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);
}
}
}
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);
}
}