sure the precursor -> transition mapping is working for the first precursor
int windowIndexOne;
Assert.IsTrue(isoMapper.TryGetDeconvFromMz(710.5, out windowIndexOne));
// Use the precursor index to get the bins mapping to this precursor
var precursorBins = new HashSet <int>(transitionBinner.BinsForDeconvWindows(new[] { windowIndexOne }));
var expectedPrecursorBins = new HashSet <int>(new[] { 0, 3, 4, 5, 7 });
var setComparer = HashSet <int> .CreateSetComparer();
Assert.IsTrue(setComparer.Equals(expectedPrecursorBins, precursorBins));
// Make sure the precursor -> transition mapping is working for the second precursor
int windowIndexTwo;
Assert.IsTrue(isoMapper.TryGetDeconvFromMz(595.0, out windowIndexTwo));
precursorBins = new HashSet <int>(transitionBinner.BinsForDeconvWindows(new[] { windowIndexOne, windowIndexTwo }));
expectedPrecursorBins = new HashSet <int>(new[] { 0, 1, 2, 3, 4, 5, 6, 7 });
Assert.IsTrue(setComparer.Equals(expectedPrecursorBins, precursorBins));
// m/z values to test mapping of m/z value -> multiplex matching transition bins
var queryVals = new[] { 252.0, 377.0, 379.92, 379.95 };
var bins = transitionBinner.BinsFromValues(queryVals, true).ToList();
var expectedBins = new List <KeyValuePair <int, int> >
{
new KeyValuePair <int, int>(1, 0),
new KeyValuePair <int, int>(2, 1),
new KeyValuePair <int, int>(2, 2),
new KeyValuePair <int, int>(2, 3),
new KeyValuePair <int, int>(3, 1),
new KeyValuePair <int, int>(3, 2),
new KeyValuePair <int, int>(3, 3),
new KeyValuePair <int, int>(3, 4)
};
AssertEx.AreEqualDeep(expectedBins, bins);
Assert.AreEqual(376.65, transitionBinner.LowerValueFromBin(0), 0.0001);
Assert.AreEqual(377.35, transitionBinner.UpperValueFromBin(0), 0.0001);
Assert.AreEqual(377.0, transitionBinner.CenterValueFromBin(0), 0.0001);
return(transitionBinner);
}
/// <summary>
/// Given an original spectrum, return two spectra each with an isolation window that is half of the original spectrum.
/// </summary>
public MsDataSpectrum[] GetDeconvolvedSpectra(int index, MsDataSpectrum originalSpectrum)
{
if (originalSpectrum.Precursors.Count != 1)
{
return(new[] { originalSpectrum });
}
MsPrecursor originalPrecursor = originalSpectrum.Precursors.First();
double? lowerMzNullable = GetLowerMz(originalPrecursor);
double? upperMzNullable = GetUpperMz(originalPrecursor);
if (!lowerMzNullable.HasValue || !upperMzNullable.HasValue)
{
return(new[] { originalSpectrum });
}
double lowerMz = lowerMzNullable.Value;
double upperMz = upperMzNullable.Value;
MsDataSpectrum earlyLow = FindOverlappingSpectrum(lowerMz, Enumerable.Range(1, index - 1).Select(i => index - i), originalPrecursor);
MsDataSpectrum earlyHigh = FindOverlappingSpectrum(upperMz, Enumerable.Range(1, index - 1).Select(i => index - i), originalPrecursor);
MsDataSpectrum lateLow = FindOverlappingSpectrum(lowerMz,
Enumerable.Range(index + 1, _dataFile.SpectrumCount - index - 1), originalPrecursor);
MsDataSpectrum lateHigh = FindOverlappingSpectrum(upperMz,
Enumerable.Range(index + 1, _dataFile.SpectrumCount - index - 1), originalPrecursor);
double?middlePrecursorMz = GetMiddlePrecursorMz(new[] { earlyLow, lateLow }, new[] { earlyHigh, lateHigh });
if (!middlePrecursorMz.HasValue)
{
return(new[] { originalSpectrum });
}
double[] mzs = originalSpectrum.Mzs;
List <KeyValuePair <double, double> > lowerPeaks = new List <KeyValuePair <double, double> >();
List <KeyValuePair <double, double> > upperPeaks = new List <KeyValuePair <double, double> >();
// ReSharper disable CollectionNeverQueried.Local
List <KeyValuePair <double, double> > removedPeaks = new List <KeyValuePair <double, double> >();
// ReSharper restore CollectionNeverQueried.Local
for (int i = 0; i < mzs.Length; i++)
{
double mz = mzs[i];
double earlyLowIntensity = GetIntensity(earlyLow, mz);
double earlyHighIntensity = GetIntensity(earlyHigh, mz);
double lateLowIntensity = GetIntensity(lateLow, mz);
double lateHighIntensity = GetIntensity(lateHigh, mz);
double totalLow = earlyLowIntensity + lateLowIntensity;
double totalHigh = earlyHighIntensity + lateHighIntensity;
double total = totalLow + totalHigh;
if (total > 0)
{
double fractionLow = totalLow / total;
if (fractionLow > 0.0f)
{
double intensity = originalSpectrum.Intensities[i] * fractionLow;
lowerPeaks.Add(new KeyValuePair <double, double>(mz, intensity));
}
double fractionHigh = totalHigh / total;
if (fractionHigh > 0.0f)
{
double intensity = originalSpectrum.Intensities[i] * fractionHigh;
upperPeaks.Add(new KeyValuePair <double, double>(mz, intensity));
}
}
else
{
removedPeaks.Add(new KeyValuePair <double, double>(mz, originalSpectrum.Intensities[i]));
}
}
MsDataSpectrum lowerSpectrum = MakeDeconvSpectrum(originalSpectrum, lowerPeaks);
lowerSpectrum.Precursors = ImmutableList.Singleton(MakeMsPrecursor(lowerMz, middlePrecursorMz.Value));
MsDataSpectrum upperSpectrum = MakeDeconvSpectrum(originalSpectrum, upperPeaks);
upperSpectrum.Precursors = ImmutableList.Singleton(MakeMsPrecursor(middlePrecursorMz.Value, upperMz));
return(new[] { lowerSpectrum, upperSpectrum });
}
