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);
}
}
}
}
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);
}
}