public void MSGeneratorOnUIMFTest1()
{
var uimfFile = FileRefs.RawDataMSFiles.UIMFStdFile3;
var run = new RunFactory().CreateRun(uimfFile);
var msgen = MSGeneratorFactory.CreateMSGenerator(run.MSFileType);
var peakDetector = new DeconToolsPeakDetectorV2(1.3, 2, Globals.PeakFitType.QUADRATIC, true);
var zeroFiller = new DeconTools.Backend.ProcessingTasks.ZeroFillers.DeconToolsZeroFiller(3);
var thrashParameters = new ThrashParameters();
thrashParameters.MinMSFeatureToBackgroundRatio = 1;
thrashParameters.MaxFit = 0.4;
var newDeconvolutor = new ThrashDeconvolutorV2(thrashParameters);
var testLCScan = 500;
var testIMSScan = 120;
var numIMSScanSummed = 7;
var lowerIMSScan = testIMSScan - (numIMSScanSummed - 1) / 2;
var upperIMSScan = testIMSScan + (numIMSScanSummed - 1) / 2;
var scanSet = new ScanSetFactory().CreateScanSet(run, testLCScan, 1);
run.CurrentScanSet = scanSet;
((UIMFRun)run).CurrentIMSScanSet = new IMSScanSet(testIMSScan, lowerIMSScan, upperIMSScan);
msgen.Execute(run.ResultCollection);
Assert.IsTrue(run.XYData.Xvalues.Length > 100);
}
public void ThrashV2OnIMSDataTest1()
{
var uimfFile =
@"\\protoapps\UserData\Slysz\DeconTools_TestFiles\UIMF\Sarc_MS2_90_6Apr11_Cheetah_11-02-19.uimf";
var run = new RunFactory().CreateRun(uimfFile);
var msgen = MSGeneratorFactory.CreateMSGenerator(run.MSFileType);
var peakDetector = new DeconToolsPeakDetectorV2(1.3, 2, Globals.PeakFitType.QUADRATIC, true);
var zeroFiller = new DeconTools.Backend.ProcessingTasks.ZeroFillers.DeconToolsZeroFiller(3);
var thrashParameters = new ThrashParameters();
thrashParameters.MinMSFeatureToBackgroundRatio = 1;
thrashParameters.MaxFit = 0.4;
var newDeconvolutor = new ThrashDeconvolutorV2(thrashParameters);
var testLCScan = 500;
var testIMSScan = 120;
var numIMSScanSummed = 7;
var lowerIMSScan = testIMSScan - (numIMSScanSummed - 1) / 2;
var upperIMSScan = testIMSScan + (numIMSScanSummed - 1) / 2;
var scanSet = new ScanSetFactory().CreateScanSet(run, testLCScan, 1);
run.CurrentScanSet = scanSet;
((UIMFRun)run).CurrentIMSScanSet = new IMSScanSet(testIMSScan, lowerIMSScan, upperIMSScan);
msgen.Execute(run.ResultCollection);
zeroFiller.Execute(run.ResultCollection);
peakDetector.Execute(run.ResultCollection);
newDeconvolutor.Execute(run.ResultCollection);
TestUtilities.DisplayMSFeatures(run.ResultCollection.ResultList);
Assert.IsTrue(run.ResultCollection.ResultList.Count > 0);
Assert.AreEqual(33, run.ResultCollection.ResultList.Count);
var result1 = run.ResultCollection.ResultList[0];
Assert.AreEqual(13084442, (decimal)Math.Round(result1.IntensityAggregate));
Assert.AreEqual(960.53365m, (decimal)Math.Round(result1.IsotopicProfile.MonoIsotopicMass, 5));
Assert.AreEqual(2, result1.IsotopicProfile.ChargeState);
}
public void find_targetMassTag_131959Test1()
{
var run = new RunFactory().CreateRun(xcaliburTestfile);
var masstagImporter = new MassTagFromTextFileImporter(massTagTestList1);
var massTagColl = masstagImporter.Import();
Assert.AreEqual(2719, massTagColl.TargetList.Count);
var chromAligner = new ChromAlignerUsingVIPERInfo();
chromAligner.Execute(run);
var peakImporter = new DeconTools.Backend.Data.PeakImporterFromText(xcaliburAllPeaksFile);
peakImporter.ImportPeaks(run.ResultCollection.MSPeakResultList);
//int mtID = 635428;
var mtID = 131959;
Task peakChromGen = new PeakChromatogramGenerator(20);
Task smoother = new DeconTools.Backend.ProcessingTasks.Smoothers.SavitzkyGolaySmoother(23, 2);
Task zeroFill = new DeconTools.Backend.ProcessingTasks.ZeroFillers.DeconToolsZeroFiller(3);
Task peakDet = new DeconTools.Backend.ProcessingTasks.PeakDetectors.ChromPeakDetector(0.5, 1);
Task msPeakDet = new DeconToolsPeakDetectorV2(1.3, 2, Globals.PeakFitType.QUADRATIC, true);
var basicChromPeakSelParam = new ChromPeakSelectorParameters();
basicChromPeakSelParam.NETTolerance = 0.1f;
basicChromPeakSelParam.PeakSelectorMode = Globals.PeakSelectorMode.ClosestToTarget;
Task chromPeakSel = new BasicChromPeakSelector(basicChromPeakSelParam);
Task msgen = MSGeneratorFactory.CreateMSGenerator(run.MSFileType);
run.CurrentMassTag = massTagColl.TargetList.Find(p => p.ID == mtID);
var mt = run.CurrentMassTag;
mt.MZ = mt.MonoIsotopicMass / mt.ChargeState + Globals.PROTON_MASS;
Task theorFeatureGen = new TomTheorFeatureGenerator(DeconTools.Backend.Globals.LabellingType.NONE, 0.005);
Task targetedFeatureFinder = new BasicTFF();
Task fitScoreCalc = new IsotopicProfileFitScoreCalculator();
theorFeatureGen.Execute(run.ResultCollection);
Console.WriteLine();
Console.WriteLine();
Console.WriteLine("------------------- MassTag = " + mt.ID + "---------------------------");
Console.WriteLine("monoMass = " + mt.MonoIsotopicMass.ToString("0.0000") + "; monoMZ = " + mt.MZ.ToString("0.0000") + "; ChargeState = " + mt.ChargeState + "; NET = " + mt.NormalizedElutionTime.ToString("0.000") + "; Sequence = " + mt.Code + "; EmpiricalFormula= " + mt.EmpiricalFormula + "\n");
peakChromGen.Execute(run.ResultCollection);
smoother.Execute(run.ResultCollection);
//TestUtilities.DisplayXYValues(run.ResultCollection);
peakDet.Execute(run.ResultCollection);
TestUtilities.DisplayPeaks(run.PeakList);
chromPeakSel.Execute(run.ResultCollection);
msgen.Execute(run.ResultCollection);
//TestUtilities.DisplayXYValues(run.ResultCollection);
msPeakDet.Execute(run.ResultCollection);
targetedFeatureFinder.Execute(run.ResultCollection);
fitScoreCalc.Execute(run.ResultCollection);
var massTagResult = run.ResultCollection.MassTagResultList[mt];
massTagResult.DisplayToConsole();
//Console.WriteLine("------------------------------ end --------------------------");
}
public void CompareOldAndNewDeconvolutorsUIMF()
{
var uimfFile =
@"\\protoapps\UserData\Slysz\DeconTools_TestFiles\UIMF\Sarc_MS2_90_6Apr11_Cheetah_11-02-19.uimf";
var run = new RunFactory().CreateRun(uimfFile);
var testLCScan = 500;
var testIMSScan = 120;
var numIMSScanSummed = 7;
var lowerIMSScan = testIMSScan - (numIMSScanSummed - 1) / 2;
var upperIMSScan = testIMSScan + (numIMSScanSummed - 1) / 2;
var scanSet = new ScanSetFactory().CreateScanSet(run, testLCScan, 1);
var msgen = MSGeneratorFactory.CreateMSGenerator(run.MSFileType);
var peakDetector = new DeconToolsPeakDetectorV2(1.3, 2, Globals.PeakFitType.QUADRATIC, true);
var zeroFiller = new DeconTools.Backend.ProcessingTasks.ZeroFillers.DeconToolsZeroFiller(3);
var thrashParameters = new ThrashParameters();
thrashParameters.MinMSFeatureToBackgroundRatio = 1;
thrashParameters.MaxFit = 0.4;
var newDeconvolutor = new ThrashDeconvolutorV2(thrashParameters);
var oldDeconvolutor = new HornDeconvolutor();
oldDeconvolutor.MinPeptideBackgroundRatio = 1;
oldDeconvolutor.MaxFitAllowed = 0.4;
run.CurrentScanSet = scanSet;
((UIMFRun)run).CurrentIMSScanSet = new IMSScanSet(testIMSScan, lowerIMSScan, upperIMSScan);
msgen.Execute(run.ResultCollection);
zeroFiller.Execute(run.ResultCollection);
//smoother.Execute(run.ResultCollection);
peakDetector.Execute(run.ResultCollection);
newDeconvolutor.Execute(run.ResultCollection);
//Console.WriteLine("\n--------------New decon ------------------");
//TestUtilities.DisplayMSFeatures(run.ResultCollection.ResultList);
var newResults = new List <IsosResult>(run.ResultCollection.ResultList);
// TestUtilities.DisplayMSFeatures(newResults);
//DisplayPPMErrorsForeachPeakOfMSFeature(newResults);
//return;
run.ResultCollection.ResultList.Clear();
run.ResultCollection.IsosResultBin.Clear();
oldDeconvolutor.Execute(run.ResultCollection);
var oldResults = new List <IsosResult>(run.ResultCollection.ResultList);
//Console.WriteLine("\n--------------Old decon ------------------");
//TestUtilities.DisplayMSFeatures(run.ResultCollection.ResultList);
var sharedIsos = new List <IsosResult>();
var uniqueToNew = new List <IsosResult>();
var uniqueToOld = new List <IsosResult>();
var toleranceForComparison = 0.05;
foreach (var newresult in newResults)
{
var foundMatch = false;
for (var i = 0; i < oldResults.Count; i++)
{
var oldResult = oldResults[i];
if (Math.Abs(newresult.IsotopicProfile.MonoIsotopicMass - oldResult.IsotopicProfile.MonoIsotopicMass) < toleranceForComparison &&
newresult.IsotopicProfile.ChargeState == oldResult.IsotopicProfile.ChargeState)
{
foundMatch = true;
}
}
if (foundMatch)
{
sharedIsos.Add(newresult);
}
else
{
uniqueToNew.Add(newresult);
}
}
foreach (var oldResult in oldResults)
{
var foundMatch = false;
for (var i = 0; i < newResults.Count; i++)
{
var newresult = newResults[i];
if (Math.Abs(newresult.IsotopicProfile.MonoIsotopicMass - oldResult.IsotopicProfile.MonoIsotopicMass) < toleranceForComparison &&
newresult.IsotopicProfile.ChargeState == oldResult.IsotopicProfile.ChargeState)
{
foundMatch = true;
}
}
if (!foundMatch)
{
uniqueToOld.Add(oldResult);
}
}
Console.WriteLine("\n--------------Common to new and Old ------------------");
TestUtilities.DisplayMSFeatures(sharedIsos);
Console.WriteLine("\n--------------Unique to new ------------------");
TestUtilities.DisplayMSFeatures(uniqueToNew);
Console.WriteLine("\n--------------Unique to old ------------------");
TestUtilities.DisplayMSFeatures(uniqueToOld);
}
