/// <summary>
/// Gets the LC Scanset used in generating a mass spectrum, based on the width of the Chrom peak.
/// </summary>
/// <param name="chromPeak"></param>
/// <param name="run"></param>
/// <param name="peakWidthInSigma">number of sigma. In Gaussian peak theory, 4 sigma is often used to define
/// the base of a Gaussian peak. 2.35 sigma is the peak at half height. </param>
/// <param name="maxScansToSum"></param>
/// <returns></returns>
public ScanSet GetLCScanSetForChromPeakBasedOnPeakWidth(Peak chromPeak, Run run, double peakWidthInSigma = 2, int maxScansToSum = 100)
{
ScanSet scanset;
if (chromPeak == null || chromPeak.XValue == 0)
{
return(null);
//throw new NullReferenceException("Trying to use chromPeak to generate mass spectrum, but chrompeak is null");
}
var bestScan = (int)chromPeak.XValue;
bestScan = run.GetClosestMSScan(bestScan, DeconTools.Backend.Globals.ScanSelectionMode.CLOSEST);
var sigma = chromPeak.Width / 2.35;
var lowerScan = (int)Math.Round(chromPeak.XValue - (peakWidthInSigma * sigma / 2));
var closestLowerScan = run.GetClosestMSScan(lowerScan, DeconTools.Backend.Globals.ScanSelectionMode.CLOSEST);
var upperScan = (int)Math.Round(chromPeak.XValue + (peakWidthInSigma * sigma / 2));
var closestUpperScan = run.GetClosestMSScan(upperScan, DeconTools.Backend.Globals.ScanSelectionMode.CLOSEST);
scanset = _scansetFactory.CreateScanSet(run, bestScan, closestLowerScan, closestUpperScan);
_scansetFactory.TrimScans(scanset, maxScansToSum);
if (run.MSFileType == DeconTools.Backend.Globals.MSFileType.PNNL_UIMF)
{
// GORD: Update this when fixing CurrentFrameSet
throw new NotSupportedException("UIMF worflows should use a UIMF specific peak selector.");
}
return(scanset);
}
public void TrimScansTest1()
{
var startScan = 5970;
var stopScan = 6035;
var rf = new RunFactory();
var run = rf.CreateRun(FileRefs.RawDataMSFiles.OrbitrapStdFile1);
var ssf = new ScanSetFactory();
var scan = ssf.CreateScanSet(run, 6005, startScan, stopScan);
Assert.AreEqual("6005 {5970, 5977, 5984, 5991, 5998, 6005, 6012, 6019, 6026, 6033}", scan.ToString());
var maxScansAllowed = 7;
ssf.TrimScans(scan, maxScansAllowed);
Assert.AreEqual("6005 {5984, 5991, 5998, 6005, 6012, 6019}", scan.ToString());
}
