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 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 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);
}
}
}
}