C# Class Coon.Compass.TagQuant.TagQuant

Show file Open project: dbaileychess/Compass Class Usage Examples

Public Properties

Property	Type	Description
CalculatePurity	bool
DontQuantifyETD	bool
ETDQuantPosition	int
FtMassTolerance	CSMSL.Tolerance
InputFiles	List
ItMassTolerance	CSMSL.Tolerance
MS3Quant	bool
NoisebandCap	bool
OutputDirectory	string
PurityMatrices	IsobaricTagPurityCorrection>.Dictionary
PurityWindowInTh	double
RawFileDirectory	string
RawFiles	ThermoRawFile>.Dictionary
UsedTags	TagInformation>.SortedList

Public Methods

Method	Description
Run ( ) : void
TagQuant ( string outputDirectory, string rawFileDirectory, IEnumerable inputFiles, IEnumerable tags, Tolerance itTolerance, Tolerance ftTolerance, bool isMS3Quant = false, int etdQuantPosition, bool nosiebasecap = false, bool isETDQuantified = true, bool calculatePurity = false ) : System

Protected Methods

Method	Description
OnUpdateLog ( string message ) : void

Private Methods

Method	Description
BuildPurityMatrixes ( IEnumerable inputTags ) : void
DeterminePurity ( MSDataScan scan, double mz, int charge, DoubleRange isolationRange ) : double
LoadFiles ( IEnumerable filePaths, bool ms3Quant = false ) : IEnumerable
Log ( string msg ) : void
Normalize ( IEnumerable quantFiles ) : void
OnProgressUpdate ( int percent ) : void
PurityCorrect ( IEnumerable peaks, bool isDecoy ) : void
WriteLog ( ) : void
WriteOutputFiles ( IEnumerable quantFiles ) : void

Method Details

OnUpdateLog() protected method

protected OnUpdateLog ( string message ) : void
message	string
return	void

Run() public method

public Run ( ) : void
return	void

TagQuant() public method

public TagQuant ( string outputDirectory, string rawFileDirectory, IEnumerable inputFiles, IEnumerable tags, Tolerance itTolerance, Tolerance ftTolerance, bool isMS3Quant = false, int etdQuantPosition, bool nosiebasecap = false, bool isETDQuantified = true, bool calculatePurity = false ) : System
outputDirectory	string
rawFileDirectory	string
inputFiles	IEnumerable
tags	IEnumerable
itTolerance	CSMSL.Tolerance
ftTolerance	CSMSL.Tolerance
isMS3Quant	bool
etdQuantPosition	int
nosiebasecap	bool
isETDQuantified	bool
calculatePurity	bool
return	System

Property Details

CalculatePurity public property

public bool CalculatePurity
return	bool

DontQuantifyETD public property

public bool DontQuantifyETD
return	bool

ETDQuantPosition public property

public int ETDQuantPosition
return	int

FtMassTolerance public property

public Tolerance,CSMSL FtMassTolerance
return	CSMSL.Tolerance

InputFiles public property

public List InputFiles
return	List

ItMassTolerance public property

public Tolerance,CSMSL ItMassTolerance
return	CSMSL.Tolerance

MS3Quant public property

public bool MS3Quant
return	bool

NoisebandCap public property

public bool NoisebandCap
return	bool

OutputDirectory public property

public string OutputDirectory
return	string

PurityMatrices public property

public Dictionary PurityMatrices
return	IsobaricTagPurityCorrection>.Dictionary

PurityWindowInTh public property

public double PurityWindowInTh
return	double

RawFileDirectory public property

public string RawFileDirectory
return	string

RawFiles public property

public Dictionary RawFiles
return	ThermoRawFile>.Dictionary

UsedTags public property

public SortedList UsedTags
return	TagInformation>.SortedList