public void OldDeconvolutorTest_temp1()
{
Run run = new XCaliburRun2(FileRefs.RawDataMSFiles.OrbitrapStdFile1);
#if !Disable_DeconToolsV2
var parameters = new DeconEngineClasses.OldDecon2LSParameters();
var paramFile =
@"\\protoapps\UserData\Slysz\DeconTools_TestFiles\ParameterFiles\LTQ_Orb_SN2_PeakBR1pt3_PeptideBR1_Thrash_MaxFit1.xml";
parameters.Load(paramFile);
var scanSet = new ScanSetFactory().CreateScanSet(run, 6005, 1);
var msgen = MSGeneratorFactory.CreateMSGenerator(run.MSFileType);
var peakDetector = new DeconToolsPeakDetectorV2(1.3, 2, DeconTools.Backend.Globals.PeakFitType.QUADRATIC, true);
var deconvolutor = new HornDeconvolutor(parameters.GetDeconToolsParameters());
run.CurrentScanSet = scanSet;
msgen.Execute(run.ResultCollection);
peakDetector.Execute(run.ResultCollection);
deconvolutor.Execute(run.ResultCollection);
run.ResultCollection.ResultList = run.ResultCollection.ResultList.OrderByDescending(p => p.IntensityAggregate).ToList();
TestUtilities.DisplayMSFeatures(run.ResultCollection.ResultList);
//IsosResult testIso = run.ResultCollection.ResultList[0];
//TestUtilities.DisplayIsotopicProfileData(testIso.IsotopicProfile);
//TestUtilities.DisplayMSFeatures(run.ResultCollection.ResultList);
//TestUtilities.DisplayPeaks(run.PeakList);
#endif
}
public void deconWithTHRASH_Then_ValidateTest1()
{
Run run = new XCaliburRun2(FileRefs.RawDataMSFiles.OrbitrapStdFile1);
var scanSet = new ScanSet(6005);
run.CurrentScanSet = scanSet;
var msgen = MSGeneratorFactory.CreateMSGenerator(run.MSFileType);
var peakDetector = new DeconToolsPeakDetectorV2(1.3, 2, DeconTools.Backend.Globals.PeakFitType.QUADRATIC, true);
var decon = new HornDeconvolutor();
var validator = new ResultValidatorTask();
msgen.Execute(run.ResultCollection);
peakDetector.Execute(run.ResultCollection);
decon.Execute(run.ResultCollection);
validator.Execute(run.ResultCollection);
Assert.AreEqual(93, run.ResultCollection.ResultList.Count);
var testResult = run.ResultCollection.ResultList[0];
Assert.AreEqual(0.0532199478712594m, (decimal)testResult.InterferenceScore);
//TestUtilities.DisplayMSFeatures(run.ResultCollection.ResultList);
}
public void PeakDetectorOnCentroidedDataTest1()
{
var run = new RunFactory().CreateRun(FileRefs.RawDataMSFiles.OrbitrapStdFile1);
var scan = new ScanSet(6006); //this is a centroided MS2 scan
var msgen = MSGeneratorFactory.CreateMSGenerator(run.MSFileType);
var peakDetector = new DeconToolsPeakDetectorV2(0, 0, Globals.PeakFitType.QUADRATIC, true);
peakDetector.RawDataType = Globals.RawDataType.Centroided;
peakDetector.IsDataThresholded = true;
run.CurrentScanSet = scan;
msgen.Execute(run.ResultCollection);
peakDetector.Execute(run.ResultCollection);
Console.WriteLine("Num XY datapoints in mass spectrum= " + run.XYData.Xvalues.Length);
Console.WriteLine("numPeaks = " + run.PeakList.Count);
Assert.AreEqual(run.XYData.Xvalues.Length, run.PeakList.Count);
//TestUtilities.DisplayXYValues(run.XYData);
//TestUtilities.DisplayPeaks(run.PeakList);
}
public void PeakDetectorOnCentroidedDataTest2()
{
var run = new RunFactory().CreateRun(FileRefs.RawDataMSFiles.OrbitrapStdFile1);
var scan = new ScanSet(6006); //this is a MS2 scan
var msgen = MSGeneratorFactory.CreateMSGenerator(run.MSFileType);
// Note that setting the PeakFitType to Apex will not matter since RawDataType is Centroided
// It would only matter if the RawDataType was Profile
var peakDetector = new DeconToolsPeakDetectorV2(0, 0, Globals.PeakFitType.APEX, true);
peakDetector.RawDataType = Globals.RawDataType.Centroided;
peakDetector.SignalToNoiseThreshold = 0;
peakDetector.PeakToBackgroundRatio = 0;
peakDetector.IsDataThresholded = true;
run.CurrentScanSet = scan;
msgen.Execute(run.ResultCollection);
peakDetector.Execute(run.ResultCollection);
Console.WriteLine("Num XY datapoints in mass spectrum= " + run.XYData.Xvalues.Length);
Console.WriteLine("numPeaks = " + run.PeakList.Count);
Assert.AreEqual(run.XYData.Xvalues.Length, run.PeakList.Count);
//TestUtilities.DisplayXYValues(run.XYData);
//TestUtilities.DisplayPeaks(run.PeakList);
}
public void test1()
{
Run run = new XCaliburRun(bsaO16O18file1);
MSGeneratorFactory msgenFact = new MSGeneratorFactory();
Task msgen = msgenFact.CreateMSGenerator(run.MSFileType);
DeconToolsPeakDetector peakDet = new DeconToolsPeakDetector(1.3, 2, DeconTools.Backend.Globals.PeakFitType.QUADRATIC, true);
O16O18FeatureFinder finder = new O16O18FeatureFinder();
List <MassTag> massTagList = TestUtilities.CreateO16O18TestMassTagList1();
run.CurrentMassTag = massTagList[0];
TomTheorFeatureGenerator theorFeatureGen = new TomTheorFeatureGenerator();
theorFeatureGen.GenerateTheorFeature(run.CurrentMassTag);
run.CurrentScanSet = new ScanSet(3294);
msgen.Execute(run.ResultCollection);
peakDet.Execute(run.ResultCollection);
IsotopicProfile o16O18profile = finder.FindFeature(run.PeakList, run.CurrentMassTag.IsotopicProfile, 10, true);
TestUtilities.DisplayIsotopicProfileData(o16O18profile);
}
public void CheckBackgroundIntensityTest1()
{
Run run = new XCaliburRun2(FileRefs.RawDataMSFiles.OrbitrapStdFile1);
var scan = new ScanSet(6005);
var msgen = MSGeneratorFactory.CreateMSGenerator(run.MSFileType);
var peakDetector = new DeconToolsPeakDetectorV2();
peakDetector.PeakToBackgroundRatio = 1.3;
peakDetector.SignalToNoiseThreshold = 2;
peakDetector.PeakFitType = Globals.PeakFitType.QUADRATIC;
peakDetector.IsDataThresholded = true;
var oldPeakDetector = new DeconToolsPeakDetectorV2(1.3, 2, DeconTools.Backend.Globals.PeakFitType.QUADRATIC, true);
peakDetector.IsDataThresholded = true;
run.CurrentScanSet = scan;
msgen.Execute(run.ResultCollection);
peakDetector.Execute(run.ResultCollection);
oldPeakDetector.Execute(run.ResultCollection);
//Assert.AreEqual(peakDetector.BackgroundIntensity, oldPeakDetector.BackgroundIntensity);
}
//public override WorkflowParameters WorkflowParameters
//{
// get
// {
// throw new NotImplementedException();
// }
// set
// {
// throw new NotImplementedException();
// }
//}
public void InitializeWorkflow()
{
NumMSScansToSumWhenBuildingMasterPeakList = 3;
MasterPeakListPeakDetector = new DeconToolsPeakDetectorV2();
MasterPeakListPeakDetector.PeakToBackgroundRatio = 4;
MasterPeakListPeakDetector.SignalToNoiseThreshold = 3;
MasterPeakListPeakDetector.IsDataThresholded = false;
MasterPeakListPeakDetector.PeaksAreStored = true;
msgen = MSGeneratorFactory.CreateMSGenerator(DeconTools.Backend.Globals.MSFileType.PNNL_UIMF);
this.DriftTimeProfileExtractionPPMTolerance = 15;
this.ChromSmoother = new SavitzkyGolaySmoother(23, 2);
this.ChromPeakDetector = new ChromPeakDetector(0.5, 0.5);
this.ChromGenerator = new ChromatogramGenerator();
processedMSPeaks = new List <MSPeakResult>();
}
public void agilentDeconTest1()
{
RunFactory runFact = new RunFactory();
Run run = runFact.CreateRun(agilentFile);
MSGeneratorFactory msfactory = new MSGeneratorFactory();
Task msgen = msfactory.CreateMSGenerator(run.MSFileType);
DeconToolsPeakDetector peakDet = new DeconToolsPeakDetector();
peakDet.PeakBackgroundRatio = 7;
peakDet.SigNoiseThreshold = 3;
HornDeconvolutor decon = new HornDeconvolutor();
ScanSet scan1821 = new ScanSet(1821);
run.CurrentScanSet = scan1821;
msgen.Execute(run.ResultCollection);
run.XYData = run.XYData.TrimData(450, 520, TODO);
peakDet.Execute(run.ResultCollection);
decon.Execute(run.ResultCollection);
TestUtilities.DisplayMSFeatures(run.ResultCollection.ResultList);
}
public List <Task> getStandardTaskList(Run run)
{
Task peakChromGen = new PeakChromatogramGenerator(chromPPMTolerance);
Task smoother = new DeconTools.Backend.ProcessingTasks.Smoothers.DeconToolsSavitzkyGolaySmoother(11, 11, 2);
Task peakDet = new DeconTools.Backend.ProcessingTasks.PeakDetectors.ChromPeakDetector(0.5, 0.5);
Task chromPeakSel = new DeconTools.Backend.ProcessingTasks.ChromPeakSelector(1, 0.01, Globals.PeakSelectorMode.CLOSEST_TO_TARGET);
MSGeneratorFactory msgenFactory = new MSGeneratorFactory();
Task msgen = msgenFactory.CreateMSGenerator(run.MSFileType);
DeconToolsV2.Peaks.clsPeakProcessorParameters peakParams = new DeconToolsV2.Peaks.clsPeakProcessorParameters(2, 3, false, DeconToolsV2.Peaks.PEAK_FIT_TYPE.QUADRATIC);
Task mspeakDet = new DeconToolsPeakDetector(peakParams);
Task theorFeatureGen = new TomTheorFeatureGenerator();
Task finder = new N14N15TFFTask(5);
Task quant = new N14N15QuantifierTask(1);
Task fitScoreCalc = new IsotopicProfileFitScoreCalculator();
List <Task> taskList = new List <Task>();
taskList.Add(peakChromGen);
taskList.Add(smoother);
taskList.Add(peakDet);
taskList.Add(chromPeakSel);
taskList.Add(msgen);
taskList.Add(mspeakDet);
taskList.Add(theorFeatureGen);
taskList.Add(finder);
taskList.Add(quant);
taskList.Add(fitScoreCalc);
return(taskList);
}
public void deconWithRAPID_Then_ValidateTest1()
{
Run run = new XCaliburRun2(FileRefs.RawDataMSFiles.OrbitrapStdFile1);
ScanSet scanSet = new ScanSet(6005);
run.CurrentScanSet = scanSet;
MSGenerator msgen = MSGeneratorFactory.CreateMSGenerator(run.MSFileType);
DeconToolsPeakDetectorV2 peakDetector = new DeconToolsPeakDetectorV2(1.3, 2, DeconTools.Backend.Globals.PeakFitType.QUADRATIC, true);
RapidDeconvolutor decon = new RapidDeconvolutor();
ResultValidatorTask validator = new ResultValidatorTask();
msgen.Execute(run.ResultCollection);
peakDetector.Execute(run.ResultCollection);
decon.Execute(run.ResultCollection);
validator.Execute(run.ResultCollection);
Assert.AreEqual(190, run.ResultCollection.ResultList.Count);
IsosResult testResult = run.ResultCollection.ResultList[0];
Assert.AreEqual(0.0213668719893332m, (decimal)testResult.InterferenceScore);
//TestUtilities.DisplayMSFeatures(run.ResultCollection.ResultList);
}
public void Test1()
{
string testfile = @"D:\Data\From_Nicola\AC2_Neg_highpH_14Apr13_Sauron_13-04-03.raw";
Run run = new RunFactory().CreateRun(testfile);
TestUtilities.DisplayRunInformation(run);
var msgen = MSGeneratorFactory.CreateMSGenerator(run.MSFileType);
ScanSet scanSet = new ScanSet(4100);
run.CurrentScanSet = scanSet;
msgen.Execute(run.ResultCollection);
DeconToolsPeakDetectorV2 peakDetector = new DeconToolsPeakDetectorV2();
peakDetector.Execute(run.ResultCollection);
run.PeakList = run.PeakList.Where(p => p.XValue > 742 && p.XValue < 749).ToList();
HornDeconvolutor hornDeconvolutor = new HornDeconvolutor();
hornDeconvolutor.ChargeCarrierMass = -1.00727649;
hornDeconvolutor.Execute(run.ResultCollection);
TestUtilities.DisplayMSFeatures(run.ResultCollection.ResultList);
}
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 DetectPeaksTest1()
{
var peakBR = 1.3;
double sigNoise = 2;
var isThresholded = true;
var peakfitType = DeconTools.Backend.Globals.PeakFitType.QUADRATIC;
var testFile = FileRefs.RawDataMSFiles.OrbitrapStdFile1;
Run run = new XCaliburRun2(testFile);
var msgen = MSGeneratorFactory.CreateMSGenerator(run.MSFileType);
run.CurrentScanSet = new ScanSet(6005);
msgen.Execute(run.ResultCollection);
var peakDet = new DeconToolsPeakDetectorV2(peakBR, sigNoise, peakfitType, isThresholded);
peakDet.PeaksAreStored = true;
var peakList = peakDet.FindPeaks(run.XYData, 0, 50000);
TestUtilities.DisplayPeaks(peakList);
}
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 virtual void InitializeRunRelatedTasks()
{
if (Run != null)
{
MSGenerator = MSGeneratorFactory.CreateMSGenerator(this.Run.MSFileType);
}
}
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 override void InitializeRunRelatedTasks()
{
if (Run != null)
{
MSGenerator = MSGeneratorFactory.CreateMSGenerator(Run.MSFileType);
int minLCScan;
int maxLCScan;
if (this._workflowParameters.LCScanMax == -1 || this._workflowParameters.LCScanMin == -1)
{
if (Run is UIMFRun)
{
minLCScan = ((UIMFRun)Run).MinLCScan;
maxLCScan = ((UIMFRun)Run).MaxLCScan;
}
else
{
minLCScan = Run.MinLCScan;
maxLCScan = Run.MaxLCScan;
}
}
else
{
minLCScan = this._workflowParameters.LCScanMin;
maxLCScan = this._workflowParameters.LCScanMax;
}
if (Run.MSFileType == DeconTools.Backend.Globals.MSFileType.PNNL_UIMF)
{
var uimfRun = Run as UIMFRun;
uimfRun.ScanSetCollection.Create(uimfRun, minLCScan, maxLCScan,
_workflowParameters.Num_LC_TimePointsSummed, 1,
_workflowParameters.ProcessMSMS);
bool sumAllIMSScans = (_workflowParameters.NumIMSScansSummed == -1 ||
_workflowParameters.NumIMSScansSummed > uimfRun.MaxLCScan);
if (sumAllIMSScans)
{
int primaryIMSScan = Run.MinLCScan;
uimfRun.IMSScanSetCollection.ScanSetList.Clear();
var imsScanset = new IMSScanSet(primaryIMSScan, uimfRun.MinIMSScan, uimfRun.MaxIMSScan);
uimfRun.IMSScanSetCollection.ScanSetList.Add(imsScanset);
}
else
{
uimfRun.IMSScanSetCollection.Create(Run, uimfRun.MinIMSScan, uimfRun.MaxIMSScan,
_workflowParameters.NumIMSScansSummed, 1);
}
}
else
{
Run.ScanSetCollection.Create(Run, minLCScan, maxLCScan,
this._workflowParameters.Num_LC_TimePointsSummed, 1, this._workflowParameters.ProcessMSMS);
}
}
}
public void uimfTest1()
{
UIMFRun run = new UIMFRun(uimfFile1);
MSGeneratorFactory msgenFactory = new MSGeneratorFactory();
Task msgen = msgenFactory.CreateMSGenerator(run.MSFileType);
Task peakDetector = new DeconToolsPeakDetector();
Task decon = new HornDeconvolutor();
Task suspPeakFlagger = new LeftOfMonoPeakLooker();
run.CurrentFrameSet = new FrameSet(501, 500, 502);
run.CurrentScanSet = new ScanSet(250, 246, 254);
msgen.Execute(run.ResultCollection);
peakDetector.Execute(run.ResultCollection);
decon.Execute(run.ResultCollection);
foreach (var result in run.ResultCollection.ResultList)
{
((LeftOfMonoPeakLooker)suspPeakFlagger).CurrentResult = result;
suspPeakFlagger.Execute(run.ResultCollection);
}
Assert.AreEqual(38, run.ResultCollection.ResultList.Count);
List <IsosResult> flaggedResults = run.ResultCollection.ResultList.Where(p => p.Flags.Count > 0).ToList();
Assert.AreEqual(13, flaggedResults.Count);
TestUtilities.DisplayIsotopicProfileData(flaggedResults[0].IsotopicProfile);
Console.WriteLine();
TestUtilities.DisplayIsotopicProfileData(flaggedResults[1].IsotopicProfile);
}
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 criticalErrorInPeakDetectorTest1()
{
UIMFRun run = new DeconTools.Backend.Runs.UIMFRun(fpgaUIMFFilePath2);
FrameSetCollectionCreator ffcc = new FrameSetCollectionCreator(run, 425, 432, 3, 1);
ffcc.Create();
ScanSetCollectionCreator sscc = new ScanSetCollectionCreator(run, 1, 500, 9, 1);
sscc.Create();
MSGeneratorFactory factory = new MSGeneratorFactory();
Task msgen = factory.CreateMSGenerator(run.MSFileType);
DeconToolsPeakDetector peakDet = new DeconToolsPeakDetector();
peakDet.PeakBackgroundRatio = 4;
peakDet.SigNoiseThreshold = 3;
foreach (var frame in run.FrameSetCollection.FrameSetList)
{
run.CurrentFrameSet = frame;
foreach (var scan in run.ScanSetCollection.ScanSetList)
{
run.CurrentScanSet = scan;
msgen.Execute(run.ResultCollection);
peakDet.Execute(run.ResultCollection);
}
}
}
public void DetectPeaksInOrbitrapData()
{
var peakBR = 1.3;
double sigNoise = 2;
var isThresholded = true;
var peakfitType = DeconTools.Backend.Globals.PeakFitType.QUADRATIC;
var testFile = FileRefs.RawDataMSFiles.OrbitrapStdFile1;
Run run = new XCaliburRun2(testFile);
//create list of target scansets
run.ScanSetCollection.Create(run, 6000, 6015, 1, 1);
//in the 'run' object there is now a list of scans : run.ScanSetCollection
var msgen = MSGeneratorFactory.CreateMSGenerator(run.MSFileType);
var peakDet = new DeconToolsPeakDetectorV2(peakBR, sigNoise, peakfitType, isThresholded);
peakDet.PeaksAreStored = true;
foreach (var scan in run.ScanSetCollection.ScanSetList)
{
//set the target scan:
run.CurrentScanSet = scan;
msgen.Execute(run.ResultCollection);
peakDet.Execute(run.ResultCollection);
}
}
public void peak_interference_UIMF_expectInterference_test1()
{
var uimfFrame1200_142 = FileRefs.RawDataBasePath + @"\UIMF\Sarc_MS_90_21Aug10_Cheetah_10-08-02_0000_frame1200_scan142.txt";
Run run = new DeconTools.Backend.Runs.MSScanFromTextFileRun(uimfFrame1200_142);
var scanSet = new ScanSet(0);
run.CurrentScanSet = scanSet;
var msgen = MSGeneratorFactory.CreateMSGenerator(run.MSFileType);
msgen.MinMZ = 200;
msgen.MaxMZ = 2000;
var peakDetector = new DeconToolsPeakDetectorV2(4, 3, DeconTools.Backend.Globals.PeakFitType.QUADRATIC, true);
var decon = new HornDeconvolutor();
decon.MinIntensityForScore = 10;
decon.DeleteIntensityThreshold = 10;
decon.MaxFitAllowed = 0.4;
decon.MinMZ = 200;
decon.MaxMZ = 2000;
decon.IsMZRangeUsed = false;
var zeroFiller = new DeconToolsZeroFiller();
msgen.Execute(run.ResultCollection);
zeroFiller.Execute(run.ResultCollection);
peakDetector.Execute(run.ResultCollection);
decon.Execute(run.ResultCollection);
//Assert.AreEqual(93, run.ResultCollection.ResultList.Count);
var testResult = run.ResultCollection.ResultList.Where(p => p.IsotopicProfile.MonoPeakMZ > 428 && p.IsotopicProfile.MonoPeakMZ < 430).First();
var monoPeak = testResult.IsotopicProfile.getMonoPeak();
var lastPeak = testResult.IsotopicProfile.Peaklist[testResult.IsotopicProfile.Peaklist.Count - 1];
var startIndexOfXYData = MathUtils.BinarySearchWithTolerance(run.XYData.Xvalues, monoPeak.XValue - 3, 0, (run.XYData.Xvalues.Length - 1), 2);
//interference scorer
var interferenceScorer = new InterferenceScorer();
var stopwatch = new Stopwatch();
stopwatch.Start();
var scanPeaks = run.PeakList.Select <Peak, MSPeak>(i => (MSPeak)i).ToList();
var interferenceScore = interferenceScorer.GetInterferenceScore(scanPeaks, testResult.IsotopicProfile.Peaklist, monoPeak.XValue - 1.1,
lastPeak.XValue + lastPeak.Width);
stopwatch.Stop();
Console.WriteLine("interference= " + interferenceScore);
Console.WriteLine("Time taken = " + stopwatch.ElapsedMilliseconds);
}
public void PeakDetectorDemo1()
{
//In this list on Scan 6005 we can see what the peak of the parent is. Slide 4 1059.45898 is the Monoisotopic peak of Scan 6009
var run = new RunFactory().CreateRun(FileRefs.RawDataMSFiles.OrbitrapStdFile1);
var testScan = new ScanSet(6009);
run.CurrentScanSet = testScan;
var msgen = MSGeneratorFactory.CreateMSGenerator(run.MSFileType);
var peakDetector = new DeconToolsPeakDetectorV2();
msgen.Execute(run.ResultCollection);
peakDetector.Execute(run.ResultCollection);
var sb = new StringBuilder();
foreach (var peak in run.PeakList)
{
sb.Append(peak.XValue + "\t" + peak.Height + "\t" + peak.Width + "\n");
}
Console.WriteLine("----------------------PeakList---------------");
Console.WriteLine("m/z\tintensity\twidth");
Console.WriteLine(sb.ToString());
}
public void getMSMSDataTest1()
{
//Create the run
var runFactory = new RunFactory();
var run = runFactory.CreateRun(FileRefs.RawDataMSFiles.OrbitrapStdFile1);
//Create the task
Task msgen = MSGeneratorFactory.CreateMSGenerator(run.MSFileType);
var peakdetector = new DeconToolsPeakDetectorV2();
var startScan = 6000;
var stopScan = 7000;
for (var i = startScan; i < stopScan; i++)
{
if (run.GetMSLevel(i) == 2)
{
var scanset = new ScanSet(i);
run.CurrentScanSet = scanset;
msgen.Execute(run.ResultCollection);
peakdetector.Execute(run.ResultCollection);
Console.Write("Working on Scan " + scanset.PrimaryScanNumber);
Console.WriteLine("; XYPair count = " + run.XYData.Xvalues.Length);
Console.WriteLine("num peaks= " + run.PeakList.Count);
}
}
}
public void createRunAndReadMSSpectraTest1()
{
//Create the run
var runFactory = new RunFactory();
var run = runFactory.CreateRun(FileRefs.RawDataMSFiles.OrbitrapStdFile1);
//Create the task
var msgen = MSGeneratorFactory.CreateMSGenerator(run.MSFileType);
//Create the target scan list (MS1 scans from 6005 - 6020).
run.ScanSetCollection.Create(run, 6005, 6020, 1, 1);
//iterate over each scan in the target collection get the mass spectrum
foreach (var scan in run.ScanSetCollection.ScanSetList)
{
Console.WriteLine("Working on Scan " + scan.PrimaryScanNumber);
run.CurrentScanSet = scan;
msgen.Execute(run.ResultCollection);
Console.WriteLine("XYPair count = " + run.XYData.Xvalues.Length);
}
}
public void findMSFeaturesInOrbitrapData_Test1()
{
Run run = new XCaliburRun2(FileRefs.RawDataMSFiles.OrbitrapStdFile1);
var scanSet = new ScanSet(6005);
run.CurrentScanSet = scanSet;
var msgen = MSGeneratorFactory.CreateMSGenerator(run.MSFileType);
var peakDetector = new DeconToolsPeakDetectorV2(1.3, 2, DeconTools.Backend.Globals.PeakFitType.QUADRATIC, true);
var decon = new HornDeconvolutor();
msgen.Execute(run.ResultCollection);
peakDetector.Execute(run.ResultCollection);
decon.Execute(run.ResultCollection);
Assert.AreEqual(93, run.ResultCollection.ResultList.Count);
//order and get the most intense msfeature
run.ResultCollection.ResultList = run.ResultCollection.ResultList.OrderByDescending(p => p.IntensityAggregate).ToList();
var testIso = run.ResultCollection.ResultList[0];
Assert.AreEqual(13084442, testIso.IntensityAggregate);
Assert.AreEqual(2, testIso.IsotopicProfile.ChargeState);
Assert.AreEqual(0.01012m, (decimal)Math.Round(testIso.IsotopicProfile.Score, 5));
Assert.AreEqual(3, testIso.IsotopicProfile.Peaklist.Count);
Assert.AreEqual(481.274105402604m, (decimal)testIso.IsotopicProfile.Peaklist[0].XValue);
Assert.AreEqual(481.775412188198m, (decimal)testIso.IsotopicProfile.Peaklist[1].XValue);
Assert.AreEqual(482.276820274024m, (decimal)testIso.IsotopicProfile.Peaklist[2].XValue);
TestUtilities.DisplayMSFeatures(run.ResultCollection.ResultList);
// TestUtilities.DisplayPeaks(run.PeakList);
}
public void ZeroFillerCompareNewAndOld()
{
Run run = new MSScanFromTextFileRun(FileRefs.RawDataMSFiles.TextFileMS_std1);
var msgen = MSGeneratorFactory.CreateMSGenerator(run.MSFileType);
var zeroFiller = new DeconToolsZeroFiller(3);
msgen.Execute(run.ResultCollection);
var numZerosToFill = 3;
var newZeroFilled = zeroFiller.ZeroFill(run.XYData.Xvalues, run.XYData.Yvalues, numZerosToFill);
// var oldZeroFilled = zeroFiller.ZeroFillOld(run.XYData.Xvalues, run.XYData.Yvalues, numZerosToFill);
var lowerMZ = 625.48;
var upperMZ = 626.18;
run.XYData = run.XYData.TrimData(lowerMZ, upperMZ);
newZeroFilled = newZeroFilled.TrimData(lowerMZ, upperMZ);
// oldZeroFilled = oldZeroFilled.TrimData(lowerMZ, upperMZ);
Console.WriteLine("---------- before zerofilling ---------------");
TestUtilities.DisplayXYValues(run.XYData);
Console.WriteLine("---------- after zerofilling ---------------");
TestUtilities.DisplayXYValues(newZeroFilled);
// Console.WriteLine("---------- after zerofilling using DeconEngine ---------------");
// TestUtilities.DisplayXYValues(oldZeroFilled);
}
public void InitializeRunRelatedTasks()
{
if (Run != null)
{
MSGenerator = MSGeneratorFactory.CreateMSGenerator(Run.MSFileType);
int minLCScan;
int maxLCScan;
if (WorkflowParameters.LCScanMax == -1 || WorkflowParameters.LCScanMin == -1)
{
if (Run is UIMFRun thisUimfRun)
{
minLCScan = thisUimfRun.MinLCScan;
maxLCScan = thisUimfRun.MaxLCScan;
}
else
{
minLCScan = Run.MinLCScan;
maxLCScan = Run.MaxLCScan;
}
}
else
{
minLCScan = WorkflowParameters.LCScanMin;
maxLCScan = WorkflowParameters.LCScanMax;
}
if (Run.MSFileType == Globals.MSFileType.PNNL_UIMF && Run is UIMFRun uimfRun)
{
uimfRun.ScanSetCollection.Create(uimfRun, minLCScan, maxLCScan,
WorkflowParameters.Num_LC_TimePointsSummed, 1,
WorkflowParameters.ProcessMSMS);
var sumAllIMSScans = WorkflowParameters.NumIMSScansSummed == -1 ||
WorkflowParameters.NumIMSScansSummed > uimfRun.MaxLCScan;
if (sumAllIMSScans)
{
var primaryIMSScan = Run.MinLCScan;
uimfRun.IMSScanSetCollection.ScanSetList.Clear();
var imsScanSet = new IMSScanSet(primaryIMSScan, uimfRun.MinIMSScan, uimfRun.MaxIMSScan);
uimfRun.IMSScanSetCollection.ScanSetList.Add(imsScanSet);
}
else
{
uimfRun.IMSScanSetCollection.Create(Run, uimfRun.MinIMSScan, uimfRun.MaxIMSScan,
WorkflowParameters.NumIMSScansSummed, 1);
}
}
else
{
Run.ScanSetCollection.Create(Run, minLCScan, maxLCScan,
WorkflowParameters.Num_LC_TimePointsSummed, 1, WorkflowParameters.ProcessMSMS);
}
}
}
public void checkIntegrityOfUIMF_RawDataTest1()
{
UIMFRun run = new DeconTools.Backend.Runs.UIMFRun(fpgaUIMFFilePath2);
FrameSetCollectionCreator ffcc = new FrameSetCollectionCreator(run, 696, 696, 3, 1);
ffcc.Create();
ScanSetCollectionCreator sscc = new ScanSetCollectionCreator(run, 350, 500, 9, 1);
sscc.Create();
MSGeneratorFactory factory = new MSGeneratorFactory();
Task msgen = factory.CreateMSGenerator(run.MSFileType);
DeconToolsPeakDetector peakDet = new DeconToolsPeakDetector();
peakDet.PeakBackgroundRatio = 6;
peakDet.SigNoiseThreshold = 3;
StringBuilder sb = new StringBuilder();
sb.Append("frame\tscan\tmaxIntens\tnumZeros\n");
foreach (var frame in run.FrameSetCollection.FrameSetList)
{
run.CurrentFrameSet = frame;
foreach (var scan in run.ScanSetCollection.ScanSetList)
{
run.CurrentScanSet = scan;
msgen.Execute(run.ResultCollection);
List <int> indices = getIndicesOf0MZValues(run.XYData.Xvalues);
double maxY = run.XYData.GetMaxY();
if (indices.Count > -1)
{
sb.Append(frame.PrimaryFrame);
sb.Append("\t");
sb.Append(scan.PrimaryScanNumber);
sb.Append("\t");
sb.Append(maxY);
sb.Append("\t");
sb.Append(indices.Count);
sb.Append("\n");
}
}
}
Console.WriteLine(sb.ToString());
}
public void test1()
{
Run run = new XCaliburRun(xcaliburTestfile);
List <MassTag> mass_tagList = TestUtilities.CreateTestMassTagList();
MassTag mt = mass_tagList[0];
run.CurrentScanSet = new ScanSet(9017, new int[] { 9010, 9017, 9024 });
run.CurrentMassTag = mt;
MSGeneratorFactory msgenFactory = new MSGeneratorFactory();
Task msgen = msgenFactory.CreateMSGenerator(run.MSFileType);
DeconToolsV2.Peaks.clsPeakProcessorParameters peakParams = new DeconToolsV2.Peaks.clsPeakProcessorParameters(2, 1.3, true, DeconToolsV2.Peaks.PEAK_FIT_TYPE.QUADRATIC);
Task mspeakDet = new DeconToolsPeakDetector(peakParams);
Task theorFeatureGen = new TomTheorFeatureGenerator();
Task targetedFeatureFinder = new BasicTFF(0.01);
IsotopicProfileFitScoreCalculator fitScoreCalc = new IsotopicProfileFitScoreCalculator();
msgen.Execute(run.ResultCollection);
//run.XYData.Display();
mspeakDet.Execute(run.ResultCollection);
theorFeatureGen.Execute(run.ResultCollection);
targetedFeatureFinder.Execute(run.ResultCollection);
fitScoreCalc.Execute(run.ResultCollection);
MassTagResultBase result = run.ResultCollection.GetMassTagResult(mt);
TestUtilities.DisplayIsotopicProfileData(result.IsotopicProfile);
Console.WriteLine("Fit val = " + result.IsotopicProfile.Score);
/*
*
*
* ------------------- MassTag = 24769---------------------------
* monoMass = 2086.0595; monoMZ = 1044.0370; ChargeState = 2; NET = 0.452; Sequence = DFNEALVHQVVVAYAANAR
*
****** Match ******
******NET = 0.452
******ChromPeak ScanNum = 9016.48992535631
******ChromPeak NETVal = 0.453
******ScanSet = { 9010, 9017, 9024, }
******Observed MZ and intensity = 1044.03290771556 1.269842E+07
******------------------------------ end --------------------------
*
*
*
*
*
*/
}