public void tempGetMSMSDataTest2()
{
var reader = new ThermoRawFileReader.XRawFileIO(FileRefs.RawDataMSFiles.OrbitrapStdFile1);
var startScan = 6000;
var stopScan = 7000;
for (var i = startScan; i < stopScan; i++)
{
ThermoRawFileReader.clsScanInfo scanInfo;
var success = reader.GetScanInfo(i, out scanInfo);
Console.Write("Working on Scan " + i);
Console.WriteLine("; Scan info = " + scanInfo.ToString());
}
}
public void TestGetScanDataSumScans(string rawFileName, int scanStart, int scanEnd)
{
var expectedData = new Dictionary<string, Dictionary<int, Dictionary<string, string>>>();
// Keys in this dictionary are the start scan for summing
var file1Data = new Dictionary<int, Dictionary<string, string>>
{
{1513, new Dictionary<string, string>()}
};
// The KeySpec for each dictionary entry is MaxDataCount_Centroid
file1Data[1513].Add("0_False", "1390 409.769 2.7E+5 1241.231 4.0E+5 + c ESI Full ms [400.00-2000.00]");
file1Data[1513].Add("0_True", "1390 409.769 2.7E+5 1241.231 4.0E+5 + c ESI Full ms [400.00-2000.00]");
file1Data[1513].Add("50_False", " 50 883.357 5.5E+6 1213.223 2.0E+6 + c ESI Full ms [400.00-2000.00]");
file1Data[1513].Add("50_True", " 50 883.357 5.5E+6 1213.223 2.0E+6 + c ESI Full ms [400.00-2000.00]");
expectedData.Add("Shew_246a_LCQa_15Oct04_Andro_0904-2_4-20", file1Data);
var file2Data = new Dictionary<int, Dictionary<string, string>>
{
{16121, new Dictionary<string, string>()}
};
// The KeySpec for each dictionary entry is MaxDataCount_Centroid
file2Data[16121].Add("0_False", "26057 346.518 0.0E+0 753.312 8.7E+0 FTMS + p NSI Full ms [350.0000-1550.0000]");
file2Data[16121].Add("0_True", " 818 351.230 3.2E+5 820.778 2.3E+5 FTMS + p NSI Full ms [350.0000-1550.0000]");
file2Data[16121].Add("50_False", " 50 503.553 1.2E+7 521.201 1.6E+7 FTMS + p NSI Full ms [350.0000-1550.0000]");
file2Data[16121].Add("50_True", " 50 371.885 2.6E+7 650.717 9.8E+6 FTMS + p NSI Full ms [350.0000-1550.0000]");
expectedData.Add("HCC-38_ETciD_EThcD_4xdil_20uL_3hr_3_08Jan16_Pippin_15-08-53", file2Data);
var dataFile = GetRawDataFile(rawFileName);
using (var reader = new XRawFileIO(dataFile.FullName))
{
Console.WriteLine("Scan data for {0}", dataFile.Name);
Console.WriteLine("{0} {1,3} {2,8} {3,-8} {4,-8} {5,-8} {6,-8} {7,-8} {8}",
"Scan", "Max#", "Centroid", "DataCount",
"FirstMz", "FirstInt", "MidMz", "MidInt", "ScanFilter");
for (var iteration = 1; iteration <= 4; iteration++)
{
int maxNumberOfPeaks;
bool centroidData;
switch (iteration)
{
case 1:
maxNumberOfPeaks = 0;
centroidData = false;
break;
case 2:
maxNumberOfPeaks = 0;
centroidData = true;
break;
case 3:
maxNumberOfPeaks = 50;
centroidData = false;
break;
default:
maxNumberOfPeaks = 50;
centroidData = true;
break;
}
double[,] massIntensityPairs;
var dataPointsRead = reader.GetScanDataSumScans(scanStart, scanEnd, out massIntensityPairs, maxNumberOfPeaks, centroidData);
Assert.IsTrue(dataPointsRead > 0, string.Format("GetScanDataSumScans returned 0 summing scans {0} to {1}", scanStart, scanEnd));
clsScanInfo scanInfo;
var success = reader.GetScanInfo(scanStart, out scanInfo);
Assert.IsTrue(success, "GetScanInfo returned false for scan {0}", scanStart);
var lastIndex = massIntensityPairs.GetUpperBound(1);
int dataCount;
if (maxNumberOfPeaks > 0)
{
dataCount = maxNumberOfPeaks;
// Make sure the 2D array has values of 0 for mass and intensity beyond index maxNumberOfPeaks
for (var dataIndex = maxNumberOfPeaks; dataIndex < lastIndex; dataIndex++)
{
if (massIntensityPairs[0, dataIndex] > 0)
{
Console.WriteLine("Non-zero m/z value found at index {0} for scan {1}", dataIndex, scanStart);
Assert.AreEqual(0, massIntensityPairs[0, dataIndex], "Non-zero m/z value found in 2D array beyond expected index");
}
if (massIntensityPairs[1, dataIndex] > 0)
{
Console.WriteLine("Non-zero intensity value found at index {0} for scan {1}", dataIndex, scanStart);
Assert.AreEqual(0, massIntensityPairs[1, dataIndex], "Non-zero intensity value found in 2D array beyond expected index");
}
}
}
else
{
dataCount = lastIndex + 1;
}
Assert.AreEqual(dataPointsRead, dataCount, "Data count mismatch vs. function return value");
var midPoint = (int)(dataCount / 2f);
var scanSummary =
string.Format(
"{0} {1,3} {2,8} {3,8} {4,8} {5,8} {6,8} {7,8} {8}",
scanStart, maxNumberOfPeaks, centroidData,
dataCount,
massIntensityPairs[0, 0].ToString("0.000"), massIntensityPairs[1, 0].ToString("0.0E+0"),
massIntensityPairs[0, midPoint].ToString("0.000"), massIntensityPairs[1, midPoint].ToString("0.0E+0"),
scanInfo.FilterText);
Dictionary<int, Dictionary<string, string>> expectedDataThisFile;
if (!expectedData.TryGetValue(Path.GetFileNameWithoutExtension(dataFile.Name), out expectedDataThisFile))
{
Assert.Fail("Dataset {0} not found in dictionary expectedData", dataFile.Name);
}
Dictionary<string, string> expectedDataByType;
if (expectedDataThisFile.TryGetValue(scanStart, out expectedDataByType))
{
var keySpec = maxNumberOfPeaks + "_" + centroidData;
string expectedDataDetails;
if (expectedDataByType.TryGetValue(keySpec, out expectedDataDetails))
{
Assert.AreEqual(expectedDataDetails, scanSummary.Substring(22),
"Scan details mismatch, scan " + scanStart + ", keySpec " + keySpec);
}
}
Console.WriteLine(scanSummary);
}
}
}
public void TestGetScanInfo(string rawFileName, 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>
{
{1513, "1 1 851 44.57 400 2000 6.3E+8 1089.978 1.2E+7 0.00 CID Positive True False 11 79 1.50 + c ESI Full..."},
{1514, "2 2 109 44.60 230 1780 5.0E+6 528.128 7.2E+5 884.41 CID cid Positive True False 11 79 28.96 + c d Full m..."},
{1515, "2 3 290 44.63 305 2000 2.6E+7 1327.414 6.0E+6 1147.67 CID cid Positive True False 11 79 14.13 + c d Full m..."},
{1516, "2 4 154 44.66 400 2000 7.6E+5 1251.554 3.7E+4 1492.90 CID cid Positive True False 11 79 123.30 + c d Full m..."},
{1517, "1 1 887 44.69 400 2000 8.0E+8 1147.613 1.0E+7 0.00 CID Positive True False 11 79 1.41 + c ESI Full..."},
{1518, "2 2 190 44.71 380 2000 4.6E+6 1844.618 2.7E+5 1421.21 CID cid Positive True False 11 79 40.91 + c d Full m..."},
{1519, "2 3 165 44.74 380 2000 6.0E+6 1842.547 6.9E+5 1419.24 CID cid Positive True False 11 79 37.84 + c d Full m..."},
{1520, "2 4 210 44.77 265 2000 1.5E+6 1361.745 4.2E+4 1014.93 CID cid Positive True False 11 79 96.14 + c d Full m..."},
{1521, "1 1 860 44.80 400 2000 6.9E+8 1126.627 2.9E+7 0.00 CID Positive True False 11 79 1.45 + c ESI Full..."}
};
expectedData.Add("Shew_246a_LCQa_15Oct04_Andro_0904-2_4-20", file1Data);
// Note that for this dataset NumPeaks does not accurately reflect the number of data in each mass spectrum (it's much higher than it should be)
// For example, scan 16121 has NumPeaks = 45876, but TestGetScanData() correctly finds 11888 data points for that scan
var file2Data = new Dictionary<int, string>
{
{16121, "1 1 45876 47.68 350 1550 1.9E+9 503.565 3.4E+8 0.00 CID Positive False True 46 219 0.44 FTMS + p NSI..."},
{16122, "2 2 4124 47.68 106 817 1.6E+6 550.309 2.1E+5 403.22 CID cid Positive True False 46 219 11.82 ITMS + c NSI..."},
{16123, "2 2 6484 47.68 143 1627 5.5E+5 506.272 4.9E+4 538.84 CID cid Positive True False 46 219 26.07 ITMS + c NSI..."},
{16124, "2 2 8172 47.68 208 2000 7.8E+5 737.530 7.0E+4 776.27 CID cid Positive True False 46 219 24.65 ITMS + c NSI..."},
{16125, "2 2 5828 47.68 120 1627 2.1E+5 808.486 2.2E+4 538.84 ETD etd Positive True False 46 219 42.48 ITMS + c NSI..."},
{16126, "2 2 6228 47.68 120 1627 1.4E+5 536.209 9.0E+3 538.84 ETD ETciD Positive True False 46 219 58.96 ITMS + c NSI..."},
{16127, "2 2 7180 47.68 120 1627 1.3E+5 808.487 1.4E+4 538.84 ETD EThcD Positive True False 46 219 58.96 ITMS + c NSI..."},
{16128, "2 2 7980 47.69 225 1682 4.4E+5 805.579 2.3E+4 835.88 CID cid Positive True False 46 219 42.71 ITMS + c NSI..."},
{16129, "2 2 7700 47.69 266 1986 3.4E+5 938.679 2.9E+4 987.89 CID cid Positive True False 46 219 35.75 ITMS + c NSI..."},
{16130, "2 2 5180 47.69 110 853 2.7E+5 411.977 1.2E+4 421.26 CID cid Positive True False 46 219 50.98 ITMS + c NSI..."},
{16131, "2 2 436 47.69 120 1986 2.1E+4 984.504 9.5E+3 987.89 ETD etd Positive True False 46 219 26.55 ITMS + c NSI..."},
{16132, "2 2 2116 47.69 120 853 1.2E+4 421.052 6.8E+2 421.26 ETD etd Positive True False 46 219 127.21 ITMS + c NSI..."},
{16133, "2 2 2444 47.70 120 853 1.5E+4 421.232 1.2E+3 421.26 ETD ETciD Positive True False 46 219 110.22 ITMS + c NSI..."},
{16134, "2 2 2948 47.70 120 853 1.4E+4 838.487 7.5E+2 421.26 ETD EThcD Positive True False 46 219 110.22 ITMS + c NSI..."},
{16135, "2 2 508 47.70 120 1986 2.1E+4 984.498 9.2E+3 987.89 ETD ETciD Positive True False 46 219 31.82 ITMS + c NSI..."},
{16136, "2 2 948 47.71 120 1986 2.3E+4 984.491 9.4E+3 987.89 ETD EThcD Positive True False 46 219 31.82 ITMS + c NSI..."},
{16137, "2 2 9580 47.71 336 2000 3.5E+5 1536.038 4.7E+3 1241.01 CID cid Positive True False 46 219 30.70 ITMS + c NSI..."},
{16138, "2 2 7604 47.72 235 1760 2.9E+5 826.095 2.5E+4 874.84 CID cid Positive True False 46 219 40.56 ITMS + c NSI..."},
{16139, "2 2 972 47.72 120 1760 1.6E+4 875.506 2.1E+3 874.84 ETD etd Positive True False 46 219 45.88 ITMS + c NSI..."},
{16140, "2 2 1596 47.72 120 1760 1.8E+4 1749.846 2.0E+3 874.84 ETD ETciD Positive True False 46 219 54.15 ITMS + c NSI..."},
{16141, "2 2 2124 47.72 120 1760 1.6E+4 874.664 1.6E+3 874.84 ETD EThcD Positive True False 46 219 54.15 ITMS + c NSI..."},
{16142, "1 1 51976 47.73 350 1550 1.3E+9 503.565 1.9E+8 0.00 CID Positive False True 46 219 0.79 FTMS + p NSI..."},
{16143, "2 2 5412 47.73 128 981 6.5E+5 444.288 6.4E+4 485.28 CID cid Positive True False 46 219 22.26 ITMS + c NSI..."},
{16144, "2 2 4300 47.73 101 1561 5.0E+5 591.309 4.0E+4 387.66 CID cid Positive True False 46 219 28.20 ITMS + c NSI..."},
{16145, "2 2 6740 47.73 162 1830 4.0E+5 567.912 2.8E+4 606.62 CID cid Positive True False 46 219 37.30 ITMS + c NSI..."},
{16146, "2 2 4788 47.73 99 770 1.9E+5 532.308 3.4E+4 379.72 CID cid Positive True False 46 219 100.00 ITMS + c NSI..."},
{16147, "2 2 6708 47.74 120 1830 3.8E+5 603.095 3.1E+4 606.62 ETD etd Positive True False 46 219 25.47 ITMS + c NSI..."},
{16148, "2 2 7260 47.74 120 1830 1.5E+5 603.076 1.3E+4 606.62 ETD ETciD Positive True False 46 219 61.48 ITMS + c NSI..."},
{16149, "2 2 9172 47.74 120 1830 1.6E+5 603.027 1.1E+4 606.62 ETD EThcD Positive True False 46 219 61.48 ITMS + c NSI..."},
{16150, "2 2 5204 47.74 95 1108 3.8E+5 418.536 1.2E+5 365.88 CID cid Positive True False 46 219 134.71 ITMS + c NSI..."},
{16151, "2 2 5636 47.75 146 1656 2.8E+5 501.523 4.3E+4 548.54 CID cid Positive True False 46 219 30.60 ITMS + c NSI..."},
{16152, "2 2 9572 47.75 328 2000 1.8E+5 848.497 2.2E+3 1210.30 CID cid Positive True False 46 219 38.05 ITMS + c NSI..."},
{16153, "2 2 5004 47.75 120 1656 1.3E+5 548.396 1.3E+4 548.54 ETD etd Positive True False 46 219 50.35 ITMS + c NSI..."},
{16154, "2 2 4732 47.75 120 1656 4.2E+4 548.450 4.2E+3 548.54 ETD ETciD Positive True False 46 219 122.26 ITMS + c NSI..."},
{16155, "2 2 6228 47.76 120 1656 4.2E+4 550.402 3.6E+3 548.54 ETD EThcD Positive True False 46 219 122.26 ITMS + c NSI..."},
{16156, "2 2 9164 47.76 324 2000 1.5E+5 1491.872 1.0E+4 1197.57 CID cid Positive True False 46 219 63.61 ITMS + c NSI..."},
{16157, "2 2 5916 47.76 124 950 2.2E+5 420.689 2.2E+4 469.71 CID cid Positive True False 46 219 100.00 ITMS + c NSI..."},
{16158, "2 2 5740 47.76 306 2000 1.3E+5 1100.042 3.5E+3 1132.02 CID cid Positive True False 46 219 27.79 ITMS + c NSI..."},
{16159, "2 2 5540 47.76 122 935 1.9E+5 445.117 2.7E+4 462.15 CID cid Positive True False 46 219 69.09 ITMS + c NSI..."},
{16160, "2 2 5756 47.77 145 1646 3.4E+5 539.065 6.0E+4 545.18 CID cid Positive True False 46 219 28.97 ITMS + c NSI..."},
{16161, "2 2 6100 47.77 157 1191 2.8E+5 541.462 6.0E+4 590.28 CID cid Positive True False 46 219 37.92 ITMS + c NSI..."},
{16162, "2 2 2508 47.77 120 1191 8.4E+4 1180.615 5.1E+3 590.28 ETD etd Positive True False 46 219 38.31 ITMS + c NSI..."},
{16163, "2 2 2644 47.77 120 1191 1.8E+4 1184.614 9.0E+2 590.28 ETD ETciD Positive True False 46 219 109.20 ITMS + c NSI..."},
{16164, "2 2 3180 47.77 120 1191 1.7E+4 1184.644 8.7E+2 590.28 ETD EThcD Positive True False 46 219 109.20 ITMS + c NSI..."},
{16165, "1 1 53252 47.78 350 1550 1.2E+9 503.565 1.6E+8 0.00 CID Positive False True 46 219 0.76 FTMS + p NSI..."}
};
expectedData.Add("HCC-38_ETciD_EThcD_4xdil_20uL_3hr_3_08Jan16_Pippin_15-08-53", file2Data);
var dataFile = GetRawDataFile(rawFileName);
using (var reader = new XRawFileIO(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} {18} {19}",
"Scan", "MSLevel", "Event",
"NumPeaks", "RetentionTime",
"LowMass", "HighMass", "TotalIonCurrent",
"BasePeakMZ", "BasePeakIntensity",
"ParentIonMZ", "ActivationType", "CollisionMode",
"IonMode", "IsCentroided", "IsFTMS",
"ScanEvents.Count", "StatusLog.Count",
"IonInjectionTime" ,"FilterText");
var scanCountMS1 = 0;
var scanCountMS2 = 0;
for (var scanNumber = scanStart; scanNumber <= scanEnd; scanNumber++)
{
clsScanInfo scanInfo;
var success = reader.GetScanInfo(scanNumber, out scanInfo);
Assert.IsTrue(success, "GetScanInfo returned false for scan {0}", scanNumber);
string injectionTimeText;
double ionInjectionTime;
if (scanInfo.TryGetScanEvent("Ion Injection Time (ms)", out injectionTimeText, true))
{
double.TryParse(injectionTimeText, out ionInjectionTime);
}
else
{
ionInjectionTime = 0;
}
var scanSummary =
string.Format(
"{0} {1} {2} {3,5} {4} {5,3} {6,4} {7} {8,8} {9} {10,8} {11} {12,5} {13} {14} {15} {16} {17} {18,6} {19}",
scanInfo.ScanNumber, scanInfo.MSLevel, scanInfo.EventNumber,
scanInfo.NumPeaks, scanInfo.RetentionTime.ToString("0.00"),
scanInfo.LowMass.ToString("0"), scanInfo.HighMass.ToString("0"),
scanInfo.TotalIonCurrent.ToString("0.0E+0"), scanInfo.BasePeakMZ.ToString("0.000"),
scanInfo.BasePeakIntensity.ToString("0.0E+0"), scanInfo.ParentIonMZ.ToString("0.00"),
scanInfo.ActivationType, scanInfo.CollisionMode,
scanInfo.IonMode, scanInfo.IsCentroided,
scanInfo.IsFTMS, scanInfo.ScanEvents.Count, scanInfo.StatusLog.Count,
ionInjectionTime.ToString("0.00"),
scanInfo.FilterText.Substring(0, 12) + "...");
Console.WriteLine(scanSummary);
if (scanInfo.MSLevel > 1)
scanCountMS2++;
else
scanCountMS1++;
Dictionary<int, string> expectedDataThisFile;
if (!expectedData.TryGetValue(Path.GetFileNameWithoutExtension(dataFile.Name), out expectedDataThisFile))
{
Assert.Fail("Dataset {0} not found in dictionary expectedData", dataFile.Name);
}
string expectedScanSummary;
if (expectedDataThisFile.TryGetValue(scanNumber, out expectedScanSummary))
{
Assert.AreEqual(scanNumber + " " + expectedScanSummary, scanSummary,
"Scan summary mismatch, scan " + 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 TestGetScanData(string rawFileName, int scanStart, int scanEnd)
{
var expectedData = new Dictionary<string, Dictionary<int, Dictionary<string, string>>>();
// Keys in this dictionary are the scan number of data being retrieved
var file1Data = new Dictionary<int, Dictionary<string, string>>
{
{1513, new Dictionary<string, string>()},
{1514, new Dictionary<string, string>()},
{1515, new Dictionary<string, string>()},
{1516, new Dictionary<string, string>()},
{1517, new Dictionary<string, string>()}
};
// The KeySpec for each dictionary entry is MaxDataCount_Centroid
file1Data[1513].Add("0_False", " 851 851 409.615 4.8E+5 1227.956 1.6E+6 + c ESI Full ms [400.00-2000.00]");
file1Data[1514].Add("0_False", " 109 109 281.601 2.4E+4 633.151 4.4E+4 + c d Full ms2 [email protected] [230.00-1780.00]");
file1Data[1515].Add("0_False", " 290 290 335.798 3.8E+4 1034.194 1.6E+4 + c d Full ms2 [email protected] [305.00-2000.00]");
file1Data[1516].Add("0_False", " 154 154 461.889 7.3E+3 1203.274 2.6E+3 + c d Full ms2 [email protected] [400.00-2000.00]");
file1Data[1517].Add("0_False", " 887 887 420.016 9.7E+5 1232.206 8.0E+5 + c ESI Full ms [400.00-2000.00]");
file1Data[1513].Add("0_True", " 851 851 409.615 4.8E+5 1227.956 1.6E+6 + c ESI Full ms [400.00-2000.00]");
file1Data[1514].Add("0_True", " 109 109 281.601 2.4E+4 633.151 4.4E+4 + c d Full ms2 [email protected] [230.00-1780.00]");
file1Data[1515].Add("0_True", " 290 290 335.798 3.8E+4 1034.194 1.6E+4 + c d Full ms2 [email protected] [305.00-2000.00]");
file1Data[1516].Add("0_True", " 154 154 461.889 7.3E+3 1203.274 2.6E+3 + c d Full ms2 [email protected] [400.00-2000.00]");
file1Data[1517].Add("0_True", " 887 887 420.016 9.7E+5 1232.206 8.0E+5 + c ESI Full ms [400.00-2000.00]");
file1Data[1513].Add("50_False", " 50 50 747.055 2.5E+6 1148.485 3.4E+6 + c ESI Full ms [400.00-2000.00]");
file1Data[1514].Add("50_False", " 50 50 281.601 2.4E+4 632.089 2.6E+4 + c d Full ms2 [email protected] [230.00-1780.00]");
file1Data[1515].Add("50_False", " 50 50 353.590 9.7E+4 1157.949 3.6E+5 + c d Full ms2 [email protected] [305.00-2000.00]");
file1Data[1516].Add("50_False", " 50 50 461.889 7.3E+3 1146.341 1.4E+4 + c d Full ms2 [email protected] [400.00-2000.00]");
file1Data[1517].Add("50_False", " 50 50 883.347 8.9E+6 1206.792 5.5E+6 + c ESI Full ms [400.00-2000.00]");
file1Data[1513].Add("50_True", " 50 50 747.055 2.5E+6 1148.485 3.4E+6 + c ESI Full ms [400.00-2000.00]");
file1Data[1514].Add("50_True", " 50 50 281.601 2.4E+4 632.089 2.6E+4 + c d Full ms2 [email protected] [230.00-1780.00]");
file1Data[1515].Add("50_True", " 50 50 353.590 9.7E+4 1157.949 3.6E+5 + c d Full ms2 [email protected] [305.00-2000.00]");
file1Data[1516].Add("50_True", " 50 50 461.889 7.3E+3 1146.341 1.4E+4 + c d Full ms2 [email protected] [400.00-2000.00]");
file1Data[1517].Add("50_True", " 50 50 883.347 8.9E+6 1206.792 5.5E+6 + c ESI Full ms [400.00-2000.00]");
expectedData.Add("Shew_246a_LCQa_15Oct04_Andro_0904-2_4-20", file1Data);
var file2Data = new Dictionary<int, Dictionary<string, string>>
{
{16121, new Dictionary<string, string>()},
{16122, new Dictionary<string, string>()},
{16126, new Dictionary<string, string>()},
{16131, new Dictionary<string, string>()},
{16133, new Dictionary<string, string>()},
{16141, new Dictionary<string, string>()}
};
// The KeySpec for each dictionary entry is MaxDataCount_Centroid
file2Data[16121].Add("0_False", "11888 11888 346.518 0.0E+0 706.844 9.8E+4 FTMS + p NSI Full ms [350.0000-1550.0000]");
file2Data[16122].Add("0_False", " 490 490 116.232 7.0E+1 403.932 1.1E+3 ITMS + c NSI r d Full ms2 [email protected] [106.0000-817.0000]");
file2Data[16126].Add("0_False", " 753 753 231.045 1.1E+1 1004.586 2.0E+1 ITMS + c NSI r d sa Full ms2 [email protected]@cid20.00 [120.0000-1627.0000]");
file2Data[16131].Add("0_False", " 29 29 984.504 9.5E+3 1931.917 2.4E+1 ITMS + c NSI r d Full ms2 [email protected] [120.0000-1986.0000]");
file2Data[16133].Add("0_False", " 280 280 260.118 2.3E+1 663.160 7.7E+0 ITMS + c NSI r d sa Full ms2 [email protected]@cid20.00 [120.0000-853.0000]");
file2Data[16141].Add("0_False", " 240 240 304.425 1.3E+1 1447.649 3.0E+1 ITMS + c NSI r d sa Full ms2 [email protected]@hcd20.00 [120.0000-1760.0000]");
file2Data[16121].Add("0_True", " 833 833 351.231 2.9E+5 712.813 2.9E+5 FTMS + p NSI Full ms [350.0000-1550.0000]");
file2Data[16122].Add("0_True", " 490 490 116.232 7.0E+1 403.932 1.1E+3 ITMS + c NSI r d Full ms2 [email protected] [106.0000-817.0000]");
file2Data[16126].Add("0_True", " 753 753 231.045 1.1E+1 1004.586 2.0E+1 ITMS + c NSI r d sa Full ms2 [email protected]@cid20.00 [120.0000-1627.0000]");
file2Data[16131].Add("0_True", " 29 29 984.504 9.5E+3 1931.917 2.4E+1 ITMS + c NSI r d Full ms2 [email protected] [120.0000-1986.0000]");
file2Data[16133].Add("0_True", " 280 280 260.118 2.3E+1 663.160 7.7E+0 ITMS + c NSI r d sa Full ms2 [email protected]@cid20.00 [120.0000-853.0000]");
file2Data[16141].Add("0_True", " 240 240 304.425 1.3E+1 1447.649 3.0E+1 ITMS + c NSI r d sa Full ms2 [email protected]@hcd20.00 [120.0000-1760.0000]");
file2Data[16121].Add("50_False", " 50 50 503.553 2.0E+7 504.571 2.1E+7 FTMS + p NSI Full ms [350.0000-1550.0000]");
file2Data[16122].Add("50_False", " 50 50 157.049 2.0E+4 385.181 6.0E+3 ITMS + c NSI r d Full ms2 [email protected] [106.0000-817.0000]");
file2Data[16126].Add("50_False", " 50 50 535.311 2.5E+3 798.982 1.3E+3 ITMS + c NSI r d sa Full ms2 [email protected]@cid20.00 [120.0000-1627.0000]");
file2Data[16131].Add("50_False", " 29 29 984.504 9.5E+3 1931.917 2.4E+1 ITMS + c NSI r d Full ms2 [email protected] [120.0000-1986.0000]");
file2Data[16133].Add("50_False", " 50 50 356.206 7.5E+1 795.543 1.3E+2 ITMS + c NSI r d sa Full ms2 [email protected]@cid20.00 [120.0000-853.0000]");
file2Data[16141].Add("50_False", " 50 50 853.937 5.6E+1 1705.974 9.8E+1 ITMS + c NSI r d sa Full ms2 [email protected]@hcd20.00 [120.0000-1760.0000]");
file2Data[16121].Add("50_True", " 833 833 351.231 2.9E+5 712.813 2.9E+5 FTMS + p NSI Full ms [350.0000-1550.0000]");
file2Data[16122].Add("50_True", " 50 50 157.049 2.0E+4 385.181 6.0E+3 ITMS + c NSI r d Full ms2 [email protected] [106.0000-817.0000]");
file2Data[16126].Add("50_True", " 50 50 535.311 2.5E+3 798.982 1.3E+3 ITMS + c NSI r d sa Full ms2 [email protected]@cid20.00 [120.0000-1627.0000]");
file2Data[16131].Add("50_True", " 29 29 984.504 9.5E+3 1931.917 2.4E+1 ITMS + c NSI r d Full ms2 [email protected] [120.0000-1986.0000]");
file2Data[16133].Add("50_True", " 50 50 356.206 7.5E+1 795.543 1.3E+2 ITMS + c NSI r d sa Full ms2 [email protected]@cid20.00 [120.0000-853.0000]");
file2Data[16141].Add("50_True", " 50 50 853.937 5.6E+1 1705.974 9.8E+1 ITMS + c NSI r d sa Full ms2 [email protected]@hcd20.00 [120.0000-1760.0000]");
expectedData.Add("HCC-38_ETciD_EThcD_4xdil_20uL_3hr_3_08Jan16_Pippin_15-08-53", file2Data);
var dataFile = GetRawDataFile(rawFileName);
using (var reader = new XRawFileIO(dataFile.FullName))
{
for (var iteration = 1; iteration <= 4; iteration++)
{
int maxNumberOfPeaks;
bool centroidData;
switch (iteration)
{
case 1:
maxNumberOfPeaks = 0;
centroidData = false;
break;
case 2:
maxNumberOfPeaks = 0;
centroidData = true;
break;
case 3:
maxNumberOfPeaks = 50;
centroidData = false;
break;
default:
maxNumberOfPeaks = 50;
centroidData = true;
break;
}
if (iteration == 1)
{
Console.WriteLine("Scan data for {0}", dataFile.Name);
Console.WriteLine("{0} {1,3} {2,8} {3,-8} {4,-8} {5,-8} {6,-8} {7,-8} {8,-8} {9}",
"Scan", "Max#", "Centroid", "MzCount", "IntCount",
"FirstMz", "FirstInt", "MidMz", "MidInt", "ScanFilter");
}
for (var scanNumber = scanStart; scanNumber <= scanEnd; scanNumber++)
{
double[] mzList;
double[] intensityList;
var dataPointsRead = reader.GetScanData(scanNumber, out mzList, out intensityList, maxNumberOfPeaks, centroidData);
Assert.IsTrue(dataPointsRead > 0, "GetScanData returned 0 for scan {0}", scanNumber);
Assert.AreEqual(dataPointsRead, mzList.Length, "Data count mismatch vs. function return value");
var midPoint = (int)(intensityList.Length / 2f);
clsScanInfo scanInfo;
var success = reader.GetScanInfo(scanNumber, out scanInfo);
Assert.IsTrue(success, "GetScanInfo returned false for scan {0}", scanNumber);
var scanSummary =
string.Format(
"{0} {1,3} {2,8} {3,8} {4,8} {5,8} {6,8} {7,8} {8,8} {9}",
scanNumber, maxNumberOfPeaks, centroidData,
mzList.Length, intensityList.Length,
mzList[0].ToString("0.000"), intensityList[0].ToString("0.0E+0"),
mzList[midPoint].ToString("0.000"), intensityList[midPoint].ToString("0.0E+0"),
scanInfo.FilterText);
Console.WriteLine(scanSummary);
Dictionary<int, Dictionary<string, string>> expectedDataThisFile;
if (!expectedData.TryGetValue(Path.GetFileNameWithoutExtension(dataFile.Name), out expectedDataThisFile))
{
Assert.Fail("Dataset {0} not found in dictionary expectedData", dataFile.Name);
}
Dictionary<string, string> expectedDataByType;
if (expectedDataThisFile.TryGetValue(scanNumber, out expectedDataByType))
{
var keySpec = maxNumberOfPeaks + "_" + centroidData;
string expectedDataDetails;
if (expectedDataByType.TryGetValue(keySpec, out expectedDataDetails))
{
Assert.AreEqual(expectedDataDetails, scanSummary.Substring(22),
"Scan details mismatch, scan " + scanNumber + ", keySpec " + keySpec);
}
}
}
}
}
}
public void TestGetScanData2D(string rawFileName, int scanStart, int scanEnd)
{
var expectedData = new Dictionary<string, Dictionary<int, Dictionary<string, string>>>();
// Keys in this dictionary are the scan number of data being retrieved
var file1Data = new Dictionary<int, Dictionary<string, string>>
{
{1513, new Dictionary<string, string>()},
{1514, new Dictionary<string, string>()}
};
// The KeySpec for each dictionary entry is MaxDataCount_Centroid
file1Data[1513].Add("0_False", " 851 409.615 4.8E+5 1227.956 1.6E+6 + c ESI Full ms [400.00-2000.00]");
file1Data[1514].Add("0_False", " 109 281.601 2.4E+4 633.151 4.4E+4 + c d Full ms2 [email protected] [230.00-1780.00]");
file1Data[1513].Add("0_True", " 851 409.615 4.8E+5 1227.956 1.6E+6 + c ESI Full ms [400.00-2000.00]");
file1Data[1514].Add("0_True", " 109 281.601 2.4E+4 633.151 4.4E+4 + c d Full ms2 [email protected] [230.00-1780.00]");
file1Data[1513].Add("50_False", " 50 747.055 2.5E+6 1148.485 3.4E+6 + c ESI Full ms [400.00-2000.00]");
file1Data[1514].Add("50_False", " 50 281.601 2.4E+4 632.089 2.6E+4 + c d Full ms2 [email protected] [230.00-1780.00]");
file1Data[1513].Add("50_True", " 50 747.055 2.5E+6 1148.485 3.4E+6 + c ESI Full ms [400.00-2000.00]");
file1Data[1514].Add("50_True", " 50 281.601 2.4E+4 632.089 2.6E+4 + c d Full ms2 [email protected] [230.00-1780.00]");
expectedData.Add("Shew_246a_LCQa_15Oct04_Andro_0904-2_4-20", file1Data);
var file2Data = new Dictionary<int, Dictionary<string, string>>
{
{16121, new Dictionary<string, string>()},
{16122, new Dictionary<string, string>()}
};
// The KeySpec for each dictionary entry is MaxDataCount_Centroid
file2Data[16121].Add("0_False", "11888 346.518 0.0E+0 706.844 9.8E+4 FTMS + p NSI Full ms [350.0000-1550.0000]");
file2Data[16122].Add("0_False", " 490 116.232 7.0E+1 403.932 1.1E+3 ITMS + c NSI r d Full ms2 [email protected] [106.0000-817.0000]");
file2Data[16121].Add("0_True", " 833 351.231 2.9E+5 712.813 2.9E+5 FTMS + p NSI Full ms [350.0000-1550.0000]");
file2Data[16122].Add("0_True", " 490 116.232 7.0E+1 403.932 1.1E+3 ITMS + c NSI r d Full ms2 [email protected] [106.0000-817.0000]");
file2Data[16121].Add("50_False", " 50 503.553 2.0E+7 504.571 2.1E+7 FTMS + p NSI Full ms [350.0000-1550.0000]");
file2Data[16122].Add("50_False", " 50 157.049 2.0E+4 385.181 6.0E+3 ITMS + c NSI r d Full ms2 [email protected] [106.0000-817.0000]");
file2Data[16121].Add("50_True", " 833 351.231 2.9E+5 712.813 2.9E+5 FTMS + p NSI Full ms [350.0000-1550.0000]");
file2Data[16122].Add("50_True", " 50 157.049 2.0E+4 385.181 6.0E+3 ITMS + c NSI r d Full ms2 [email protected] [106.0000-817.0000]");
expectedData.Add("HCC-38_ETciD_EThcD_4xdil_20uL_3hr_3_08Jan16_Pippin_15-08-53", file2Data);
var dataFile = GetRawDataFile(rawFileName);
using (var reader = new XRawFileIO(dataFile.FullName))
{
Console.WriteLine("Scan data for {0}", dataFile.Name);
Console.WriteLine("{0} {1,3} {2,8} {3,-8} {4,-8} {5,-8} {6,-8} {7,-8} {8}",
"Scan", "Max#", "Centroid", "DataCount",
"FirstMz", "FirstInt", "MidMz", "MidInt", "ScanFilter");
for (var iteration = 1; iteration <= 4; iteration++)
{
int maxNumberOfPeaks;
bool centroidData;
switch (iteration)
{
case 1:
maxNumberOfPeaks = 0;
centroidData = false;
break;
case 2:
maxNumberOfPeaks = 0;
centroidData = true;
break;
case 3:
maxNumberOfPeaks = 50;
centroidData = false;
break;
default:
maxNumberOfPeaks = 50;
centroidData = true;
break;
}
for (var scanNumber = scanStart; scanNumber <= scanEnd; scanNumber++)
{
double[,] massIntensityPairs;
var dataPointsRead = reader.GetScanData2D(scanNumber, out massIntensityPairs, maxNumberOfPeaks, centroidData);
Assert.IsTrue(dataPointsRead > 0, "GetScanData2D returned 0 for scan {0}", scanNumber);
clsScanInfo scanInfo;
var success = reader.GetScanInfo(scanNumber, out scanInfo);
Assert.IsTrue(success, "GetScanInfo returned false for scan {0}", scanNumber);
var lastIndex = massIntensityPairs.GetUpperBound(1);
int dataCount;
if (maxNumberOfPeaks > 0)
{
if (centroidData && scanInfo.IsFTMS)
{
// When centroiding FTMS data, the maxNumberOfPeaks value is ignored
dataCount = lastIndex + 1;
var pointToCheck = maxNumberOfPeaks + (int)((lastIndex - maxNumberOfPeaks) / 2f);
Assert.IsTrue(massIntensityPairs[0, pointToCheck] > 50, "m/z value in 2D array is unexpectedly less than 50");
}
else
{
dataCount = maxNumberOfPeaks;
// Make sure the 2D array has values of 0 for mass and intensity beyond index maxNumberOfPeaks
for (var dataIndex = maxNumberOfPeaks; dataIndex < lastIndex; dataIndex++)
{
if (massIntensityPairs[0, dataIndex] > 0)
{
Console.WriteLine("Non-zero m/z value found at index {0} for scan {1}", dataIndex, scanNumber);
Assert.AreEqual(0, massIntensityPairs[0, dataIndex], "Non-zero m/z value found in 2D array beyond expected index");
}
if (massIntensityPairs[1, dataIndex] > 0)
{
Console.WriteLine("Non-zero intensity value found at index {0} for scan {1}", dataIndex, scanNumber);
Assert.AreEqual(0, massIntensityPairs[1, dataIndex], "Non-zero intensity value found in 2D array beyond expected index");
}
}
}
}
else
{
dataCount = lastIndex + 1;
}
Assert.AreEqual(dataPointsRead, dataCount, "Data count mismatch vs. function return value");
var midPoint = (int)(dataCount / 2f);
var scanSummary =
string.Format(
"{0} {1,3} {2,8} {3,8} {4,8} {5,8} {6,8} {7,8} {8}",
scanNumber, maxNumberOfPeaks, centroidData,
dataCount,
massIntensityPairs[0, 0].ToString("0.000"), massIntensityPairs[1,0].ToString("0.0E+0"),
massIntensityPairs[0, midPoint].ToString("0.000"), massIntensityPairs[1, midPoint].ToString("0.0E+0"),
scanInfo.FilterText);
Console.WriteLine(scanSummary);
Dictionary<int, Dictionary<string, string>> expectedDataThisFile;
if (!expectedData.TryGetValue(Path.GetFileNameWithoutExtension(dataFile.Name), out expectedDataThisFile))
{
Assert.Fail("Dataset {0} not found in dictionary expectedData", dataFile.Name);
}
Dictionary<string, string> expectedDataByType;
if (expectedDataThisFile.TryGetValue(scanNumber, out expectedDataByType))
{
var keySpec = maxNumberOfPeaks + "_" + centroidData;
string expectedDataDetails;
if (expectedDataByType.TryGetValue(keySpec, out expectedDataDetails))
{
Assert.AreEqual(expectedDataDetails, scanSummary.Substring(22),
"Scan details mismatch, scan " + scanNumber + ", keySpec " + keySpec);
}
}
}
}
}
}
public void TestGetNumScans(string rawFileName, int expectedResult)
{
var dataFile = GetRawDataFile(rawFileName);
using (var reader = new XRawFileIO(dataFile.FullName))
{
var scanCount = reader.GetNumScans();
Console.WriteLine("Scan count for {0}: {1}", dataFile.Name, scanCount);
Assert.AreEqual(expectedResult, scanCount, "Scan count mismatch");
}
}
public void TestGetScanCountsByScanType(
string rawFileName,
int scanStart,
int scanEnd,
int expectedMS1,
int expectedMS2,
int expectedTotalScanCount)
{
// Keys in this Dictionary are filename, values are ScanCounts by collision mode, where the key is a Tuple of ScanType and FilterString
var expectedData = new Dictionary<string, Dictionary<Tuple<string, string>, int>>();
// Keys in this dictionary are scan type, values are a Dictionary of FilterString and the number of scans with that filter string
AddExpectedTupleAndCount(expectedData, "B5_50uM_MS_r1", "Q1MS", "+ c NSI Q1MS", 20);
AddExpectedTupleAndCount(expectedData, "MNSLTFKK_ms", "Q1MS", "+ p NSI Q1MS", 88);
AddExpectedTupleAndCount(expectedData, "QCShew200uL", "Q3MS", "+ c NSI Q3MS", 101);
AddExpectedTupleAndCount(expectedData, "Wrighton_MT2_SPE_200avg_240k_neg_330-380", "SIM ms", "FTMS - p NSI SIM ms", 200);
const string file5 = "1229_02blk1";
AddExpectedTupleAndCount(expectedData, file5, "MS", "ITMS + c NSI Full ms", 8);
AddExpectedTupleAndCount(expectedData, file5, "CID-MSn", "ITMS + c NSI d Full ms2 [email protected]", 24);
AddExpectedTupleAndCount(expectedData, file5, "SIM ms", "ITMS + p NSI SIM ms", 69);
const string file6 = "MCF7_histone_32_49B_400min_HCD_ETD_01172014_b";
AddExpectedTupleAndCount(expectedData, file6, "HMS", "FTMS + p NSI Full ms", 9);
AddExpectedTupleAndCount(expectedData, file6, "ETD-HMSn", "FTMS + p NSI d Full ms2 [email protected]", 46);
AddExpectedTupleAndCount(expectedData, file6, "HCD-HMSn", "FTMS + p NSI d Full ms2 [email protected]", 37);
AddExpectedTupleAndCount(expectedData, file6, "SIM ms", "FTMS + p NSI d SIM ms", 9);
const string file7 = "lowdose_IMAC_iTRAQ1_PQDMSA";
AddExpectedTupleAndCount(expectedData, file7, "HMS", "FTMS + p NSI Full ms", 16);
AddExpectedTupleAndCount(expectedData, file7, "CID-MSn", "ITMS + c NSI d Full ms2 [email protected]", 43);
AddExpectedTupleAndCount(expectedData, file7, "PQD-MSn", "ITMS + c NSI d Full ms2 [email protected]", 42);
const string file8 = "MZ20150721blank2";
AddExpectedTupleAndCount(expectedData, file8, "HMS", "FTMS + p NSI Full ms", 62);
AddExpectedTupleAndCount(expectedData, file8, "ETD-HMSn", "FTMS + p NSI d Full ms2 [email protected]", 186);
AddExpectedTupleAndCount(expectedData, file8, "ETD-HMSn", "FTMS + p NSI d Full ms2 [email protected]", 186);
const string file9 = "OG_CEPC_PU_22Oct13_Legolas_13-05-12";
AddExpectedTupleAndCount(expectedData, file9, "HMS", "FTMS + p NSI Full ms", 9);
AddExpectedTupleAndCount(expectedData, file9, "CID-MSn", "ITMS + c NSI d Full ms2 [email protected]", 46);
AddExpectedTupleAndCount(expectedData, file9, "ETD-MSn", "ITMS + c NSI d Full ms2 [email protected]", 1);
AddExpectedTupleAndCount(expectedData, file9, "ETD-MSn", "ITMS + c NSI d Full ms2 [email protected]", 1);
AddExpectedTupleAndCount(expectedData, file9, "ETD-MSn", "ITMS + c NSI d Full ms2 [email protected]", 8);
AddExpectedTupleAndCount(expectedData, file9, "ETD-MSn", "ITMS + c NSI d Full ms2 [email protected]", 8);
AddExpectedTupleAndCount(expectedData, file9, "ETD-MSn", "ITMS + c NSI d Full ms2 [email protected]", 56);
AddExpectedTupleAndCount(expectedData, file9, "SA_ETD-MSn", "ITMS + c NSI d sa Full ms2 [email protected]", 5);
AddExpectedTupleAndCount(expectedData, file9, "SA_ETD-MSn", "ITMS + c NSI d sa Full ms2 [email protected]", 1);
AddExpectedTupleAndCount(expectedData, file9, "SA_ETD-MSn", "ITMS + c NSI d sa Full ms2 [email protected]", 1);
AddExpectedTupleAndCount(expectedData, file9, "SA_ETD-MSn", "ITMS + c NSI d sa Full ms2 [email protected]", 14);
AddExpectedTupleAndCount(expectedData, file9, "SA_ETD-MSn", "ITMS + c NSI d sa Full ms2 [email protected]", 32);
AddExpectedTupleAndCount(expectedData, file9, "SA_ETD-MSn", "ITMS + c NSI d sa Full ms2 [email protected]", 260);
const string file10 = "blank_MeOH-3_18May16_Rainier_Thermo_10344958";
AddExpectedTupleAndCount(expectedData, file10, "HMS", "FTMS - p ESI Full ms", 190);
AddExpectedTupleAndCount(expectedData, file10, "CID-HMSn", "FTMS - c ESI d Full ms2 [email protected]", 207);
AddExpectedTupleAndCount(expectedData, file10, "CID-HMSn", "FTMS - c ESI d Full ms3 [email protected] [email protected]", 4);
const string file11 = "HCC-38_ETciD_EThcD_07Jan16_Pippin_15-08-53";
AddExpectedTupleAndCount(expectedData, file11, "HMS", "FTMS + p NSI Full ms", 20);
AddExpectedTupleAndCount(expectedData, file11, "CID-MSn", "ITMS + c NSI r d Full ms2 [email protected]", 231);
AddExpectedTupleAndCount(expectedData, file11, "ETciD-MSn", "ITMS + c NSI r d sa Full ms2 [email protected]@cid20.00", 46);
AddExpectedTupleAndCount(expectedData, file11, "ETciD-MSn", "ITMS + c NSI r d sa Full ms2 [email protected]@cid20.00", 4);
AddExpectedTupleAndCount(expectedData, file11, "ETD-MSn", "ITMS + c NSI r d Full ms2 [email protected]", 46);
AddExpectedTupleAndCount(expectedData, file11, "ETD-MSn", "ITMS + c NSI r d Full ms2 [email protected]", 4);
AddExpectedTupleAndCount(expectedData, file11, "EThcD-MSn", "ITMS + c NSI r d sa Full ms2 [email protected]@hcd20.00", 46);
AddExpectedTupleAndCount(expectedData, file11, "EThcD-MSn", "ITMS + c NSI r d sa Full ms2 [email protected]@hcd20.00", 4);
const string file12 = "MeOHBlank03POS_11May16_Legolas_HSS-T3_A925";
AddExpectedTupleAndCount(expectedData, file12, "HMS", "FTMS + p ESI Full ms", 8);
AddExpectedTupleAndCount(expectedData, file12, "CID-MSn", "ITMS + c ESI d Full ms2 [email protected]", 47);
AddExpectedTupleAndCount(expectedData, file12, "HCD-HMSn", "FTMS + c ESI d Full ms2 [email protected]", 38);
AddExpectedTupleAndCount(expectedData, file12, "HCD-HMSn", "FTMS + c ESI d Full ms2 [email protected]", 8);
AddExpectedTupleAndCount(expectedData, "IPA-blank-07_25Oct13_Gimli", "Zoom-MS", "ITMS + p NSI Z ms", 101);
var dataFile = GetRawDataFile(rawFileName);
using (var reader = new XRawFileIO(dataFile.FullName))
{
Console.WriteLine("Parsing scan headers for {0}", dataFile.Name);
var scanCount = reader.GetNumScans();
Console.WriteLine("Total scans: {0}", scanCount);
Assert.AreEqual(expectedTotalScanCount, scanCount, "Total scan count mismatch");
Console.WriteLine();
var scanCountMS1 = 0;
var scanCountMS2 = 0;
var scanTypeCountsActual = new Dictionary<Tuple<string, string>, int>();
for (var scanNumber = scanStart; scanNumber <= scanEnd; scanNumber++)
{
clsScanInfo scanInfo;
var success = reader.GetScanInfo(scanNumber, out scanInfo);
Assert.IsTrue(success, "GetScanInfo returned false for scan {0}", scanNumber);
var scanType = XRawFileIO.GetScanTypeNameFromFinniganScanFilterText(scanInfo.FilterText);
var genericScanFilter = XRawFileIO.MakeGenericFinniganScanFilter(scanInfo.FilterText);
var scanTypeKey = new Tuple<string, string>(scanType, genericScanFilter);
int observedScanCount;
if (scanTypeCountsActual.TryGetValue(scanTypeKey, out observedScanCount))
{
scanTypeCountsActual[scanTypeKey] = observedScanCount + 1;
}
else
{
scanTypeCountsActual.Add(scanTypeKey, 1);
}
if (scanInfo.MSLevel > 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");
Dictionary<Tuple<string, string>, int> expectedScanInfo;
if (!expectedData.TryGetValue(Path.GetFileNameWithoutExtension(dataFile.Name), out expectedScanInfo))
{
Assert.Fail("Dataset {0} not found in dictionary expectedData", dataFile.Name);
}
Console.WriteLine("{0,-5} {1,5} {2}", "Valid", "Count", "ScanType");
foreach (var scanType in (from item in scanTypeCountsActual orderby item.Key select item))
{
int expectedScanCount;
if (expectedScanInfo.TryGetValue(scanType.Key, out expectedScanCount))
{
var isValid = scanType.Value == expectedScanCount;
Console.WriteLine("{0,-5} {1,5} {2}", isValid, scanType.Value, scanType.Key);
Assert.AreEqual(expectedScanCount, scanType.Value, "Scan type count mismatch");
}
else
{
Console.WriteLine("Unexpected scan type found: {0}", scanType.Key);
Assert.Fail("Unexpected scan type found: {0}", scanType.Key);
}
}
}
}
public void TestScanInfoCopyFromStruct(string rawFileName, int scanStart, int scanEnd)
{
var dataFile = GetRawDataFile(rawFileName);
using (var reader = new XRawFileIO(dataFile.FullName))
{
Console.WriteLine("Checking clsScanInfo initializing from a struct using {0}", dataFile.Name);
for (var scanNumber = scanStart; scanNumber <= scanEnd; scanNumber++)
{
clsScanInfo scanInfo;
var success = reader.GetScanInfo(scanNumber, out scanInfo);
Assert.IsTrue(success, "GetScanInfo returned false for scan {0}", scanNumber);
#pragma warning disable 618
var udtScanHeaderInfo = new udtScanHeaderInfoType
{
MSLevel = scanInfo.MSLevel,
EventNumber = scanInfo.EventNumber,
SIMScan = scanInfo.SIMScan,
MRMScanType = scanInfo.MRMScanType,
ZoomScan = scanInfo.ZoomScan,
NumPeaks = scanInfo.NumPeaks,
RetentionTime = scanInfo.RetentionTime,
LowMass = scanInfo.LowMass,
HighMass = scanInfo.HighMass,
TotalIonCurrent = scanInfo.TotalIonCurrent,
BasePeakMZ = scanInfo.BasePeakMZ,
BasePeakIntensity = scanInfo.BasePeakIntensity,
FilterText = scanInfo.FilterText,
ParentIonMZ = scanInfo.ParentIonMZ,
ActivationType = scanInfo.ActivationType,
CollisionMode = scanInfo.CollisionMode,
IonMode = scanInfo.IonMode,
MRMInfo = scanInfo.MRMInfo,
NumChannels = scanInfo.NumChannels,
UniformTime = scanInfo.UniformTime,
Frequency = scanInfo.Frequency,
IsCentroidScan = scanInfo.IsCentroided,
ScanEventNames = new string[scanInfo.ScanEvents.Count],
ScanEventValues = new string[scanInfo.ScanEvents.Count],
StatusLogNames = new string[scanInfo.StatusLog.Count],
StatusLogValues = new string[scanInfo.StatusLog.Count]
};
#pragma warning restore 618
var targetIndex = 0;
foreach (var scanEvent in scanInfo.ScanEvents)
{
udtScanHeaderInfo.ScanEventNames[targetIndex] = scanEvent.Key;
udtScanHeaderInfo.ScanEventValues[targetIndex] = scanEvent.Value;
targetIndex++;
}
targetIndex = 0;
foreach (var scanEvent in scanInfo.StatusLog)
{
udtScanHeaderInfo.StatusLogNames[targetIndex] = scanEvent.Key;
udtScanHeaderInfo.StatusLogValues[targetIndex] = scanEvent.Value;
targetIndex++;
}
#pragma warning disable 618
var scanInfoFromStruct = new clsScanInfo(scanInfo.ScanNumber, udtScanHeaderInfo);
#pragma warning restore 618
Assert.AreEqual(scanInfoFromStruct.MSLevel, scanInfo.MSLevel);
Assert.AreEqual(scanInfoFromStruct.IsCentroided, scanInfo.IsCentroided);
Assert.AreEqual(scanInfoFromStruct.FilterText, scanInfo.FilterText);
Assert.AreEqual(scanInfoFromStruct.BasePeakIntensity, scanInfo.BasePeakIntensity, 0.0001);
Assert.AreEqual(scanInfoFromStruct.TotalIonCurrent, scanInfo.TotalIonCurrent, 0.0001);
}
}
}
public void TestCorruptDataHandling(
string rawFileName,
int scanStart,
int scanEnd,
int expectedMS1,
int expectedMS2,
int corruptScanStart,
int corruptScanEnd)
{
var dataFile = GetRawDataFile(rawFileName);
try
{
using (var reader = new XRawFileIO(dataFile.FullName))
{
var scanCount = reader.GetNumScans();
Console.WriteLine("Scan count for {0}: {1}", dataFile.Name, scanCount);
if (expectedMS1 + expectedMS2 == 0)
{
Assert.IsTrue(reader.FileInfo.CorruptFile, "CorruptFile is false while we expected it to be true");
Assert.IsTrue(scanCount == 0, "ScanCount is non-zero, while we expected it to be 0");
}
else
{
Assert.IsFalse(reader.FileInfo.CorruptFile, "CorruptFile is true while we expected it to be false");
Assert.IsTrue(scanCount > 0, "ScanCount is zero, while we expected it to be > 0");
}
var scanCountMS1 = 0;
var scanCountMS2 = 0;
for (var scanNumber = scanStart; scanNumber <= scanEnd; scanNumber++)
{
try
{
clsScanInfo scanInfo;
reader.GetScanInfo(scanNumber, out scanInfo);
if (reader.FileInfo.CorruptFile)
{
Assert.IsTrue(string.IsNullOrEmpty(scanInfo.FilterText), "FilterText is not empty but should be since corrupt file");
}
else
{
Assert.IsFalse(string.IsNullOrEmpty(scanInfo.FilterText), "FilterText is empty but should not be");
if (scanInfo.MSLevel > 1)
scanCountMS2++;
else
scanCountMS1++;
}
double[] mzList;
double[] intensityList;
// Note: this function call will fail randomly with file Corrupt_Scans6920-7021_AID_STM_013_101104_06_LTQ_16Nov04_Earth_0904-8.raw
// Furthermore, we are unable to catch the exception that occurs (or no exception is thrown) and adding
// [System.Runtime.ExceptionServices.HandleProcessCorruptedStateExceptions] to the function does not help
var dataPointCount = reader.GetScanData(scanNumber, out mzList, out intensityList);
if (reader.FileInfo.CorruptFile)
{
Assert.IsTrue(dataPointCount == 0, "GetScanData unexpectedly reported a non-zero data count for scan {0}", scanNumber);
Assert.IsTrue(mzList.Length == 0, "GetScanData unexpectedly returned m/z data for scan {0}", scanNumber);
Assert.IsTrue(intensityList.Length == 0, "GetScanData unexpectedly returned intensity data for scan {0}", scanNumber);
}
else
{
if (dataPointCount == 0)
{
Console.WriteLine("Corrupt scan encountered: {0}", scanNumber);
Assert.IsTrue(scanNumber >= corruptScanStart && scanNumber <= corruptScanEnd, "Unexpected corrupt scan found, scan {0}", scanNumber);
Assert.IsTrue(mzList.Length == 0, "GetScanData unexpectedly returned m/z data for scan {0}", scanNumber);
Assert.IsTrue(intensityList.Length == 0, "GetScanData unexpectedly returned intensity data for scan {0}", scanNumber);
}
else
{
Assert.IsTrue(dataPointCount > 0, "GetScanData reported a data point count of 0 for scan {0}", scanNumber);
Assert.IsTrue(mzList.Length > 0, "GetScanData unexpectedly returned no m/z data for scan {0}", scanNumber);
Assert.IsTrue(intensityList.Length > 0, "GetScanData unexpectedly returned no intensity data for scan {0}", scanNumber);
Assert.IsTrue(mzList.Length == intensityList.Length, "Array length mismatch for m/z and intensity data for scan {0}", scanNumber);
Assert.IsTrue(dataPointCount == mzList.Length, "Array length does not agree with dataPointCount 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)
{
var msg = string.Format("Exception opening .raw file {0}:\n{1}", rawFileName, ex.Message);
Console.WriteLine(msg);
Assert.Fail(msg);
}
}
public void TestGetCollisionEnergy(string rawFileName)
{
// Keys in this Dictionary are filename, values are Collision Energies by scan
var expectedData = new Dictionary<string, Dictionary<int, List<double>>>();
var ce30 = new List<double> { 30.00 };
var ce45 = new List<double> { 45.00 };
var ce20_120 = new List<double> { 20.00, 120.550003 };
var ce120 = new List<double> { 120.550003 };
var ms1Scan = new List<double>();
// Keys in this dictionary are scan number and values are collision energies
var file1Data = new Dictionary<int, List<double>>
{
{2250, ce45},
{2251, ce45},
{2252, ce45},
{2253, ms1Scan},
{2254, ce45},
{2255, ce45},
{2256, ce45},
{2257, ms1Scan},
{2258, ce45},
{2259, ce45},
{2260, ce45}
};
expectedData.Add("Shew_246a_LCQa_15Oct04_Andro_0904-2_4-20", file1Data);
var file2Data = new Dictionary<int, List<double>>
{
{39000, ce30},
{39001, ce30},
{39002, ms1Scan},
{39003, ce30},
{39004, ce30},
{39005, ce30},
{39006, ce120},
{39007, ce20_120},
{39008, ce20_120},
{39009, ce30},
{39010, ce30}
};
expectedData.Add("HCC-38_ETciD_EThcD_4xdil_20uL_3hr_3_08Jan16_Pippin_15-08-53", file2Data);
var file3Data = new Dictionary<int, List<double>>
{
{19000, ce120},
{19001, ce20_120},
{19002, ce20_120},
{19003, ms1Scan},
{19004, ce30},
{19005, ce30},
{19006, ce30},
{19007, ce120},
{19008, ce20_120},
{19009, ce20_120},
{19010, ce30}
};
expectedData.Add("HCC-38_ETciD_EThcD_07Jan16_Pippin_15-08-53", file3Data);
var file4Data = new Dictionary<int, List<double>>
{
{1, ce30},
{2, ce30}
};
expectedData.Add("MZ0210MnxEF889ETD", file4Data);
var dataFile = GetRawDataFile(rawFileName);
Dictionary<int, List<double>> collisionEnergiesThisFile;
if (!expectedData.TryGetValue(Path.GetFileNameWithoutExtension(dataFile.Name), out collisionEnergiesThisFile))
{
Assert.Fail("Dataset {0} not found in dictionary expectedData", dataFile.Name);
}
// Keys are scan number, values are the list of collision energies
var collisionEnergiesActual = new Dictionary<int, List<double>>();
// Keys are scan number, values are msLevel
var msLevelsActual = new Dictionary<int, int>();
// Keys are scan number, values are the ActivationType, for example cid, etd, hcd
var activationTypesActual = new Dictionary<int, string>();
using (var reader = new XRawFileIO(dataFile.FullName))
{
foreach (var scanNumber in collisionEnergiesThisFile.Keys)
{
clsScanInfo scanInfo;
var success = reader.GetScanInfo(scanNumber, out scanInfo);
Assert.IsTrue(success, "GetScanInfo returned false for scan {0}", scanNumber);
var collisionEnergiesThisScan = reader.GetCollisionEnergy(scanNumber);
collisionEnergiesActual.Add(scanNumber, collisionEnergiesThisScan);
msLevelsActual.Add(scanNumber, scanInfo.MSLevel);
activationTypesActual.Add(scanNumber, scanInfo.ActivationType.ToString());
}
Console.WriteLine("{0,-5} {1,-5} {2}", "Valid", "Scan", "Collision Energy");
foreach (var actualEnergiesOneScan in (from item in collisionEnergiesActual orderby item.Key select item))
{
var scanNumber = actualEnergiesOneScan.Key;
var expectedEnergies = collisionEnergiesThisFile[scanNumber];
var activationTypes = string.Join(", ", activationTypesActual[scanNumber]);
if (actualEnergiesOneScan.Value.Count == 0)
{
var msLevel = msLevelsActual[scanNumber];
if (msLevel != 1)
{
var msg = string.Format(
"Scan {0} has no collision energies, which should only be true for spectra with msLevel=1. This scan has msLevel={1} and activationType={2}",
scanNumber, msLevel, activationTypes);
Console.WriteLine(msg);
Assert.Fail(msg);
}
else
{
Console.WriteLine("{0,-5} {1,-5} {2}", true, scanNumber, "MS1 scan");
}
}
else
{
foreach (var actualEnergy in actualEnergiesOneScan.Value)
{
var isValid = expectedEnergies.Any(expectedEnergy => Math.Abs(actualEnergy - expectedEnergy) < 0.00001);
Console.WriteLine("{0,-5} {1,-5} {2}", isValid, scanNumber, actualEnergy.ToString("0.00"));
Assert.IsTrue(isValid, "Unexpected collision energy {0} for scan {1}", actualEnergy.ToString("0.00"), scanNumber);
}
}
if (expectedEnergies.Count != actualEnergiesOneScan.Value.Count)
{
var msg = string.Format("Collision energy count mismatch for scan {0}", scanNumber);
Console.WriteLine(msg);
Assert.AreEqual(expectedEnergies.Count, actualEnergiesOneScan.Value.Count, msg);
}
}
}
}
public void TestScanEventData(string rawFileName, int scanStart, int scanEnd)
{
// Keys in this Dictionary are filename, values are ScanCounts by event, where the key is a Tuple of EventName and EventValue
var expectedData = new Dictionary<string, Dictionary<Tuple<string, string>, int>>();
AddExpectedTupleAndCount(expectedData, "Shew_246a_LCQa_15Oct04_Andro_0904-2_4-20", "Resolution:", "Low", 101);
AddExpectedTupleAndCount(expectedData, "Shew_246a_LCQa_15Oct04_Andro_0904-2_4-20", "Scan Event:", "1", 25);
AddExpectedTupleAndCount(expectedData, "Shew_246a_LCQa_15Oct04_Andro_0904-2_4-20", "Scan Event:", "2", 25);
AddExpectedTupleAndCount(expectedData, "Shew_246a_LCQa_15Oct04_Andro_0904-2_4-20", "Scan Event:", "3", 25);
AddExpectedTupleAndCount(expectedData, "Shew_246a_LCQa_15Oct04_Andro_0904-2_4-20", "Scan Event:", "4", 26);
AddExpectedTupleAndCount(expectedData, "HCC-38_ETciD_EThcD_4xdil_20uL_3hr_3_08Jan16_Pippin_15-08-53", "Charge State:", "0", 21);
AddExpectedTupleAndCount(expectedData, "HCC-38_ETciD_EThcD_4xdil_20uL_3hr_3_08Jan16_Pippin_15-08-53", "Charge State:", "2", 134);
AddExpectedTupleAndCount(expectedData, "HCC-38_ETciD_EThcD_4xdil_20uL_3hr_3_08Jan16_Pippin_15-08-53", "Charge State:", "3", 30);
AddExpectedTupleAndCount(expectedData, "HCC-38_ETciD_EThcD_4xdil_20uL_3hr_3_08Jan16_Pippin_15-08-53", "Charge State:", "4", 14);
AddExpectedTupleAndCount(expectedData, "HCC-38_ETciD_EThcD_4xdil_20uL_3hr_3_08Jan16_Pippin_15-08-53", "Charge State:", "7", 1);
AddExpectedTupleAndCount(expectedData, "HCC-38_ETciD_EThcD_4xdil_20uL_3hr_3_08Jan16_Pippin_15-08-53", "Charge State:", "8", 1);
AddExpectedTupleAndCount(expectedData, "HCC-38_ETciD_EThcD_4xdil_20uL_3hr_3_08Jan16_Pippin_15-08-53", "MS2 Isolation Width:", "2.000", 180);
AddExpectedTupleAndCount(expectedData, "HCC-38_ETciD_EThcD_4xdil_20uL_3hr_3_08Jan16_Pippin_15-08-53", "MS2 Isolation Width:", "1200.000", 21);
var dataFile = GetRawDataFile(rawFileName);
Dictionary<Tuple<string, string>, int> expectedEventsThisFile;
if (!expectedData.TryGetValue(Path.GetFileNameWithoutExtension(dataFile.Name), out expectedEventsThisFile))
{
Assert.Fail("Dataset {0} not found in dictionary expectedData", dataFile.Name);
}
var eventsToCheck = (from item in expectedEventsThisFile select item.Key.Item1).Distinct().ToList();
var eventCountsActual = new Dictionary<Tuple<string, string>, int>();
using (var reader = new XRawFileIO(dataFile.FullName))
{
for (var scanNumber = scanStart; scanNumber <= scanEnd; scanNumber++)
{
clsScanInfo scanInfo;
var success = reader.GetScanInfo(scanNumber, out scanInfo);
Assert.IsTrue(success, "GetScanInfo returned false for scan {0}", scanNumber);
foreach (var eventName in eventsToCheck)
{
string eventValue;
scanInfo.TryGetScanEvent(eventName, out eventValue);
var eventKey = new Tuple<string, string>(eventName, eventValue);
int scanCount;
if (eventCountsActual.TryGetValue(eventKey, out scanCount))
{
eventCountsActual[eventKey] = scanCount + 1;
}
else
{
eventCountsActual.Add(eventKey, 1);
}
}
}
Console.WriteLine("{0,-5} {1,5} {2}", "Valid", "Count", "Event");
foreach (var observedEvent in (from item in eventCountsActual orderby item.Key select item))
{
int expectedScanCount;
if (expectedEventsThisFile.TryGetValue(observedEvent.Key, out expectedScanCount))
{
var isValid = observedEvent.Value == expectedScanCount;
Console.WriteLine("{0,-5} {1,5} {2} {3}", isValid, observedEvent.Value, observedEvent.Key.Item1, observedEvent.Key.Item2);
Assert.AreEqual(expectedScanCount, observedEvent.Value, "Event count mismatch");
}
else
{
Console.WriteLine("Unexpected event/value found: {0} {1}", observedEvent.Key.Item1, observedEvent.Key.Item2);
Assert.Fail("Unexpected event/value found: {0} {1}", observedEvent.Key.Item1, observedEvent.Key.Item2);
}
}
}
}
public void TestGetScanPrecisionData(string rawFileName, int scanStart, int scanEnd)
{
var expectedData = new Dictionary<string, Dictionary<int, string>>();
var noMatch = " 0 ";
var file1Data = new Dictionary<int, string>
{
{1513, noMatch + "+ c ESI Full ms [400.00-2000.00]"},
{1514, noMatch + "+ c d Full ms2 [email protected] [230.00-1780.00]"}
};
expectedData.Add("Shew_246a_LCQa_15Oct04_Andro_0904-2_4-20", file1Data);
var file2Data = new Dictionary<int, string>
{
{16121, "833 712.813 2.9E+5 22100.000 2.138 3.000 FTMS + p NSI Full ms [350.0000-1550.0000]"},
{16122, noMatch + "ITMS + c NSI r d Full ms2 [email protected] [106.0000-817.0000]"},
{16123, noMatch + "ITMS + c NSI r d Full ms2 [email protected] [143.0000-1627.0000]"},
{16124, noMatch + "ITMS + c NSI r d Full ms2 [email protected] [208.0000-2000.0000]"},
{16125, noMatch + "ITMS + c NSI r d Full ms2 [email protected] [120.0000-1627.0000]"},
{16126, noMatch + "ITMS + c NSI r d sa Full ms2 [email protected]@cid20.00 [120.0000-1627.0000]"},
{16127, noMatch + "ITMS + c NSI r d sa Full ms2 [email protected]@hcd20.00 [120.0000-1627.0000]"},
{16128, noMatch + "ITMS + c NSI r d Full ms2 [email protected] [225.0000-1682.0000]"},
{16129, noMatch + "ITMS + c NSI r d Full ms2 [email protected] [266.0000-1986.0000]"},
{16130, noMatch + "ITMS + c NSI r d Full ms2 [email protected] [110.0000-853.0000]"},
{16131, noMatch + "ITMS + c NSI r d Full ms2 [email protected] [120.0000-1986.0000]"},
{16132, noMatch + "ITMS + c NSI r d Full ms2 [email protected] [120.0000-853.0000]"},
{16133, noMatch + "ITMS + c NSI r d sa Full ms2 [email protected]@cid20.00 [120.0000-853.0000]"},
{16134, noMatch + "ITMS + c NSI r d sa Full ms2 [email protected]@hcd20.00 [120.0000-853.0000]"},
{16135, noMatch + "ITMS + c NSI r d sa Full ms2 [email protected]@cid20.00 [120.0000-1986.0000]"},
{16136, noMatch + "ITMS + c NSI r d sa Full ms2 [email protected]@hcd20.00 [120.0000-1986.0000]"},
{16137, noMatch + "ITMS + c NSI r d Full ms2 [email protected] [336.0000-2000.0000]"},
{16138, noMatch + "ITMS + c NSI r d Full ms2 [email protected] [235.0000-1760.0000]"},
{16139, noMatch + "ITMS + c NSI r d Full ms2 [email protected] [120.0000-1760.0000]"},
{16140, noMatch + "ITMS + c NSI r d sa Full ms2 [email protected]@cid20.00 [120.0000-1760.0000]"},
{16141, noMatch + "ITMS + c NSI r d sa Full ms2 [email protected]@hcd20.00 [120.0000-1760.0000]"},
{16142, "928 740.322 2.1E+5 28700.000 2.221 3.000 FTMS + p NSI Full ms [350.0000-1550.0000]"}
};
expectedData.Add("HCC-38_ETciD_EThcD_4xdil_20uL_3hr_3_08Jan16_Pippin_15-08-53", file2Data);
var dataFile = GetRawDataFile(rawFileName);
using (var reader = new XRawFileIO(dataFile.FullName))
{
Console.WriteLine("Scan label data for {0}", dataFile.Name);
Console.WriteLine("{0} {1,3} {2,8} {3,8} {4,8} {5,8} {6,8} {7}",
"Scan", "Count", "Mass", "Intensity",
"Resolution", "AccuracyMMU", "AccuracyPPM", "ScanFilter");
for (var scanNumber = scanStart; scanNumber <= scanEnd; scanNumber++)
{
// List of Intensity, Mass, AccuracyMMU, AccuracyPPM, and Resolution for each data point
udtMassPrecisionInfoType[] massResolutionData;
var dataPointsRead = reader.GetScanPrecisionData(scanNumber, out massResolutionData);
if (dataPointsRead == -1)
Assert.AreEqual(0, massResolutionData.Length, "Data count mismatch vs. function return value");
else
Assert.AreEqual(dataPointsRead, massResolutionData.Length, "Data count mismatch vs. function return value");
clsScanInfo scanInfo;
var success = reader.GetScanInfo(scanNumber, out scanInfo);
Assert.IsTrue(success, "GetScanInfo returned false for scan {0}", scanStart);
if (massResolutionData.Length == 0 && scanInfo.IsFTMS)
{
Assert.Fail("GetScanPrecisionData returned no data for FTMS scan " + scanNumber);
}
string scanSummary;
if (massResolutionData.Length == 0)
{
scanSummary = string.Format("{0} {1,3} {2,8} {3,8} {4,8} {5,8} {6,8} {7}",
scanNumber, massResolutionData.Length,
string.Empty,
string.Empty,
string.Empty,
string.Empty,
string.Empty,
scanInfo.FilterText);
}
else
{
var midPoint = (int)(massResolutionData.Length / 2f);
scanSummary = string.Format("{0} {1,3} {2,8} {3,8} {4,8} {5,8} {6,8} {7}",
scanNumber, massResolutionData.Length,
massResolutionData[midPoint].Mass.ToString("0.000"),
massResolutionData[midPoint].Intensity.ToString("0.0E+0"),
massResolutionData[midPoint].Resolution.ToString("0.000"),
massResolutionData[midPoint].AccuracyMMU.ToString("0.000"),
massResolutionData[midPoint].AccuracyPPM.ToString("0.000"),
scanInfo.FilterText);
}
Dictionary<int, string> expectedDataThisFile;
if (!expectedData.TryGetValue(Path.GetFileNameWithoutExtension(dataFile.Name), out expectedDataThisFile))
{
Assert.Fail("Dataset {0} not found in dictionary expectedData", dataFile.Name);
}
string expectedScanSummary;
if (expectedDataThisFile.TryGetValue(scanNumber, out expectedScanSummary))
{
Assert.AreEqual(scanNumber + " " + expectedScanSummary, scanSummary,
"Scan summary mismatch, scan " + scanNumber);
}
Console.WriteLine(scanSummary);
}
}
}
public void TestGetScanInfoStruct(string rawFileName, int scanStart, int scanEnd)
{
var dataFile = GetRawDataFile(rawFileName);
using (var reader = new XRawFileIO(dataFile.FullName))
{
Console.WriteLine("Checking GetScanInfo initializing from a struct using {0}", dataFile.Name);
for (var scanNumber = scanStart; scanNumber <= scanEnd; scanNumber++)
{
clsScanInfo scanInfo;
var success = reader.GetScanInfo(scanNumber, out scanInfo);
Assert.IsTrue(success, "GetScanInfo returned false for scan {0}", scanNumber);
#pragma warning disable 618
udtScanHeaderInfoType scanInfoStruct;
success = reader.GetScanInfo(scanNumber, out scanInfoStruct);
#pragma warning restore 618
Assert.IsTrue(success, "GetScanInfo (struct) returned false for scan {0}", scanNumber);
Assert.AreEqual(scanInfoStruct.MSLevel, scanInfo.MSLevel);
Assert.AreEqual(scanInfoStruct.IsCentroidScan, scanInfo.IsCentroided);
Assert.AreEqual(scanInfoStruct.FilterText, scanInfo.FilterText);
Assert.AreEqual(scanInfoStruct.BasePeakIntensity, scanInfo.BasePeakIntensity, 0.0001);
Assert.AreEqual(scanInfoStruct.TotalIonCurrent, scanInfo.TotalIonCurrent, 0.0001);
}
}
}
public void TestGetScanInfoMRM(string rawFileName, int scanStart, int scanEnd)
{
// Keys in this Dictionary are filename, values are the expected SIM scan counts
var expectedData = new Dictionary<string, KeyValuePair<string, int>>
{
{"B5_50uM_MS_r1", new KeyValuePair<string, int>("200.0_600.0_1000.0", 20)},
{"MNSLTFKK_ms", new KeyValuePair<string, int>("200.1_700.0_1200.0", 88)},
{"QCShew200uL", new KeyValuePair<string, int>("400.0_900.0_1400.0", 101)}
};
var dataFile = GetRawDataFile(rawFileName);
using (var reader = new XRawFileIO(dataFile.FullName))
{
Console.WriteLine("Examining MRM details in {0}", dataFile.Name);
var mrmRangeCountsActual = new Dictionary<string, int>();
for (var scanNumber = scanStart; scanNumber <= scanEnd; scanNumber++)
{
clsScanInfo scanInfo;
var success = reader.GetScanInfo(scanNumber, out scanInfo);
Assert.IsTrue(success, "GetScanInfo returned false for scan {0}", scanNumber);
foreach (var mrmRange in scanInfo.MRMInfo.MRMMassList)
{
var mrmRangeKey =
mrmRange.StartMass.ToString("0.0") + "_" +
mrmRange.CentralMass.ToString("0.0") + "_" +
mrmRange.EndMass.ToString("0.0");
int observedScanCount;
if (mrmRangeCountsActual.TryGetValue(mrmRangeKey, out observedScanCount))
{
mrmRangeCountsActual[mrmRangeKey] = observedScanCount + 1;
}
else
{
mrmRangeCountsActual.Add(mrmRangeKey, 1);
}
}
Assert.IsTrue(mrmRangeCountsActual.Count == 1, "Found {0} MRM scan ranges; espected to only find 1", mrmRangeCountsActual.Count);
}
KeyValuePair<string, int> expectedMRMInfo;
if (!expectedData.TryGetValue(Path.GetFileNameWithoutExtension(dataFile.Name), out expectedMRMInfo))
{
Assert.Fail("Dataset {0} not found in dictionary expectedData", dataFile.Name);
}
Console.WriteLine("{0,-5} {1,-5} {2}", "Valid", "Count", "MRMScanRange");
var mrmRangeActual = mrmRangeCountsActual.First();
if (expectedMRMInfo.Key == mrmRangeActual.Key)
{
var isValid = mrmRangeActual.Value == expectedMRMInfo.Value;
Console.WriteLine("{0,-5} {1,5} {2}", isValid, mrmRangeActual.Value, mrmRangeActual.Key);
Assert.AreEqual(expectedMRMInfo.Value, mrmRangeActual.Value, "Scan type count mismatch");
}
else
{
Console.WriteLine("Unexpected MRM scan range found: {0}", mrmRangeActual.Key);
Assert.Fail("Unexpected MRM scan range found: {0}", mrmRangeActual.Key);
}
}
}
private static void TestReader(string rawFilePath, bool centroid = false, bool testSumming = false, int scanStart = 0, int scanEnd = 0)
{
try {
if (!File.Exists(rawFilePath)) {
Console.WriteLine("File not found, skipping: " + rawFilePath);
return;
}
using (var oReader = new XRawFileIO(rawFilePath))
{
foreach(var method in oReader.FileInfo.InstMethods) {
Console.WriteLine(method);
}
var iNumScans = oReader.GetNumScans();
var strCollisionEnergies = string.Empty;
ShowMethod(oReader);
var scanStep = 1;
if (scanStart < 1)
scanStart = 1;
if (scanEnd < 1) {
scanEnd = iNumScans;
scanStep = 21;
} else {
if (scanEnd < scanStart) {
scanEnd = scanStart;
}
}
for (var iScanNum = scanStart; iScanNum <= scanEnd; iScanNum += scanStep) {
clsScanInfo oScanInfo;
var bSuccess = oReader.GetScanInfo(iScanNum, out oScanInfo);
if (bSuccess) {
Console.Write("Scan " + iScanNum + " at " + oScanInfo.RetentionTime.ToString("0.00") + " minutes: " + oScanInfo.FilterText);
var lstCollisionEnergies = oReader.GetCollisionEnergy(iScanNum);
if (lstCollisionEnergies.Count == 0) {
strCollisionEnergies = string.Empty;
} else if (lstCollisionEnergies.Count >= 1) {
strCollisionEnergies = lstCollisionEnergies[0].ToString("0.0");
if (lstCollisionEnergies.Count > 1) {
for (var intIndex = 1; intIndex <= lstCollisionEnergies.Count - 1; intIndex++) {
strCollisionEnergies += ", " + lstCollisionEnergies[intIndex].ToString("0.0");
}
}
}
if (string.IsNullOrEmpty(strCollisionEnergies)) {
Console.WriteLine();
} else {
Console.WriteLine("; CE " + strCollisionEnergies);
}
string monoMZ;
string chargeState;
string isolationWidth;
if (oScanInfo.TryGetScanEvent("Monoisotopic M/Z:", out monoMZ, false)) {
Console.WriteLine("Monoisotopic M/Z: " + monoMZ);
}
if (oScanInfo.TryGetScanEvent("Charge State", out chargeState, true))
{
Console.WriteLine("Charge State: " + chargeState);
}
if (oScanInfo.TryGetScanEvent("MS2 Isolation Width", out isolationWidth, true))
{
Console.WriteLine("MS2 Isolation Width: " + isolationWidth);
}
if (iScanNum % 50 == 0 || scanEnd - scanStart <= 50) {
// Get the data for scan iScanNum
Console.WriteLine();
Console.WriteLine("Spectrum for scan " + iScanNum);
double[] dblMzList;
double[] dblIntensityList;
var intDataCount = oReader.GetScanData(iScanNum, out dblMzList, out dblIntensityList, 0, centroid);
var mzDisplayStepSize = 50;
if (centroid) {
mzDisplayStepSize = 1;
}
for (var iDataPoint = 0; iDataPoint <= dblMzList.Length - 1; iDataPoint += mzDisplayStepSize) {
Console.WriteLine(" " + dblMzList[iDataPoint].ToString("0.000") + " mz " + dblIntensityList[iDataPoint].ToString("0"));
}
Console.WriteLine();
const int scansToSum = 15;
if (iScanNum + scansToSum < iNumScans & testSumming) {
// Get the data for scan iScanNum through iScanNum + 15
double[,] dblMassIntensityPairs;
var dataCount = oReader.GetScanDataSumScans(iScanNum, iScanNum + scansToSum, out dblMassIntensityPairs, 0, centroid);
Console.WriteLine("Summed spectrum, scans " + iScanNum + " through " + (iScanNum + scansToSum));
for (var iDataPoint = 0; iDataPoint <= dblMassIntensityPairs.GetLength(1) - 1; iDataPoint += 50) {
Console.WriteLine(" " + dblMassIntensityPairs[0, iDataPoint].ToString("0.000") + " mz " + dblMassIntensityPairs[1, iDataPoint].ToString("0"));
}
Console.WriteLine();
}
if (oScanInfo.IsFTMS) {
udtFTLabelInfoType[] ftLabelData;
var dataCount = oReader.GetScanLabelData(iScanNum, out ftLabelData);
Console.WriteLine();
Console.WriteLine("{0,12}{1,12}{2,12}{3,12}{4,12}{5,12}", "Mass", "Intensity", "Resolution", "Baseline", "Noise", "Charge");
for (var iDataPoint = 0; iDataPoint <= dataCount - 1; iDataPoint += 50) {
Console.WriteLine("{0,12}{1,12}{2,12}{3,12}{4,12}{5,12}", ftLabelData[iDataPoint].Mass.ToString("0.000"), ftLabelData[iDataPoint].Intensity.ToString("0"), ftLabelData[iDataPoint].Resolution.ToString("0"), ftLabelData[iDataPoint].Baseline.ToString("0.0"), ftLabelData[iDataPoint].Noise.ToString("0"), ftLabelData[iDataPoint].Charge.ToString("0"));
}
udtMassPrecisionInfoType[] ftPrecisionData;
dataCount = oReader.GetScanPrecisionData(iScanNum, out ftPrecisionData);
Console.WriteLine();
Console.WriteLine("{0,12}{1,12}{2,12}{3,12}{4,12}", "Mass", "Intensity", "AccuracyMMU", "AccuracyPPM", "Resolution");
for (var iDataPoint = 0; iDataPoint <= dataCount - 1; iDataPoint += 50) {
Console.WriteLine("{0,12}{1,12}{2,12}{3,12}{4,12}", ftPrecisionData[iDataPoint].Mass.ToString("0.000"), ftPrecisionData[iDataPoint].Intensity.ToString("0"), ftPrecisionData[iDataPoint].AccuracyMMU.ToString("0.000"), ftPrecisionData[iDataPoint].AccuracyPPM.ToString("0.000"), ftPrecisionData[iDataPoint].Resolution.ToString("0"));
}
}
}
}
}
}
} catch (Exception ex) {
Console.WriteLine("Error in sub TestReader: " + ex.Message);
}
}
private static void ShowMethod(XRawFileIO oReader)
{
try
{
var intIndex = 0;
foreach (var method in oReader.FileInfo.InstMethods) {
if (intIndex == 0 & oReader.FileInfo.InstMethods.Count == 1) {
} else {
}
Console.WriteLine("Instrument model: " + oReader.FileInfo.InstModel);
Console.WriteLine("Instrument name: " + oReader.FileInfo.InstName);
Console.WriteLine("Instrument description: " + oReader.FileInfo.InstrumentDescription);
Console.WriteLine("Instrument serial number: " + oReader.FileInfo.InstSerialNumber);
Console.WriteLine();
Console.WriteLine(method);
intIndex++;
}
} catch (Exception ex)
{
Console.WriteLine("Error loading the MS Method: " + ex.Message);
}
}
