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;
}