public UIMFRun()
{
XYData = new XYData();
MSFileType = Globals.MSFileType.PNNL_UIMF;
IMSScanSetCollection = new IMSScanSetCollection();
_framePressuresUnsmoothed = new Dictionary <int, double>();
//_frameTypeForMS1 = DataReader.FrameType.MS1; //default is MS1
}
public void BasePeakChromatogramTests()
{
var filename = @"D:\Data\UIMF\Sarc_P13_C10_1186_23Sep11_Cheetah_11-09-06.uimf";
var run = new RunFactory().CreateRun(filename);
var scanSetCollection = new ScanSetCollection();
//scanSetCollection.Create(run, 500, 550,1,1);
scanSetCollection.Create(run, run.MinLCScan, run.MaxLCScan, 1, 1);
var imsScanSetCollection = new IMSScanSetCollection();
imsScanSetCollection.Create(run, 60, 250, 1, 1);
var msgen = MSGeneratorFactory.CreateMSGenerator(run.MSFileType);
var peakDet = new DeconToolsPeakDetectorV2();
peakDet.PeakToBackgroundRatio = 4;
peakDet.SignalToNoiseThreshold = 2;
peakDet.IsDataThresholded = true;
var outputFile = @"C:\Users\d3x720\Documents\PNNL\My_DataAnalysis\2013\Saturation_Correction\chromOuput.txt";
using (var writer = new StreamWriter(outputFile))
{
for (var lcscan = 0; lcscan < scanSetCollection.ScanSetList.Count; lcscan++)
{
Console.WriteLine("lcscan= " + lcscan);
var scanSet = scanSetCollection.ScanSetList[lcscan];
run.CurrentScanSet = scanSet;
var sb = new StringBuilder();
var numImsScans = imsScanSetCollection.ScanSetList.Count;
for (var imsScan = 0; imsScan < numImsScans; imsScan++)
{
var imsscanSet = (IMSScanSet)imsScanSetCollection.ScanSetList[imsScan];
((UIMFRun)run).CurrentIMSScanSet = imsscanSet;
var basePeakIntensity = 0;
try
{
msgen.Execute(run.ResultCollection);
peakDet.Execute(run.ResultCollection);
basePeakIntensity = GetMaxPeak(run.PeakList);
}
catch (Exception ex)
{
Console.WriteLine("skipping lcscan " + lcscan + " --- it is empty");
}
sb.Append(basePeakIntensity);
if (imsScan != numImsScans - 1) // if not the last value, add delimiter
{
sb.Append("\t");
}
}
writer.WriteLine(sb.ToString());
}
}
}
