/// <summary>
/// Tests the dynamic connection for ThermoRawFileReader
/// </summary>
public static void TestDynamicConnectionRawFileReader()
{
Stopwatch stopwatch = new Stopwatch();
stopwatch.Start();
var path1 = Path.Combine(TestContext.CurrentContext.TestDirectory, "DataFiles", "small.raw");
var dynamicConnection1 = new ThermoDynamicData(path1);
var path2 = Path.Combine(TestContext.CurrentContext.TestDirectory, "DataFiles", "testFileWMS2.raw");
var dynamicConnection2 = new ThermoDynamicData(path2);
var msOrders = dynamicConnection1.MsOrdersByScan;
Assert.That(msOrders != null && msOrders.Length > 0);
var a = dynamicConnection1.GetOneBasedScanFromDynamicConnection(1);
Assert.That(a != null);
var b = dynamicConnection2.GetOneBasedScanFromDynamicConnection(1);
Assert.That(b != null);
Assert.That(a.MassSpectrum.XArray.Length != b.MassSpectrum.XArray.Length);
a = dynamicConnection1.GetOneBasedScanFromDynamicConnection(10000);
Assert.That(a == null);
dynamicConnection1.CloseDynamicConnection();
dynamicConnection2.CloseDynamicConnection();
Console.WriteLine($"Analysis time for TestDynamicConnectionRawFileReader: {stopwatch.Elapsed.Hours}h {stopwatch.Elapsed.Minutes}m {stopwatch.Elapsed.Seconds}s");
}
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 bool IndexMassSpectralPeaks(SpectraFileInfo fileInfo, bool silent, Dictionary <SpectraFileInfo, Ms1ScanInfo[]> _ms1Scans)
{
if (!silent)
{
Console.WriteLine("Reading spectra file");
}
MsDataScan[] msDataScans = null;
// read spectra file
var ext = Path.GetExtension(fileInfo.FullFilePathWithExtension).ToUpperInvariant();
if (ext == ".MZML")
{
try
{
msDataScans = Mzml.LoadAllStaticData(fileInfo.FullFilePathWithExtension).GetAllScansList()
.OrderBy(p => p.OneBasedScanNumber).ToArray();
}
catch (FileNotFoundException)
{
if (!silent)
{
Console.WriteLine("\nCan't find .mzML file" + fileInfo.FullFilePathWithExtension + "\n");
}
return(false);
}
catch (Exception e)
{
if (!silent)
{
Console.WriteLine("Problem opening .mzML file " + fileInfo.FullFilePathWithExtension + "; " +
e.Message);
}
return(false);
}
for (int i = 0; i < msDataScans.Length; i++)
{
if (msDataScans[i].MsnOrder > 1)
{
msDataScans[i] = null;
}
}
}
else if (ext == ".RAW")
{
var tempList = new List <MsDataScan>();
ThermoDynamicData dynamicConnection = null;
try
{
dynamicConnection = new ThermoDynamicData(fileInfo.FullFilePathWithExtension);
// use thermo dynamic connection to get the ms1 scans and then dispose of the connection
for (int i = 0; i < dynamicConnection.MsOrdersByScan.Length; i++)
{
if (dynamicConnection.MsOrdersByScan[i] == 1)
{
tempList.Add(dynamicConnection.GetOneBasedScanFromDynamicConnection(i + 1));
}
else
{
tempList.Add(null);
}
}
dynamicConnection.CloseDynamicConnection();
}
catch (FileNotFoundException)
{
if (dynamicConnection != null)
{
dynamicConnection.CloseDynamicConnection();
}
if (!silent)
{
Console.WriteLine("\nCan't find .raw file" + fileInfo.FullFilePathWithExtension + "\n");
}
return(false);
}
catch (Exception e)
{
if (dynamicConnection != null)
{
dynamicConnection.CloseDynamicConnection();
}
if (!silent)
{
throw new MzLibException("FlashLFQ Error: Problem opening .raw file " + fileInfo.FullFilePathWithExtension + "; " + e.Message);
}
}
msDataScans = tempList.ToArray();
}
else
{
if (!silent)
{
Console.WriteLine("Unsupported file type " + ext);
return(false);
}
}
if (!silent)
{
Console.WriteLine("Indexing MS1 peaks");
}
if (!msDataScans.Any(p => p != null))
{
_indexedPeaks = new List <IndexedMassSpectralPeak> [0];
return(false);
}
_indexedPeaks = new List <IndexedMassSpectralPeak> [(int)Math.Ceiling(msDataScans.Where(p => p != null &&
p.MassSpectrum.LastX != null).Max(p => p.MassSpectrum.LastX.Value) * BinsPerDalton) + 1];
int scanIndex = 0;
List <Ms1ScanInfo> scanInfo = new List <Ms1ScanInfo>();
for (int i = 0; i < msDataScans.Length; i++)
{
if (msDataScans[i] == null)
{
continue;
}
scanInfo.Add(new Ms1ScanInfo(msDataScans[i].OneBasedScanNumber, scanIndex, msDataScans[i].RetentionTime));
for (int j = 0; j < msDataScans[i].MassSpectrum.XArray.Length; j++)
{
int roundedMz = (int)Math.Round(msDataScans[i].MassSpectrum.XArray[j] * BinsPerDalton, 0);
if (_indexedPeaks[roundedMz] == null)
{
_indexedPeaks[roundedMz] = new List <IndexedMassSpectralPeak>();
}
_indexedPeaks[roundedMz].Add(new IndexedMassSpectralPeak(msDataScans[i].MassSpectrum.XArray[j],
msDataScans[i].MassSpectrum.YArray[j], scanIndex, msDataScans[i].RetentionTime));
}
scanIndex++;
}
_ms1Scans.Add(fileInfo, scanInfo.ToArray());
if (_indexedPeaks == null || _indexedPeaks.Length == 0)
{
if (!silent)
{
Console.WriteLine("FlashLFQ Error: The file " + fileInfo.FilenameWithoutExtension + " contained no MS1 peaks!");
}
return(false);
}
return(true);
}