C# Class CSMSL.IO.PepXML.PepXmlWriter

Inheritance: IDisposable
Show file Open project: dbaileychess/CSMSL Class Usage Examples

Public Methods

Method Description
Dispose ( ) : void
EndSpectrum ( ) : void
PepXmlWriter ( string filePath ) : System
SetCurrentStage ( Stage stage, bool endPreviousStage = true ) : void
StartSearchSummary ( string searchEngine, bool isPrecursorMassMonoisotopic, bool isProductMassMonoisotopic ) : void
StartSpectrum ( int spectrumNumbner, double rt, double precursorNeutralMass, int chargeState, string title = "" ) : void
WriteComment ( string comment ) : void
WriteModification ( IMass modification, ModificationSites sites, bool fixedModification = true ) : void
WritePSM ( PeptideSpectralMatch psm, int hitRank = 1 ) : void
WriteParameter ( string name, string value ) : void
WriteProteinDatabase ( string fastaFilePath, string name = "", string releaseDate = "" ) : void
WriteSampleProtease ( Protease protease ) : void
WriteSearchProtease ( Protease protease, int maxMissedClevages, bool semiDigested = false ) : void

Method Details

Dispose() public method

public Dispose ( ) : void
return void

EndSpectrum() public method

public EndSpectrum ( ) : void
return void

PepXmlWriter() public method

public PepXmlWriter ( string filePath ) : System
filePath string
return System

SetCurrentStage() public method

public SetCurrentStage ( Stage stage, bool endPreviousStage = true ) : void
stage Stage
endPreviousStage bool
return void

StartSearchSummary() public method

public StartSearchSummary ( string searchEngine, bool isPrecursorMassMonoisotopic, bool isProductMassMonoisotopic ) : void
searchEngine string
isPrecursorMassMonoisotopic bool
isProductMassMonoisotopic bool
return void

StartSpectrum() public method

public StartSpectrum ( int spectrumNumbner, double rt, double precursorNeutralMass, int chargeState, string title = "" ) : void
spectrumNumbner int
rt double
precursorNeutralMass double
chargeState int
title string
return void

WriteComment() public method

public WriteComment ( string comment ) : void
comment string
return void

WriteModification() public method

public WriteModification ( IMass modification, ModificationSites sites, bool fixedModification = true ) : void
modification IMass
sites ModificationSites
fixedModification bool
return void

WritePSM() public method

public WritePSM ( PeptideSpectralMatch psm, int hitRank = 1 ) : void
psm PeptideSpectralMatch
hitRank int
return void

WriteParameter() public method

public WriteParameter ( string name, string value ) : void
name string
value string
return void

WriteProteinDatabase() public method

public WriteProteinDatabase ( string fastaFilePath, string name = "", string releaseDate = "" ) : void
fastaFilePath string
name string
releaseDate string
return void

WriteSampleProtease() public method

public WriteSampleProtease ( Protease protease ) : void
protease CSMSL.Proteomics.Protease
return void

WriteSearchProtease() public method

public WriteSearchProtease ( Protease protease, int maxMissedClevages, bool semiDigested = false ) : void
protease CSMSL.Proteomics.Protease
maxMissedClevages int
semiDigested bool
return void