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] = ThermoRawFileReader.LoadAllStaticData(origDataFile, filter, commonParameters.MaxThreadsToUsePerFile);
}
return(MyMsDataFiles[origDataFile]);
}
}
public static void TestDynamicRaw(string fileName)
{
string filePath = Path.Combine(TestContext.CurrentContext.TestDirectory, "DataFiles", fileName);
ThermoRawFileReader staticRaw = ThermoRawFileReader.LoadAllStaticData(filePath);
ThermoDynamicData dynamicRaw = new ThermoDynamicData(filePath);
foreach (MsDataScan staticScan in staticRaw.GetAllScansList())
{
MsDataScan dynamicScan = dynamicRaw.GetOneBasedScanFromDynamicConnection(staticScan.OneBasedScanNumber);
Assert.That(dynamicScan.OneBasedScanNumber == staticScan.OneBasedScanNumber);
Assert.That(dynamicScan.MsnOrder == staticScan.MsnOrder);
Assert.That(dynamicScan.RetentionTime == staticScan.RetentionTime);
Assert.That(dynamicScan.Polarity == staticScan.Polarity);
Assert.That(dynamicScan.ScanWindowRange.Minimum == staticScan.ScanWindowRange.Minimum);
Assert.That(dynamicScan.ScanWindowRange.Maximum == staticScan.ScanWindowRange.Maximum);
Assert.That(dynamicScan.ScanFilter == staticScan.ScanFilter);
Assert.That(dynamicScan.NativeId == staticScan.NativeId);
Assert.That(dynamicScan.IsCentroid == staticScan.IsCentroid);
Assert.That(dynamicScan.IsCentroid == staticScan.IsCentroid);
Assert.That(dynamicScan.InjectionTime == staticScan.InjectionTime);
Assert.That(dynamicScan.NoiseData == staticScan.NoiseData);
Assert.That(dynamicScan.IsolationMz == staticScan.IsolationMz);
Assert.That(dynamicScan.SelectedIonChargeStateGuess == staticScan.SelectedIonChargeStateGuess);
Assert.That(dynamicScan.SelectedIonIntensity == staticScan.SelectedIonIntensity);
Assert.That(dynamicScan.SelectedIonMZ == staticScan.SelectedIonMZ);
Assert.That(dynamicScan.DissociationType == staticScan.DissociationType);
Assert.That(dynamicScan.IsolationWidth == staticScan.IsolationWidth);
Assert.That(dynamicScan.OneBasedPrecursorScanNumber == staticScan.OneBasedPrecursorScanNumber);
Assert.That(dynamicScan.SelectedIonMonoisotopicGuessIntensity == staticScan.SelectedIonMonoisotopicGuessIntensity);
Assert.That(dynamicScan.SelectedIonMonoisotopicGuessMz == staticScan.SelectedIonMonoisotopicGuessMz);
if (dynamicScan.IsolationRange != null || staticScan.IsolationRange != null)
{
Assert.That(dynamicScan.IsolationRange.Minimum == staticScan.IsolationRange.Minimum);
Assert.That(dynamicScan.IsolationRange.Maximum == staticScan.IsolationRange.Maximum);
}
Assert.That(dynamicScan.MassSpectrum.XArray.Length == staticScan.MassSpectrum.XArray.Length);
Assert.That(dynamicScan.MassSpectrum.YArray.Length == staticScan.MassSpectrum.YArray.Length);
for (int i = 0; i < staticScan.MassSpectrum.XArray.Length; i++)
{
double staticMz = staticScan.MassSpectrum.XArray[i];
double staticIntensity = staticScan.MassSpectrum.YArray[i];
double dynamicMz = dynamicScan.MassSpectrum.XArray[i];
double dynamicIntensity = dynamicScan.MassSpectrum.YArray[i];
Assert.That(dynamicMz == staticMz);
Assert.That(dynamicIntensity == staticIntensity);
}
}
}
public static void TestEthcdReading()
{
string filePath = Path.Combine(TestContext.CurrentContext.TestDirectory, "DataFiles", "sliced_ethcd.raw");
var spectra = ThermoRawFileReader.LoadAllStaticData(filePath, null, 1);
var hcdScan = spectra.GetOneBasedScan(5);
Assert.That(hcdScan.DissociationType == DissociationType.HCD);
var ethcdScan = spectra.GetOneBasedScan(6);
Assert.That(ethcdScan.DissociationType == DissociationType.EThcD);
}
static void Thermo()
{
string rawPath = @"C:\Work\primaqdev\testdata\06042010HSRE3mem117.RAW";
string runID = "run_1";
using (var reader = new ThermoRawFileReader(rawPath))
using (ITransactionScope txn = reader.BeginTransaction())
{
foreach (var ms in reader.ReadMassSpectra(runID))
{
var peaks = reader.ReadSpectrumPeaks(ms.ID);
Console.Out.WriteLine(ms.ID);
}
}
}
/// <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 = ThermoRawFileReader.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 " +
$"{stopwatch.Elapsed.Minutes}m {stopwatch.Elapsed.Seconds}s");
}
/// <summary>
/// Tests LoadAllStaticData for ThermoRawFileReader
/// </summary>
public static void TestLoadAllStaticDataRawFileReader(string infile, string outfile1, string outfile2)
{
var path = Path.Combine(TestContext.CurrentContext.TestDirectory, "DataFiles", infile);
outfile1 = Path.Combine(TestContext.CurrentContext.TestDirectory, "DataFiles", outfile1);
outfile2 = Path.Combine(TestContext.CurrentContext.TestDirectory, "DataFiles", outfile2);
Stopwatch stopwatch = new Stopwatch();
stopwatch.Start();
var a = ThermoRawFileReader.LoadAllStaticData(path, maxThreads: 1);
MzmlMethods.CreateAndWriteMyMzmlWithCalibratedSpectra(a, outfile1, false);
var aa = Mzml.LoadAllStaticData(outfile1);
MzmlMethods.CreateAndWriteMyMzmlWithCalibratedSpectra(aa, outfile2, true);
Mzml.LoadAllStaticData(outfile2);
Console.WriteLine($"Analysis time for TestLoadAllStaticDataRawFileReader({infile}): {stopwatch.Elapsed.Hours}h {stopwatch.Elapsed.Minutes}m {stopwatch.Elapsed.Seconds}s");
}
public static List <ScanHeaderInfo> FileScanHeaderInfo(string fullFilePathWithExtension)
{
string filename = Path.GetFileName(fullFilePathWithExtension);
List <ScanHeaderInfo> scanHeaderInfoList = new();
switch (GetDataFileType(fullFilePathWithExtension))
{
case DataFileType.Thermo:
ThermoRawFileReader staticRaw = ThermoRawFileReader.LoadAllStaticData(fullFilePathWithExtension);
foreach (MsDataScan item in staticRaw)
{
scanHeaderInfoList.Add(new ScanHeaderInfo(fullFilePathWithExtension, filename, item.OneBasedScanNumber, item.RetentionTime));
}
break;
case DataFileType.mzML:
List <MsDataScan> mzmlDataScans = Mzml.LoadAllStaticData(fullFilePathWithExtension).GetAllScansList();
foreach (MsDataScan item in mzmlDataScans)
{
scanHeaderInfoList.Add(new ScanHeaderInfo(fullFilePathWithExtension, filename, item.OneBasedScanNumber, item.RetentionTime));
}
break;
case DataFileType.mgf:
List <MsDataScan> mgfDataScans = Mgf.LoadAllStaticData(fullFilePathWithExtension).GetAllScansList();
foreach (MsDataScan item in mgfDataScans)
{
scanHeaderInfoList.Add(new ScanHeaderInfo(fullFilePathWithExtension, filename, item.OneBasedScanNumber, item.RetentionTime));
}
break;
case DataFileType.unknown:
default:
break;
}
return(scanHeaderInfoList);
}
