public Xic GetProductExtractedIonChromatogram(double productIonMz, double precursorIonMz, Tolerance tolerance, int minScanNum, int maxScanNum)
{
var productXic = new Xic();
for (var scanNum = minScanNum; scanNum <= maxScanNum; scanNum++)
{
if (GetMsLevel(scanNum) == 1)
{
continue;
}
var productSpec = _scanNumSpecMap[scanNum] as ProductSpectrum;
if (productSpec == null)
{
continue;
}
if (!productSpec.IsolationWindow.Contains(precursorIonMz))
{
continue;
}
var peak = productSpec.FindPeak(productIonMz, tolerance);
if (peak != null)
{
productXic.Add(new XicPoint(scanNum, peak.Mz, peak.Intensity));
}
}
return(productXic);
}
private static Xic GetExtractedIonChromatogram(double minMz, double maxMz, List <LcMsPeak> peakList)
{
var xic = GetXicPointsWithin(minMz, maxMz, peakList);
xic.Sort();
return(Xic.GetSelectedXic(xic));
}
/// <summary>
/// Smooth and snip tails off a single XIC.
/// </summary>
/// <param name="xic">The XIC to refine.</param>
/// <returns>Refined XIC.</returns>
public Xic RefineXic(Xic xic)
{
// Here we smooth the points...and remove any features with from and trailing zero points
if (xic.Count == 0)
{
return(xic);
}
var unsmoothedPoints = xic.Select(xicp => new XYData(xicp.ScanNum, xicp.Intensity))
.OrderBy(p => p.X).ToList();
var points = smoother.Smooth(unsmoothedPoints);
// Find the biggest peak...
var maxScanIndex = 0;
double maxAbundance = 0;
for (var i = 0; i < xic.Count; i++)
{
if (maxAbundance < xic[i].Intensity)
{
maxScanIndex = i;
maxAbundance = xic[i].Intensity;
}
}
// Then find when the feature goes to zero
// Start from max to left
var startIndex = maxScanIndex;
// If we hit zero, then keep
for (; startIndex > 0; startIndex--)
{
if ((xic[startIndex].Intensity / maxAbundance) < this.relativeIntensityThreshold)
{
break;
}
}
// Start from max to right
var stopIndex = maxScanIndex;
for (; stopIndex < xic.Count - 1; stopIndex++)
{
if ((xic[stopIndex].Intensity / maxAbundance) < this.relativeIntensityThreshold)
{
break;
}
}
// Add the features back
for (var i = startIndex; i <= stopIndex; i++)
{
xic[i] = new XicPoint(Convert.ToInt32(xic[i].ScanNum), xic[i].Mz, Convert.ToInt64(points[i].Y));
}
return(xic);
}
public new Xic GetFullProductExtractedIonChromatogram(double minMz, double maxMz, double precursorIonMz)
{
var xic = GetProductExtractedIonChromatogram(minMz, maxMz, precursorIonMz);
var scanToXicPoint = new XicPoint[MaxLcScan - MinLcScan + 1];
foreach (var xicPoint in xic) scanToXicPoint[xicPoint.ScanNum - MinLcScan] = xicPoint;
var newXic = new Xic();
newXic.AddRange(GetFragmentationSpectraScanNums(precursorIonMz).Select(scanNum => scanToXicPoint[scanNum - MinLcScan] ?? new XicPoint(scanNum, 0, 0)));
return newXic;
}
public Xic GetProductExtractedIonChromatogram(double minMz, double maxMz, double precursorIonMz)
{
var xic = new Xic();
foreach (var isolationWindow in GetIsoWindows(precursorIonMz))
{
var peakList = _isoWindowToChromPeaks[isolationWindow];
xic.AddRange(GetXicPointsWithin(minMz, maxMz, peakList));
}
xic.Sort();
return Xic.GetSelectedXic(xic);
}
public Xic GetProductExtractedIonChromatogram(double minMz, double maxMz, double precursorIonMz)
{
var xic = new Xic();
foreach (var isolationWindow in GetIsoWindows(precursorIonMz))
{
var peakList = _isoWindowToChromPeaks[isolationWindow];
xic.AddRange(GetXicPointsWithin(minMz, maxMz, peakList));
}
xic.Sort();
return(Xic.GetSelectedXic(xic));
}
public new Xic GetFullProductExtractedIonChromatogram(double minMz, double maxMz, double precursorIonMz)
{
var xic = GetProductExtractedIonChromatogram(minMz, maxMz, precursorIonMz);
var scanToXicPoint = new XicPoint[MaxLcScan - MinLcScan + 1];
foreach (var xicPoint in xic)
{
scanToXicPoint[xicPoint.ScanNum - MinLcScan] = xicPoint;
}
var newXic = new Xic();
newXic.AddRange(GetFragmentationSpectraScanNums(precursorIonMz).Select(scanNum => scanToXicPoint[scanNum - MinLcScan] ?? new XicPoint(scanNum, 0, 0)));
return(newXic);
}
private List <Xic> ReadXicDatabase(string path)
{
var lines = File.ReadAllLines(path).ToList();
var xic = new Xic();
var data = new List <Xic>();
var found = false;
foreach (var line in lines)
{
if (line.Contains("id"))
{
if (found)
{
data.Add(xic);
}
found = true;
xic = new Xic();
var splitLine = line.Split('\t');
xic.id = Convert.ToInt32(splitLine[1]);
xic.charge = Convert.ToInt32(splitLine[3]);
xic.x = new List <double>();
xic.y = new List <double>();
}
else if (line.Contains("score"))
{
var splitLine = line.Split('\t');
xic.score = Convert.ToInt32(splitLine[1]);
xic.scoreName = splitLine[3];
}
else if (line.Contains("reviewer"))
{
var splitLine = line.Split('\t');
xic.reviewer = splitLine[1];
}
else if (!line.Contains("mz"))
{
var splitLine = line.Split('\t');
xic.x.Add(Convert.ToDouble(splitLine[1]));
xic.y.Add(Convert.ToDouble(splitLine[2]));
xic.mz = Convert.ToDouble(splitLine[0]);
}
}
if (found)
{
data.Add(xic);
}
return(data);
}
public SpectrumSearchResult(ProductSpectrum hcdSpectrum, ProductSpectrum cidSpectrum, Spectrum precursorSpectrum, List <MsMsSearchResult> hcdSearchResultList, List <MsMsSearchResult> cidSearchResultList, Xic xic, LcMsRun lcMsRun, ScoreModel scoreModel = null, LipidTarget lipidTarget = null)
{
HcdSpectrum = hcdSpectrum;
CidSpectrum = cidSpectrum;
PrecursorSpectrum = precursorSpectrum;
HcdSearchResultList = hcdSearchResultList;
CidSearchResultList = cidSearchResultList;
Xic = xic;
LcMsRun = lcMsRun;
PeakArea = null;
RunLength = lcMsRun.GetElutionTime(lcMsRun.MaxLcScan);
ApexScanNum = Xic.GetNearestApexScanNum(PrecursorSpectrum.ScanNum, performSmoothing: true);
ApexIntensity = Xic.Where(x => x.ScanNum == ApexScanNum).Sum(x => x.Intensity);
RetentionTime = LcMsRun.GetElutionTime(ApexScanNum);
if (scoreModel != null && lipidTarget != null)
{
ModelScore = scoreModel.ScoreLipid(lipidTarget, this);
}
}
private static Xic GetXicPointsWithin(double minMz, double maxMz, List <LcMsPeak> peakList)
{
var xic = new Xic();
var index = peakList.BinarySearch(new LcMsPeak((minMz + maxMz) / 2, 0, 0));
if (index < 0)
{
index = ~index;
}
// go down
var i = index - 1;
while (i >= 0 && i < peakList.Count)
{
var peak = peakList[i];
if (peak.Mz <= minMz)
{
break;
}
xic.Add(new XicPoint(peak));
--i;
}
// go up
i = index;
while (i >= 0 && i < peakList.Count)
{
var peak = peakList[i];
if (peak.Mz >= maxMz)
{
break;
}
xic.Add(new XicPoint(peak));
++i;
}
return(xic);
}
/// <summary>
/// Gets the extracted ion chromatogram of the specified m/z range (using only MS2 spectra)
/// </summary>
/// <param name="minMz">min m/z</param>
/// <param name="maxMz">max m/z</param>
/// <param name="precursorIonMz">precursor m/z of the precursor ion</param>
/// <param name="minScanNum">minimum scan number (inclusive)</param>
/// <param name="maxScanNum">maximum scan number (inclusive)</param>
/// <returns>XIC as an Xic object</returns>
public Xic GetProductExtractedIonChromatogram(double minMz, double maxMz, double precursorIonMz, int minScanNum, int maxScanNum)
{
var xic = new Xic();
//for (var scanNum = minScanNum; scanNum <= maxScanNum; scanNum++)
foreach (var scanNum in GetFragmentationSpectraScanNums(precursorIonMz))
{
if (scanNum < minScanNum || scanNum > maxScanNum)
{
continue;
}
var spec = GetSpectrum(scanNum) as ProductSpectrum;
if (spec == null)
{
continue;
}
var peak = spec.FindPeak(minMz, maxMz);
xic.Add(peak != null ? new XicPoint(scanNum, peak.Mz, peak.Intensity) : new XicPoint(scanNum, 0, 0));
}
return(xic);
}
/// <summary>
/// Get a segment of Xic containing the targetScanNum
/// </summary>
/// <param name="xic">xic to be trimmed</param>
/// <param name="targetScanNum">target scan number to generate xic</param>
/// <param name="tolerance">number of scans that can be tolerated</param>
/// <returns>Trimmed XIC around targetScanNum</returns>
public Xic GetTrimmedXic(Xic xic, int targetScanNum, int tolerance = 3)
{
var index = xic.BinarySearch(new XicPoint(targetScanNum, 0, 0));
if (index < 0) index = ~index;
var xicSegment = new Xic();
var curScanNum = targetScanNum;
// go down
var i = index - 1;
while (i >= 0 && i < xic.Count)
{
var xicPeak = xic[i];
// check whether there's no MS1 scan in between
var isConsecutive = true;
var numMissingScans = 0;
for (var scanNum = xicPeak.ScanNum + 1; scanNum < curScanNum; scanNum++)
{
if (GetMsLevel(scanNum) == 1) ++numMissingScans;
if (numMissingScans > tolerance)
{
isConsecutive = false;
break;
}
}
if (isConsecutive) xicSegment.Add(xicPeak);
else break;
curScanNum = xicPeak.ScanNum;
--i;
}
// go up
i = index;
curScanNum = targetScanNum;
while (i >= 0 && i < xic.Count)
{
var xicPeak = xic[i];
// check whether there's no MS1 scan in between
var numMissingScans = 0;
var isConsecutive = true;
for (var scanNum = curScanNum + 1; scanNum < xicPeak.ScanNum; scanNum++)
{
if (GetMsLevel(scanNum) == 1) ++numMissingScans;
if (numMissingScans > tolerance)
{
isConsecutive = false;
break;
}
}
if (isConsecutive) xicSegment.Add(xicPeak);
else break;
curScanNum = xicPeak.ScanNum;
++i;
}
xicSegment.Sort();
return xicSegment;
}
/// <summary>
/// Get a segment of Xic containing the targetScanNum
/// </summary>
/// <param name="xic">xic to be trimmed</param>
/// <param name="targetScanNum">target scan number to generate xic</param>
/// <param name="tolerance">number of scans that can be tolerated</param>
/// <returns>Trimmed XIC around targetScanNum</returns>
public Xic GetTrimmedXic(Xic xic, int targetScanNum, int tolerance = 3)
{
var index = xic.BinarySearch(new XicPoint(targetScanNum, 0, 0));
if (index < 0)
{
index = ~index;
}
var xicSegment = new Xic();
var curScanNum = targetScanNum;
// go down
var i = index - 1;
while (i >= 0 && i < xic.Count)
{
var xicPeak = xic[i];
// check whether there's no MS1 scan in between
var isConsecutive = true;
var numMissingScans = 0;
for (var scanNum = xicPeak.ScanNum + 1; scanNum < curScanNum; scanNum++)
{
if (GetMsLevel(scanNum) == 1)
{
++numMissingScans;
}
if (numMissingScans > tolerance)
{
isConsecutive = false;
break;
}
}
if (isConsecutive)
{
xicSegment.Add(xicPeak);
}
else
{
break;
}
curScanNum = xicPeak.ScanNum;
--i;
}
// go up
i = index;
curScanNum = targetScanNum;
while (i >= 0 && i < xic.Count)
{
var xicPeak = xic[i];
// check whether there's no MS1 scan in between
var numMissingScans = 0;
var isConsecutive = true;
for (var scanNum = curScanNum + 1; scanNum < xicPeak.ScanNum; scanNum++)
{
if (GetMsLevel(scanNum) == 1)
{
++numMissingScans;
}
if (numMissingScans > tolerance)
{
isConsecutive = false;
break;
}
}
if (isConsecutive)
{
xicSegment.Add(xicPeak);
}
else
{
break;
}
curScanNum = xicPeak.ScanNum;
++i;
}
xicSegment.Sort();
return(xicSegment);
}
public void SolveAsymmetricGaussianFactory(string path, BasisFunctionsEnum functionChoise)
{
var data = ReadXicDatabase(Path.Combine(TestPathSingleton.TestDirectory, path));
var newData = new List <Xic>();
foreach (var xic in data)
{
var basisFunction = BasisFunctionFactory.BasisFunctionSelector(functionChoise);
var coefficients = basisFunction.Coefficients;
var start = xic.x.Min() - .5;
var stop = xic.x.Max() + .5;
var A = xic.y.Max();
A += (A * .05);
var width = Math.Abs(stop - start);
coefficients[0] = start + ((stop - start) / 2);
coefficients[1] = A;
coefficients[2] = width * .5;
coefficients[3] = coefficients[2];
//Console.WriteLine("Xic {0}", xic.id);
//Console.WriteLine();
for (var i = 0; i < xic.x.Count; i++)
{
// Console.WriteLine("{0}\t{1}", xic.x[i], xic.y[i]);
}
SolverReport worked = null;
Console.WriteLine();
var showDetails = false;
try
{
worked = EvaluateFunction(xic.x, xic.y, basisFunction, ref coefficients, showDetails);
}
catch (Exception)
{
continue;
}
// First solve for the function
var solver = new LevenburgMarquadtSolver();
var numberOfSamples = 100;
// Calculate the width an spacing of each of the trapezoids.
var delta = width / Convert.ToDouble(numberOfSamples);
var x = start;
var newXic = new Xic();
newXic.x = new List <double>();
newXic.y = new List <double>();
newXic.charge = xic.charge;
newXic.scoreName = xic.scoreName;
newXic.score = xic.score;
newXic.id = xic.id;
newXic.prevXic = xic;
newXic.report = worked;
newXic.reviewer = xic.reviewer;
// We already evaluated the first point, now for each element within
for (var i = 0; i < numberOfSamples + 1; i++)
{
x += delta;
var y = basisFunction.Evaluate(coefficients, x);
newXic.x.Add(x);
newXic.y.Add(y);
// Console.WriteLine("{0}\t{1}", x, y);
}
//Console.WriteLine();
newData.Add(newXic);
}
var newPath = path.Replace(".xic", functionChoise + "_fit.xic");
using (TextWriter writer = File.CreateText(newPath))
{
foreach (var feature in newData)
{
writer.WriteLine("id\t{0}\tcharge\t{1}", feature.id, feature.charge);
writer.WriteLine("score\t{0}\tscoreName\t{1}", feature.score, feature.scoreName);
writer.WriteLine("reviewer\t{0}", feature.reviewer);
writer.WriteLine("R2\t{0}", feature.report.RSquared);
writer.WriteLine("Rms\t{0}", feature.report.RmsError);
writer.WriteLine("Converged\t{0}", feature.report.DidConverge);
writer.WriteLine("mz\ttime\tintensity");
var prev = feature.prevXic;
for (var i = 0; i < feature.x.Count; i++)
{
var prevTime = "";
var prevInt = "";
if (prev != null && i < prev.x.Count)
{
prevTime = prev.x[i].ToString();
prevInt = prev.y[i].ToString();
}
writer.WriteLine("{0}\t{1}\t{2}\t{3}\t{4}", feature.mz, feature.x[i], feature.y[i], prevTime, prevInt);
}
writer.WriteLine();
}
}
}
/// <summary>
/// Gets the extracted ion chromatogram of the specified m/z range (using only MS2 spectra)
/// </summary>
/// <param name="minMz">min m/z</param>
/// <param name="maxMz">max m/z</param>
/// <param name="precursorIonMz">precursor m/z of the precursor ion</param>
/// <param name="minScanNum">minimum scan number (inclusive)</param>
/// <param name="maxScanNum">maximum scan number (inclusive)</param>
/// <returns>XIC as an Xic object</returns>
public Xic GetProductExtractedIonChromatogram(double minMz, double maxMz, double precursorIonMz, int minScanNum, int maxScanNum)
{
var xic = new Xic();
//for (var scanNum = minScanNum; scanNum <= maxScanNum; scanNum++)
foreach (var scanNum in GetFragmentationSpectraScanNums(precursorIonMz))
{
if (scanNum < minScanNum || scanNum > maxScanNum) continue;
var spec = GetSpectrum(scanNum) as ProductSpectrum;
if (spec == null) continue;
var peak = spec.FindPeak(minMz, maxMz);
xic.Add(peak != null ? new XicPoint(scanNum, peak.Mz, peak.Intensity) : new XicPoint(scanNum, 0, 0));
}
return xic;
}
public Xic GetProductExtractedIonChromatogram(double productIonMz, double precursorIonMz, Tolerance tolerance, int minScanNum, int maxScanNum)
{
var productXic = new Xic();
for (var scanNum = minScanNum; scanNum <= maxScanNum; scanNum++)
{
if (GetMsLevel(scanNum) == 1) continue;
var productSpec = _scanNumSpecMap[scanNum] as ProductSpectrum;
if (productSpec == null) continue;
if (!productSpec.IsolationWindow.Contains(precursorIonMz)) continue;
var peak = productSpec.FindPeak(productIonMz, tolerance);
if (peak != null) productXic.Add(new XicPoint(scanNum, peak.Mz, peak.Intensity));
}
return productXic;
}
private static Xic GetXicPointsWithin(double minMz, double maxMz, List<LcMsPeak> peakList)
{
var xic = new Xic();
var index = peakList.BinarySearch(new LcMsPeak((minMz + maxMz) / 2, 0, 0));
if (index < 0) index = ~index;
// go down
var i = index - 1;
while (i >= 0 && i < peakList.Count)
{
var peak = peakList[i];
if (peak.Mz <= minMz) break;
xic.Add(new XicPoint(peak));
--i;
}
// go up
i = index;
while (i >= 0 && i < peakList.Count)
{
var peak = peakList[i];
if (peak.Mz >= maxMz) break;
xic.Add(new XicPoint(peak));
++i;
}
return xic;
}
