/// <summary>
/// Test ScanOrAcqTimeToAbsolute
/// </summary>
/// <param name="scanList"></param>
/// <param name="scanNumScanConverter"></param>
/// <param name="scanNumber">Absolute scan number</param>
/// <param name="relativeTime">Relative scan (value between 0 and 1)</param>
/// <param name="scanTime">Scan time</param>
private void TestScanConversionToAbsolute(
clsScanList scanList,
clsScanNumScanTimeConversion scanNumScanConverter,
KeyValuePair <int, int> scanNumber,
KeyValuePair <float, float> relativeTime,
KeyValuePair <float, float> scanTime)
{
try
{
// Find the scan number corresponding to each of these values
float result1 = scanNumScanConverter.ScanOrAcqTimeToAbsolute(scanList, scanNumber.Key, clsCustomSICList.eCustomSICScanTypeConstants.Absolute, false);
Console.WriteLine(scanNumber.Key + " -> " + result1);
Assert.AreEqual(scanNumber.Value, result1, 1E-05);
float result2 = scanNumScanConverter.ScanOrAcqTimeToAbsolute(scanList, relativeTime.Key, clsCustomSICList.eCustomSICScanTypeConstants.Relative, false);
Console.WriteLine(relativeTime.Key + " -> " + result2);
Assert.AreEqual(relativeTime.Value, result2, 1E-05);
float result3 = scanNumScanConverter.ScanOrAcqTimeToAbsolute(scanList, scanTime.Key, clsCustomSICList.eCustomSICScanTypeConstants.AcquisitionTime, false);
Console.WriteLine(scanTime.Key + " -> " + result3);
Assert.AreEqual(scanTime.Value, result3, 1E-05);
Console.WriteLine();
}
catch (Exception ex)
{
Console.WriteLine("Error caught: " + ex.Message);
}
}
public void TestScanConversions()
{
const double MZ_MINIMUM = 100;
const float INTENSITY_MINIMUM = 10000;
const float SCAN_TIME_SCALAR = 10;
var scanList = new clsScanList();
var oRand = new Random();
var intLastSurveyScanIndexInMasterSeqOrder = -1;
// Populate scanList with example scan data
for (var scanNumber = 1; scanNumber <= 1750; scanNumber++)
{
if (scanNumber % 10 == 0)
{
// Add a survey scan
// If this is a mzXML file that was processed with ReadW, .ScanHeaderText and .ScanTypeName will get updated by UpdateMSXMLScanType
var newSurveyScan = new MASIC.clsScanInfo
{
ScanNumber = scanNumber,
ScanTime = scanNumber / SCAN_TIME_SCALAR,
ScanHeaderText = string.Empty,
ScanTypeName = "MS",
BasePeakIonMZ = MZ_MINIMUM + oRand.NextDouble() * 1000,
BasePeakIonIntensity = INTENSITY_MINIMUM + (float)oRand.NextDouble() * 1000
};
// Survey scans typically lead to multiple parent ions; we do not record them here
newSurveyScan.FragScanInfo.ParentIonInfoIndex = -1;
newSurveyScan.TotalIonIntensity = newSurveyScan.BasePeakIonIntensity * (float)(0.25 + oRand.NextDouble() * 5);
// Determine the minimum positive intensity in this scan
newSurveyScan.MinimumPositiveIntensity = INTENSITY_MINIMUM;
// If this is a mzXML file that was processed with ReadW, then these values will get updated by UpdateMSXMLScanType
newSurveyScan.ZoomScan = false;
newSurveyScan.SIMScan = false;
newSurveyScan.MRMScanType = MRMScanTypeConstants.NotMRM;
newSurveyScan.LowMass = MZ_MINIMUM;
newSurveyScan.HighMass = Math.Max(newSurveyScan.BasePeakIonMZ * 1.1, MZ_MINIMUM * 10);
newSurveyScan.IsFTMS = false;
scanList.SurveyScans.Add(newSurveyScan);
var intLastSurveyScanIndex = scanList.SurveyScans.Count - 1;
scanList.AddMasterScanEntry(clsScanList.eScanTypeConstants.SurveyScan, intLastSurveyScanIndex);
intLastSurveyScanIndexInMasterSeqOrder = scanList.MasterScanOrderCount - 1;
}
else
{
// If this is a mzXML file that was processed with ReadW, .ScanHeaderText and .ScanTypeName will get updated by UpdateMSXMLScanType
var newFragScan = new MASIC.clsScanInfo
{
ScanNumber = scanNumber,
ScanTime = scanNumber / SCAN_TIME_SCALAR,
ScanHeaderText = string.Empty,
ScanTypeName = "MSn",
BasePeakIonMZ = MZ_MINIMUM + oRand.NextDouble() * 1000,
BasePeakIonIntensity = INTENSITY_MINIMUM + (float)oRand.NextDouble() * 1000
};
// 1 for the first MS/MS scan after the survey scan, 2 for the second one, etc.
newFragScan.FragScanInfo.FragScanNumber = (scanList.MasterScanOrderCount - 1) - intLastSurveyScanIndexInMasterSeqOrder;
newFragScan.FragScanInfo.MSLevel = 2;
newFragScan.TotalIonIntensity = newFragScan.BasePeakIonIntensity * (float)(0.25 + oRand.NextDouble() * 2);
// Determine the minimum positive intensity in this scan
newFragScan.MinimumPositiveIntensity = INTENSITY_MINIMUM;
// If this is a mzXML file that was processed with ReadW, then these values will get updated by UpdateMSXMLScanType
newFragScan.ZoomScan = false;
newFragScan.SIMScan = false;
newFragScan.MRMScanType = MRMScanTypeConstants.NotMRM;
newFragScan.MRMScanInfo.MRMMassCount = 0;
newFragScan.LowMass = MZ_MINIMUM;
newFragScan.HighMass = Math.Max(newFragScan.BasePeakIonMZ * 1.1, MZ_MINIMUM * 10);
newFragScan.IsFTMS = false;
scanList.FragScans.Add(newFragScan);
scanList.AddMasterScanEntry(clsScanList.eScanTypeConstants.FragScan, scanList.FragScans.Count - 1);
}
}
var scanNumScanConverter = new clsScanNumScanTimeConversion();
RegisterEvents(scanNumScanConverter);
// Convert absolute values
// Scan 500, relative scan 0.5, and the scan at 30 minutes
TestScanConversionToAbsolute(
scanList, scanNumScanConverter,
new KeyValuePair <int, int>(500, 500),
new KeyValuePair <float, float>(0.5F, 876),
new KeyValuePair <float, float>(30, 300));
TestScanConversionToTime(
scanList, scanNumScanConverter,
new KeyValuePair <int, int>(500, 50),
new KeyValuePair <float, float>(0.5F, 87.55F),
new KeyValuePair <float, float>(30, 30));
// Convert ranges
// 50 scans wide, 10% of the run, and 5 minutes
TestScanConversionToAbsolute(
scanList, scanNumScanConverter,
new KeyValuePair <int, int>(50, 50),
new KeyValuePair <float, float>(0.1F, 176),
new KeyValuePair <float, float>(5, 50));
TestScanConversionToTime(
scanList, scanNumScanConverter,
new KeyValuePair <int, int>(50, 5),
new KeyValuePair <float, float>(0.1F, 17.59F),
new KeyValuePair <float, float>(5, 5));
}
