C# Class ImsInformed.Workflows.LcImsPeptideExtraction.LcImsPeptideSearchWorkfow

The informed workflow.
Mostrar archivo 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