C# Class CSMSL.IO.PsmReader

Inheritance: IDisposable

Show file Open project: dbaileychess/CSMSL

Protected Properties

Property	Type	Description
_dataFiles	MSDataFile>.Dictionary
_disposed	bool
_extraColumns	List
_fixedMods	List
_proteins	Protein>.Dictionary
_variableMods	IMass>.Dictionary

Public Methods

Method	Description
AddFixedModification ( Modification modification ) : IMass
AddFixedModifications ( IEnumerable modifications ) : void
AddMSDataFile ( MSDataFile dataFile ) : void
AddMSDataFiles ( IEnumerable dataFiles ) : void
AddVariableModification ( IMass modification, string name ) : void
AddVariableModification ( string chemicalFormula, string name ) : void
Dispose ( ) : void
LoadProteins ( IEnumerable proteins ) : void
LoadProteins ( string fastaFile ) : void
ReadExtra ( string p ) : void
ReadNextPsm ( ) : IEnumerable

Protected Methods

Method	Description
Dispose ( bool disposing ) : void
PsmReader ( string filePath ) : System
SetFixedMods ( AminoAcidPolymer peptide ) : void
SetVariableMods ( AminoAcidPolymer peptide, string modname, int residue ) : void

Method Details

AddFixedModification() public method

public AddFixedModification ( Modification modification ) : IMass
modification	Modification
return	IMass

AddFixedModifications() public method

public AddFixedModifications ( IEnumerable modifications ) : void
modifications	IEnumerable
return	void

AddMSDataFile() public method

public AddMSDataFile ( MSDataFile dataFile ) : void
dataFile	MSDataFile
return	void

AddMSDataFiles() public method

public AddMSDataFiles ( IEnumerable dataFiles ) : void
dataFiles	IEnumerable
return	void

AddVariableModification() public method

public AddVariableModification ( IMass modification, string name ) : void
modification	IMass
name	string
return	void

AddVariableModification() public method

public AddVariableModification ( string chemicalFormula, string name ) : void
chemicalFormula	string
name	string
return	void

Dispose() public method

public Dispose ( ) : void
return	void

Dispose() protected method

protected Dispose ( bool disposing ) : void
disposing	bool
return	void

LoadProteins() public method

public LoadProteins ( IEnumerable proteins ) : void
proteins	IEnumerable
return	void

LoadProteins() public method

public LoadProteins ( string fastaFile ) : void
fastaFile	string
return	void

PsmReader() protected method

protected PsmReader ( string filePath ) : System
filePath	string
return	System

ReadExtra() public method

public ReadExtra ( string p ) : void
p	string
return	void

ReadNextPsm() public abstract method

public abstract ReadNextPsm ( ) : IEnumerable
return	IEnumerable

SetFixedMods() protected method

protected SetFixedMods ( AminoAcidPolymer peptide ) : void
peptide	AminoAcidPolymer
return	void

SetVariableMods() protected method

protected SetVariableMods ( AminoAcidPolymer peptide, string modname, int residue ) : void
peptide	AminoAcidPolymer
modname	string
residue	int
return	void

Property Details

_dataFiles protected property

protected Dictionary> _dataFiles
return	MSDataFile>.Dictionary

_disposed protected property

protected bool _disposed
return	bool

_extraColumns protected property

protected List _extraColumns
return	List

_fixedMods protected property

protected List _fixedMods
return	List

_proteins protected property

protected Dictionary _proteins
return	Protein>.Dictionary

_variableMods protected property

protected Dictionary _variableMods
return	IMass>.Dictionary