public void SpeedTest1()
{
var fileName = FileRefs.RawDataMSFiles.OrbitrapStdFile1;
var run = new RunFactory().CreateRun(fileName);
run.ScanSetCollection.Create(run, 5500, 5550, 1, 1, false);
var msgen = MSGeneratorFactory.CreateMSGenerator(run.MSFileType);
var peakBr = 1.3;//0.25;
var peakDetector = new DeconToolsPeakDetectorV2(peakBr, 2, DeconTools.Backend.Globals.PeakFitType.QUADRATIC, true);
var thrashParameters = new ThrashParameters();
thrashParameters.MinMSFeatureToBackgroundRatio = peakBr;
thrashParameters.MaxFit = 0.4;
var newDeconvolutor = new InformedThrashDeconvolutor(thrashParameters);
var watch = new Stopwatch();
watch.Start();
foreach (var scanSet in run.ScanSetCollection.ScanSetList)
{
run.CurrentScanSet = scanSet;
msgen.Execute(run.ResultCollection);
peakDetector.Execute(run.ResultCollection);
run.CurrentScanSet.BackgroundIntensity = peakDetector.BackgroundIntensity;
newDeconvolutor.Execute(run.ResultCollection);
}
watch.Stop();
Console.WriteLine("Time per scan (INFORMED) = " + watch.ElapsedMilliseconds / run.ScanSetCollection.ScanSetList.Count);
}
public void CompareToScottsData1()
{
var fileName = FileRefs.RawDataMSFiles.OrbitrapStdFile1;
var run = new RunFactory().CreateRun(fileName);
run.ScanSetCollection.Create(run, 5509, 5509, 1, 1, false);
var msgen = MSGeneratorFactory.CreateMSGenerator(run.MSFileType);
var peakBr = 1.9;//1.3;
var peakDetector = new DeconToolsPeakDetectorV2(peakBr, 2, DeconTools.Backend.Globals.PeakFitType.QUADRATIC, true);
var thrashParameters = new ThrashParameters();
thrashParameters.MinMSFeatureToBackgroundRatio = peakBr;
thrashParameters.MaxFit = 0.4;
var newDeconvolutor = new InformedThrashDeconvolutor(thrashParameters);
var scanset = new ScanSet(5509);
run.CurrentScanSet = scanset;
msgen.Execute(run.ResultCollection);
peakDetector.Execute(run.ResultCollection);
run.CurrentScanSet.BackgroundIntensity = peakDetector.BackgroundIntensity;
newDeconvolutor.Execute(run.ResultCollection);
var scottMzVals = ReadScottsAnnotationsScan5509().ToArray();
var myMzVals = run.ResultCollection.ResultList.Select(p => p.IsotopicProfile.MonoPeakMZ).OrderBy(p => p).ToArray();
var comparisions = new Dictionary <decimal, double>();
foreach (var scottVal in scottMzVals)
{
var tolerance = 0.01;
var indexInThrash = MathUtils.BinarySearchWithTolerance(myMzVals, scottVal, 0, myMzVals.Length - 1, tolerance);
var myMzVal = indexInThrash == -1 ? 0.0d : myMzVals[indexInThrash];
comparisions.Add((decimal)scottVal, myMzVal);
}
var numCorrect = comparisions.Values.Count(p => p > 0);
var numMissing = scottMzVals.Count() - numCorrect;
Console.WriteLine("Total annotated= \t" + scottMzVals.Count());
Console.WriteLine("Number correct = \t" + numCorrect);
Console.WriteLine("Number missing = \t" + numMissing);
}
public static Deconvolutor CreateDeconvolutor(DeconToolsParameters parameters)
{
Check.Require(parameters != null, "Factory cannot create Deconvolutor class. DeconToolsParameters are null.");
if (parameters == null)
{
return(new NullDeconvolutor());
}
Deconvolutor decon;
switch (parameters.ScanBasedWorkflowParameters.DeconvolutionType)
{
case Globals.DeconvolutionType.None:
return(new NullDeconvolutor());
case Globals.DeconvolutionType.ThrashV1:
// 2016 Port of ThrashV1 in DeconEngineV2 to C#, .NET 4
// This is the preferred deconvoluter as of Fall 2017
decon = new HornDeconvolutor(parameters);
return(decon);
case Globals.DeconvolutionType.ThrashV2:
// 2012 port of DeconEngine to C#
// As of 2016, not used because results do not agree with ThrashV1, C++
#pragma warning disable 618
decon = new InformedThrashDeconvolutor(parameters.ThrashParameters);
#pragma warning restore 618
return(decon);
case Globals.DeconvolutionType.Rapid:
// To include support for Rapid, you must add a reference to DeconEngine.dll, which was compiled with Visual Studio 2003 and uses MSVCP71.dll
// Note that DeconEngine.dll also depends on xerces-c_2_7.dll while DeconEngineV2.dll depends on xerces-c_2_8.dll
#if INCLUDE_RAPID
return(new RapidDeconvolutor(parameters.ThrashParameters.MinMSFeatureToBackgroundRatio,
Deconvolutor.DeconResultComboMode.simplyAddIt));
#else
throw new NotSupportedException("Support for Rapid is not included in this version of the DLL");
#endif
default:
throw new ArgumentOutOfRangeException(nameof(parameters),
"Trying to create the deconvolutor, but an incorrect Deconvolutor type was given. Good example: 'ThrashV1'");
}
}
public void Stolen_ThrashV2OnOrbitrapTest1()
{
//Run run = new XCaliburRun2(FileRefs.RawDataMSFiles.OrbitrapStdFile1);
var fileName =
@"\\protoapps\UserData\Slysz\DeconTools_TestFiles\Orbitrap\QC_Shew_08_04-pt5-2_11Jan09_Sphinx_08-11-18.raw";
//Run run = RunUtilities.CreateAndLoadPeaks(fileName);
var run = new RunFactory().CreateRun(fileName);
run.ScanSetCollection.Create(run, 6005, 6005, 1, 1, false);
var msgen = MSGeneratorFactory.CreateMSGenerator(run.MSFileType);
var peakDetector = new DeconToolsPeakDetectorV2(1.3, 2, Globals.PeakFitType.QUADRATIC, true);
peakDetector.IsDataThresholded = true;
var parameters = new ThrashParameters();
parameters.MinMSFeatureToBackgroundRatio = 1;
parameters.MaxFit = 0.3;
var deconvolutor = new InformedThrashDeconvolutor(parameters);
//var deconvolutor2 = new
var scan = new ScanSet(6005);
run.CurrentScanSet = scan;
msgen.Execute(run.ResultCollection);
peakDetector.Execute(run.ResultCollection);
deconvolutor.Execute(run.ResultCollection);
Console.WriteLine(run.ResultCollection.MSPeakResultList);
// TestUtilities.DisplayMSFeatures(run.ResultCollection.ResultList);
Assert.IsTrue(run.ResultCollection.ResultList.Count > 0);
//Assert.AreEqual(187, 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 static Deconvolutor CreateDeconvolutor(DeconToolsParameters parameters)
{
Check.Require(parameters != null, "Factory cannot create Deconvolutor class. DeconToolsParameters are null.");
Deconvolutor decon;
switch (parameters.ScanBasedWorkflowParameters.DeconvolutionType)
{
case Globals.DeconvolutionType.None:
return(new NullDeconvolutor());
case Globals.DeconvolutionType.ThrashV1:
//#if Disable_DeconToolsV2
// throw new NotSupportedException(
// "Deconvolution method ThrashV1 is not supported since support for C++ based DeconToolsV2 is disabled; update the parameter file to use <DeconvolutionType>ThrashV2</DeconvolutionType>");
//#else
decon = new HornDeconvolutor(parameters);
return(decon);
//#endif
case Globals.DeconvolutionType.ThrashV2:
decon = new InformedThrashDeconvolutor(parameters.ThrashParameters);
return(decon);
case Globals.DeconvolutionType.Rapid:
// To include support for Rapid, you must add a reference to DeconEngine.dll, which was compiled with Visual Studio 2003 and uses MSVCP71.dll
// Note that DeconEngine.dll also depends on xerces-c_2_7.dll while DeconEngineV2.dll depends on xerces-c_2_8.dll
#if INCLUDE_RAPID
return(new RapidDeconvolutor(parameters.ThrashParameters.MinMSFeatureToBackgroundRatio,
Deconvolutor.DeconResultComboMode.simplyAddIt));
#else
throw new NotSupportedException("Support for Rapid is not included in this version of the DLL");
#endif
default:
throw new ArgumentOutOfRangeException("parameters",
"Trying to create the deconvolutor, but an incorrect Deconvolutor type was given. Good example: 'ThrashV1'");
}
}
public void TestAndComparingScottsData()
{
var fileName = @"\\protoapps\UserData\Slysz\DeconTools_TestFiles\Orbitrap\QC_Shew_08_04-pt5-2_11Jan09_Sphinx_08-11-18.raw";
var run = new RunFactory().CreateRun(fileName);
run.ScanSetCollection.Create(run, 5509, 5509, 1, 1, false);
var msgen = MSGeneratorFactory.CreateMSGenerator(run.MSFileType);
var peakBr = 0.5;
var peakDetector = new DeconToolsPeakDetectorV2(peakBr, 2, DeconTools.Backend.Globals.PeakFitType.QUADRATIC, true);
var thrashParameters = new ThrashParameters();
thrashParameters.MinMSFeatureToBackgroundRatio = peakBr;//3;
thrashParameters.MaxFit = 0.4;
//var newDeconvolutor = new ThrashDeconvolutorV2(thrashParameters);
var newDeconvolutor = new InformedThrashDeconvolutor(thrashParameters);
var scanset = new ScanSet(5509);
//For summing mass spectra:
//scanset = new ScanSetFactory().CreateScanSet(run, 6005, 5);
run.CurrentScanSet = scanset;
var oldDeconvolutor = new HornDeconvolutor();
oldDeconvolutor.MinPeptideBackgroundRatio = peakBr;
oldDeconvolutor.MaxFitAllowed = 0.4;
msgen.Execute(run.ResultCollection);
peakDetector.Execute(run.ResultCollection);
//run.PeakList = run.PeakList.Where(p => p.XValue > 634 && p.XValue < 642).ToList();
//run.DeconToolsPeakList = run.DeconToolsPeakList.Where(p => p.mdbl_mz > 634 && p.mdbl_mz < 642).ToArray();
run.CurrentScanSet.BackgroundIntensity = peakDetector.BackgroundIntensity;
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);
//return;
// DisplayPPMErrorsForeachPeakOfMSFeature(newResults);
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>();
GetComparisons(newResults, oldResults, sharedIsos, uniqueToNew, uniqueToOld);
var scottsData = GetScottsData();
var scottsDataArray = scottsData.ToArray();
GetScottComparisons(sharedIsos, uniqueToNew, uniqueToOld, scottsDataArray);
Console.WriteLine("\n--------------Common to new and Old ------------------");
TestUtilities.DisplayMSFeatures(sharedIsos);
Console.WriteLine("\n--------------Unique to new ------------------");
TestUtilities.DisplayMSFeatures(uniqueToNew);
var outputFilename = @"C:\Temp\ThrashTesting\exportedIsos.csv";
var exporter = IsosExporterFactory.CreateIsosExporter(run.ResultCollection.ResultType, Globals.ExporterType.Text, outputFilename);
exporter.ExportIsosResults(uniqueToNew);
Console.WriteLine("\n--------------Unique to old ------------------");
TestUtilities.DisplayMSFeatures(uniqueToOld);
}
