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);
}
public void smartChromPeakSelectorTest_withDynamicSumming()
{
var 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 basicChromPeakSelector = new BasicChromPeakSelector(new ChromPeakSelectorParameters());
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 = new XYData();
run.XYData.Xvalues = xydata.Xvalues;
run.XYData.Yvalues = xydata.Yvalues;
// 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);
//first run the standard peak selector
basicChromPeakSelector.Execute(run.ResultCollection);
var result = run.ResultCollection.GetTargetedResult(run.CurrentMassTag);
Assert.AreEqual(10066, (int)Math.Round(result.ChromPeakSelected.XValue));
//now run the smart chrom peak selector
run.XYData = new XYData();
run.XYData.Xvalues = xydata.Xvalues;
run.XYData.Yvalues = xydata.Yvalues;
chromPeakDet.Execute(run.ResultCollection);
smartChromPeakSelector.Parameters.NETTolerance = 0.025f;
smartChromPeakSelector.Parameters.MaxScansSummedInDynamicSumming = 51;
smartChromPeakSelector.Parameters.SummingMode = SummingModeEnum.SUMMINGMODE_DYNAMIC;
smartChromPeakSelector.Parameters.AreaOfPeakToSumInDynamicSumming = 1;
smartChromPeakSelector.Execute(run.ResultCollection);
msgen.Execute(run.ResultCollection);
iterativeTff.Execute(run.ResultCollection);
fitscoreCalc.Execute(run.ResultCollection);
Console.WriteLine(result.ScanSet);
Assert.AreEqual(14, result.ScanSet.IndexValues.Count);
Assert.AreEqual(0.0104m, (decimal)Math.Round(result.Score, 4));
Assert.AreEqual("9575 {9534, 9540, 9547, 9554, 9561, 9568, 9575, 9582, 9589, 9596, 9603, 9610, 9617, 9624}", result.ScanSet.ToString());
run.XYData = new XYData();
run.XYData.Xvalues = xydata.Xvalues;
run.XYData.Yvalues = xydata.Yvalues;
chromPeakDet.Execute(run.ResultCollection);
smartChromPeakSelector.Parameters.NETTolerance = 0.025f;
smartChromPeakSelector.Parameters.MaxScansSummedInDynamicSumming = 51;
smartChromPeakSelector.Parameters.SummingMode = SummingModeEnum.SUMMINGMODE_DYNAMIC;
smartChromPeakSelector.Parameters.AreaOfPeakToSumInDynamicSumming = 2;
smartChromPeakSelector.Execute(run.ResultCollection);
msgen.Execute(run.ResultCollection);
iterativeTff.Execute(run.ResultCollection);
fitscoreCalc.Execute(run.ResultCollection);
result.DisplayToConsole();
Assert.AreEqual(9579, (int)Math.Round(result.ChromPeakSelected.XValue));
Assert.AreEqual(0.025m, (decimal)(Math.Round(result.Score, 4)));
//Console.WriteLine(result.ScanSet);
Assert.AreEqual(26, result.ScanSet.IndexValues.Count);
Assert.AreEqual("9575 {9493, 9500, 9506, 9513, 9520, 9527, 9534, 9540, 9547, 9554, 9561, 9568, 9575, 9582, 9589, 9596, 9603, 9610, 9617, 9624, 9631, 9638, 9645, 9652, 9658, 9665}", result.ScanSet.ToString());
}