C# Class ImsInformed.Workflows.CrossSectionExtraction.CrossSectionWorkfow

Find molecules with a given empirical formula and given ionization methods. Developed based on LCMS Peptide Search Workflow

Inheritance: IDisposable

Public Properties

Property	Type	Description
peakDetector	ChromPeakDetector
smoother	SavitzkyGolaySmoother
theoreticalFeatureGenerator	ITheorFeatureGenerator

Method	Description
CrossSectionWorkfow ( string uimfFileLocation, string outputDirectory, CrossSectionSearchParameters parameters ) : System	Initializes a new instance of the CrossSectionWorkfow class.
Dispose ( ) : void	The dispose.
Dispose ( bool disposing ) : void	The dispose.
RunCrossSectionWorkFlow ( IImsTarget target, bool detailedVerbose = true ) : CrossSectionWorkflowResult	The run molecule informed work flow.
RunCrossSectionWorkFlow ( IEnumerable targetList, bool detailedVerbose = true ) : IList	The run cross section work flow.

Method	Description
FindPeaksBasedOnXIC ( VoltageGroup voltageGroup, ExtractedIonChromatogram chromatogram, IImsTarget target ) : List	The find peaks based on xic.
ReportAnslysisResultAndMetrics ( CrossSectionWorkflowResult informedResult, bool detailedVerbose = true ) : void	The report anslysis result and metrics.
ReportFeatureEvaluation ( StandardImsPeak peak, PeakScores scores, bool verbose, IImsTarget target, bool badScanRange, bool lowAbsoluteIntensity, bool lowRelativeIntensity, bool badPeakShape, bool lowIsotopicAffinity ) : string	The report feature evaluation.
ReportIsomersInfo ( IEnumerable allIsomers ) : void	The report isomers info.
ReportTargetInfo ( IImsTarget target, bool verbose ) : void	The report target info.
ReportTrackInformation ( AssociationHypothesis hypothesis, bool hasCompositionInfo, bool verbose ) : void	The report track information.
ResetTraceListenerToTarget ( IImsTarget target, string datasetName ) : FileStream	The reset trace listener to target.

Initializes a new instance of the CrossSectionWorkfow class.

public CrossSectionWorkfow ( string uimfFileLocation, string outputDirectory, CrossSectionSearchParameters parameters ) : System
uimfFileLocation	string	/// The uimf file location. ///
outputDirectory	string	/// The output directory. ///
parameters	CrossSectionSearchParameters	/// The parameters. ///
return	System

The dispose.

public Dispose ( ) : void
return	void

The dispose.

public Dispose ( bool disposing ) : void
disposing	bool	/// The disposing. ///
return	void

The run molecule informed work flow.

public RunCrossSectionWorkFlow ( IImsTarget target, bool detailedVerbose = true ) : CrossSectionWorkflowResult
target	IImsTarget	/// The Target. ///
detailedVerbose	bool	///
return	CrossSectionWorkflowResult

The run cross section work flow.

public RunCrossSectionWorkFlow ( IEnumerable targetList, bool detailedVerbose = true ) : IList
targetList	IEnumerable	/// The target list. ///
detailedVerbose	bool	/// The detailed verbose. ///
return	IList

The number of frames.

public int NumberOfFrames
return	int

The number of scans.

public int NumberOfScans
return	int

The _peak detector.

protected ChromPeakDetector peakDetector
return	ChromPeakDetector

The smoother.

protected SavitzkyGolaySmoother smoother
return	SavitzkyGolaySmoother

The theoretical feature generator.

protected ITheorFeatureGenerator theoreticalFeatureGenerator
return	ITheorFeatureGenerator

The UIMF reader.

public DataReader uimfReader
return	DataReader