C# Class Coon.Compass.Lotor.Lotor

Show file Open project: dbaileychess/Compass Class Usage Examples

Public Properties

Property	Type	Description
FixedModifications	List
QuantifiedModifications	List

Public Methods

Method	Description
GetPValue ( PSM psm, Tolerance prod_tolerance, double cutoff ) : double
Localize ( ) : void
LocalizedIsoform ( double data ) : Tuple
Log ( string message, bool isError = false ) : void
Lotor ( string rawFileDirectory, string inputcsvFile, string outputDirectory, List fixedModifications, List quantifiedModifications, Tolerance prod_Tolerance, int scoreCutoff, bool separateGroups, double productThreshold, bool ignoreCTerminal, bool reduceSites, FragmentTypes fragType, bool phosphoNeutralLoss = false ) : System
ProgressUpdate ( double percent ) : void

Protected Methods

Method	Description
OnFinished ( ) : void

Private Methods

Method	Description
CalculateBestIsoforms ( List psms, FragmentTypes fragType, Tolerance prod_tolerance, double productThreshold, bool phosphoNeutralLosses ) : List
CompileResults ( List hits, string csvFile, string outputDirectory, bool breakProteinsApart = false ) : List
LoadAllPSMs ( string csvFile, string rawFileDirectory, List fixedMods ) : List
LocalizedIsoformSimple ( PSM psm ) : Tuple
WriteResults ( List proteins, string csvFile, string outDirectory, int firstQuant, int lastQuant ) : void

Method Details

GetPValue() public static method

public static GetPValue ( PSM psm, Tolerance prod_tolerance, double cutoff ) : double
psm	PSM
prod_tolerance	CSMSL.Tolerance
cutoff	double
return	double

Localize() public method

public Localize ( ) : void
return	void

LocalizedIsoform() public static method

public static LocalizedIsoform ( double data ) : Tuple
data	double
return	Tuple

Log() public method

public Log ( string message, bool isError = false ) : void
message	string
isError	bool
return	void

Lotor() public method

public Lotor ( string rawFileDirectory, string inputcsvFile, string outputDirectory, List fixedModifications, List quantifiedModifications, Tolerance prod_Tolerance, int scoreCutoff, bool separateGroups, double productThreshold, bool ignoreCTerminal, bool reduceSites, FragmentTypes fragType, bool phosphoNeutralLoss = false ) : System
rawFileDirectory	string
inputcsvFile	string
outputDirectory	string
fixedModifications	List
quantifiedModifications	List
prod_Tolerance	CSMSL.Tolerance
scoreCutoff	int
separateGroups	bool
productThreshold	double
ignoreCTerminal	bool
reduceSites	bool
fragType	FragmentTypes
phosphoNeutralLoss	bool
return	System

OnFinished() protected method

protected OnFinished ( ) : void
return	void

ProgressUpdate() public method

public ProgressUpdate ( double percent ) : void
percent	double
return	void

Property Details

FixedModifications public static property

public static List FixedModifications
return	List

QuantifiedModifications public static property

public static List QuantifiedModifications
return	List