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 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 ThrashPreferPlusOneChargeStateTest1()
{
Run run = new XCaliburRun2(FileRefs.RawDataMSFiles.OrbitrapStdFile1);
run.ScanSetCollection.Create(run, 6005, 6005, 1, 1, false);
var msgen = MSGeneratorFactory.CreateMSGenerator(run.MSFileType);
var peakDetector = new DeconToolsPeakDetectorV2(0.5, 2, Globals.PeakFitType.QUADRATIC, true);
peakDetector.IsDataThresholded = true;
var parameters = new ThrashParameters();
parameters.MinMSFeatureToBackgroundRatio = 1;
parameters.MaxFit = 0.3;
parameters.CheckAllPatternsAgainstChargeState1 = true;
var deconvolutor = new ThrashDeconvolutorV2(parameters);
var scan = new ScanSet(6005);
run.CurrentScanSet = scan;
msgen.Execute(run.ResultCollection);
peakDetector.Execute(run.ResultCollection);
run.PeakList = run.PeakList.Where(p => p.XValue > 750 && p.XValue < 753).ToList();
deconvolutor.Execute(run.ResultCollection);
Assert.IsTrue(run.ResultCollection.ResultList.Count > 0);
var result1 = run.ResultCollection.ResultList.First();
Assert.AreEqual(1, result1.IsotopicProfile.ChargeState);
Console.WriteLine("--------- Prefer +1 charge state ----------------");
TestUtilities.DisplayMSFeatures(run.ResultCollection.ResultList);
run.ResultCollection.ResultList.Clear();
run.ResultCollection.IsosResultBin.Clear();
deconvolutor.Parameters.CheckAllPatternsAgainstChargeState1 = false;
deconvolutor.Execute(run.ResultCollection);
Console.WriteLine("\n--------- No charge state bias ----------------");
TestUtilities.DisplayMSFeatures(run.ResultCollection.ResultList);
Assert.IsTrue(run.ResultCollection.ResultList.Count > 0);
result1 = run.ResultCollection.ResultList.First();
Assert.AreEqual(3, result1.IsotopicProfile.ChargeState);
}
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 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 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 void UIMFTesting1()
{
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(2, 2, DeconTools.Backend.Globals.PeakFitType.QUADRATIC, true);
var thrashParameters = new ThrashParameters();
thrashParameters.MinMSFeatureToBackgroundRatio = 2;
thrashParameters.MaxFit = 0.4;
var newDeconvolutor = new ThrashDeconvolutorV2(thrashParameters);
run.CurrentScanSet = scanSet;
((UIMFRun)run).CurrentIMSScanSet = new IMSScanSet(testIMSScan, lowerIMSScan, upperIMSScan);
msgen.Execute(run.ResultCollection);
peakDetector.Execute(run.ResultCollection);
//6 500 728.6907 729.69800 1 34678 0.252 0.000
run.PeakList = (from n in run.PeakList where n.XValue > 729 && n.XValue < 731 select n).ToList();
newDeconvolutor.Execute(run.ResultCollection);
TestUtilities.DisplayMSFeatures(run.ResultCollection.ResultList);
}
public void ThrashV2OnOrbitrapTest1()
{
Run run = new XCaliburRun2(FileRefs.RawDataMSFiles.OrbitrapStdFile1);
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 ThrashDeconvolutorV2(parameters);
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 InformedThrashDeconvolutor(ThrashParameters parameters)
{
Parameters = parameters;
}
public ThrashDeconvolutorV2(ThrashParameters parameters)
{
Parameters = parameters;
}
public void Stolen_CompareOldAndNewDeconvolutorsOrbitrap()
{
Run run = new XCaliburRun2(FileRefs.RawDataMSFiles.OrbitrapStdFile1);
//string fileName = @"C:\Users\Klin638\Documents\Visual Studio 2010\Backup Files\New folder\QC_Shew_08_04-pt5-2_11Jan09_Sphinx_08-11-18.RAW";
//@"\\protoapps\UserData\Slysz\DeconTools_TestFiles\Orbitrap\QC_Shew_08_04-pt5-2_11Jan09_Sphinx_08-11-18.raw";
//@"\\protoapps\UserData\Slysz\DeconTools_TestFiles\Orbitrap\Vorbi\Yellow_C12_099_18Mar10_Griffin_10-01-13.raw";
//@"C:\Users\Klin638\Documents\Visual Studio 2010\Backup Files\New folder\QC_Shew_08_04-pt5-2_11Jan09_Sphinx_08-11-18.RAW";
//
//Run run = RunUtilities.CreateAndLoadPeaks(fileName);
//Run run = new RunFactory().CreateRun(fileName);
run.ScanSetCollection.Create(run, 6005, 6005, 1, 1, false);
//to sum
//run.ScanSetCollection.Create(run, 6005, 6005, 5, 1, false);
var msgen = MSGeneratorFactory.CreateMSGenerator(run.MSFileType);
var peakDetector = new DeconToolsPeakDetectorV2(1.3, 2, DeconTools.Backend.Globals.PeakFitType.QUADRATIC, true);
var thrashParameters = new ThrashParameters();
thrashParameters.MinMSFeatureToBackgroundRatio = 3;
thrashParameters.MaxFit = 0.4;
var newDeconvolutor = new ThrashDeconvolutorV2(thrashParameters);
//var newDeconvolutor = new InformedThrashDeconvolutor(thrashParameters);
var scanset = new ScanSet(6005);
//For summing mass spectra:
//scanset = new ScanSetFactory().CreateScanSet(run, 6005, 5);
run.CurrentScanSet = scanset;
var oldDeconvolutor = new HornDeconvolutor();
oldDeconvolutor.MinPeptideBackgroundRatio = 3;
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);
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);
}
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);
}
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);
}
public void CompareOldAndNewDeconvolutorsOrbitrap()
{
Run run = new XCaliburRun2(FileRefs.RawDataMSFiles.OrbitrapStdFile1);
//run.ScanSetCollection.Create(run, 6005, 6005, 1, 1, false);
//to sum
run.ScanSetCollection.Create(run, 6005, 6005, 5, 1, false);
var msgen = MSGeneratorFactory.CreateMSGenerator(run.MSFileType);
var peakDetector = new DeconToolsPeakDetectorV2(1.3, 2, DeconTools.Backend.Globals.PeakFitType.QUADRATIC, true);
var thrashParameters = new ThrashParameters();
thrashParameters.MinMSFeatureToBackgroundRatio = 3;
thrashParameters.MaxFit = 0.4;
var newDeconvolutor = new ThrashDeconvolutorV2(thrashParameters);
var scanset = new ScanSet(6005);
//For summing mass spectra:
//scanset = new ScanSetFactory().CreateScanSet(run, 6005, 5);
run.CurrentScanSet = scanset;
var oldDeconvolutor = new HornDeconvolutor();
oldDeconvolutor.MinPeptideBackgroundRatio = 3;
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);
Console.WriteLine("\n--------------Common to new and Old ------------------");
TestUtilities.DisplayMSFeatures(sharedIsos);
Console.WriteLine("\n--------------Unique to new ------------------");
TestUtilities.DisplayMSFeatures(uniqueToNew);
var diOutputFolder = new DirectoryInfo(@"C:\Temp\ThrashTesting");
if (!diOutputFolder.Exists)
{
diOutputFolder.Create();
}
var outputFilename = Path.Combine(diOutputFolder.FullName, "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);
}
