C# Class ImsInformed.Workflows.LcImsPeptideExtraction.LcImsPeptideSearchWorkfow

The informed workflow.

Show file 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 property

The number of frames.

public double NumberOfFrames
return	double

NumberOfScans public property

The number of scans.

public double NumberOfScans
return	double

_buildWatershedStopWatch protected property

protected Stopwatch _buildWatershedStopWatch
return	Stopwatch

_featureFindCount protected property

The _feature find count.

protected double _featureFindCount
return	double

_featureFindStopWatch protected property

The _feature find stop watch.

protected Stopwatch _featureFindStopWatch
return	Stopwatch

_isotopicPeakFitScoreCalculator protected property

The _isotopic peak fit score calculator.

protected PeakLeastSquaresFitter _isotopicPeakFitScoreCalculator
return	PeakLeastSquaresFitter

_leftOfMonoPeakLooker protected property

The _left of mono peak looker.

protected LeftOfMonoPeakLooker _leftOfMonoPeakLooker
return	LeftOfMonoPeakLooker

_msFeatureFinder protected property

The _ms feature finder.

protected IterativeTFF _msFeatureFinder
return	IterativeTFF

_parameters public property

The _parameters.

public LcImsPeptideSearchParameters,ImsInformed.Workflows.LcImsPeptideExtraction _parameters
return	LcImsPeptideSearchParameters

_peakDetector protected property

The _peak detector.

protected ChromPeakDetector _peakDetector
return	ChromPeakDetector

_pointCount protected property

The _point count.

protected double _pointCount
return	double

_smoothStopwatch protected property

The _smooth stopwatch.

protected Stopwatch _smoothStopwatch
return	Stopwatch

_smoother protected property

The smoother.

protected SavitzkyGolaySmoother _smoother
return	SavitzkyGolaySmoother

_theoreticalFeatureGenerator protected property

The _theoretical feature generator.

protected ITheorFeatureGenerator _theoreticalFeatureGenerator
return	ITheorFeatureGenerator

_uimfFileLocation protected property

The _uimf file location.

protected string _uimfFileLocation
return	string

_uimfReader public property

The _uimf reader.

public DataReader _uimfReader
return	DataReader