//[TestCase(@"MzML\QC_Shew_16_01-15f_MPA_02redo_8Nov16_Tiger_16-02-14.mzML.gz", 9293)] // implemented, but decompresses first
public void ReadMzMLChromatogramsTestRandom(string inputFileRelativePath, int expectedChromatograms)
{
if (!TestPath.FindInputFile(inputFileRelativePath, out var sourceFile))
{
Console.WriteLine("File not found: " + inputFileRelativePath);
return;
}
using (var reader = new SimpleMzMLReader(sourceFile.FullName, true, true))
{
Assert.AreEqual(expectedChromatograms, reader.NumChromatograms);
var chromCount = 0;
foreach (var chrom in reader.ReadAllChromatograms(true))
{
if (chrom == null)
{
Console.WriteLine("ReadAllChromatograms returned null for chromatogram index {0}", chromCount);
}
else
{
Console.WriteLine("Chromatogram {0}, NativeID {1,-45} has {2:N0} data points", chrom.Index, chrom.Id, chrom.Intensities.Length);
}
chromCount++;
}
Assert.AreEqual(expectedChromatograms, chromCount);
}
}
public void ReadMzMLChromatogramsTestNonRandom(string inputFileRelativePath, int expectedSpectra, int expectedChromatograms)
{
if (!TestPath.FindInputFile(inputFileRelativePath, out var sourceFile))
{
Console.WriteLine("File not found: " + inputFileRelativePath);
return;
}
using (var reader = new SimpleMzMLReader(sourceFile.FullName, false, true))
{
Assert.AreEqual(expectedSpectra, reader.NumSpectra);
if (expectedSpectra != 0)
{
Assert.AreEqual(0, reader.NumChromatograms);
}
var specCount = 0;
foreach (var spec in reader.ReadAllSpectra(true))
{
if (specCount < 100 || specCount >= expectedSpectra - 100)
{
Console.WriteLine("Spectrum {0,4}, NativeID {1,-45} has {2:N0} data points", spec.ScanNumber, spec.NativeId, spec.Peaks.Length);
}
else if (specCount == 100)
{
Console.WriteLine("...");
}
specCount++;
}
Assert.AreEqual(expectedSpectra, specCount);
Assert.AreEqual(expectedChromatograms, reader.NumChromatograms);
var chromCount = 0;
foreach (var chrom in reader.ReadAllChromatograms(false))
{
if (chrom == null)
{
Console.WriteLine("ReadAllChromatograms returned null for chromatogram index {0}", chromCount);
}
else
{
Console.WriteLine("Chromatogram {0}, NativeID {1,-45} has {2:N0} data points", chrom.Index, chrom.Id, chrom.Intensities.Length);
}
chromCount++;
}
Assert.AreEqual(expectedChromatograms, reader.NumChromatograms);
Assert.AreEqual(expectedChromatograms, chromCount);
}
}
public List <CompoundData> ReadSpectraData(List <CompoundData> combinedTransitions)
{
using (var reader = new SimpleMzMLReader(DatasetPath))
{
foreach (var spectrum in reader.ReadAllSpectra(true))
{
if (spectrum.Precursors.Count == 0)
{
continue;
}
var time = spectrum.ScanStartTime;
var precursorMz = spectrum.Precursors[0].SelectedIons[0].SelectedIonMz;
var matches = combinedTransitions.Where(x => x.StartTimeMinutes <= time && time <= x.StopTimeMinutes && Math.Abs(x.PrecursorMz - precursorMz) < 0.01);
foreach (var match in matches)
{
foreach (var trans in match.Transitions)
{
foreach (var scanWindow in spectrum.ScanWindows.Where(x => x.LowerLimit <= trans.ProductMz && trans.ProductMz <= x.UpperLimit))
{
//foreach (var peakMatch in srmSpec.Peaks.Where(x => Math.Abs(trans.ProductMz - x.Mz) < 0.01))
foreach (var peakMatch in spectrum.Peaks.Where(x => scanWindow.LowerLimit <= x.Mz && x.Mz <= scanWindow.UpperLimit))
{
var intensity = peakMatch.Intensity;
trans.IntensitySum += intensity;
trans.Intensities.Add(new TransitionData.DataPoint(spectrum.ScanNumber, time, intensity));
if (intensity > trans.MaxIntensity)
{
trans.MaxIntensity = intensity;
trans.MaxIntensityTime = time;
}
}
}
}
}
}
var medianScanTimeDiff = 0.001;
foreach (var chromatogram in reader.ReadAllChromatograms(true))
{
if (chromatogram.CVParams.Any(x => x.TermInfo.Cvid == CV.CVID.MS_total_ion_current_chromatogram))
{
// First chromatogram, use it to determine approximate scan times
var diffs = new List <double>(chromatogram.Times.Length);
var lastTime = 0.0;
foreach (var time in chromatogram.Times)
{
diffs.Add(time - lastTime);
lastTime = time;
}
diffs.Sort();
medianScanTimeDiff = diffs[diffs.Count / 2];
}
if (!chromatogram.CVParams.Any(x => x.TermInfo.Cvid == CV.CVID.MS_selected_reaction_monitoring_chromatogram))
{
continue;
}
var precursorMz = chromatogram.Precursor.IsolationWindow.TargetMz;
var productMz = chromatogram.Product.TargetMz;
var matches = combinedTransitions.Where(x => Math.Abs(x.PrecursorMz - precursorMz) < 0.01);
foreach (var match in matches)
{
foreach (var trans in match.Transitions.Where(x => Math.Abs(x.ProductMz - productMz) < 0.01))
{
for (var i = 0; i < chromatogram.Times.Length; i++)
{
var time = chromatogram.Times[i];
var intensity = chromatogram.Intensities[i];
trans.IntensitySum += intensity;
var estimatedScanNum = (int)Math.Round(time / medianScanTimeDiff, MidpointRounding.AwayFromZero);
trans.Intensities.Add(new TransitionData.DataPoint(estimatedScanNum, time, intensity));
if (intensity > trans.MaxIntensity)
{
trans.MaxIntensity = intensity;
trans.MaxIntensityTime = time;
}
}
}
}
}
}
return(combinedTransitions.ToList());
}
