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 static Run CreateResultsFromThreeScansOfStandardOrbitrapData()
{
Run run = new XCaliburRun2(FileRefs.RawDataMSFiles.OrbitrapStdFile1);
run.ScanSetCollection.Create(run, 6000, 6020, 1, 1, false);
Task msgen = MSGeneratorFactory.CreateMSGenerator(run.MSFileType);
Task peakDetector = new DeconToolsPeakDetectorV2();
Task decon = new ThrashDeconvolutorV2();
Task msScanInfoCreator = new ScanResultUpdater();
Task flagger = new ResultValidatorTask();
foreach (var scan in run.ScanSetCollection.ScanSetList)
{
run.CurrentScanSet = scan;
msgen.Execute(run.ResultCollection);
peakDetector.Execute(run.ResultCollection);
decon.Execute(run.ResultCollection);
msScanInfoCreator.Execute(run.ResultCollection);
flagger.Execute(run.ResultCollection);
}
return(run);
}
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 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 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 static Run CreateResultsFromTwoFramesOfStandardUIMFData()
{
var run = new UIMFRun(FileRefs.RawDataMSFiles.UIMFStdFile1);
run.ResultCollection.ResultType = Globals.ResultType.UIMF_TRADITIONAL_RESULT;
run.ScanSetCollection.Create(run, 500, 501, 3, 1);
run.IMSScanSetCollection.Create(run, 250, 270, 9, 1);
Task msgen = new UIMF_MSGenerator();
Task peakDetector = new DeconToolsPeakDetectorV2();
Task decon = new ThrashDeconvolutorV2();
Task msScanInfoCreator = new ScanResultUpdater();
Task flagger = new ResultValidatorTask();
Task ticExtractor = new DeconTools.Backend.ProcessingTasks.UIMF_TICExtractor();
Task driftTimeextractor = new UIMFDriftTimeExtractor();
foreach (var frame in run.ScanSetCollection.ScanSetList)
{
run.CurrentScanSet = frame;
foreach (IMSScanSet scan in run.IMSScanSetCollection.ScanSetList)
{
run.CurrentIMSScanSet = scan;
msgen.Execute(run.ResultCollection);
peakDetector.Execute(run.ResultCollection);
decon.Execute(run.ResultCollection);
flagger.Execute(run.ResultCollection);
driftTimeextractor.Execute(run.ResultCollection);
msScanInfoCreator.Execute(run.ResultCollection);
ticExtractor.Execute(run.ResultCollection);
}
}
return(run);
}
public static Run CreatePeakDataFromStandardOrbitrapData()
{
Run run = new XCaliburRun2(FileRefs.RawDataMSFiles.OrbitrapStdFile1);
run.ScanSetCollection.Create(run, 6000, 6050, 1, 1, false);
Task msgen = new GenericMSGenerator();
var peakDetector = new DeconToolsPeakDetectorV2();
peakDetector.PeaksAreStored = true;
Task decon = new ThrashDeconvolutorV2();
Task msScanInfoCreator = new ScanResultUpdater();
Task flagger = new ResultValidatorTask();
foreach (var scan in run.ScanSetCollection.ScanSetList)
{
run.CurrentScanSet = scan;
msgen.Execute(run.ResultCollection);
peakDetector.Execute(run.ResultCollection);
}
return(run);
}
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 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 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);
}
public void BPISaturationCorrectedTest1()
{
var filename = @"D:\Data\UIMF\Sarc_P13_C10_1186_23Sep11_Cheetah_11-09-06.uimf";
var run = new RunFactory().CreateRun(filename);
run.ScanSetCollection = new ScanSetCollection();
//scanSetCollection.Create(run, 500, 550,1,1);
var startFrame = 477;
var stopFrame = 477;
//startFrame = run.MinLCScan;
//stopFrame = run.MaxLCScan;
run.ScanSetCollection.Create(run, startFrame, stopFrame, 1, 1);
((UIMFRun)run).IMSScanSetCollection = new IMSScanSetCollection();
((UIMFRun)run).IMSScanSetCollection.Create(run, 122, 122, 1, 1);
var msgen = MSGeneratorFactory.CreateMSGenerator(run.MSFileType);
var peakDet = new DeconToolsPeakDetectorV2();
peakDet.PeakToBackgroundRatio = 2;
peakDet.SignalToNoiseThreshold = 2;
peakDet.IsDataThresholded = true;
var _zeroFiller = new DeconToolsZeroFiller();
var _deconvolutor = new ThrashDeconvolutorV2();
_deconvolutor.UseAutocorrelationChargeDetermination = true;
_deconvolutor.Parameters.MaxFit = 0.8;
var saturationWorkflow = new SaturationIMSScanBasedWorkflow(new DeconToolsParameters(), run);
var outputFile = @"C:\Users\d3x720\Documents\PNNL\My_DataAnalysis\2013\Saturation_Correction\chromOuputSatCorrected.txt";
using (var writer = new StreamWriter(outputFile))
{
var uimfRun = (UIMFRun)run;
var _unsummedMSFeatures = new List <IsosResult>();
foreach (var lcScanSet in run.ScanSetCollection.ScanSetList)
{
Console.WriteLine("Scanset= " + lcScanSet);
uimfRun.ResultCollection.MSPeakResultList.Clear();
_unsummedMSFeatures.Clear();
var unsummedFrameSet = new ScanSet(lcScanSet.PrimaryScanNumber);
//get saturated MSFeatures for unsummed data
uimfRun.CurrentScanSet = unsummedFrameSet;
var sb = new StringBuilder();
var errorInFrame = false;
var numIMSScans = uimfRun.IMSScanSetCollection.ScanSetList.Count;
for (var imsScanNum = 0; imsScanNum < numIMSScans; imsScanNum++)
{
var imsScanSet = uimfRun.IMSScanSetCollection.ScanSetList[imsScanNum];
uimfRun.ResultCollection.IsosResultBin.Clear(); //clear any previous MSFeatures
var unsummedIMSScanset = new IMSScanSet(imsScanSet.PrimaryScanNumber);
uimfRun.CurrentIMSScanSet = unsummedIMSScanset;
try
{
msgen.Execute(run.ResultCollection);
_zeroFiller.Execute(run.ResultCollection);
peakDet.Execute(run.ResultCollection);
_deconvolutor.Deconvolute(uimfRun.ResultCollection); //adds to IsosResultBin
}
catch (Exception ex)
{
errorInFrame = true;
}
_unsummedMSFeatures.AddRange(run.ResultCollection.IsosResultBin);
var basePeakIntensity = 0;
//iterate over unsummed MSFeatures and check for saturation
foreach (var isosResult in uimfRun.ResultCollection.IsosResultBin)
{
var isPossiblySaturated = isosResult.IntensityAggregate > 1e7;
if (isPossiblySaturated)
{
var theorIso = new IsotopicProfile();
saturationWorkflow.RebuildSaturatedIsotopicProfile(run.XYData, isosResult, uimfRun.PeakList, out theorIso);
saturationWorkflow.AdjustSaturatedIsotopicProfile(isosResult.IsotopicProfile, theorIso, true, true);
}
TestUtilities.DisplayIsotopicProfileData(isosResult.IsotopicProfile);
var height = (int)isosResult.IsotopicProfile.getMostIntensePeak().Height;
if (height > basePeakIntensity)
{
basePeakIntensity = height;
}
}
sb.Append(basePeakIntensity);
var isNotLastIMSScan = imsScanNum != numIMSScans - 1;
if (isNotLastIMSScan)
{
sb.Append("\t");
}
}
if (errorInFrame)
{
}
else
{
writer.WriteLine(sb.ToString());
}
}
}
}
