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);
}
}
}