public void Test1()
{
var rawfilename = @"D:\Data\O16O18\GlueGrant\GG_MO_Trauma_374020_20May11_Sphinx_11-03-28.RAW";
var exportedIsos = Path.Combine(Path.GetDirectoryName(rawfilename), Path.GetFileName(rawfilename).Replace(".RAW", "_test_isos.csv"));
if (File.Exists(exportedIsos))
{
File.Delete(exportedIsos);
}
var run = new RunFactory().CreateRun(rawfilename);
run.ResultCollection.ResultType = Backend.Globals.ResultType.O16O18_TRADITIONAL_RESULT;
run.ScanSetCollection.Create(run, 5000, 5000, 1, 1);
run.CurrentScanSet = run.ScanSetCollection.ScanSetList[0];
var msgen = MSGeneratorFactory.CreateMSGenerator(run.MSFileType);
var peakDet = new DeconToolsPeakDetectorV2();
peakDet.PeakToBackgroundRatio = 1.3;
peakDet.SignalToNoiseThreshold = 2;
var decon = new HornDeconvolutor();
decon.IsO16O18Data = true;
var appender = new O16O18PeakDataAppender();
var exporter = IsosExporterFactory.CreateIsosExporter(run.ResultCollection.ResultType, Backend.Globals.ExporterType.Text, exportedIsos);
msgen.Execute(run.ResultCollection);
peakDet.Execute(run.ResultCollection);
decon.Execute(run.ResultCollection);
appender.Execute(run.ResultCollection);
var testResult = (O16O18IsosResult)run.ResultCollection.ResultList[1];
Assert.AreEqual(DeconTools.Backend.Globals.ResultType.O16O18_TRADITIONAL_RESULT, run.ResultCollection.ResultType);
Assert.AreEqual(5905390, testResult.IsotopicProfile.GetMonoAbundance());
Assert.AreEqual(3017899, testResult.MonoPlus2Abundance);
Assert.AreEqual(162389, testResult.MonoPlus4Abundance);
exporter.Execute(run.ResultCollection);
run.Close();
}
public void smartChromPeakSelectorTest_noSumming()
{
var run = new RunFactory().CreateRun(xcaliburTestfile);
run.Close();
run = new RunFactory().CreateRun(xcaliburTestfile);
var massTagColl = new TargetCollection();
var masstagImporter = new MassTagFromTextFileImporter(massTagTestList1);
massTagColl = masstagImporter.Import();
var chromAligner = new ChromAlignerUsingVIPERInfo();
chromAligner.Execute(run);
var theorFeatureGen = new TomTheorFeatureGenerator(DeconTools.Backend.Globals.LabellingType.NONE, 0.005);
var chromPeakDet = new ChromPeakDetector(0.5, 1);
var smartchromParam = new SmartChromPeakSelectorParameters();
var smartChromPeakSelector = new SmartChromPeakSelector(smartchromParam);
var basicChromParam = new ChromPeakSelectorParameters();
var basicChromPeakSelector = new BasicChromPeakSelector(basicChromParam);
var msgen = MSGeneratorFactory.CreateMSGenerator(run.MSFileType);
var iterativeTff = new IterativeTFF(new IterativeTFFParameters());
var fitscoreCalc = new IsotopicProfileFitScoreCalculator();
var testChromatogramDataFile = @"\\protoapps\UserData\Slysz\DeconTools_TestFiles\TargetedWorkflowStandards\massTag635428_chromatogramData.txt";
var xydata = TestUtilities.LoadXYDataFromFile(testChromatogramDataFile);
Assert.IsNotNull(xydata);
run.XYData = xydata;
// run.XYData.Display();
run.CurrentMassTag = massTagColl.TargetList.Where(p => p.ID == 635428).First();
Console.WriteLine("------MT = " + run.CurrentMassTag.ToString());
theorFeatureGen.Execute(run.ResultCollection);
chromPeakDet.Execute(run.ResultCollection);
var result = run.ResultCollection.GetTargetedResult(run.CurrentMassTag);
//first run the standard peak selector
basicChromPeakSelector.Execute(run.ResultCollection);
Assert.AreEqual(10066, (int)Math.Round(result.ChromPeakSelected.XValue));
//now run the smart chrom peak selector
run.XYData = xydata;
chromPeakDet.Execute(run.ResultCollection);
smartChromPeakSelector.Parameters.NETTolerance = 0.025f;
smartChromPeakSelector.Execute(run.ResultCollection);
msgen.Execute(run.ResultCollection);
iterativeTff.Execute(run.ResultCollection);
TestUtilities.DisplayPeaks(run.PeakList);
fitscoreCalc.Execute(run.ResultCollection);
Assert.AreEqual(9579, (int)Math.Round(result.ChromPeakSelected.XValue));
//result.DisplayToConsole();
TestUtilities.DisplayIsotopicProfileData(result.Target.IsotopicProfile);
}
