public MsDataFile LoadFile(string origDataFile, CommonParameters commonParameters)
{
FilteringParams filter = new FilteringParams(commonParameters.NumberOfPeaksToKeepPerWindow, commonParameters.MinimumAllowedIntensityRatioToBasePeak, commonParameters.WindowWidthThomsons, commonParameters.NumberOfWindows, commonParameters.NormalizePeaksAccrossAllWindows, commonParameters.TrimMs1Peaks, commonParameters.TrimMsMsPeaks);
if (commonParameters.DissociationType == DissociationType.LowCID || commonParameters.MS2ChildScanDissociationType == DissociationType.LowCID || commonParameters.MS3ChildScanDissociationType == DissociationType.LowCID)
{
filter = null;
}
if (MyMsDataFiles.TryGetValue(origDataFile, out MsDataFile value) && value != null)
{
return(value);
}
// By now know that need to load this file!!!
lock (FileLoadingLock) // Lock because reading is sequential
{
if (Path.GetExtension(origDataFile).Equals(".mzML", StringComparison.OrdinalIgnoreCase))
{
MyMsDataFiles[origDataFile] = Mzml.LoadAllStaticData(origDataFile, filter, commonParameters.MaxThreadsToUsePerFile);
}
else if (Path.GetExtension(origDataFile).Equals(".mgf", StringComparison.OrdinalIgnoreCase))
{
MyMsDataFiles[origDataFile] = Mgf.LoadAllStaticData(origDataFile, filter);
}
else
{
MyMsDataFiles[origDataFile] = ThermoRawFileReaderData.LoadAllStaticData(origDataFile, filter, commonParameters.MaxThreadsToUsePerFile);
}
return(MyMsDataFiles[origDataFile]);
}
}
/// <summary>
/// Tests peak filtering for ThermoRawFileReader
/// </summary>
public static void TestPeakFilteringRawFileReader(string infile)
{
Stopwatch stopwatch = new Stopwatch();
stopwatch.Start();
var filterParams = new FilteringParams(200, 0.01, 0, 1, false, true, true);
var path = Path.Combine(TestContext.CurrentContext.TestDirectory, "DataFiles", infile);
var a = ThermoRawFileReaderData.LoadAllStaticData(path, filterParams, maxThreads: 1);
var rawScans = a.GetAllScansList();
foreach (var scan in rawScans)
{
Assert.That(scan.MassSpectrum.XArray.Length <= 200);
}
string outfile1 = Path.Combine(TestContext.CurrentContext.TestDirectory, "DataFiles", Path.GetFileNameWithoutExtension(infile) + ".mzML");
MzmlMethods.CreateAndWriteMyMzmlWithCalibratedSpectra(a, outfile1, false);
var mzml = Mzml.LoadAllStaticData(outfile1, filterParams, maxThreads: 1);
var mzmlScans = mzml.GetAllScansList();
for (int i = 0; i < mzmlScans.Count; i++)
{
var mzmlScan = mzmlScans[i];
var rawScan = rawScans[i];
for (int j = 0; j < mzmlScan.MassSpectrum.XArray.Length; j++)
{
double roundedMzmlMz = Math.Round(mzmlScan.MassSpectrum.XArray[j], 2);
double roundedRawMz = Math.Round(rawScan.MassSpectrum.XArray[j], 2);
Assert.AreEqual(roundedMzmlMz, roundedRawMz);
double roundedMzmlIntensity = Math.Round(mzmlScan.MassSpectrum.XArray[j], 0);
double roundedRawIntensity = Math.Round(rawScan.MassSpectrum.XArray[j], 0);
Assert.AreEqual(roundedMzmlIntensity, roundedRawIntensity);
}
}
Console.WriteLine($"Analysis time for TestPeakFilteringRawFileReader: {stopwatch.Elapsed.Hours}h " +
$"{stopwatch.Elapsed.Minutes}m {stopwatch.Elapsed.Seconds}s");
}
/// <summary>
/// Tests LoadAllStaticData for ThermoRawFileReader
/// </summary>
public static void TestLoadAllStaticDataRawFileReader(string infile, string outfile1, string outfile2)
{
var path = Path.Combine(TestContext.CurrentContext.TestDirectory, "DataFiles", infile);
outfile1 = Path.Combine(TestContext.CurrentContext.TestDirectory, "DataFiles", outfile1);
outfile2 = Path.Combine(TestContext.CurrentContext.TestDirectory, "DataFiles", outfile2);
Stopwatch stopwatch = new Stopwatch();
stopwatch.Start();
var a = ThermoRawFileReaderData.LoadAllStaticData(path, maxThreads: 1);
MzmlMethods.CreateAndWriteMyMzmlWithCalibratedSpectra(a, outfile1, false);
var aa = Mzml.LoadAllStaticData(outfile1);
MzmlMethods.CreateAndWriteMyMzmlWithCalibratedSpectra(aa, outfile2, true);
Mzml.LoadAllStaticData(outfile2);
Console.WriteLine($"Analysis time for TestLoadAllStaticDataRawFileReader({infile}): {stopwatch.Elapsed.Hours}h {stopwatch.Elapsed.Minutes}m {stopwatch.Elapsed.Seconds}s");
}
