/// <summary>
/// Gets the appropriate IMassSpecDataReader for the supplied path.
/// It is recommended that "NormalizeDatasetPath" be called prior to calling this function, and that the returned string be used instead of the original path
/// </summary>
/// <param name="filePath"></param>
/// <returns></returns>
/// <remarks>It is recommended that "NormalizeDatasetPath" be called prior to calling this function, and that the returned string be used instead of the original path</remarks>
public static IMassSpecDataReader GetMassSpecDataReader(string filePath)
{
filePath = NormalizeDatasetPath(filePath);
var type = GetMassSpecDataType(filePath);
IMassSpecDataReader reader = null;
switch (type)
{
case MassSpecDataType.XCaliburRun:
reader = new XCaliburReader(filePath);
break;
case MassSpecDataType.MzMLFile:
reader = new MzMLReader(filePath);
break;
case MassSpecDataType.PbfFile:
reader = new PbfLcMsRun(filePath);
break;
case MassSpecDataType.Unknown:
if (_pwizAvailable)
{
reader = new ProteoWizardReader(filePath);
}
break;
}
return reader;
}
[TestCase(@"\\proto-2\UnitTest_Files\InformedProteomics_TestFiles\MZML\VA139IMSMS_compressed.mzML", 3145)] // Centroid, Agilent QTOF, compressed binary data
public void TestReadMzML(string filePath, int expectedSpectra)
{
var methodName = MethodBase.GetCurrentMethod().Name;
TestUtils.ShowStarting(methodName, filePath);
Stopwatch timer = new Stopwatch();
timer.Start();
var reader = new MzMLReader(filePath);
var constTime = timer.Elapsed;
Console.WriteLine(@"Constructor time: " + constTime);
var numSpectra = reader.NumSpectra;
var metaTime = timer.Elapsed - constTime;
Console.WriteLine(@"Metadata read time: " + metaTime);
var spectra = reader.ReadAllSpectra();
var spectraCount = spectra.Count();
timer.Stop();
Console.WriteLine(@"Spectra Read time: " + (timer.Elapsed - metaTime));
Console.WriteLine(@"Time: " + timer.Elapsed);
Assert.AreEqual(expectedSpectra, numSpectra, "NumSpectra");
Assert.AreEqual(expectedSpectra, spectraCount, "SpectraCount");
Assert.AreEqual(numSpectra, spectraCount, "NumSpectra vs. SpectraCount");
reader.Close();
}