public void TestCorruptDataHandling(
string dotDFolderName,
int scanStart,
int scanEnd,
int expectedMS1,
int expectedMS2)
{
var dataFolder = GetBrukerDataFolder(dotDFolderName);
try
{
using (var reader = new MSDataFileReader(dataFolder.FullName))
{
var scanCount = reader.SpectrumCount;
Console.WriteLine("Scan count for {0}: {1}", dataFolder.Name, scanCount);
if (expectedMS1 + expectedMS2 == 0)
{
Assert.IsTrue(scanCount == 0, "ScanCount is non-zero, while we expected it to be 0");
}
else
{
Assert.IsTrue(scanCount > 0, "ScanCount is zero, while we expected it to be > 0");
}
var scanNumberToIndexMap = reader.GetScanToIndexMapping();
var scanCountMS1 = 0;
var scanCountMS2 = 0;
foreach (var scan in scanNumberToIndexMap.Where(x => x.Key >= scanStart && x.Key <= scanEnd))
{
var scanNumber = scan.Key;
var spectrumIndex = scan.Value;
try
{
var spectrum = reader.GetSpectrum(spectrumIndex, true);
var cvScanInfo = reader.GetSpectrumScanInfo(spectrumIndex);
Assert.IsTrue(cvScanInfo != null, "GetSpectrumScanInfo returned a null object for scan {0}", scanNumber);
if (spectrum.Level > 1)
{
scanCountMS2++;
}
else
{
scanCountMS1++;
}
var dataPointCount = spectrum.Mzs.Length;
Assert.IsTrue(dataPointCount > 0, "Data point count is 0 for scan {0}", scanNumber);
Assert.IsTrue(spectrum.Mzs.Length > 0, "m/z data is empty for scan {0}", scanNumber);
Assert.IsTrue(spectrum.Intensities.Length > 0, "Intensity data is empty for scan {0}", scanNumber);
Assert.IsTrue(spectrum.Mzs.Length == spectrum.Intensities.Length, "Array length mismatch for m/z and intensity data for scan {0}", scanNumber);
}
catch (Exception ex)
{
Console.WriteLine("Exception reading scan {0}: {1}", scanNumber, ex.Message);
Assert.Fail("Exception reading scan {0}", scanNumber);
}
}
Console.WriteLine("scanCountMS1={0}", scanCountMS1);
Console.WriteLine("scanCountMS2={0}", scanCountMS2);
Assert.AreEqual(expectedMS1, scanCountMS1, "MS1 scan count mismatch");
Assert.AreEqual(expectedMS2, scanCountMS2, "MS2 scan count mismatch");
}
}
catch (Exception ex)
{
if (expectedMS1 + expectedMS2 == 0)
{
Console.WriteLine("Error opening .D folder (this was expected):\n{0}", ex.Message);
}
else
{
var msg = string.Format("Exception opening .D folder {0}:\n{1}", dotDFolderName, ex.Message);
Console.WriteLine(msg);
Assert.Fail(msg);
}
}
}
public void TestGetScanInfo(string uimfFileName, int frameStart, int frameEnd, int expectedMS1, int expectedMS2)
{
var expectedData = new Dictionary <string, Dictionary <KeyValuePair <int, int>, string> >();
// Keys in this dictionary are the FrameNum, ScanNum whose metadata is being retrieved
var file1Data = new Dictionary <KeyValuePair <int, int>, string>
{
// Scan MSLevel NumPeaks RetentionTime DriftTimeMsec IonMobilityDriftTime LowMass HighMass TotalIonCurrent BasePeakMZ BasePeakIntensity ParentIonMZ ActivationType IonMode IsCentroided ScanStartTime IonInjectionTime FilterText
{ new KeyValuePair <int, int>(1, 0), " 1 0 1 3 0.01 0.01 0.00 0.00 0 14384 0.0E+0 0.000 0.0E+0 0.00 positive False 7192.23" },
{ new KeyValuePair <int, int>(1, 100), " 1 100 1 1317 0.01 0.01 24.68 24.68 0 14384 0.0E+0 0.000 0.0E+0 0.00 positive False 7192.23" },
{ new KeyValuePair <int, int>(1, 200), " 1 200 1 3 0.01 0.01 49.36 49.36 0 14384 0.0E+0 0.000 0.0E+0 0.00 positive False 7192.23" },
{ new KeyValuePair <int, int>(2, 0), " 2 0 1 16 0.25 0.25 0.00 0.00 0 14384 0.0E+0 0.000 0.0E+0 0.00 positive False 7192.23" },
{ new KeyValuePair <int, int>(2, 1), " 2 1 1 6 0.25 0.25 0.25 0.25 0 14384 0.0E+0 0.000 0.0E+0 0.00 positive False 7192.23" },
{ new KeyValuePair <int, int>(2, 100), " 2 100 1 3429 0.25 0.25 24.70 24.70 0 14384 0.0E+0 0.000 0.0E+0 0.00 positive False 7192.23" },
{ new KeyValuePair <int, int>(2, 200), " 2 200 1 9 0.25 0.25 49.39 49.39 0 14384 0.0E+0 0.000 0.0E+0 0.00 positive False 7192.23" },
{ new KeyValuePair <int, int>(3, 0), " 3 0 1 21 0.50 0.50 0.00 0.00 0 14384 0.0E+0 0.000 0.0E+0 0.00 positive False 7192.23" },
{ new KeyValuePair <int, int>(3, 100), " 3 100 1 4216 0.50 0.50 24.65 24.65 0 14384 0.0E+0 0.000 0.0E+0 0.00 positive False 7192.23" },
{ new KeyValuePair <int, int>(3, 200), " 3 200 1 3 0.50 0.50 49.31 49.31 0 14384 0.0E+0 0.000 0.0E+0 0.00 positive False 7192.23" },
{ new KeyValuePair <int, int>(4, 0), " 4 0 1 3 0.75 0.75 0.00 0.00 0 14384 0.0E+0 0.000 0.0E+0 0.00 positive False 7192.23" },
{ new KeyValuePair <int, int>(4, 1), " 4 1 1 6 0.75 0.75 0.25 0.25 0 14384 0.0E+0 0.000 0.0E+0 0.00 positive False 7192.23" },
{ new KeyValuePair <int, int>(4, 100), " 4 100 1 5640 0.75 0.75 24.58 24.58 0 14384 0.0E+0 0.000 0.0E+0 0.00 positive False 7192.23" },
{ new KeyValuePair <int, int>(4, 200), " 4 200 1 6 0.75 0.75 49.16 49.16 0 14384 0.0E+0 0.000 0.0E+0 0.00 positive False 7192.23" },
{ new KeyValuePair <int, int>(5, 0), " 5 0 1 9 1.00 1.00 0.00 0.00 0 14384 0.0E+0 0.000 0.0E+0 0.00 positive False 7192.23" },
{ new KeyValuePair <int, int>(5, 100), " 5 100 1 4605 1.00 1.00 24.70 24.70 0 14384 0.0E+0 0.000 0.0E+0 0.00 positive False 7192.23" },
{ new KeyValuePair <int, int>(5, 200), " 5 200 1 3 1.00 1.00 49.39 49.39 0 14384 0.0E+0 0.000 0.0E+0 0.00 positive False 7192.23" }
};
expectedData.Add("9_Peptide_Mix_16Oct14_Cedar_Infuse", file1Data);
var file2Data = new Dictionary <KeyValuePair <int, int>, string>
{
{ new KeyValuePair <int, int>(1, 38), " 1 38 1 15 0.01 0.01 6.11 6.11 0 2646 0.0E+0 0.000 0.0E+0 0.00 positive False 1322.76" },
{ new KeyValuePair <int, int>(1, 114), " 1 114 1 1215 0.01 0.01 18.34 18.34 0 2646 0.0E+0 0.000 0.0E+0 0.00 positive False 1322.76" },
{ new KeyValuePair <int, int>(1, 152), " 1 152 1 222 0.01 0.01 24.45 24.45 0 2646 0.0E+0 0.000 0.0E+0 0.00 positive False 1322.76" },
{ new KeyValuePair <int, int>(1, 228), " 1 228 1 3 0.01 0.01 36.67 36.67 0 2646 0.0E+0 0.000 0.0E+0 0.00 positive False 1322.76" },
{ new KeyValuePair <int, int>(1, 304), " 1 304 1 9 0.01 0.01 48.89 48.89 0 2646 0.0E+0 0.000 0.0E+0 0.00 positive False 1322.76" }
};
expectedData.Add("9pep_mix_1uM_4bit_50_3Jun16", file2Data);
var file3Data = new Dictionary <KeyValuePair <int, int>, string>
{
{ new KeyValuePair <int, int>(1, 100), " 1 100 1 504 0.01 0.01 16.37 16.37 0 2646 0.0E+0 0.000 0.0E+0 0.00 positive False 1322.79" },
{ new KeyValuePair <int, int>(2, 100), " 2 100 1 494 0.06 0.06 16.42 16.42 0 2646 0.0E+0 0.000 0.0E+0 0.00 positive False 1322.79" },
{ new KeyValuePair <int, int>(3, 100), " 3 100 1 1109 0.11 0.11 16.43 16.43 0 2646 0.0E+0 0.000 0.0E+0 0.00 positive False 1322.79" },
{ new KeyValuePair <int, int>(4, 0), " 4 0 1 3 0.17 0.17 0.00 0.00 0 2646 0.0E+0 0.000 0.0E+0 0.00 positive False 1322.79" },
{ new KeyValuePair <int, int>(4, 100), " 4 100 1 1061 0.17 0.17 16.41 16.41 0 2646 0.0E+0 0.000 0.0E+0 0.00 positive False 1322.79" },
{ new KeyValuePair <int, int>(5, 0), " 5 0 1 3 0.22 0.22 0.00 0.00 0 2646 0.0E+0 0.000 0.0E+0 0.00 positive False 1322.79" },
{ new KeyValuePair <int, int>(5, 100), " 5 100 1 1087 0.22 0.22 16.44 16.44 0 2646 0.0E+0 0.000 0.0E+0 0.00 positive False 1322.79" },
};
expectedData.Add("QC_Shew_IMER_500ng_Run-1_4May16_Oak_15-01-16", file3Data);
var file4Data = new Dictionary <KeyValuePair <int, int>, string>
{
{ new KeyValuePair <int, int>(1, 1), " 1 1 1 344 0.00 0.00 0.12 0.12 0 1700 0.0E+0 0.000 0.0E+0 0.00 positive False 849.87" },
{ new KeyValuePair <int, int>(1, 100), " 1 100 1 345 0.00 0.00 12.10 12.10 0 1700 0.0E+0 0.000 0.0E+0 0.00 positive False 849.87" },
{ new KeyValuePair <int, int>(1, 200), " 1 200 1 577 0.00 0.00 24.20 24.20 0 1700 0.0E+0 0.000 0.0E+0 0.00 positive False 849.87" },
{ new KeyValuePair <int, int>(1, 300), " 1 300 1 996 0.00 0.00 36.30 36.30 0 1700 0.0E+0 0.000 0.0E+0 0.00 positive False 849.87" },
{ new KeyValuePair <int, int>(1, 400), " 1 400 1 469 0.00 0.00 48.40 48.40 0 1700 0.0E+0 0.000 0.0E+0 0.00 positive False 849.87" },
{ new KeyValuePair <int, int>(1, 500), " 1 500 1 336 0.00 0.00 60.50 60.50 0 1700 0.0E+0 0.000 0.0E+0 0.00 positive False 849.87" },
{ new KeyValuePair <int, int>(1, 600), " 1 600 1 369 0.00 0.00 72.60 72.60 0 1700 0.0E+0 0.000 0.0E+0 0.00 positive False 849.87" },
{ new KeyValuePair <int, int>(1, 700), " 1 700 1 423 0.00 0.00 84.70 84.70 0 1700 0.0E+0 0.000 0.0E+0 0.00 positive False 849.87" },
{ new KeyValuePair <int, int>(2, 1), " 2 1 1 381 0.00 0.00 0.12 0.12 0 1700 0.0E+0 0.000 0.0E+0 0.00 positive False 849.87" },
{ new KeyValuePair <int, int>(2, 100), " 2 100 1 243 0.00 0.00 12.10 12.10 0 1700 0.0E+0 0.000 0.0E+0 0.00 positive False 849.87" },
{ new KeyValuePair <int, int>(2, 200), " 2 200 1 669 0.00 0.00 24.20 24.20 0 1700 0.0E+0 0.000 0.0E+0 0.00 positive False 849.87" },
{ new KeyValuePair <int, int>(2, 300), " 2 300 1 770 0.00 0.00 36.30 36.30 0 1700 0.0E+0 0.000 0.0E+0 0.00 positive False 849.87" },
{ new KeyValuePair <int, int>(2, 400), " 2 400 1 372 0.00 0.00 48.40 48.40 0 1700 0.0E+0 0.000 0.0E+0 0.00 positive False 849.87" },
{ new KeyValuePair <int, int>(2, 500), " 2 500 1 355 0.00 0.00 60.50 60.50 0 1700 0.0E+0 0.000 0.0E+0 0.00 positive False 849.87" },
{ new KeyValuePair <int, int>(2, 600), " 2 600 1 441 0.00 0.00 72.60 72.60 0 1700 0.0E+0 0.000 0.0E+0 0.00 positive False 849.87" },
{ new KeyValuePair <int, int>(2, 700), " 2 700 1 328 0.00 0.00 84.70 84.70 0 1700 0.0E+0 0.000 0.0E+0 0.00 positive False 849.87" },
{ new KeyValuePair <int, int>(3, 1), " 3 1 1 405 0.00 0.00 0.12 0.12 0 1700 0.0E+0 0.000 0.0E+0 0.00 positive False 849.87" },
{ new KeyValuePair <int, int>(3, 100), " 3 100 1 419 0.00 0.00 12.10 12.10 0 1700 0.0E+0 0.000 0.0E+0 0.00 positive False 849.87" },
{ new KeyValuePair <int, int>(3, 200), " 3 200 1 705 0.00 0.00 24.20 24.20 0 1700 0.0E+0 0.000 0.0E+0 0.00 positive False 849.87" },
{ new KeyValuePair <int, int>(3, 300), " 3 300 1 1080 0.00 0.00 36.30 36.30 0 1700 0.0E+0 0.000 0.0E+0 0.00 positive False 849.87" },
{ new KeyValuePair <int, int>(3, 400), " 3 400 1 387 0.00 0.00 48.40 48.40 0 1700 0.0E+0 0.000 0.0E+0 0.00 positive False 849.87" },
{ new KeyValuePair <int, int>(3, 500), " 3 500 1 423 0.00 0.00 60.50 60.50 0 1700 0.0E+0 0.000 0.0E+0 0.00 positive False 849.87" },
{ new KeyValuePair <int, int>(3, 600), " 3 600 1 402 0.00 0.00 72.60 72.60 0 1700 0.0E+0 0.000 0.0E+0 0.00 positive False 849.87" },
{ new KeyValuePair <int, int>(3, 700), " 3 700 1 333 0.00 0.00 84.70 84.70 0 1700 0.0E+0 0.000 0.0E+0 0.00 positive False 849.87" },
{ new KeyValuePair <int, int>(4, 1), " 4 1 1 348 0.00 0.00 0.12 0.12 0 1700 0.0E+0 0.000 0.0E+0 0.00 positive False 849.87" },
{ new KeyValuePair <int, int>(4, 100), " 4 100 1 343 0.00 0.00 12.10 12.10 0 1700 0.0E+0 0.000 0.0E+0 0.00 positive False 849.87" },
{ new KeyValuePair <int, int>(4, 200), " 4 200 1 625 0.00 0.00 24.20 24.20 0 1700 0.0E+0 0.000 0.0E+0 0.00 positive False 849.87" },
{ new KeyValuePair <int, int>(4, 300), " 4 300 1 1125 0.00 0.00 36.29 36.29 0 1700 0.0E+0 0.000 0.0E+0 0.00 positive False 849.87" },
{ new KeyValuePair <int, int>(4, 400), " 4 400 1 384 0.00 0.00 48.39 48.39 0 1700 0.0E+0 0.000 0.0E+0 0.00 positive False 849.87" },
{ new KeyValuePair <int, int>(4, 500), " 4 500 1 399 0.00 0.00 60.49 60.49 0 1700 0.0E+0 0.000 0.0E+0 0.00 positive False 849.87" },
{ new KeyValuePair <int, int>(4, 600), " 4 600 1 362 0.00 0.00 72.59 72.59 0 1700 0.0E+0 0.000 0.0E+0 0.00 positive False 849.87" },
{ new KeyValuePair <int, int>(4, 700), " 4 700 1 360 0.00 0.00 84.69 84.69 0 1700 0.0E+0 0.000 0.0E+0 0.00 positive False 849.87" }
};
expectedData.Add("20160524_TuneMix_1574V_neg_001", file4Data);
var dataFile = GetUimfDataFile(uimfFileName);
using (var reader = new MSDataFileReader(dataFile.FullName))
{
Console.WriteLine("Scan info for {0}", dataFile.Name);
Console.WriteLine("{0} {1} {2} {3} {4} {5} {6} {7} {8} {9} {10} {11} {12} {13} {14} {15} {16} {17}",
"Frame", "Scan", "MSLevel",
"NumPeaks", "RetentionTime",
"ScanStartTime",
"DriftTimeMsec",
"IonMobilityDriftTime",
"LowMass", "HighMass", "TotalIonCurrent",
"BasePeakMZ", "BasePeakIntensity",
"ParentIonMZ", "ActivationType",
"IonMode", "IsCentroided",
"IsolationMZ");
var frameScanPairToIndexMap = reader.GetUimfFrameScanPairToIndexMapping();
var scanCountMS1 = 0;
var scanCountMS2 = 0;
foreach (var frame in frameScanPairToIndexMap)
{
var frameNumber = frame.Key.Key;
var scanNumber = frame.Key.Value;
var spectrumIndex = frame.Value;
if (frameNumber < frameStart || frameNumber > frameEnd)
{
continue;
}
if (string.Equals(uimfFileName, "9pep_mix_1uM_4bit_50_3Jun16.uimf", StringComparison.InvariantCultureIgnoreCase))
{
if (!(scanNumber == 1 || scanNumber % 38 == 0))
{
continue;
}
}
else
{
if (!(scanNumber == 1 || scanNumber % 100 == 0))
{
continue;
}
}
var spectrum = reader.GetSpectrum(spectrumIndex, true);
var spectrumParams = reader.GetSpectrumCVParamData(spectrumIndex);
var cvScanInfo = reader.GetSpectrumScanInfo(spectrumIndex);
Assert.IsTrue(spectrum != null, "GetSpectrum returned a null object for frame {0}, scan {1} ", frameNumber, scanNumber);
var totalIonCurrent = cvParamUtilities.GetCvParamValueDbl(spectrumParams, cvParamUtilities.CVIDs.MS_TIC);
var basePeakMZ = cvParamUtilities.GetCvParamValueDbl(spectrumParams, cvParamUtilities.CVIDs.MS_base_peak_m_z);
var basePeakIntensity = cvParamUtilities.GetCvParamValueDbl(spectrumParams, cvParamUtilities.CVIDs.MS_base_peak_intensity);
double isolationMZ = 0;
double parentIonMZ = 0;
var activationType = string.Empty;
if (spectrum.Precursors.Length > 0)
{
var precursor = spectrum.Precursors[0];
isolationMZ = precursor.IsolationMz.GetValueOrDefault();
parentIonMZ = precursor.PrecursorMz.GetValueOrDefault();
if (precursor.ActivationTypes != null)
{
activationType = string.Join(", ", precursor.ActivationTypes);
}
}
GetScanMetadata(cvScanInfo, out var scanStartTime, out var ionMobilityDriftTime, out var lowMass, out var highMass);
var retentionTime = cvParamUtilities.CheckNull(spectrum.RetentionTime);
var numPeaks = spectrum.Mzs.Length;
var ionMode = spectrum.NegativeCharge ? "negative" : "positive";
var scanSummary =
string.Format(
"{0,4} {1,4} {2} {3,5} {4,6:0.00} {5,6:0.00} {6,8:0.00} {7,8:0.00} {8,3:0} {9,5:0} {10,6:0.0E+0} {11,8:0.000} {12,6:0.0E+0} {13,8:0.00} {14,-8} {15} {16,-5} {17,8:0.00}",
frameNumber, scanNumber, spectrum.Level,
numPeaks, retentionTime, scanStartTime,
cvParamUtilities.CheckNull(spectrum.DriftTimeMsec),
ionMobilityDriftTime,
lowMass, highMass,
totalIonCurrent, basePeakMZ, basePeakIntensity, parentIonMZ,
activationType, ionMode,
spectrum.Centroided, isolationMZ);
Console.WriteLine(scanSummary);
if (spectrum.Level > 1)
{
scanCountMS2++;
}
else
{
scanCountMS1++;
}
if (!expectedData.TryGetValue(Path.GetFileNameWithoutExtension(dataFile.Name), out var expectedDataThisFile))
{
Assert.Fail("Dataset {0} not found in dictionary expectedData", dataFile.Name);
}
if (expectedDataThisFile.TryGetValue(new KeyValuePair <int, int>(frameNumber, scanNumber), out var expectedScanSummary))
{
if (!string.Equals(expectedScanSummary, scanSummary))
{
Console.WriteLine(
"{0,4} {1,4} {2} {3,5} {4,6} {5,6} {6,8} {7,8} {8,3} {9,5} {10,6} {11,8} {12,6} {13,8} {14,-8} {15} {16,-5} {17,8}",
"Frame", "Scan", "MSLevel",
"NumPeaks", "RetentionTime", "ScanStartTime",
"DriftTimeMsec",
"IonMobilityDriftTime",
"LowMass", "HighMass",
"TIC", "BasePeakMZ", "BPI", "ParentIonMZ",
"ActivationType", "IonMode",
"Centroided?", "IsolationMZ");
}
Assert.AreEqual(expectedScanSummary, scanSummary,
"Scan summary mismatch, scan " + scanNumber);
}
var expectedNativeId = string.Format("frame={0} scan={1} frameType=1", frameNumber, scanNumber);
Assert.AreEqual(spectrum.NativeId, expectedNativeId, "NativeId is not in the expected format for frame {0}, scan {1} ", frameNumber, scanNumber);
}
Console.WriteLine("scanCountMS1={0}", scanCountMS1);
Console.WriteLine("scanCountMS2={0}", scanCountMS2);
Assert.AreEqual(expectedMS1, scanCountMS1, "MS1 scan count mismatch");
Assert.AreEqual(expectedMS2, scanCountMS2, "MS2 scan count mismatch");
}
}
public void TestGetScanInfo(string dotDFolderName, int scanStart, int scanEnd, int expectedMS1, int expectedMS2)
{
var expectedData = new Dictionary <string, Dictionary <int, string> >();
// Keys in this dictionary are the scan number whose metadata is being retrieved
var file1Data = new Dictionary <int, string>
{
// Scan MSLevel NumPeaks RetentionTime ScanStartTime DriftTimeMsec LowMass HighMass TotalIonCurrent BasePeakMZ BasePeakIntensity ParentIonMZ
{ 1, "1 1 7794096 0.59 35.34 0 92 1300 7.1E+9 0.000 5.5E+8 0.00 positive False 696.00" },
{ 2, "2 1 7794096 1.10 66.27 0 92 1300 7.2E+9 0.000 5.6E+8 0.00 positive False 696.00" },
{ 3, "3 1 7794096 1.62 97.18 0 92 1300 7.2E+9 0.000 5.5E+8 0.00 positive False 696.00" },
{ 4, "4 1 7794096 2.14 128.17 0 92 1300 7.1E+9 0.000 5.3E+8 0.00 positive False 696.00" },
{ 5, "5 1 7794096 2.65 159.12 0 92 1300 7.1E+9 0.000 5.4E+8 0.00 positive False 696.00" }
};
expectedData.Add("2016_04_12_Background_000001", file1Data);
var file2Data = new Dictionary <int, string>
{
{ 1, "1 1 7615807 3.58 214.92 0 111 1200 3.6E+10 0.000 3.1E+9 0.00 negative False 655.50" }
};
expectedData.Add("Blank-2_05May16_Leopard_Infuse_1_01_7976", file2Data);
var file3Data = new Dictionary <int, string>
{
{ 15, "15 1 39775 2.38 142.89 0 983 984 0.0E+0 0.000 0.0E+0 0.00 positive False 983.50" },
{ 16, "16 1 39775 2.53 152.06 0 983 984 0.0E+0 0.000 0.0E+0 0.00 positive False 983.50" },
{ 17, "17 1 39775 2.69 161.24 0 983 984 0.0E+0 0.000 0.0E+0 0.00 positive False 983.50" },
{ 18, "18 1 39775 2.84 170.41 0 983 984 0.0E+0 0.000 0.0E+0 0.00 positive False 983.50" },
{ 19, "19 1 39775 2.99 179.58 0 983 984 0.0E+0 0.000 0.0E+0 0.00 positive False 983.50" },
{ 20, "20 1 39775 3.15 188.76 0 983 984 0.0E+0 0.000 0.0E+0 0.00 positive False 983.50" }
};
expectedData.Add("Humira_100fmol_20121026_hi_res_9_01_716", file3Data);
var file4Data = new Dictionary <int, string>
{
{ 1, "1 2 8214787 2.20 131.89 0 207 10000 6.0E+8 0.000 1.3E+7 1600.00 cid negative False 1600.00" }
};
expectedData.Add("MZ20160603PPS_edta_000004", file4Data);
var dataFolder = GetBrukerDataFolder(dotDFolderName);
using (var reader = new MSDataFileReader(dataFolder.FullName))
{
Console.WriteLine("Scan info for {0}", dataFolder.Name);
Console.WriteLine("{0} {1} {2} {3} {4} {5} {6} {7} {8} {9} {10} {11} {12} {13} {14} {15}",
"Scan", "MSLevel",
"NumPeaks", "RetentionTime",
"ScanStartTime",
"DriftTimeMsec",
"LowMass", "HighMass", "TotalIonCurrent",
"BasePeakMZ", "BasePeakIntensity",
"ParentIonMZ", "ActivationType",
"IonMode", "IsCentroided",
"IsolationMZ");
var scanNumberToIndexMap = reader.GetScanToIndexMapping();
var scanCountMS1 = 0;
var scanCountMS2 = 0;
foreach (var scan in scanNumberToIndexMap.Where(x => x.Key >= scanStart && x.Key <= scanEnd))
{
var scanNumber = scan.Key;
var spectrumIndex = scan.Value;
var spectrum = reader.GetSpectrum(spectrumIndex, true);
var spectrumParams = reader.GetSpectrumCVParamData(spectrumIndex);
var cvScanInfo = reader.GetSpectrumScanInfo(spectrumIndex);
Assert.IsTrue(spectrum != null, "GetSpectrum returned a null object for scan " + scanNumber);
var totalIonCurrent = cvParamUtilities.GetCvParamValueDbl(spectrumParams, cvParamUtilities.CVIDs.MS_TIC);
var basePeakMZ = cvParamUtilities.GetCvParamValueDbl(spectrumParams, cvParamUtilities.CVIDs.MS_base_peak_m_z);
var basePeakIntensity = cvParamUtilities.GetCvParamValueDbl(spectrumParams, cvParamUtilities.CVIDs.MS_base_peak_intensity);
double isolationMZ = 0;
double parentIonMZ = 0;
var activationType = string.Empty;
if (spectrum.Precursors.Length > 0)
{
var precursor = spectrum.Precursors[0];
isolationMZ = precursor.IsolationMz.GetValueOrDefault();
parentIonMZ = precursor.PrecursorMz.GetValueOrDefault();
if (precursor.ActivationTypes != null)
{
activationType = string.Join(", ", precursor.ActivationTypes);
}
}
GetScanMetadata(cvScanInfo, out var scanStartTime, out var lowMass, out var highMass);
var retentionTime = cvParamUtilities.CheckNull(spectrum.RetentionTime);
var numPeaks = spectrum.Mzs.Length;
var ionMode = spectrum.NegativeCharge ? "negative" : "positive";
var scanSummary =
string.Format(
"{0} {1} {2,5} {3,6:0.00} {4,6:0.00} {5:0} {6,3:0} {7,5:0} {8,6:0.0E+0} {9,8:0.000} {10,6:0.0E+0} {11,8:0.00} {12,-8} {13} {14,-5} {15,8:0.00}",
scanNumber, spectrum.Level,
numPeaks, retentionTime, scanStartTime,
cvParamUtilities.CheckNull(spectrum.DriftTimeMsec),
lowMass, highMass,
totalIonCurrent,
basePeakMZ, basePeakIntensity, parentIonMZ,
activationType,
ionMode, spectrum.Centroided, isolationMZ);
Console.WriteLine(scanSummary);
if (spectrum.Level > 1)
{
scanCountMS2++;
}
else
{
scanCountMS1++;
}
if (!expectedData.TryGetValue(Path.GetFileNameWithoutExtension(dataFolder.Name), out var expectedDataThisFile))
{
Assert.Fail("Dataset {0} not found in dictionary expectedData", dataFolder.Name);
}
if (expectedDataThisFile.TryGetValue(scanNumber, out var expectedScanSummary))
{
Assert.AreEqual(expectedScanSummary, scanSummary,
"Scan summary mismatch, scan " + scanNumber);
}
var expectedNativeId = string.Format("scan={0}", scanNumber);
Assert.AreEqual(spectrum.NativeId, expectedNativeId, "NativeId is not in the expected format for scan {0}", scanNumber);
}
Console.WriteLine("scanCountMS1={0}", scanCountMS1);
Console.WriteLine("scanCountMS2={0}", scanCountMS2);
Assert.AreEqual(expectedMS1, scanCountMS1, "MS1 scan count mismatch");
Assert.AreEqual(expectedMS2, scanCountMS2, "MS2 scan count mismatch");
}
}
public void TestCorruptDataHandling(
string uimfFileName,
int frameStart,
int frameEnd,
int expectedMS1,
int expectedMS2,
int expectedScansWithData)
{
var dataFile = GetUimfDataFile(uimfFileName);
try
{
using (var reader = new MSDataFileReader(dataFile.FullName))
{
var scanCount = reader.SpectrumCount;
Console.WriteLine("Scan count for {0}: {1}", dataFile.Name, scanCount);
if (expectedMS1 + expectedMS2 == 0)
{
Assert.IsTrue(scanCount == 0, "ScanCount is non-zero, while we expected it to be 0");
}
else
{
Assert.IsTrue(scanCount > 0, "ScanCount is zero, while we expected it to be > 0");
}
var frameScanPairToIndexMap = reader.GetUimfFrameScanPairToIndexMapping();
var scanCountMS1 = 0;
var scanCountMS2 = 0;
var scansWithData = 0;
foreach (var frame in frameScanPairToIndexMap)
{
var frameNumber = frame.Key.Key;
var scanNumber = frame.Key.Value;
var spectrumIndex = frame.Value;
if (frameNumber < frameStart || frameNumber > frameEnd)
{
continue;
}
try
{
var spectrum = reader.GetSpectrum(spectrumIndex, true);
var cvScanInfo = reader.GetSpectrumScanInfo(spectrumIndex);
Assert.IsTrue(cvScanInfo != null, "GetSpectrumScanInfo returned a null object for frame {0}, scan {1} ", frameNumber, scanNumber);
if (spectrum.Level > 1)
{
scanCountMS2++;
}
else
{
scanCountMS1++;
}
var dataPointCount = spectrum.Mzs.Length;
if (dataPointCount > 0)
{
scansWithData++;
}
Assert.IsTrue(spectrum.Mzs.Length == spectrum.Intensities.Length, "Array length mismatch for m/z and intensity data for frame {0}, scan {1} ", frameNumber, scanNumber);
}
catch (Exception ex)
{
Console.WriteLine("Exception reading scan {0}: {1}", scanNumber, ex.Message);
Assert.Fail("Exception reading scan {0}", scanNumber);
}
}
Console.WriteLine("scanCountMS1={0}", scanCountMS1);
Console.WriteLine("scanCountMS2={0}", scanCountMS2);
Console.WriteLine("scansWithData={0}", scansWithData);
Assert.AreEqual(expectedMS1, scanCountMS1, "MS1 scan count mismatch");
Assert.AreEqual(expectedMS2, scanCountMS2, "MS2 scan count mismatch");
Assert.AreEqual(expectedScansWithData, scansWithData, "ScansWithData count mismatch");
}
}
catch (Exception ex)
{
if (expectedMS1 + expectedMS2 == 0)
{
Console.WriteLine("Error opening .uimf file (this was expected):\n{0}", ex.Message);
}
else
{
var msg = string.Format("Exception opening .uimf file {0}:\n{1}", uimfFileName, ex.Message);
Console.WriteLine(msg);
Assert.Fail(msg);
}
}
}
