public LcMsPeakMatrix(LcMsRun run, LcMsFeatureLikelihood scorer = null, int minScanCharge = 1, int maxScanCharge = 60, int maxThreadCount = 0)
{
Run = run;
_maxThreadCount = maxThreadCount;
_ms1PeakList = new List<Ms1Peak>();
Ms1Spectra = new List<Ms1Spectrum>();
var ms1ScanNums = run.GetMs1ScanVector();
NColumns = ms1ScanNums.Length;
MinSearchCharge = minScanCharge;
MaxSearchCharge = maxScanCharge;
NRows = Math.Min(MaxSearchCharge - MinSearchCharge + 1, 35);
for (var i = 0; i < Math.Min(ms1ScanNums.Length, ushort.MaxValue); i++)
{
var ms1Spec = run.GetMs1Spectrum(ms1ScanNums[i]);
Ms1Spectra.Add(ms1Spec);
foreach (var peak in ms1Spec.Peaks) _ms1PeakList.Add(peak as Ms1Peak);
}
_ms1PeakList.Sort();
_distProfileAcrossCharge = new double[NRows];
_corrProfileAcrossCharge = new double[NRows];
_intensityAcrossCharge = new double[NRows];
_summedEnvelopeColRange = new int[NRows, 2];
_featureMatrix = null;
Comparer = new MzComparerWithBinning(27); // 16ppm
_scorer = scorer;
_seedEnvelopes = new List<KeyValuePair<double, ObservedIsotopeEnvelope>>();
_ms1Filter = null;
}
public ProteinSpectrumMatch FindByFeature(double mass, int minScanNum, int maxScanNum, Tolerance tolerance)
{
var massComparerWithBinning = new MzComparerWithBinning(29); // 4ppm
var massBin = massComparerWithBinning.GetBinNumber(mass);
ProteinSpectrumMatch ret = null;
for (var scanNum = minScanNum + 1; scanNum < maxScanNum; scanNum++)
{
if (_scanNumToMatchMap[scanNum] == null)
{
continue;
}
if (Math.Abs(massBin - massComparerWithBinning.GetBinNumber(_scanNumToMatchMap[scanNum].Mass)) <= 1)
{
if (ret == null)
{
ret = _scanNumToMatchMap[scanNum];
}
else
{
if (ret.Score < _scanNumToMatchMap[scanNum].Score)
{
ret = _scanNumToMatchMap[scanNum];
}
}
}
}
return(ret);
}
public LcMsPeakScorer(Ms1Spectrum spec, int numBits4WinSize = 19) // 19 bits -> 4096 ppm, 20 bits -> 2048
{
Spectrum = spec;
var peaks = spec.Peaks;
_windowComparer = new MzComparerWithBinning(numBits4WinSize);
_minBinNum = _windowComparer.GetBinNumber(peaks[0].Mz);
_maxBinNum = _windowComparer.GetBinNumber(peaks[peaks.Length - 1].Mz);
var numberOfbins = _maxBinNum - _minBinNum + 1;
_peakStartIndex = new int[2][];
_peakRanking = new int[2][][];
var intensities = new List<double>[2][];
for (var i = 0; i < 2; i++)
{
_peakStartIndex[i] = new int[numberOfbins];
_peakRanking[i] = new int[numberOfbins][];
intensities[i] = new List<double>[numberOfbins];
for (var j = 0; j < numberOfbins; j++)
{
_peakStartIndex[i][j] = peaks.Length - 1;
intensities[i][j] = new List<double>();
}
}
for (var i = 0; i < peaks.Length; i++)
{
var binNum = _windowComparer.GetBinNumber(peaks[i].Mz);
var binMzAverage = _windowComparer.GetMzAverage(binNum);
var binIdx = binNum - _minBinNum;
intensities[0][binIdx].Add(peaks[i].Intensity);
if (i < _peakStartIndex[0][binIdx]) _peakStartIndex[0][binIdx] = i;
if (peaks[i].Mz < binMzAverage)
{
intensities[1][binIdx].Add(peaks[i].Intensity);
if (i < _peakStartIndex[1][binIdx]) _peakStartIndex[1][binIdx] = i;
}
else if (binNum < _maxBinNum) // skip this at the rightmost bin
{
intensities[1][binIdx + 1].Add(peaks[i].Intensity);
if (i < _peakStartIndex[1][binIdx + 1]) _peakStartIndex[1][binIdx + 1] = i;
}
}
for (var i = 0; i < 2; i++)
{
for (var binIdx = 0; binIdx < numberOfbins; binIdx++)
{
if (intensities[i][binIdx].Count < 1) continue;
double medianIntensity;
_peakRanking[i][binIdx] = GetRankings(intensities[i][binIdx].ToArray(), out medianIntensity);
}
}
}
public ProteinMassBinning(double minMass = 50, double maxMass = 50000, bool padZeroMassBin = false, int numBits = 28)
{
_mzComparer = new MzComparerWithBinning(numBits);
MinMass = minMass;
MaxMass = maxMass;
_minBinIndex = _mzComparer.GetBinNumber(MinMass);
_maxBinIndex = _mzComparer.GetBinNumber(MaxMass);
_padZeroMassBin = padZeroMassBin;
NumberOfBins = (_padZeroMassBin) ? _maxBinIndex - _minBinIndex + 2 : _maxBinIndex - _minBinIndex + 1;
}
public ProteinMassBinning(double minMass = 50, double maxMass = 50000, bool padZeroMassBin = false, int numBits = 28)
{
_mzComparer = new MzComparerWithBinning(numBits);
MinMass = minMass;
MaxMass = maxMass;
_minBinIndex = _mzComparer.GetBinNumber(MinMass);
_maxBinIndex = _mzComparer.GetBinNumber(MaxMass);
_padZeroMassBin = padZeroMassBin;
NumberOfBins = (_padZeroMassBin) ? _maxBinIndex - _minBinIndex + 2 : _maxBinIndex - _minBinIndex + 1;
}
public void UpdateWithDecoyScore(List <Ms1Spectrum> ms1Spectra, int targetMinCharge, int targetMaxCharge)
{
var ms1ScanNumToIndex = _run.GetMs1ScanNumToIndex();
var ms1ScanNums = _run.GetMs1ScanVector();
var minCol = ms1ScanNumToIndex[MinScanNum];
var maxCol = ms1ScanNumToIndex[MaxScanNum];
MinCharge = targetMinCharge;
MaxCharge = targetMaxCharge;
var rnd = new Random();
var comparer = new MzComparerWithBinning(28);
var mostAbuInternalIndex = TheoreticalEnvelope.IndexOrderByRanking[0];
var nRows = MaxCharge - MinCharge + 1;
var nCols = maxCol - minCol + 1;
Envelopes = new ObservedIsotopeEnvelope[nRows][];
for (var i = 0; i < nRows; i++)
{
Envelopes[i] = new ObservedIsotopeEnvelope[nCols];
}
for (var charge = targetMinCharge; charge <= targetMaxCharge; charge++)
{
var mostAbuMz = TheoreticalEnvelope.GetIsotopeMz(charge, mostAbuInternalIndex);
if (_run.MaxMs1Mz < mostAbuMz || mostAbuMz < _run.MinMs1Mz)
{
continue;
}
for (var col = minCol; col <= maxCol; col++)
{
var localWin = ms1Spectra[col].GetLocalMzWindow(mostAbuMz);
var numMzBins = comparer.GetBinNumber(localWin.MaxMz) - comparer.GetBinNumber(localWin.MinMz) + 1;
var peakSet = new Ms1Peak[TheoreticalEnvelope.Size];
for (var k = 0; k < peakSet.Length; k++)
{
var r = rnd.Next(0, numMzBins);
if (r < localWin.PeakCount)
{
peakSet[k] = (Ms1Peak)ms1Spectra[col].Peaks[r + localWin.PeakStartIndex];
}
}
var env = new ObservedIsotopeEnvelope(Mass, charge, ms1ScanNums[col], peakSet, TheoreticalEnvelope);
//AddObservedEnvelope(env);
Envelopes[charge - MinCharge][col - minCol] = env;
}
}
UpdateScore(ms1Spectra, false);
}
/// <summary>
/// MaxEnt deconvolution algorithm constructor
/// </summary>
/// <param name="spec">Specrum</param>
/// <param name="tolerance">tolerance</param>
/// <param name="massBinning">mass binning interface</param>
/// <param name="minCharge">maximum charge to be considered</param>
/// <param name="maxCharge">minimum charge to be considered</param>
/// <param name="minMass">minimum mass to be considered</param>
/// <param name="maxMass">maximum mass to be considered</param>
public MaxEntDeconvoluter(Spectrum spec, Tolerance tolerance, MzComparerWithBinning massBinning, int minCharge = 1, int maxCharge = 100, double minMass = 10000, double maxMass = 100000)
{
_minCharge = minCharge;
_maxCharge = maxCharge;
_minMass = minMass;
_maxMass = maxMass;
_tolerance = tolerance;
_massBinning = massBinning;
_spectrum = spec;
_deconvolutedSpectrum = null;
}
/// <summary>
/// MaxEnt deconvolution algorithm constructor
/// </summary>
/// <param name="tolerance">tolerance</param>
/// <param name="massBinning">mass binning interface</param>
/// <param name="minCharge">maximum charge to be considered</param>
/// <param name="maxCharge">minimum charge to be considered</param>
/// <param name="minMass">minimum mass to be considered</param>
/// <param name="maxMass">maximum mass to be considered</param>
public MaxEntDeconvoluter(Spectrum spec, Tolerance tolerance, MzComparerWithBinning massBinning, int minCharge = 1, int maxCharge = 100, double minMass = 10000, double maxMass = 100000)
{
_minCharge = minCharge;
_maxCharge = maxCharge;
_minMass = minMass;
_maxMass = maxMass;
_tolerance = tolerance;
_massBinning = massBinning;
_spectrum = spec;
_deconvolutedSpectrum = null;
}
/// <summary>
/// Produce a summed spectrum using the data in the scans specified by <paramref name="scanNums"/>
/// </summary>
/// <param name="scanNums"></param>
/// <param name="repScanNum">Representative scan number</param>
/// <returns></returns>
public SummedSpectrum GetSummedSpectrum(IList <int> scanNums, int repScanNum = 0)
{
var mzComparer = new MzComparerWithBinning();
var mzDic = new Dictionary <int, List <double> >();
var intDic = new Dictionary <int, double>();
foreach (var scanNum in scanNums)
{
var spec = GetSpectrum(scanNum);
if (spec == null)
{
continue;
}
foreach (var peak in spec.Peaks)
{
var mzBin = mzComparer.GetBinNumber(peak.Mz);
List <double> mzList;
if (mzDic.TryGetValue(mzBin, out mzList))
{
mzList.Add(peak.Mz);
intDic[mzBin] += peak.Intensity;
}
else
{
mzDic.Add(mzBin, new List <double> {
peak.Mz
});
intDic.Add(mzBin, peak.Intensity);
}
}
}
var summedPeakList = new List <Peak>();
foreach (var entry in mzDic)
{
var binNum = entry.Key;
var mzList = entry.Value;
var medianMz = mzList.Median();
var intensity = intDic[binNum];
summedPeakList.Add(new Peak(medianMz, intensity));
}
summedPeakList.Sort();
var summedSpec = new SummedSpectrum(summedPeakList, repScanNum)
{
ScanNums = scanNums
};
return(summedSpec);
}
public void TestFloatBinning()
{
var methodName = MethodBase.GetCurrentMethod().Name;
ShowStarting(methodName);
const double minMass = 200;
const double maxMass = 50000;
const int numBits = 29;
var comparer = new MzComparerWithBinning(numBits);
Console.WriteLine(comparer.GetBinNumber(maxMass));
Console.WriteLine(comparer.GetBinNumber(maxMass) - comparer.GetBinNumber(minMass) + 1);
Console.WriteLine(LcMsMatchMap.GetBinNumber(maxMass) - LcMsMatchMap.GetBinNumber(minMass) + 1);
}
public LcMsPeakMatrixLowResolution(LcMsRun run, int maxFeaturesPerSpec = 100, double tolerancePpm = 64, int minScanCharge = 20, int maxScanCharge = 100, double minScanMass = 20000, double maxScanMass = 60000)
{
Run = run;
_tolerance = new Tolerance(Math.Max(tolerancePpm, 32));
_minCharge = minScanCharge;
_maxCharge = maxScanCharge;
_minMass = minScanMass;
_maxMass = maxScanMass;
_ms1Features = new NodeSet <Ms1Feature>();
var nBits = (int)Math.Round(27 - Math.Log(_tolerance.GetValue() / 16, 2));
_comparer = new MzComparerWithBinning(nBits);
_maxFeaturesPerSpec = maxFeaturesPerSpec;
}
public void TestFloatBinning()
{
var methodName = MethodBase.GetCurrentMethod().Name;
ShowStarting(methodName);
const double minMass = 200;
const double maxMass = 50000;
const int numBits = 29;
var comparer = new MzComparerWithBinning(numBits);
Console.WriteLine(comparer.GetBinNumber(maxMass));
Console.WriteLine(comparer.GetBinNumber(maxMass) - comparer.GetBinNumber(minMass) + 1);
Console.WriteLine(LcMsMatchMap.GetBinNumber(maxMass) - LcMsMatchMap.GetBinNumber(minMass) + 1);
}
public void TestGeneringAllXics()
{
var methodName = MethodBase.GetCurrentMethod().Name;
Utils.ShowStarting(methodName);
if (!File.Exists(TestRawFilePath))
{
Assert.Ignore(@"Skipping test " + methodName + @" since file not found: " + TestRawFilePath);
}
var run = PbfLcMsRun.GetLcMsRun(TestRawFilePath, 0.0, 0.0);
Assert.True(run != null);
var ms1Scans = run.GetMs1ScanVector();
var comparer = new MzComparerWithBinning(27);
const double minMz = 600.0; // 600.0
const double maxMz = 2000.0; // 2000.0
var minBinNum = comparer.GetBinNumber(minMz);
var maxBinNum = comparer.GetBinNumber(maxMz);
//var scanCount = run.MaxLcScan - run.MinLcScan + 1;
var scanCount = run.NumSpectra;
var sw = new Stopwatch();
sw.Start();
var numBinsProcessed = 0;
for (var binNum = minBinNum; binNum <= maxBinNum; binNum++)
{
var mzStart = comparer.GetMzStart(binNum);
var mzEnd = comparer.GetMzEnd(binNum);
var vec1 = run.GetFullPrecursorIonExtractedIonChromatogramVector(mzStart, mzEnd);
if (++numBinsProcessed % 2500 == 0)
{
Console.WriteLine(@"{0,5} / {1,5}, {2:0.00} m/z", numBinsProcessed, maxBinNum - minBinNum + 1, mzStart);
}
Assert.IsTrue(vec1.Length == ms1Scans.Length);
}
sw.Stop();
Console.WriteLine(@"{0:f4} sec", sw.Elapsed.TotalSeconds);
}
public void TestGetNumBins()
{
var methodName = MethodBase.GetCurrentMethod().Name;
Utils.ShowStarting(methodName);
var comparer = new MzComparerWithBinning(26);
const double minMz = 5000.0; // 600.0
const double maxMz = 10000.0; // 2000.0
var minBinNum = comparer.GetBinNumber(minMz);
var maxBinNum = comparer.GetBinNumber(maxMz);
var numBins = maxBinNum - minBinNum;
Console.WriteLine(@"NumBins: " + numBins);
Assert.IsTrue(numBins == 16384);
}
public void UpdateWithDecoyScore(List<Ms1Spectrum> ms1Spectra, int targetMinCharge, int targetMaxCharge)
{
var ms1ScanNumToIndex = _run.GetMs1ScanNumToIndex();
var ms1ScanNums = _run.GetMs1ScanVector();
var minCol = ms1ScanNumToIndex[MinScanNum];
var maxCol = ms1ScanNumToIndex[MaxScanNum];
MinCharge = targetMinCharge;
MaxCharge = targetMaxCharge;
var rnd = new Random();
var comparer = new MzComparerWithBinning(28);
var mostAbuInternalIndex = TheoreticalEnvelope.IndexOrderByRanking[0];
var nRows = MaxCharge - MinCharge + 1;
var nCols = maxCol - minCol + 1;
Envelopes = new ObservedIsotopeEnvelope[nRows][];
for (var i = 0; i < nRows; i++) Envelopes[i] = new ObservedIsotopeEnvelope[nCols];
for (var charge = targetMinCharge; charge <= targetMaxCharge; charge++)
{
var mostAbuMz = TheoreticalEnvelope.GetIsotopeMz(charge, mostAbuInternalIndex);
if (_run.MaxMs1Mz < mostAbuMz || mostAbuMz < _run.MinMs1Mz) continue;
for (var col = minCol; col <= maxCol; col++)
{
var localWin = ms1Spectra[col].GetLocalMzWindow(mostAbuMz);
var numMzBins = comparer.GetBinNumber(localWin.MaxMz) - comparer.GetBinNumber(localWin.MinMz) + 1;
var peakSet = new Ms1Peak[TheoreticalEnvelope.Size];
for (var k = 0; k < peakSet.Length; k++)
{
var r = rnd.Next(0, numMzBins);
if (r < localWin.PeakCount)
peakSet[k] = (Ms1Peak) ms1Spectra[col].Peaks[r + localWin.PeakStartIndex];
}
var env = new ObservedIsotopeEnvelope(Mass, charge, ms1ScanNums[col], peakSet, TheoreticalEnvelope);
//AddObservedEnvelope(env);
Envelopes[charge - MinCharge][col - minCol] = env;
}
}
UpdateScore(ms1Spectra, false);
}
public LcMsChargeMap(LcMsRun run, Tolerance tolerance, int maxNumMs2ScansPerMass = MaxNumMs2ScansPerFeature)
{
_run = run;
_scanToIsolationWindow = new Dictionary<int, IsolationWindow>();
_maxNumMs2ScansPerMass = maxNumMs2ScansPerMass;
foreach (var ms2ScanNum in _run.GetScanNumbers(2))
{
var isoWindow = _run.GetIsolationWindow(ms2ScanNum);
if (isoWindow != null) _scanToIsolationWindow.Add(ms2ScanNum, isoWindow);
}
_tolerance = tolerance;
_map = new Dictionary<int, BitArray>();
_comparer = new MzComparerWithBinning(30); // 2 ppm binning
_sequenceMassBinToScanNumsMap = new Dictionary<int, IEnumerable<int>>();
_scanNumToMassBin = new Dictionary<int, List<int>>();
}
public ProteinSpectrumMatch FindByFeature(double mass, int minScanNum, int maxScanNum, Tolerance tolerance)
{
var massComparerWithBinning = new MzComparerWithBinning(29); // 4ppm
var massBin = massComparerWithBinning.GetBinNumber(mass);
ProteinSpectrumMatch ret = null;
for (var scanNum = minScanNum + 1; scanNum < maxScanNum; scanNum++)
{
if (_scanNumToMatchMap[scanNum] == null) continue;
if (Math.Abs(massBin - massComparerWithBinning.GetBinNumber(_scanNumToMatchMap[scanNum].Mass)) <= 1)
{
if (ret == null) ret = _scanNumToMatchMap[scanNum];
else
{
if (ret.Score < _scanNumToMatchMap[scanNum].Score) ret = _scanNumToMatchMap[scanNum];
}
}
}
return ret;
}
public SummedSpectrum GetSummedSpectrum(IList<int> scanNums, int repScanNum = 0)
{
var mzComparer = new MzComparerWithBinning();
var mzDic = new Dictionary<int, List<double>>();
var intDic = new Dictionary<int, double>();
foreach (var scanNum in scanNums)
{
var spec = GetSpectrum(scanNum);
if (spec == null) continue;
foreach (var peak in spec.Peaks)
{
var mzBin = mzComparer.GetBinNumber(peak.Mz);
List<double> mzList;
if (mzDic.TryGetValue(mzBin, out mzList))
{
mzList.Add(peak.Mz);
intDic[mzBin] += peak.Intensity;
}
else
{
mzDic.Add(mzBin, new List<double> { peak.Mz });
intDic.Add(mzBin, peak.Intensity);
}
}
}
var summedPeakList = new List<Peak>();
foreach (var entry in mzDic)
{
var binNum = entry.Key;
var mzList = entry.Value;
var medianMz = mzList.Median();
var intensity = intDic[binNum];
summedPeakList.Add(new Peak(medianMz, intensity));
}
summedPeakList.Sort();
var summedSpec = new SummedSpectrum(summedPeakList, repScanNum) {ScanNums = scanNums};
return summedSpec;
}
public void TestGeneringAllXics()
{
var methodName = MethodBase.GetCurrentMethod().Name;
TestUtils.ShowStarting(methodName);
if (!File.Exists(TestRawFilePath))
{
Assert.Ignore(@"Skipping test " + methodName + @" since file not found: " + TestRawFilePath);
}
var run = PbfLcMsRun.GetLcMsRun(TestRawFilePath, 0.0, 0.0);
Assert.True(run != null);
var ms1Scans = run.GetMs1ScanVector();
var comparer = new MzComparerWithBinning(27);
const double minMz = 600.0; // 600.0
const double maxMz = 2000.0; // 2000.0
var minBinNum = comparer.GetBinNumber(minMz);
var maxBinNum = comparer.GetBinNumber(maxMz);
var scanCount = run.MaxLcScan - run.MinLcScan + 1;
var sw = new Stopwatch();
sw.Start();
var numBinsProcessed = 0;
for (var binNum = minBinNum; binNum <= maxBinNum; binNum++)
{
var mzStart = comparer.GetMzStart(binNum);
var mzEnd = comparer.GetMzEnd(binNum);
var vec1 = run.GetFullPrecursorIonExtractedIonChromatogramVector(mzStart, mzEnd);
if (++numBinsProcessed % 2500 == 0)
{
Console.WriteLine(@"{0,5} / {1,5}, {2:0.00} m/z", numBinsProcessed, maxBinNum - minBinNum + 1, mzStart);
}
Assert.IsTrue(vec1.Length == ms1Scans.Length);
}
sw.Stop();
Console.WriteLine(@"{0:f4} sec", sw.Elapsed.TotalSeconds);
}
public void TestGettingXicVector()
{
var methodName = MethodBase.GetCurrentMethod().Name;
TestUtils.ShowStarting(methodName);
if (!File.Exists(TestRawFilePath))
{
Assert.Ignore(@"Skipping test " + methodName + @" since file not found: " + TestRawFilePath);
}
var run1 = PbfLcMsRun.GetLcMsRun(TestRawFilePath, 0.0, 0.0);
var run2 = InMemoryLcMsRun.GetLcMsRun(TestRawFilePath, 0.0, 0.0);
Assert.True(run1 != null && run2 != null);
var comparer = new MzComparerWithBinning(27);
const double minMz = 600.0; // 600.0
const double maxMz = 2000.0; // 2000.0
var minBinNum = comparer.GetBinNumber(minMz);
var maxBinNum = comparer.GetBinNumber(maxMz);
Console.WriteLine(@"NumBins: " + (maxBinNum - minBinNum));
var warnCount = 0;
var sw = new Stopwatch();
sw.Start();
for (var binNum = minBinNum; binNum <= maxBinNum; binNum++)
{
var mzStart = comparer.GetMzStart(binNum);
var mzEnd = comparer.GetMzEnd(binNum);
var vec1 = run1.GetFullPrecursorIonExtractedIonChromatogramVector(mzStart, mzEnd);
var vec2 = run2.GetFullPrecursorIonExtractedIonChromatogramVector(mzStart, mzEnd);
Assert.True(vec1.Length == vec2.Length,
"Extracted Ion Chromatogram vector length mismatch, {0} vs. {1}", vec1.Length, vec2.Length);
var matchCount = 0;
var misMatchCount = 0;
var positiveCount = 0;
for (var i = 0; i < vec2.Length; i++)
{
if (vec1[i] > 0 || vec2[i] > 0)
{
positiveCount++;
}
if (Math.Abs(vec1[i] - vec2[i]) < float.Epsilon)
{
matchCount++;
}
else
{
misMatchCount++;
}
}
if (misMatchCount <= 0 || positiveCount == 0)
{
continue;
}
var fractionAgreement = 1 - misMatchCount / (double)positiveCount;
if (fractionAgreement < 0.80 && misMatchCount > 2)
{
Console.WriteLine(@"{0}/{1} Xic values do not match for bin {2} ({3:0.00} m/z); {4:0.0}% agreement",
misMatchCount, positiveCount, binNum, mzStart, fractionAgreement * 100);
warnCount++;
}
}
sw.Stop();
Console.WriteLine(@"{0:f4} sec", sw.Elapsed.TotalSeconds);
Assert.IsTrue(warnCount < 10, "Too many Xic mismatch warnings: {0}", warnCount);
}
public void TestGettingXicVector()
{
var methodName = MethodBase.GetCurrentMethod().Name;
TestUtils.ShowStarting(methodName);
if (!File.Exists(TestRawFilePath))
{
Assert.Ignore(@"Skipping test " + methodName + @" since file not found: " + TestRawFilePath);
}
var run1 = PbfLcMsRun.GetLcMsRun(TestRawFilePath, 0.0, 0.0);
var run2 = InMemoryLcMsRun.GetLcMsRun(TestRawFilePath, 0.0, 0.0);
Assert.True(run1 != null && run2 != null);
var comparer = new MzComparerWithBinning(27);
const double minMz = 600.0; // 600.0
const double maxMz = 2000.0; // 2000.0
var minBinNum = comparer.GetBinNumber(minMz);
var maxBinNum = comparer.GetBinNumber(maxMz);
Console.WriteLine(@"NumBins: " + (maxBinNum - minBinNum));
var warnCount = 0;
var sw = new Stopwatch();
sw.Start();
for (var binNum = minBinNum; binNum <= maxBinNum; binNum++)
{
var mzStart = comparer.GetMzStart(binNum);
var mzEnd = comparer.GetMzEnd(binNum);
var vec1 = run1.GetFullPrecursorIonExtractedIonChromatogramVector(mzStart, mzEnd);
var vec2 = run2.GetFullPrecursorIonExtractedIonChromatogramVector(mzStart, mzEnd);
Assert.True(vec1.Length == vec2.Length,
"Extracted Ion Chromatogram vector length mismatch, {0} vs. {1}", vec1.Length, vec2.Length);
var matchCount = 0;
var misMatchCount = 0;
var positiveCount = 0;
for (var i = 0; i < vec2.Length; i++)
{
if (vec1[i] > 0 || vec2[i] > 0)
{
positiveCount++;
}
if (Math.Abs(vec1[i] - vec2[i]) < float.Epsilon)
{
matchCount++;
}
else
{
misMatchCount++;
}
}
if (misMatchCount <= 0 || positiveCount == 0)
{
continue;
}
var fractionAgreement = 1 - misMatchCount / (double)positiveCount;
if (fractionAgreement < 0.80 && misMatchCount > 2)
{
Console.WriteLine(@"{0}/{1} Xic values do not match for bin {2} ({3:0.00} m/z); {4:0.0}% agreement",
misMatchCount, positiveCount, binNum, mzStart, fractionAgreement * 100);
warnCount++;
}
}
sw.Stop();
Console.WriteLine(@"{0:f4} sec", sw.Elapsed.TotalSeconds);
Assert.IsTrue(warnCount < 10, "Too many Xic mismatch warnings: {0}", warnCount);
}
static MatchedPeakPostScorer()
{
BaseIonTypesCID = new[] { BaseIonType.B, BaseIonType.Y };
BaseIonTypesETD = new[] { BaseIonType.C, BaseIonType.Z };
Comparer = new MzComparerWithBinning(28);
}
public void TestGetNumBins()
{
var methodName = MethodBase.GetCurrentMethod().Name;
TestUtils.ShowStarting(methodName);
var comparer = new MzComparerWithBinning(26);
const double minMz = 5000.0; // 600.0
const double maxMz = 10000.0; // 2000.0
var minBinNum = comparer.GetBinNumber(minMz);
var maxBinNum = comparer.GetBinNumber(maxMz);
var numBins = maxBinNum - minBinNum;
Console.WriteLine(@"NumBins: " + numBins);
Assert.IsTrue(numBins == 16384);
}
} // true: target and decoy, false: target only, null: decoy only
public void QuickId()
{
const string rawFilePath = @"H:\Research\QCShew_TopDown\Production\QC_Shew_Intact_26Sep14_Bane_C2Column3.raw";
const string fastaFilePath = @"H:\Research\QCShew_TopDown\Production\ID_002216_235ACCEA.fasta";
const string modFilePath = @"H:\Research\QCShew_TopDown\Production\Mods.txt";
const int numBits = 29; // max error: 4ppm
const int minCharge = 1;
const int maxCharge = 20;
var tolerance = new Tolerance(10);
const double corrThreshold = 0.7;
var comparer = new MzComparerWithBinning(numBits);
const double minFragmentMass = 200.0;
const double maxFragmentMass = 50000.0;
var minFragMassBin = comparer.GetBinNumber(minFragmentMass);
var maxFragMassBin = comparer.GetBinNumber(maxFragmentMass);
var aminoAcidSet = new AminoAcidSet(modFilePath);
var run = PbfLcMsRun.GetLcMsRun(rawFilePath);
var ms2ScanNumArr = run.GetScanNumbers(2).ToArray();
var sw = new Stopwatch();
sw.Start();
Console.Write("Building Spectrum Arrays...");
var massVectors = new BitArray[maxFragMassBin - minFragMassBin + 1];
for (var i = minFragMassBin; i <= maxFragMassBin; i++)
{
massVectors[i - minFragMassBin] = new BitArray(run.MaxLcScan + 1);
}
foreach (var ms2ScanNum in ms2ScanNumArr)
{
var productSpec = run.GetSpectrum(ms2ScanNum) as ProductSpectrum;
if (productSpec == null)
{
continue;
}
var deconvolutedPeaks = Deconvoluter.GetDeconvolutedPeaks(productSpec.Peaks, minCharge, maxCharge, 2, 1.1, tolerance, corrThreshold);
if (deconvolutedPeaks == null)
{
continue;
}
foreach (var p in deconvolutedPeaks)
{
var mass = p.Mass;
var deltaMass = tolerance.GetToleranceAsDa(mass, 1);
var minMass = mass - deltaMass;
var maxMass = mass + deltaMass;
var minBinNum = comparer.GetBinNumber(minMass);
var maxBinNum = comparer.GetBinNumber(maxMass);
for (var binNum = minBinNum; binNum <= maxBinNum; binNum++)
{
if (binNum >= minFragMassBin && binNum <= maxFragMassBin)
{
massVectors[binNum - minFragMassBin][ms2ScanNum] = true;
}
}
}
}
sw.Stop();
Console.WriteLine(@"{0:f1} sec.", sw.Elapsed.TotalSeconds);
sw.Reset();
sw.Start();
var fastaDb = new FastaDatabase(fastaFilePath);
fastaDb.Read();
var indexedDb = new IndexedDatabase(fastaDb);
var numProteins = 0;
var intactProteinAnnotationAndOffsets =
indexedDb.IntactSequenceAnnotationsAndOffsets(0, int.MaxValue);
var bestProtein = new string[run.MaxLcScan + 1];
var bestScore = new int[run.MaxLcScan + 1];
foreach (var annotationAndOffset in intactProteinAnnotationAndOffsets)
{
if (++numProteins % 10 == 0)
{
Console.WriteLine(@"Processing, {0} proteins done, {1:f1} sec elapsed",
numProteins,
sw.Elapsed.TotalSeconds);
}
var annotation = annotationAndOffset.Annotation;
var offset = annotationAndOffset.Offset;
var protSequence = annotation.Substring(2, annotation.Length - 4);
// suffix
var seqGraph = SequenceGraph.CreateGraph(aminoAcidSet, AminoAcid.ProteinNTerm, protSequence,
AminoAcid.ProteinCTerm);
if (seqGraph == null)
{
continue;
}
for (var numNTermCleavage = 0; numNTermCleavage <= 1; numNTermCleavage++)
{
if (numNTermCleavage > 0)
{
seqGraph.CleaveNTerm();
}
var allCompositions = seqGraph.GetAllFragmentNodeCompositions();
var scoreArr = new int[run.MaxLcScan + 1];
foreach (var fragComp in allCompositions)
{
var suffixMass = fragComp.Mass + BaseIonType.Y.OffsetComposition.Mass;
var binNum = comparer.GetBinNumber(suffixMass);
if (binNum < minFragMassBin || binNum > maxFragMassBin)
{
continue;
}
var vector = massVectors[binNum - minFragMassBin];
foreach (var ms2ScanNum in ms2ScanNumArr)
{
if (vector[ms2ScanNum])
{
++scoreArr[ms2ScanNum];
}
}
}
foreach (var ms2ScanNum in ms2ScanNumArr)
{
if (scoreArr[ms2ScanNum] > bestScore[ms2ScanNum])
{
bestScore[ms2ScanNum] = scoreArr[ms2ScanNum];
var proteinName = fastaDb.GetProteinName(offset);
bestProtein[ms2ScanNum] = proteinName + (numNTermCleavage == 1 ? "'" : "");
}
}
}
// prefix
}
Console.WriteLine("ScanNum\tBestProtein\tScore");
foreach (var ms2ScanNum in ms2ScanNumArr)
{
Console.WriteLine("{0}\t{1}\t{2}", ms2ScanNum, bestScore[ms2ScanNum], bestProtein[ms2ScanNum] ?? "");
}
}
public void TestGeneratingXicsOfAllCharges()
{
var methodName = MethodBase.GetCurrentMethod().Name;
TestUtils.ShowStarting(methodName);
if (!File.Exists(TestRawFilePath))
{
Assert.Ignore(@"Skipping test " + methodName + @" since file not found: " + TestRawFilePath);
}
var run = PbfLcMsRun.GetLcMsRun(TestRawFilePath, 0.0, 0.0);
var comparer = new MzComparerWithBinning(27);
const string protSequence =
"AIPQSVEGQSIPSLAPMLERTTPAVVSVAVSGTHVSKQRVPDVFRYFFGPNAPQEQVQERPFRGLGSGVIIDADKGYIVTNNHVIDGADDIQVGLHDGREVKAKLIGTDSESDIALLQIEAKNLVAIKTSDSDELRVGDFAVAIGNPFGLGQTVTSGIVSALGRSGLGIEMLENFIQTDAAINSGNSGGALVNLKGELIGINTAIVAPNGGNVGIGFAIPANMVKNLIAQIAEHGEVRRGVLGIAGRDLDSQLAQGFGLDTQHGGFVNEVSAGSAAEKAGIKAGDIIVSVDGRAIKSFQELRAKVATMGAGAKVELGLIRDGDKKTVNVTLGEANQTTEKAAGAVHPMLQGASLENASKGVEITDVAQGSPAAMSGLQKGDLIVGINRTAVKDLKSLKELLKDQEGAVALKIVRGKSMLYLVLR";
//const string annotation = "_." + protSequence + "._";
var seqGraph = SequenceGraph.CreateGraph(new AminoAcidSet(), AminoAcid.ProteinNTerm, protSequence, AminoAcid.ProteinCTerm);
if (seqGraph == null) return;
seqGraph.SetSink(0);
var neutral = seqGraph.GetSinkSequenceCompositionWithH2O() - Composition.Hydrogen;
var proteinMass = neutral.Mass;
var isoEnv = Averagine.GetIsotopomerEnvelope(proteinMass);
const bool SHOW_ALL_SCANS = false;
var targetColIndex = 0;
#pragma warning disable 0162
if (SHOW_ALL_SCANS)
Console.WriteLine("Charge\t" + string.Join("\t", run.GetScanNumbers(1)));
else
{
// Just display data for scan 161
Console.WriteLine("Charge\t161");
foreach (var scanNumber in run.GetScanNumbers(1))
{
if (scanNumber == 161)
break;
targetColIndex++;
}
}
#pragma warning restore 0162
const int minCharge = 2;
const int maxCharge = 60;
for (var charge = minCharge; charge <= maxCharge; charge++)
{
var ion = new Ion(neutral, charge);
var mostAbundantIsotopeMz = ion.GetIsotopeMz(isoEnv.MostAbundantIsotopeIndex);
//var secondMostAbundantIsotopeMz = ion.GetIsotopeMz(isoEnv.MostAbundantIsotopeIndex + 1);
var binNum = comparer.GetBinNumber(mostAbundantIsotopeMz);
var mzStart = comparer.GetMzStart(binNum);
var mzEnd = comparer.GetMzEnd(binNum);
var xic = run.GetFullPrecursorIonExtractedIonChromatogram(mzStart, mzEnd);
Console.Write(charge+"\t");
#pragma warning disable 0162
if (SHOW_ALL_SCANS)
Console.WriteLine(string.Join("\t", xic.Select(p => p.Intensity)));
else
Console.WriteLine(xic[targetColIndex].Intensity);
#pragma warning restore 0162
}
}
public void TestId()
{
const string rawFilePath = @"H:\Research\QCShew_TopDown\Production\QC_Shew_Intact_26Sep14_Bane_C2Column3.raw";
// const string fastaFilePath = @"H:\Research\QCShew_TopDown\Production\ID_002216_235ACCEA.icsfldecoy.fasta";
//const string fastaFilePath = @"H:\Research\QCShew_TopDown\Production\Decoy_SO4280.fasta";
const string fastaFilePath = @"H:\Research\QCShew_TopDown\Production\SO2312.fasta";
const string modFilePath = @"H:\Research\QCShew_TopDown\Production\Mods.txt";
const int numBits = 29; // max error: 4ppm
const int minCharge = 2;
const int maxCharge = 20;
var tolerance = new Tolerance(10);
const double corrThreshold = 0.7;
var comparer = new MzComparerWithBinning(numBits);
const double minFragmentMass = 200.0;
const double maxFragmentMass = 50000.0;
var minFragMassBin = comparer.GetBinNumber(minFragmentMass);
var maxFragMassBin = comparer.GetBinNumber(maxFragmentMass);
var aminoAcidSet = new AminoAcidSet(modFilePath);
var run = PbfLcMsRun.GetLcMsRun(rawFilePath);
// var ms2ScanNumArr = run.GetScanNumbers(2).ToArray();
//var ms2ScanNumArr = new[] {4130};
var ms2ScanNumArr = new[] { 5189 };
var sw = new Stopwatch();
sw.Start();
Console.Write("Building Spectrum Arrays...");
var massVectors = new BitArray[maxFragMassBin - minFragMassBin + 1];
for (var i = minFragMassBin; i <= maxFragMassBin; i++)
{
massVectors[i - minFragMassBin] = new BitArray(run.MaxLcScan + 1);
}
foreach (var ms2ScanNum in ms2ScanNumArr)
{
var productSpec = run.GetSpectrum(ms2ScanNum) as ProductSpectrum;
if (productSpec == null) continue;
productSpec.FilterNoise();
var deconvolutedPeaks = Deconvoluter.GetDeconvolutedPeaks(productSpec, minCharge, maxCharge, 2, 1.1,
tolerance, corrThreshold);
if (deconvolutedPeaks == null) continue;
foreach (var p in deconvolutedPeaks)
{
var mass = p.Mass;
var deltaMass = tolerance.GetToleranceAsDa(mass, 1);
var minMass = mass - deltaMass;
var maxMass = mass + deltaMass;
var minBinNum = comparer.GetBinNumber(minMass);
var maxBinNum = comparer.GetBinNumber(maxMass);
for (var binNum = minBinNum; binNum <= maxBinNum; binNum++)
{
if (binNum >= minFragMassBin && binNum <= maxFragMassBin) massVectors[binNum - minFragMassBin][ms2ScanNum] = true;
}
}
}
sw.Stop();
Console.WriteLine(@"{0:f4} sec.", sw.Elapsed.TotalSeconds);
sw.Reset();
sw.Start();
var fastaDb = new FastaDatabase(fastaFilePath);
fastaDb.Read();
var indexedDb = new IndexedDatabase(fastaDb);
var numProteins = 0;
var intactProteinAnnotationAndOffsets =
indexedDb.IntactSequenceAnnotationsAndOffsets(0, int.MaxValue);
var bestProtein = new string[run.MaxLcScan + 1];
var bestScore = new int[run.MaxLcScan + 1];
foreach (var annotationAndOffset in intactProteinAnnotationAndOffsets)
{
if (++numProteins % 10 == 0)
{
Console.WriteLine("Processing {0}{1} proteins...", numProteins,
numProteins == 1 ? "st" : numProteins == 2 ? "nd" : numProteins == 3 ? "rd" : "th");
if (numProteins != 0)
{
sw.Stop();
Console.WriteLine("Elapsed Time: {0:f4} sec", sw.Elapsed.TotalSeconds);
sw.Reset();
sw.Start();
}
}
var annotation = annotationAndOffset.Annotation;
var offset = annotationAndOffset.Offset;
var protSequence = annotation.Substring(2, annotation.Length - 4);
// suffix
var seqGraph = SequenceGraph.CreateGraph(aminoAcidSet, AminoAcid.ProteinNTerm, protSequence,
AminoAcid.ProteinCTerm);
if (seqGraph == null) continue;
for (var numNTermCleavage = 0; numNTermCleavage <= 0; numNTermCleavage++)
{
if (numNTermCleavage > 0) seqGraph.CleaveNTerm();
var allCompositions = seqGraph.GetAllFragmentNodeCompositions().ToArray();
var scoreArr = new int[run.MaxLcScan + 1];
foreach (var fragComp in allCompositions)
{
var suffixMass = fragComp.Mass + BaseIonType.Y.OffsetComposition.Mass;
var binNum = comparer.GetBinNumber(suffixMass);
if (binNum < minFragMassBin || binNum > maxFragMassBin) continue;
var vector = massVectors[binNum - minFragMassBin];
foreach (var ms2ScanNum in ms2ScanNumArr)
{
if (vector[ms2ScanNum])
{
++scoreArr[ms2ScanNum];
Console.WriteLine(suffixMass);
}
}
}
foreach (var ms2ScanNum in ms2ScanNumArr)
{
if (scoreArr[ms2ScanNum] > bestScore[ms2ScanNum])
{
bestScore[ms2ScanNum] = scoreArr[ms2ScanNum];
var proteinName = fastaDb.GetProteinName(offset);
bestProtein[ms2ScanNum] = proteinName + (numNTermCleavage == 1 ? "'" : "");
}
}
}
//// prefix
//var seqGraphPrefix = SequenceGraph.CreateGraph(aminoAcidSet, AminoAcid.ProteinNTerm, protSequence,
// AminoAcid.ProteinCTerm);
//if (seqGraphPrefix == null) continue;
//{
// if (numNTermCleavage > 0) seqGraph.CleaveNTerm();
// var allCompositions = seqGraph.GetAllFragmentNodeCompositions();
// var scoreArr = new int[run.MaxLcScan + 1];
// foreach (var fragComp in allCompositions)
// {
// var suffixMass = fragComp.Mass + BaseIonType.Y.OffsetComposition.Mass;
// var binNum = comparer.GetBinNumber(suffixMass);
// if (binNum < minFragMassBin || binNum > maxFragMassBin) continue;
// var vector = massVectors[binNum - minFragMassBin];
// foreach (var ms2ScanNum in ms2ScanNumArr)
// {
// if (vector[ms2ScanNum]) ++scoreArr[ms2ScanNum];
// }
// }
// foreach (var ms2ScanNum in ms2ScanNumArr)
// {
// if (scoreArr[ms2ScanNum] > bestScore[ms2ScanNum])
// {
// bestScore[ms2ScanNum] = scoreArr[ms2ScanNum];
// var proteinName = fastaDb.GetProteinName(offset);
// bestProtein[ms2ScanNum] = proteinName + (numNTermCleavage == 1 ? "'" : "");
// }
// }
//}
}
Console.WriteLine("ScanNum\tBestProtein\tScore");
foreach (var ms2ScanNum in ms2ScanNumArr)
{
Console.WriteLine("{0}\t{1}\t{2}", ms2ScanNum, bestProtein[ms2ScanNum] ?? "", bestScore[ms2ScanNum]);
}
//sw.Stop();
//Console.WriteLine(@"Scoring: {0:f4} sec.", sw.Elapsed.TotalSeconds);
}
public void TestGeneratingXicsOfAllCharges()
{
var methodName = MethodBase.GetCurrentMethod().Name;
Utils.ShowStarting(methodName);
if (!File.Exists(TestRawFilePath))
{
Assert.Ignore(@"Skipping test " + methodName + @" since file not found: " + TestRawFilePath);
}
var run = PbfLcMsRun.GetLcMsRun(TestRawFilePath, 0.0, 0.0);
var comparer = new MzComparerWithBinning(27);
const string protSequence =
"AIPQSVEGQSIPSLAPMLERTTPAVVSVAVSGTHVSKQRVPDVFRYFFGPNAPQEQVQERPFRGLGSGVIIDADKGYIVTNNHVIDGADDIQVGLHDGREVKAKLIGTDSESDIALLQIEAKNLVAIKTSDSDELRVGDFAVAIGNPFGLGQTVTSGIVSALGRSGLGIEMLENFIQTDAAINSGNSGGALVNLKGELIGINTAIVAPNGGNVGIGFAIPANMVKNLIAQIAEHGEVRRGVLGIAGRDLDSQLAQGFGLDTQHGGFVNEVSAGSAAEKAGIKAGDIIVSVDGRAIKSFQELRAKVATMGAGAKVELGLIRDGDKKTVNVTLGEANQTTEKAAGAVHPMLQGASLENASKGVEITDVAQGSPAAMSGLQKGDLIVGINRTAVKDLKSLKELLKDQEGAVALKIVRGKSMLYLVLR";
//const string annotation = "_." + protSequence + "._";
var seqGraph = SequenceGraph.CreateGraph(new AminoAcidSet(), AminoAcid.ProteinNTerm, protSequence, AminoAcid.ProteinCTerm);
if (seqGraph == null)
{
return;
}
seqGraph.SetSink(0);
var neutral = seqGraph.GetSinkSequenceCompositionWithH2O() - Composition.Hydrogen;
var proteinMass = neutral.Mass;
var isoEnv = Averagine.GetIsotopomerEnvelope(proteinMass);
const bool SHOW_ALL_SCANS = false;
var targetColIndex = 0;
#pragma warning disable 0162
if (SHOW_ALL_SCANS)
{
Console.WriteLine("Charge\t" + string.Join("\t", run.GetScanNumbers(1)));
}
else
{
// Just display data for scan 161
Console.WriteLine("Charge\t161");
foreach (var scanNumber in run.GetScanNumbers(1))
{
if (scanNumber == 161)
{
break;
}
targetColIndex++;
}
}
#pragma warning restore 0162
const int minCharge = 2;
const int maxCharge = 60;
for (var charge = minCharge; charge <= maxCharge; charge++)
{
var ion = new Ion(neutral, charge);
var mostAbundantIsotopeMz = ion.GetIsotopeMz(isoEnv.MostAbundantIsotopeIndex);
//var secondMostAbundantIsotopeMz = ion.GetIsotopeMz(isoEnv.MostAbundantIsotopeIndex + 1);
var binNum = comparer.GetBinNumber(mostAbundantIsotopeMz);
var mzStart = comparer.GetMzStart(binNum);
var mzEnd = comparer.GetMzEnd(binNum);
var xic = run.GetFullPrecursorIonExtractedIonChromatogram(mzStart, mzEnd);
Console.Write(charge + "\t");
#pragma warning disable 0162
if (SHOW_ALL_SCANS)
{
Console.WriteLine(string.Join("\t", xic.Select(p => p.Intensity)));
}
else
{
Console.WriteLine(xic[targetColIndex].Intensity);
}
#pragma warning restore 0162
}
}
public LcMsPeakScorer(Ms1Spectrum spec, int numBits4WinSize = 19) // 19 bits -> 4096 ppm, 20 bits -> 2048
{
Spectrum = spec;
var peaks = spec.Peaks;
_windowComparer = new MzComparerWithBinning(numBits4WinSize);
_minBinNum = _windowComparer.GetBinNumber(peaks[0].Mz);
_maxBinNum = _windowComparer.GetBinNumber(peaks[peaks.Length - 1].Mz);
var numberOfbins = _maxBinNum - _minBinNum + 1;
_peakStartIndex = new int[2][];
_peakRanking = new int[2][][];
var intensities = new List <double> [2][];
for (var i = 0; i < 2; i++)
{
_peakStartIndex[i] = new int[numberOfbins];
_peakRanking[i] = new int[numberOfbins][];
intensities[i] = new List <double> [numberOfbins];
for (var j = 0; j < numberOfbins; j++)
{
_peakStartIndex[i][j] = peaks.Length - 1;
intensities[i][j] = new List <double>();
}
}
for (var i = 0; i < peaks.Length; i++)
{
var binNum = _windowComparer.GetBinNumber(peaks[i].Mz);
var binMzAverage = _windowComparer.GetMzAverage(binNum);
var binIdx = binNum - _minBinNum;
intensities[0][binIdx].Add(peaks[i].Intensity);
if (i < _peakStartIndex[0][binIdx])
{
_peakStartIndex[0][binIdx] = i;
}
if (peaks[i].Mz < binMzAverage)
{
intensities[1][binIdx].Add(peaks[i].Intensity);
if (i < _peakStartIndex[1][binIdx])
{
_peakStartIndex[1][binIdx] = i;
}
}
else if (binNum < _maxBinNum) // skip this at the rightmost bin
{
intensities[1][binIdx + 1].Add(peaks[i].Intensity);
if (i < _peakStartIndex[1][binIdx + 1])
{
_peakStartIndex[1][binIdx + 1] = i;
}
}
}
for (var i = 0; i < 2; i++)
{
for (var binIdx = 0; binIdx < numberOfbins; binIdx++)
{
if (intensities[i][binIdx].Count < 1)
{
continue;
}
double medianIntensity;
_peakRanking[i][binIdx] = GetRankings(intensities[i][binIdx].ToArray(), out medianIntensity);
}
}
}
public FilteredProteinMassBinning(AminoAcidSet aaSet, double maxProteinMass = 50000, int numBits = 27)
{
_aminoAcidSet = aaSet;
var terminalModifications = GetTerminalModifications(aaSet);
var extendedAminoAcidArray = GetExtendedAminoAcidArray(aaSet);
MaxMass = maxProteinMass;
MinMass = MaxMass;
foreach (var aa in extendedAminoAcidArray)
{
if (aa.Mass < MinMass) MinMass = aa.Mass;
foreach (var mod in terminalModifications)
{
var modAa = new ModifiedAminoAcid(aa, mod);
if (modAa.Mass < MinMass) MinMass = modAa.Mass;
}
}
_mzComparer = new MzComparerWithBinning(numBits);
_minMzBinIndex = _mzComparer.GetBinNumber(MinMass);
_maxMzBinIndex = _mzComparer.GetBinNumber(MaxMass);
var numberOfMzBins = _maxMzBinIndex - _minMzBinIndex + 2; // pad zero mass bin
_mzBinToFilteredBinMap = new int[numberOfMzBins];
for (var i = 0; i < numberOfMzBins; i++) _mzBinToFilteredBinMap[i] = -1;
var tempMap = new int[numberOfMzBins];
var fineNodes = new BitArray(Constants.GetBinNumHighPrecision(MaxMass));
fineNodes[0] = true;
var effectiveBinCounter = 0;
for (var fineBinIdx = 0; fineBinIdx < fineNodes.Length; fineBinIdx++)
{
if (!fineNodes[fineBinIdx]) continue;
var fineNodeMass = fineBinIdx / Constants.RescalingConstantHighPrecision;
foreach (var aa in extendedAminoAcidArray)
{
var validFineNodeIndex = Constants.GetBinNumHighPrecision(fineNodeMass + aa.Mass);
if (validFineNodeIndex >= fineNodes.Length) break;
fineNodes[validFineNodeIndex] = true;
if (fineBinIdx == 0 && !(aa is ModifiedAminoAcid)) // include terminal modifications
{
foreach (var terminalMod in terminalModifications)
{
var modifiedAa = new ModifiedAminoAcid(aa, terminalMod);
validFineNodeIndex = Constants.GetBinNumHighPrecision(fineNodeMass + modifiedAa.Mass);
if (validFineNodeIndex >= fineNodes.Length) break;
fineNodes[validFineNodeIndex] = true;
}
}
}
/*foreach (var m in massList)
{
var validFineNodeIndex = Constants.GetBinNumHighPrecision(fineNodeMass + m);
if (validFineNodeIndex >= fineNodes.Length) break;
fineNodes[validFineNodeIndex] = true;
}*/
var binNum = _mzComparer.GetBinNumber(fineNodeMass);
if (fineBinIdx == 0 || (binNum >= _minMzBinIndex && binNum <= _maxMzBinIndex && _mzBinToFilteredBinMap[binNum - _minMzBinIndex + 1] < 0))
{
_mzBinToFilteredBinMap[binNum == 0 ? 0 : binNum - _minMzBinIndex + 1] = effectiveBinCounter;
tempMap[effectiveBinCounter] = binNum;
effectiveBinCounter++;
}
}
_filteredBinToMzBinMap = new int[effectiveBinCounter];
Array.Copy(tempMap, _filteredBinToMzBinMap, effectiveBinCounter);
}
public FilteredProteinMassBinning(AminoAcidSet aaSet, double maxProteinMass = 50000, int numBits = 27)
{
// _aminoAcidSet = aaSet;
var terminalModifications = GetTerminalModifications(aaSet);
var extendedAminoAcidArray = GetExtendedAminoAcidArray(aaSet);
MaxMass = maxProteinMass;
MinMass = MaxMass;
foreach (var aa in extendedAminoAcidArray)
{
if (aa.Mass < MinMass)
{
MinMass = aa.Mass;
}
foreach (var mod in terminalModifications)
{
var modAa = new ModifiedAminoAcid(aa, mod);
if (modAa.Mass < MinMass)
{
MinMass = modAa.Mass;
}
}
}
_mzComparer = new MzComparerWithBinning(numBits);
_minMzBinIndex = _mzComparer.GetBinNumber(MinMass);
_maxMzBinIndex = _mzComparer.GetBinNumber(MaxMass);
var numberOfMzBins = _maxMzBinIndex - _minMzBinIndex + 2; // pad zero mass bin
_mzBinToFilteredBinMap = new int[numberOfMzBins];
for (var i = 0; i < numberOfMzBins; i++)
{
_mzBinToFilteredBinMap[i] = -1;
}
var tempMap = new int[numberOfMzBins];
// ReSharper disable once UseObjectOrCollectionInitializer
var fineNodes = new BitArray(Constants.GetBinNumHighPrecision(MaxMass));
fineNodes[0] = true;
var effectiveBinCounter = 0;
for (var fineBinIdx = 0; fineBinIdx < fineNodes.Length; fineBinIdx++)
{
if (!fineNodes[fineBinIdx])
{
continue;
}
var fineNodeMass = fineBinIdx / Constants.RescalingConstantHighPrecision;
foreach (var aa in extendedAminoAcidArray)
{
var validFineNodeIndex = Constants.GetBinNumHighPrecision(fineNodeMass + aa.Mass);
if (validFineNodeIndex >= fineNodes.Length)
{
break;
}
fineNodes[validFineNodeIndex] = true;
if (fineBinIdx == 0 && !(aa is ModifiedAminoAcid)) // include terminal modifications
{
foreach (var terminalMod in terminalModifications)
{
var modifiedAa = new ModifiedAminoAcid(aa, terminalMod);
validFineNodeIndex = Constants.GetBinNumHighPrecision(fineNodeMass + modifiedAa.Mass);
if (validFineNodeIndex >= fineNodes.Length)
{
break;
}
fineNodes[validFineNodeIndex] = true;
}
}
}
/*foreach (var m in massList)
* {
* var validFineNodeIndex = Constants.GetBinNumHighPrecision(fineNodeMass + m);
* if (validFineNodeIndex >= fineNodes.Length) break;
* fineNodes[validFineNodeIndex] = true;
* }*/
var binNum = _mzComparer.GetBinNumber(fineNodeMass);
if (fineBinIdx == 0 || (binNum >= _minMzBinIndex && binNum <= _maxMzBinIndex && _mzBinToFilteredBinMap[binNum - _minMzBinIndex + 1] < 0))
{
_mzBinToFilteredBinMap[binNum == 0 ? 0 : binNum - _minMzBinIndex + 1] = effectiveBinCounter;
tempMap[effectiveBinCounter] = binNum;
effectiveBinCounter++;
}
}
_filteredBinToMzBinMap = new int[effectiveBinCounter];
Array.Copy(tempMap, _filteredBinToMzBinMap, effectiveBinCounter);
}
static MatchedPeakPostScorer()
{
BaseIonTypesCID = new[] { BaseIonType.B, BaseIonType.Y };
BaseIonTypesETD = new[] { BaseIonType.C, BaseIonType.Z };
Comparer = new MzComparerWithBinning(28);
}
