C# Class ImsInformed.Workflows.LcImsPeptideExtraction.LcImsPeptideSearchWorkfow

The informed workflow.

显示文件 Open project: PNNL-Comp-Mass-Spec/IMS-Informed-Library Class Usage Examples

Public Properties

Property	Type	Description
NumberOfFrames	double
NumberOfScans	double
_parameters	LcImsPeptideSearchParameters
_uimfReader	DataReader

Protected Properties

Property	Type	Description
_buildWatershedStopWatch	Stopwatch
_featureFindCount	double
_featureFindStopWatch	Stopwatch
_isotopicPeakFitScoreCalculator	PeakLeastSquaresFitter
_leftOfMonoPeakLooker	LeftOfMonoPeakLooker
_msFeatureFinder	IterativeTFF
_peakDetector	ChromPeakDetector
_pointCount	double
_smoothStopwatch	Stopwatch
_smoother	SavitzkyGolaySmoother
_theoreticalFeatureGenerator	ITheorFeatureGenerator
_uimfFileLocation	string

Public Methods

Method	Description
ExtractData ( IEnumerable targetList ) : void
FindFeatures ( double targetMz, int scanLcMin, int scanLcMax ) : IEnumerable
LcImsPeptideSearchWorkfow ( string uimfFileLocation, LcImsPeptideSearchParameters parameters ) : System	Initializes a new instance of the LcImsPeptideSearchWorkfow class.
LcImsPeptideSearchWorkfow ( string uimfFileLocation, LcImsPeptideSearchParameters parameters, IInterpolation netAlignment ) : System	Initializes a new instance of the LcImsPeptideSearchWorkfow class.
PrintFeatureFindStatistics ( ) : void
RunInformedWorkflow ( PeptideTarget target ) : ChargeStateCorrelationResult	The run informed workflow.

Protected Methods

Method	Description
FindFeatures ( double targetMz ) : IEnumerable
FindFrameNumberUseForIsotopicProfile ( double targetMz, int scanLcRep, int scanImsRep ) : int
GetMassSpectrum ( int scanLcRep, int scanImsRep, double minMzForSpectrum, double maxMzForSpectrum ) : XYData
WriteMSPeakListToFile ( IEnumerable peakList, double targetMz ) : void
WritePointsToFile ( IEnumerable intensityPointList, double targetMz ) : void
WriteXYDataToFile ( XYData xyData, double targetMz ) : void

Private Methods

Method	Description
GetReverseAlignedNet ( double net ) : double

Method Details

ExtractData() public method

public ExtractData ( IEnumerable targetList ) : void
targetList	IEnumerable
return	void

FindFeatures() protected method

protected FindFeatures ( double targetMz ) : IEnumerable
targetMz	double
return	IEnumerable

FindFeatures() public method

public FindFeatures ( double targetMz, int scanLcMin, int scanLcMax ) : IEnumerable
targetMz	double
scanLcMin	int
scanLcMax	int
return	IEnumerable

FindFrameNumberUseForIsotopicProfile() protected method

protected FindFrameNumberUseForIsotopicProfile ( double targetMz, int scanLcRep, int scanImsRep ) : int
targetMz	double
scanLcRep	int
scanImsRep	int
return	int

GetMassSpectrum() protected method

protected GetMassSpectrum ( int scanLcRep, int scanImsRep, double minMzForSpectrum, double maxMzForSpectrum ) : XYData
scanLcRep	int
scanImsRep	int
minMzForSpectrum	double
maxMzForSpectrum	double
return	XYData

LcImsPeptideSearchWorkfow() public method

Initializes a new instance of the LcImsPeptideSearchWorkfow class.

public LcImsPeptideSearchWorkfow ( string uimfFileLocation, LcImsPeptideSearchParameters parameters ) : System
uimfFileLocation	string	/// The uimf file location. ///
parameters	LcImsPeptideSearchParameters	/// The parameters. ///
return	System

LcImsPeptideSearchWorkfow() public method

Initializes a new instance of the LcImsPeptideSearchWorkfow class.

public LcImsPeptideSearchWorkfow ( string uimfFileLocation, LcImsPeptideSearchParameters parameters, IInterpolation netAlignment ) : System
uimfFileLocation	string	/// The uimf file location. ///
parameters	LcImsPeptideSearchParameters	/// The parameters. ///
netAlignment	IInterpolation	/// The net alignment. ///
return	System

PrintFeatureFindStatistics() public method

public PrintFeatureFindStatistics ( ) : void
return	void

RunInformedWorkflow() public method

The run informed workflow.

public RunInformedWorkflow ( PeptideTarget target ) : ChargeStateCorrelationResult
target	ImsInformed.Targets.PeptideTarget	/// The Target. ///
return	ChargeStateCorrelationResult

WriteMSPeakListToFile() protected method

protected WriteMSPeakListToFile ( IEnumerable peakList, double targetMz ) : void
peakList	IEnumerable
targetMz	double
return	void

WritePointsToFile() protected method

protected WritePointsToFile ( IEnumerable intensityPointList, double targetMz ) : void
intensityPointList	IEnumerable
targetMz	double
return	void

WriteXYDataToFile() protected method

protected WriteXYDataToFile ( XYData xyData, double targetMz ) : void
xyData	XYData
targetMz	double
return	void

Property Details

NumberOfFrames public_oe property

The number of frames.

public double NumberOfFrames
return	double

NumberOfScans public_oe property

The number of scans.

public double NumberOfScans
return	double

_buildWatershedStopWatch protected_oe property

protected Stopwatch _buildWatershedStopWatch
return	Stopwatch

_featureFindCount protected_oe property

The _feature find count.

protected double _featureFindCount
return	double

_featureFindStopWatch protected_oe property

The _feature find stop watch.

protected Stopwatch _featureFindStopWatch
return	Stopwatch

_isotopicPeakFitScoreCalculator protected_oe property

The _isotopic peak fit score calculator.

protected PeakLeastSquaresFitter _isotopicPeakFitScoreCalculator
return	PeakLeastSquaresFitter

_leftOfMonoPeakLooker protected_oe property

The _left of mono peak looker.

protected LeftOfMonoPeakLooker _leftOfMonoPeakLooker
return	LeftOfMonoPeakLooker

_msFeatureFinder protected_oe property

The _ms feature finder.

protected IterativeTFF _msFeatureFinder
return	IterativeTFF

_parameters public_oe property

The _parameters.

public LcImsPeptideSearchParameters,ImsInformed.Workflows.LcImsPeptideExtraction _parameters
return	LcImsPeptideSearchParameters

_peakDetector protected_oe property

The _peak detector.

protected ChromPeakDetector _peakDetector
return	ChromPeakDetector

_pointCount protected_oe property

The _point count.

protected double _pointCount
return	double

_smoothStopwatch protected_oe property

The _smooth stopwatch.

protected Stopwatch _smoothStopwatch
return	Stopwatch

_smoother protected_oe property

The smoother.

protected SavitzkyGolaySmoother _smoother
return	SavitzkyGolaySmoother

_theoreticalFeatureGenerator protected_oe property

The _theoretical feature generator.

protected ITheorFeatureGenerator _theoreticalFeatureGenerator
return	ITheorFeatureGenerator

_uimfFileLocation protected_oe property

The _uimf file location.

protected string _uimfFileLocation
return	string

_uimfReader public_oe property

The _uimf reader.

public DataReader _uimfReader
return	DataReader