public void TestGetScanCountsByScanType(
string uimfFileName,
int frameStart,
int frameEnd,
int expectedMS1,
int expectedMS2,
int expectedTotalScanCount)
{
var dataFile = GetUimfDataFile(uimfFileName);
using (var reader = new MSDataFileReader(dataFile.FullName))
{
Console.WriteLine("Parsing scan headers for {0}", dataFile.Name);
var scanCount = reader.SpectrumCount;
Console.WriteLine("Total scans: {0}", scanCount);
Assert.AreEqual(expectedTotalScanCount, scanCount, "Total scan count mismatch");
Console.WriteLine();
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;
}
var spectrum = reader.GetSpectrum(spectrumIndex, false);
if (spectrum.Level > 1)
{
scanCountMS2++;
}
else
{
scanCountMS1++;
}
}
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 TestGetScanData(string uimfFileName, int frameStart, int frameEnd)
{
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>
{
{ new KeyValuePair <int, int>(21, 1), " 21 1 171 171 73.143 0 4313.446 6" },
{ new KeyValuePair <int, int>(21, 45), " 21 45 132 132 49.420 0 2871.914 0" },
{ new KeyValuePair <int, int>(21, 90), " 21 90 58061 58061 33.139 0 892.171 0" },
{ new KeyValuePair <int, int>(21, 135), " 21 135 1332 1332 59.655 0 1455.314 0" },
{ new KeyValuePair <int, int>(21, 180), " 21 180 213 213 35.827 0 3477.878 16" },
{ new KeyValuePair <int, int>(21, 225), " 21 225 198 198 34.311 0 4724.490 0" },
{ new KeyValuePair <int, int>(21, 270), " 21 270 156 156 137.671 0 4960.353 0" },
{ new KeyValuePair <int, int>(22, 1), " 22 1 171 171 33.352 0 2700.500 2" },
{ new KeyValuePair <int, int>(22, 45), " 22 45 123 123 60.048 0 2958.660 2" },
{ new KeyValuePair <int, int>(22, 90), " 22 90 57811 57811 33.519 0 893.895 0" },
{ new KeyValuePair <int, int>(22, 135), " 22 135 1558 1558 33.800 0 1442.189 141" },
{ new KeyValuePair <int, int>(22, 180), " 22 180 165 165 104.876 0 2716.046 4" },
{ new KeyValuePair <int, int>(22, 225), " 22 225 165 165 49.372 0 5356.743 8" },
{ new KeyValuePair <int, int>(22, 270), " 22 270 168 168 41.214 0 3317.148 0" },
{ new KeyValuePair <int, int>(23, 1), " 23 1 159 159 44.206 0 2656.092 1" },
{ new KeyValuePair <int, int>(23, 45), " 23 45 179 179 66.354 0 4174.595 0" },
{ new KeyValuePair <int, int>(23, 90), " 23 90 59421 59421 33.319 0 901.566 17" },
{ new KeyValuePair <int, int>(23, 135), " 23 135 1398 1398 36.437 0 1429.296 0" },
{ new KeyValuePair <int, int>(23, 180), " 23 180 228 228 124.690 0 2244.101 0" },
{ new KeyValuePair <int, int>(23, 225), " 23 225 186 186 35.140 0 2326.136 0" },
{ new KeyValuePair <int, int>(23, 270), " 23 270 162 162 134.804 0 4518.062 0" }
};
expectedData.Add("9_Peptide_Mix_16Oct14_Cedar_Infuse", file1Data);
var file2Data = new Dictionary <KeyValuePair <int, int>, string>
{
{ new KeyValuePair <int, int>(50, 90), " 50 90 304 304 166.939 0 316.855 71" },
{ new KeyValuePair <int, int>(50, 135), " 50 135 36 36 479.959 0 532.950 0" },
{ new KeyValuePair <int, int>(51, 90), " 51 90 516 516 166.939 0 320.853 0" },
{ new KeyValuePair <int, int>(51, 135), " 51 135 27 27 474.824 0 532.934 38" },
{ new KeyValuePair <int, int>(51, 315), " 51 315 3 3 250.922 0 250.922 58" },
{ new KeyValuePair <int, int>(52, 90), " 52 90 579 579 166.939 0 319.857 61" },
{ new KeyValuePair <int, int>(52, 135), " 52 135 30 30 479.959 0 532.934 0" },
{ new KeyValuePair <int, int>(52, 315), " 52 315 3 3 250.922 0 250.922 67" },
{ new KeyValuePair <int, int>(53, 90), " 53 90 625 625 164.932 0 321.351 0" },
{ new KeyValuePair <int, int>(53, 135), " 53 135 39 39 391.282 0 532.934 47" },
{ new KeyValuePair <int, int>(54, 90), " 54 90 456 456 164.941 0 318.876 0" },
{ new KeyValuePair <int, int>(54, 135), " 54 135 33 33 391.282 0 530.978 17" },
{ new KeyValuePair <int, int>(55, 90), " 55 90 467 467 164.932 0 318.888 0" },
{ new KeyValuePair <int, int>(55, 135), " 55 135 24 24 479.959 0 532.950 0" }
};
expectedData.Add("QC_Shew_IMER_500ng_Run-1_4May16_Oak_15-01-16", file2Data);
var dataFile = GetUimfDataFile(uimfFileName);
using (var reader = new MSDataFileReader(dataFile.FullName))
{
Console.WriteLine("Scan data for {0}", dataFile.Name);
Console.WriteLine("{0,4} {1,4} {2,-8} {3,-8} {4,-8} {5,-8} {6,-8} {7}",
"Frame", "Scan", "MzCount", "IntCount",
"FirstMz", "FirstInt", "MidMz", "MidInt");
var frameScanPairToIndexMap = reader.GetUimfFrameScanPairToIndexMapping();
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 (!(scanNumber == 1 || scanNumber % 45 == 0))
{
continue;
}
var spectrum = reader.GetSpectrum(spectrumIndex, true);
var dataPointsRead = spectrum.Mzs.Length;
if (dataPointsRead == 0)
{
Console.WriteLine("Frame {0}, scan {1} has no data; ignoring", frameNumber, scanNumber);
continue;
}
var midPoint = (int)(spectrum.Intensities.Length / 2f);
var scanSummary =
string.Format(
"{0,4} {1,4} {2,-8} {3,-8} {4,-8:0.000} {5,-8:0} {6,-8:0.000} {7:0}",
frameNumber, scanNumber,
spectrum.Mzs.Length, spectrum.Intensities.Length,
spectrum.Mzs[0], spectrum.Intensities[0],
spectrum.Mzs[midPoint], spectrum.Intensities[midPoint]);
Console.WriteLine(scanSummary);
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 expectedDataDetails))
{
Assert.AreEqual(expectedDataDetails, scanSummary,
"Scan details mismatch, scan " + scanNumber);
}
}
}
}
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 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);
}
}
}
