public void ReadMzMLChromatogramsTestDelayedRandom(string inputFileRelativePath, int expectedChromatograms, bool immediateRandomAccess)
{
if (!TestPath.FindInputFile(inputFileRelativePath, out var sourceFile))
{
Console.WriteLine("File not found: " + inputFileRelativePath);
return;
}
using (var reader = new SimpleMzMLReader(sourceFile.FullName, immediateRandomAccess, true))
{
if (!immediateRandomAccess)
{
// For non-random access readers, the number of chromatograms (as reported by NumChromatograms)
// will not get populated until after all the spectra (if any) have been read
// Therefore, NumChromatograms should currently be zero since immediateRandomAccess was false
Assert.AreEqual(0, reader.NumChromatograms);
// You cannot use reader.TryMakeRandomAccessCapable() to make the chromatograms available
// Thus, exit this method
return;
}
Assert.AreEqual(expectedChromatograms, reader.NumChromatograms);
var stepSize = Math.Max(1, expectedChromatograms / 100);
var chromatogramNumber = 1;
while (chromatogramNumber <= expectedChromatograms)
{
var chrom = reader.ReadChromatogram(chromatogramNumber);
Console.WriteLine("Chromatogram {0,2}, NativeID {1,-35} has {2:N0} data points", chrom.Index, chrom.Id, chrom.Intensities.Length);
chromatogramNumber += stepSize;
}
}
}
//[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 ReadMzMLTest(string inputFileRelativePath, int expectedSpectra, bool includePeaks)
{
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);
var specCount = 0;
foreach (var spec in reader.ReadAllSpectra(includePeaks))
{
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);
}
}
public MzMLFusionContainer(string filename)
{
this.filename = filename;
if (filename != null)
{
SimpleMzMLReader reader = new SimpleMzMLReader(filename);
_spectra = reader.ReadAllSpectra();
}
}
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 void ReadMzMLCompareScanNumbers(string inputFileRelativePath, string artificialScanNumberList, string expectedActualScanNumberList)
{
if (!TestPath.FindInputFile(inputFileRelativePath, out var sourceFile))
{
Console.WriteLine("File not found: " + inputFileRelativePath);
return;
}
var artificialScanNumbers = ParseOrderedIntegerList(artificialScanNumberList);
var expectedActualScanNumbers = ParseOrderedIntegerList(expectedActualScanNumberList);
// Run the test twice, first with randomAccess disabled, then with randomAccess enabled
for (var i = 0; i < 2; i++)
{
var randomAccess = i > 0;
using (var reader = new SimpleMzMLReader(sourceFile.FullName, randomAccess, true))
{
for (var j = 0; j < artificialScanNumbers.Count; j++)
{
var artificialScanNumber = artificialScanNumbers[j];
var expectedScanNumber = expectedActualScanNumbers[j];
var spectrum = reader.ReadMassSpectrum(artificialScanNumber, false);
if (expectedScanNumber <= 0)
{
Console.WriteLine("Spectrum {0,4} does not exist; this was expected", artificialScanNumber);
Assert.IsNull(spectrum);
continue;
}
Assert.IsNotNull(spectrum);
Console.WriteLine("Spectrum {0,4}, NativeID {1,-45}, scan {2,4}", spectrum.ScanNumber, spectrum.NativeId, spectrum.NativeIdScanNumber);
Assert.AreEqual(expectedScanNumber, spectrum.NativeIdScanNumber);
var comparisonSpectrum = reader.GetSpectrumForScan(spectrum.NativeIdScanNumber, false);
Assert.AreEqual(comparisonSpectrum.NativeId, spectrum.NativeId);
}
}
Console.WriteLine();
}
}
public void ReadMzMLTestRetrieveByScanNumber(string inputFileRelativePath, int expectedSpectra, bool includePeaks, string scanNumberList, string expectedMissingScanNumbers)
{
if (!TestPath.FindInputFile(inputFileRelativePath, out var sourceFile))
{
Console.WriteLine("File not found: " + inputFileRelativePath);
return;
}
var scanNumbers = ParseDelimitedIntegerList(scanNumberList);
var expectedMissingScans = ParseDelimitedIntegerList(expectedMissingScanNumbers);
using (var reader = new SimpleMzMLReader(sourceFile.FullName, true, true))
{
Assert.AreEqual(expectedSpectra, reader.NumSpectra);
foreach (var scanNumber in scanNumbers)
{
var spec = reader.GetSpectrumForScan(scanNumber, includePeaks);
if (spec == null)
{
if (expectedMissingScans.Contains(scanNumber))
{
Console.WriteLine("Scan {0} not found; this is expected", scanNumber);
continue;
}
Assert.Fail("GetSpectrumForScan returned null for scan {0}", scanNumber);
}
if (includePeaks)
{
Console.WriteLine("Spectrum {0,4}, NativeID {1,-45}, scan {2,4} has {3:N0} data points", spec.ScanNumber, spec.NativeId, spec.NativeIdScanNumber, spec.Peaks.Length);
}
else
{
Console.WriteLine("Spectrum {0,4}, NativeID {1,-45}, scan {2,4} (peaks not loaded)", spec.ScanNumber, spec.NativeId, spec.NativeIdScanNumber);
}
Assert.AreEqual(scanNumber, spec.NativeIdScanNumber);
}
}
}
public void ReadMzMLTestRandom(string inputFileRelativePath, int expectedSpectra, bool includePeaks, bool immediateRandomAccess)
{
if (!TestPath.FindInputFile(inputFileRelativePath, out var sourceFile))
{
Console.WriteLine("File not found: " + inputFileRelativePath);
return;
}
using (var reader = new SimpleMzMLReader(sourceFile.FullName, immediateRandomAccess, true))
{
if (!immediateRandomAccess)
{
reader.TryMakeRandomAccessCapable();
}
Assert.AreEqual(expectedSpectra, reader.NumSpectra);
var stepSize = Math.Max(1, expectedSpectra / 100);
// Note: calling .ReadMassSpectrum with scanNumber = 1 returns the first spectrum in the file, regardless of its actual scan number
var scanNumber = 1;
while (scanNumber <= expectedSpectra)
{
var spec = reader.ReadMassSpectrum(scanNumber, includePeaks);
if (includePeaks)
{
Console.WriteLine("Spectrum {0,4}, NativeID {1,-45}, scan {2,4} has {3:N0} data points", spec.ScanNumber, spec.NativeId, spec.NativeIdScanNumber, spec.Peaks.Length);
}
else
{
Console.WriteLine("Spectrum {0,4}, NativeID {1,-45}, scan {2,4} (peaks not loaded)", spec.ScanNumber, spec.NativeId, spec.NativeIdScanNumber);
}
scanNumber += stepSize;
}
}
}
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());
}
public void TestGetParentScan(string inputFileRelativePath, int startScan, int endScan, params int[] expectedPrecursorScans)
{
if (!TestPath.FindInputFile(inputFileRelativePath, out var sourceFile))
{
Console.WriteLine("File not found: " + inputFileRelativePath);
return;
}
using (var reader = new SimpleMzMLReader(sourceFile.FullName, true, true))
{
for (var scanNumber = startScan; scanNumber <= endScan; scanNumber++)
{
var spectrum = reader.ReadMassSpectrum(scanNumber, false);
if (spectrum == null)
{
continue;
}
var targetIndex = scanNumber - startScan;
int expectedPrecursorScan;
if (targetIndex >= 0 && targetIndex < expectedPrecursorScans.Length)
{
expectedPrecursorScan = expectedPrecursorScans[targetIndex];
}
else
{
expectedPrecursorScan = 0;
}
if (spectrum.Precursors.Count == 0)
{
Console.WriteLine("Scan {0} is not a fragmentation scan", spectrum.ScanNumber);
if (expectedPrecursorScan > 0)
{
Assert.Fail("Scan {0} was supposed to have precursor scan {1}, but it has no precursors", spectrum.ScanNumber, expectedPrecursorScan);
}
continue;
}
var precursorSpectrumReference = spectrum.Precursors[0].PrecursorSpectrumRef;
// Parse out scan number from the precursor spectrum reference
// "controllerType=0 controllerNumber=1 scan=1"
if (!NativeIdConversion.TryGetScanNumberLong(precursorSpectrumReference, out var precursorScan))
{
Assert.Fail("Invalid spectrum reference: " + precursorSpectrumReference);
}
Console.WriteLine("Scan {0} has precursor {1:F2} m/z, precursor scan {2}",
spectrum.ScanNumber,
spectrum.Precursors[0].IsolationWindow.TargetMz,
precursorScan);
if (expectedPrecursorScan != 0)
{
Assert.AreEqual(expectedPrecursorScan, precursorScan,
"Precursor scan number does not match the expected value for scan {0}",
spectrum.ScanNumber);
}
}
}
}
public void ReadSpectraData(List <IdentData> psmResults)
{
var dataByNativeId = new Dictionary <string, List <IdentData> >();
var dataByScan = new Dictionary <int, List <IdentData> >();
foreach (var psm in psmResults)
{
if (!string.IsNullOrWhiteSpace(psm.NativeId))
{
if (!dataByNativeId.TryGetValue(psm.NativeId, out var results))
{
results = new List <IdentData>();
dataByNativeId.Add(psm.NativeId, results);
}
results.Add(psm);
}
if (psm.ScanIdInt >= 0)
{
if (!dataByScan.TryGetValue(psm.ScanIdInt, out var results))
{
results = new List <IdentData>();
dataByScan.Add(psm.ScanIdInt, results);
}
results.Add(psm);
}
}
if (psmResults.Count == 0)
{
OnWarningEvent("Empty psmResults were sent to ReadSpectraData; nothing to do");
return;
}
using var reader = new SimpleMzMLReader(MzMLFilePath);
var spectraRead = 0;
var lastStatus = DateTime.UtcNow;
var maxScanId = psmResults.Max(x => x.ScanIdInt);
foreach (var spectrum in reader.ReadAllSpectra(false))
{
spectraRead++;
var nativeIdScanNumber = spectrum.NativeIdScanNumber;
if (nativeIdScanNumber > 0 && nativeIdScanNumber > maxScanId)
{
// All of the PSMs have been processed
break;
}
var spectrumScanNumber = nativeIdScanNumber == 0 ? spectrum.ScanNumber : nativeIdScanNumber;
if (spectrum.MsLevel <= 1)
{
continue;
}
// Find PSMs associated with the current spectrum
// First lookup using NativeId
// If no match, lookup using the scan number
List <IdentData> psmsForSpectrum;
if (dataByNativeId.TryGetValue(spectrum.NativeId, out var psmsFromNativeId))
{
psmsForSpectrum = psmsFromNativeId;
}
else if (dataByScan.TryGetValue(spectrumScanNumber, out var psmsFromScanNumber))
{
psmsForSpectrum = psmsFromScanNumber;
}
else
{
continue;
}
foreach (var psm in psmsForSpectrum)
{
var experimentalMzRefined = spectrum.GetThermoMonoisotopicMz();
if (Math.Abs(experimentalMzRefined) > 0)
{
psm.ExperMzRefined = experimentalMzRefined;
}
else if (spectrum.Precursors.Count > 0 && spectrum.Precursors[0].SelectedIons.Count > 0)
{
psm.ExperMzRefined = spectrum.Precursors[0].SelectedIons[0].SelectedIonMz;
}
else
{
OnWarningEvent("Could not determine the experimental precursor m/z for scan {0}", spectrumScanNumber);
}
if (psm.ScanTimeSeconds <= 0)
{
// StartTime is stored in minutes, we've been using seconds.
psm.ScanTimeSeconds = spectrum.ScanStartTime * 60;
}
}
if (DateTime.UtcNow.Subtract(lastStatus).TotalSeconds < 5)
{
continue;
}
Console.WriteLine(" {0:F0}% complete", spectraRead / (double)reader.NumSpectra * 100);
lastStatus = DateTime.UtcNow;
}
}
