public O16O18IqWorkflow(Run run, TargetedWorkflowParameters parameters) : base(run, parameters) { this.ChromatogramCorrelator = new O16O18ChromCorrelator(parameters.ChromSmootherNumPointsInSmooth, 0.01, parameters.ChromGenTolerance, parameters.ChromGenToleranceUnit); }
public ChromPeakAnalyzerIqWorkflow(TargetedWorkflowParameters parameters) : base(parameters) { var iterativeTffParameters = new IterativeTFFParameters(); TargetedMSFeatureFinder = new IterativeTFF(iterativeTffParameters); PeakFitter = new PeakLeastSquaresFitter(); }
/// <summary> /// Factory method for creating the key ChromPeakSelector algorithm /// </summary> /// <param name="workflowParameters"></param> /// <returns></returns> public static ChromPeakSelectorBase CreateChromPeakSelector(TargetedWorkflowParameters workflowParameters) { ChromPeakSelectorBase chromPeakSelector; var chromPeakSelectorParameters = new ChromPeakSelectorParameters(); chromPeakSelectorParameters.NETTolerance = (float)workflowParameters.ChromNETTolerance; chromPeakSelectorParameters.NumScansToSum = workflowParameters.NumMSScansToSum; chromPeakSelectorParameters.PeakSelectorMode = workflowParameters.ChromPeakSelectorMode; chromPeakSelectorParameters.SummingMode = workflowParameters.SummingMode; chromPeakSelectorParameters.AreaOfPeakToSumInDynamicSumming = workflowParameters.AreaOfPeakToSumInDynamicSumming; chromPeakSelectorParameters.MaxScansSummedInDynamicSumming = workflowParameters.MaxScansSummedInDynamicSumming; switch (workflowParameters.ChromPeakSelectorMode) { case DeconTools.Backend.Globals.PeakSelectorMode.ClosestToTarget: case DeconTools.Backend.Globals.PeakSelectorMode.MostIntense: case DeconTools.Backend.Globals.PeakSelectorMode.N15IntelligentMode: case DeconTools.Backend.Globals.PeakSelectorMode.RelativeToOtherChromPeak: chromPeakSelector = new BasicChromPeakSelector(chromPeakSelectorParameters); break; case DeconTools.Backend.Globals.PeakSelectorMode.Smart: var smartchrompeakSelectorParameters = new SmartChromPeakSelectorParameters(chromPeakSelectorParameters); smartchrompeakSelectorParameters.MSFeatureFinderType = DeconTools.Backend.Globals.TargetedFeatureFinderType.ITERATIVE; smartchrompeakSelectorParameters.MSPeakDetectorPeakBR = workflowParameters.MSPeakDetectorPeakBR; smartchrompeakSelectorParameters.MSPeakDetectorSigNoiseThresh = workflowParameters.MSPeakDetectorSigNoise; smartchrompeakSelectorParameters.MSToleranceInPPM = workflowParameters.MSToleranceInPPM; smartchrompeakSelectorParameters.NumChromPeaksAllowed = workflowParameters.NumChromPeaksAllowedDuringSelection; smartchrompeakSelectorParameters.MultipleHighQualityMatchesAreAllowed = workflowParameters.MultipleHighQualityMatchesAreAllowed; smartchrompeakSelectorParameters.IterativeTffMinRelIntensityForPeakInclusion = 0.66; smartchrompeakSelectorParameters.NumMSSummedInSmartSelector = workflowParameters.SmartChromPeakSelectorNumMSSummed; chromPeakSelector = new SmartChromPeakSelector(smartchrompeakSelectorParameters); break; case DeconTools.Backend.Globals.PeakSelectorMode.SmartUIMF: var smartUIMFchrompeakSelectorParameters = new SmartChromPeakSelectorParameters(chromPeakSelectorParameters); smartUIMFchrompeakSelectorParameters.MSFeatureFinderType = DeconTools.Backend.Globals.TargetedFeatureFinderType.ITERATIVE; smartUIMFchrompeakSelectorParameters.MSPeakDetectorPeakBR = workflowParameters.MSPeakDetectorPeakBR; smartUIMFchrompeakSelectorParameters.MSPeakDetectorSigNoiseThresh = workflowParameters.MSPeakDetectorSigNoise; smartUIMFchrompeakSelectorParameters.MSToleranceInPPM = workflowParameters.MSToleranceInPPM; smartUIMFchrompeakSelectorParameters.NumChromPeaksAllowed = workflowParameters.NumChromPeaksAllowedDuringSelection; smartUIMFchrompeakSelectorParameters.MultipleHighQualityMatchesAreAllowed = workflowParameters.MultipleHighQualityMatchesAreAllowed; smartUIMFchrompeakSelectorParameters.IterativeTffMinRelIntensityForPeakInclusion = 0.66; chromPeakSelector = new SmartChromPeakSelectorUIMF(smartUIMFchrompeakSelectorParameters); break; default: throw new ArgumentOutOfRangeException(); } return(chromPeakSelector); }
protected TargetedWorkflow(Run run, TargetedWorkflowParameters parameters) { Run = run; WorkflowParameters = parameters; MsLeftTrimAmount = 1e10; // set this high so, by default, nothing is trimmed MsRightTrimAmount = 1e10; // set this high so, by default, nothing is trimmed }
public O16O18ParentIqWorkflow(Run run, TargetedWorkflowParameters parameters) : base(run, parameters) { PeakFitter = new PeakLeastSquaresFitter(); _mspeakDetector = new DeconToolsPeakDetectorV2(parameters.MSPeakDetectorPeakBR, parameters.MSPeakDetectorSigNoise, DeconTools.Backend.Globals.PeakFitType.QUADRATIC, run.IsDataThresholded); }
public TargetedAlignerWorkflow(Run run, TargetedWorkflowParameters workflowParameters) : base(run, workflowParameters) { Check.Require(workflowParameters is TargetedAlignerWorkflowParameters, "Parameter object is of the wrong type."); _netGroupings = createNETGroupings(); NumSuccessesPerNETGrouping = new List <int>(); NumFailuresPerNETGrouping = new List <int>(); outputToConsole = true; }
public IqWorkflow CreateWorkflow(string workflowType, TargetedWorkflowParameters parameters) { workflowType = workflowType.ToLower(); switch (workflowType) { case "unlabeled": return(new BasicIqWorkflow(parameters)); case "o16o18": break; case "n14n15": break; default: throw new NotImplementedException("Cannot create workflow. Workflow type is not known. Input workflowType= " + workflowType); } return(null); }
public override ChromPeakSelectorBase CreateChromPeakSelector(TargetedWorkflowParameters workflowParameters) { var chromPeakSelectorParameters = new ChromPeakSelectorParameters(); chromPeakSelectorParameters.NETTolerance = (float)workflowParameters.ChromNETTolerance; chromPeakSelectorParameters.NumScansToSum = workflowParameters.NumMSScansToSum; chromPeakSelectorParameters.PeakSelectorMode = workflowParameters.ChromPeakSelectorMode; chromPeakSelectorParameters.SummingMode = workflowParameters.SummingMode; chromPeakSelectorParameters.AreaOfPeakToSumInDynamicSumming = workflowParameters.AreaOfPeakToSumInDynamicSumming; chromPeakSelectorParameters.MaxScansSummedInDynamicSumming = workflowParameters.MaxScansSummedInDynamicSumming; var smartchrompeakSelectorParameters = new SmartChromPeakSelectorParameters(chromPeakSelectorParameters); smartchrompeakSelectorParameters.MSFeatureFinderType = DeconTools.Backend.Globals.TargetedFeatureFinderType.ITERATIVE; smartchrompeakSelectorParameters.MSPeakDetectorPeakBR = workflowParameters.MSPeakDetectorPeakBR; smartchrompeakSelectorParameters.MSPeakDetectorSigNoiseThresh = workflowParameters.MSPeakDetectorSigNoise; smartchrompeakSelectorParameters.MSToleranceInPPM = workflowParameters.MSToleranceInPPM; smartchrompeakSelectorParameters.NumChromPeaksAllowed = workflowParameters.NumChromPeaksAllowedDuringSelection; smartchrompeakSelectorParameters.MultipleHighQualityMatchesAreAllowed = workflowParameters.MultipleHighQualityMatchesAreAllowed; smartchrompeakSelectorParameters.IterativeTffMinRelIntensityForPeakInclusion = 0.66; return(new IqSmartChromPeakSelector(smartchrompeakSelectorParameters)); }
public ChargeStateChildTopDownIqWorkflow(TargetedWorkflowParameters parameters) : base(parameters) { Parser = new IqCodeParser(); }
public ChromPeakDeciderIqWorkflow(Run run, TargetedWorkflowParameters parameters) : base(run, parameters) { }
public TargetedAlignerWorkflow(TargetedWorkflowParameters workflowParameters) : this(null, workflowParameters) { }
public UIMFTargetedMSMSWorkflowCollapseIMS(Run run, TargetedWorkflowParameters parameters) : base(run, parameters) { this.ChromPeakToXYDataMap = new Dictionary <ChromPeak, XYData>(); }
public O16O18ChromPeakAnalyzerIqWorkflow(Run run, TargetedWorkflowParameters parameters) : base(run, parameters) { }
public UIMFTargetedWorkflowCollapseIMS(Run run, TargetedWorkflowParameters parameters) : base(run, parameters) { }
public N14N15Workflow2(TargetedWorkflowParameters parameters) : this(null, parameters) { }
public N14N15Workflow2(Run run, TargetedWorkflowParameters parameters) : base(run, parameters) { MsLeftTrimAmount = 5; MsRightTrimAmount = 5; }
public ChargeStateChildIqWorkflow(TargetedWorkflowParameters parameters) : base(parameters) { TargetUtilities = new IqTargetUtilities(); }
public ChromPeakDeciderIqWorkflow(TargetedWorkflowParameters parameters) : base(parameters) { }
public ParentLogicIqWorkflow(Run run, TargetedWorkflowParameters parameters) : base(run, parameters) { }
protected TargetedWorkflow(TargetedWorkflowParameters parameters) : this(null, parameters) { }
public ParentLogicIqWorkflow(TargetedWorkflowParameters parameters) : base(parameters) { }
public O16O18Workflow(Run run, TargetedWorkflowParameters parameters) : base(run, parameters) { }
public UIMFTargetedMSMSWorkflowCollapseIMS(TargetedWorkflowParameters parameters) : this(null, parameters) { }
public SipperTargetedWorkflow(TargetedWorkflowParameters parameters) : this(null, parameters) { }
public O16O18ChromPeakAnalyzerIqWorkflow(TargetedWorkflowParameters parameters) : this(null, parameters) { }
public TargetedAlignerWorkflow(Run run, TargetedWorkflowParameters workflowParameters, BackgroundWorker bw) : this(run, workflowParameters) { _backgroundWorker = bw; }
public BasicTargetedWorkflow(TargetedWorkflowParameters parameters) : base(parameters) { }
public BasicTargetedWorkflow(Run run, TargetedWorkflowParameters parameters) : base(run, parameters) { }
public O16O18Workflow(TargetedWorkflowParameters parameters) : this(null, parameters) { }
public SipperTargetedWorkflow(Run run, TargetedWorkflowParameters parameters) : base(run, parameters) { MsRightTrimAmount = 100; MsLeftTrimAmount = 3; }