public void Test1()
{
var run =
new RunFactory().CreateRun(
@"D:\Data\From_Joe\MyDeconToolsTester\RawFiles\Transition_Selection_Orbitrap_HCD_8Mar13_Cougar_12-12-36.raw");
Assert.IsNotNull(run);
var msGen = MSGeneratorFactory.CreateMSGenerator(run.MSFileType);
int testScan = 2448;
run.CurrentScanSet = new ScanSet(testScan);
DeconToolsPeakDetectorV2 ms1PeakDetector = new DeconToolsPeakDetectorV2();
ms1PeakDetector.PeakToBackgroundRatio = 1.3;
ms1PeakDetector.SignalToNoiseThreshold = 2;
ms1PeakDetector.IsDataThresholded = true;
DeconToolsPeakDetectorV2 ms2PeakDetectorForCentroidedData = new DeconToolsPeakDetectorV2();
DeconToolsPeakDetectorV2 ms2PeakDetectorForProfileData = new DeconToolsPeakDetectorV2();
ms2PeakDetectorForProfileData = new DeconToolsPeakDetectorV2();
ms2PeakDetectorForProfileData.PeakToBackgroundRatio = ms1PeakDetector.PeakToBackgroundRatio;
ms2PeakDetectorForProfileData.SignalToNoiseThreshold = ms1PeakDetector.SignalToNoiseThreshold;
ms2PeakDetectorForProfileData.IsDataThresholded = ms1PeakDetector.IsDataThresholded;
ms2PeakDetectorForCentroidedData = new DeconToolsPeakDetectorV2(0, 0, Globals.PeakFitType.QUADRATIC, true);
ms2PeakDetectorForCentroidedData.RawDataType = Globals.RawDataType.Centroided;
run.ScanSetCollection.Create(run, testScan, testScan, 1, 1, true);
Console.WriteLine("scan\tz\tinfo");
foreach (var scan in run.ScanSetCollection.ScanSetList)
{
run.CurrentScanSet = scan;
msGen.Execute(run.ResultCollection);
if (run.GetMSLevel(scan.PrimaryScanNumber) == 1)
{
ms1PeakDetector.Execute(run.ResultCollection);
}
else
{
var dataIsCentroided = run.IsDataCentroided(scan.PrimaryScanNumber);
Console.WriteLine("Scan " + scan.PrimaryScanNumber + "centroided=" + dataIsCentroided);
TestUtilities.DisplayXYValues(run.XYData);
if (dataIsCentroided)
{
ms2PeakDetectorForCentroidedData.Execute(run.ResultCollection);
}
else
{
ms2PeakDetectorForProfileData.Execute(run.ResultCollection);
}
}
Console.WriteLine("---- peaks for Scan " + scan);
TestUtilities.DisplayPeaks(run.PeakList);
}
}
