protected virtual void InitializeProcessingTasks()
{
MSGenerator = MSGeneratorFactory.CreateMSGenerator(Run.MSFileType);
PeakDetector = PeakDetectorFactory.CreatePeakDetector(NewDeconToolsParameters);
Deconvolutor = DeconvolutorFactory.CreateDeconvolutor(NewDeconToolsParameters);
//the new iThrash imports the _peaks.txt file
if (Deconvolutor is DeconTools.Backend.ProcessingTasks.Deconvoluters.InformedThrashDeconvolutor)
{
_deconvolutorRequiresPeaksFile = true;
}
//Will initialize these but whether or not they are used are determined elsewhere
ZeroFiller = new DeconToolsZeroFiller(NewDeconToolsParameters.MiscMSProcessingParameters.ZeroFillingNumZerosToFill);
Smoother = new SavitzkyGolaySmoother(NewDeconToolsParameters.MiscMSProcessingParameters.SavitzkyGolayNumPointsInSmooth,
NewDeconToolsParameters.MiscMSProcessingParameters.SavitzkyGolayOrder);
FitScoreCalculator = new DeconToolsFitScoreCalculator();
ScanResultUpdater = new ScanResultUpdater(NewDeconToolsParameters.ScanBasedWorkflowParameters.ProcessMS2);
ResultValidator = new ResultValidatorTask();
IsosResultExporter = IsosExporterFactory.CreateIsosExporter(Run.ResultCollection.ResultType, ExporterType,
IsosOutputFileName);
ScanResultExporter = ScansExporterFactory.CreateScansExporter(Run.MSFileType, ExporterType,
ScansOutputFileName);
if (!_deconvolutorRequiresPeaksFile)
{
PeakListExporter = PeakListExporterFactory.Create(ExporterType, Run.MSFileType, PeakListExporterTriggerValue,
PeakListOutputFileName);
}
PeakToMSFeatureAssociator = new PeakToMSFeatureAssociator();
}
public void Test1()
{
var rawfilename = @"D:\Data\O16O18\GlueGrant\GG_MO_Trauma_374020_20May11_Sphinx_11-03-28.RAW";
var exportedIsos = Path.Combine(Path.GetDirectoryName(rawfilename), Path.GetFileName(rawfilename).Replace(".RAW", "_test_isos.csv"));
if (File.Exists(exportedIsos))
{
File.Delete(exportedIsos);
}
var run = new RunFactory().CreateRun(rawfilename);
run.ResultCollection.ResultType = Backend.Globals.ResultType.O16O18_TRADITIONAL_RESULT;
run.ScanSetCollection.Create(run, 5000, 5000, 1, 1);
run.CurrentScanSet = run.ScanSetCollection.ScanSetList[0];
var msgen = MSGeneratorFactory.CreateMSGenerator(run.MSFileType);
var peakDet = new DeconToolsPeakDetectorV2();
peakDet.PeakToBackgroundRatio = 1.3;
peakDet.SignalToNoiseThreshold = 2;
var decon = new HornDeconvolutor();
decon.IsO16O18Data = true;
var appender = new O16O18PeakDataAppender();
var exporter = IsosExporterFactory.CreateIsosExporter(run.ResultCollection.ResultType, Backend.Globals.ExporterType.Text, exportedIsos);
msgen.Execute(run.ResultCollection);
peakDet.Execute(run.ResultCollection);
decon.Execute(run.ResultCollection);
appender.Execute(run.ResultCollection);
var testResult = (O16O18IsosResult)run.ResultCollection.ResultList[1];
Assert.AreEqual(DeconTools.Backend.Globals.ResultType.O16O18_TRADITIONAL_RESULT, run.ResultCollection.ResultType);
Assert.AreEqual(5905390, testResult.IsotopicProfile.GetMonoAbundance());
Assert.AreEqual(3017899, testResult.MonoPlus2Abundance);
Assert.AreEqual(162389, testResult.MonoPlus4Abundance);
exporter.Execute(run.ResultCollection);
run.Close();
}
public void CompareOldAndNew2()
{
var newResultsFile =
@"C:\Users\d3x720\Documents\PNNL\My_DataAnalysis\Standard_Testing\DeconTools\Orbitrap\Test_Results\Version_1.0.XX_Jan6_AfterThrashRefining\QC_Shew_08_04-pt5-2_11Jan09_Sphinx_08-11-18_isos.csv";
var oldResultsFile =
@"C:\Users\d3x720\Documents\PNNL\My_DataAnalysis\Standard_Testing\DeconTools\Orbitrap\Test_Results\Version_1.0.4745_Dec28_AfterThrashRefactor\QC_Shew_08_04-pt5-2_11Jan09_Sphinx_08-11-18_isos.csv";
var importer = new IsosImporter(newResultsFile, Globals.MSFileType.Finnigan);
var newResults = importer.Import();
importer = new IsosImporter(oldResultsFile, Globals.MSFileType.Finnigan);
var oldResults = importer.Import();
//newResults = newResults.Where(p => p.ScanSet.PrimaryScanNumber == 6005).ToList();
//oldResults = oldResults.Where(p => p.ScanSet.PrimaryScanNumber == 6005).ToList();
var sharedIsos = new List <IsosResult>();
var uniqueToNew = new List <IsosResult>();
var uniqueToOld = new List <IsosResult>();
GetComparisons(newResults, oldResults, sharedIsos, uniqueToNew, uniqueToOld);
Console.WriteLine("Summary----------------------------");
Console.WriteLine("Shared =\t" + sharedIsos.Count);
Console.WriteLine("Unique to new =\t" + uniqueToNew.Count);
Console.WriteLine("Unique to old =\t" + uniqueToOld.Count);
Console.WriteLine("\n--------------Common to new and Old ------------------");
TestUtilities.DisplayMSFeatures(sharedIsos);
Console.WriteLine("\n--------------Unique to new ------------------");
TestUtilities.DisplayMSFeatures(uniqueToNew);
var outputFilename = @"D:\temp\exportedIsos.csv";
var exporter = IsosExporterFactory.CreateIsosExporter(Globals.ResultType.BASIC_TRADITIONAL_RESULT, Globals.ExporterType.Text, outputFilename);
exporter.ExportIsosResults(uniqueToNew);
Console.WriteLine("\n--------------Unique to old ------------------");
TestUtilities.DisplayMSFeatures(uniqueToOld);
}
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 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);
}