C# Class Phosphinator.Phosphinator

Show file Open project: dbaileychess/Compass Class Usage Examples

Public Methods

Method	Description
Phosphinate ( ) : void
Phosphinator ( IList csvFilepaths, string rawFolder, IEnumerable fixedModifications, double intensityThreshold, IntensityThresholdType intensityThresholdType, double mzTolerance, double ambiguityScoreThreshold, bool eliminatePrecursorInterference, double precursorInterferenceThreshold, bool motifXOutput, string motifXFastaProteinDatabaseFilepath, int motifXWindowSize, string outputFolder ) : System

Protected Methods

Method	Description
onFinished ( EventArgs e ) : void
onFinishedFile ( EventArgs e ) : void
onStarting ( EventArgs e ) : void
onStartingFile ( FilepathEventArgs e ) : void
onThrowException ( ExceptionEventArgs e ) : void
onUpdateProgress ( ProgressEventArgs e ) : void

Private Methods

Method	Description
AppendFieldToCsv ( string field, StreamWriter csv ) : void
ComparePhosphopeptidesByDescendingMatchingFragments ( PhosphopeptideStatistics left, PhosphopeptideStatistics right ) : int
Count ( string s, char c ) : int
ExtractMotifs ( int>.Dictionary motifs, ProteinDictionary proteins, string proteinDescription, string peptideSequence, int startResidueNumber, int phosphositeIndex ) : void
GetAlternativePhosphoisoformPeptides ( Peptide peptide, IEnumerable fixedModifications ) : List
MZFromMassAndCharge ( double mass, int charge ) : double
MassFromMZAndCharge ( double mz, int charge ) : double

Method Details

Phosphinate() public method

public Phosphinate ( ) : void
return	void

Phosphinator() public method

public Phosphinator ( IList csvFilepaths, string rawFolder, IEnumerable fixedModifications, double intensityThreshold, IntensityThresholdType intensityThresholdType, double mzTolerance, double ambiguityScoreThreshold, bool eliminatePrecursorInterference, double precursorInterferenceThreshold, bool motifXOutput, string motifXFastaProteinDatabaseFilepath, int motifXWindowSize, string outputFolder ) : System
csvFilepaths	IList
rawFolder	string
fixedModifications	IEnumerable
intensityThreshold	double
intensityThresholdType	IntensityThresholdType
mzTolerance	double
ambiguityScoreThreshold	double
eliminatePrecursorInterference	bool
precursorInterferenceThreshold	double
motifXOutput	bool
motifXFastaProteinDatabaseFilepath	string
motifXWindowSize	int
outputFolder	string
return	System

onFinished() protected method

protected onFinished ( EventArgs e ) : void
e	System.EventArgs
return	void

onFinishedFile() protected method

protected onFinishedFile ( EventArgs e ) : void
e	System.EventArgs
return	void

onStarting() protected method

protected onStarting ( EventArgs e ) : void
e	System.EventArgs
return	void

onStartingFile() protected method

protected onStartingFile ( FilepathEventArgs e ) : void
e	FilepathEventArgs
return	void

onThrowException() protected method

protected onThrowException ( ExceptionEventArgs e ) : void
e	ExceptionEventArgs
return	void

onUpdateProgress() protected method

protected onUpdateProgress ( ProgressEventArgs e ) : void
e	ProgressEventArgs
return	void