C# Class Morpheus.ProteomeDatabaseReader

Show file Open project: cwenger/Morpheus

Public Methods

Method	Description
CountProteins ( FileStream proteomeDatabase, bool onTheFlyDecoys, int &targetProteins, int &decoyProteins, int &onTheFlyDecoyProteins ) : int
HasDecoyProteins ( string fastaProteomeDatabaseFilepath ) : bool
ReadProteins ( FileStream proteomeDatabase, bool onTheFlyDecoys, Modification>.IDictionary knownVariableModifications ) : IEnumerable
ReadUniProtXmlModifications ( string uniProtXmlProteomeDatabaseFilepath ) : Modification>.Dictionary

Private Methods

Method	Description
CountFastaProteins ( FileStream fastaProteomeDatabase, bool onTheFlyDecoys, int &targetProteins, int &decoyProteins, int &onTheFlyDecoyProteins ) : int
CountUniProtXmlProteins ( FileStream uniProtXmlProteomeDatabase, bool onTheFlyDecoys, int &targetProteins, int &decoyProteins, int &onTheFlyDecoyProteins ) : int
InitializeDictionaries ( ) : void
ReadFastaProteins ( FileStream fastaProteomeDatabase, bool onTheFlyDecoys ) : IEnumerable
ReadUniProtXmlProteins ( FileStream uniProtXmlProteomeDatabase, bool onTheFlyDecoys, Modification>.IDictionary knownVariableModifications ) : IEnumerable

Method Details

CountProteins() public static method

public static CountProteins ( FileStream proteomeDatabase, bool onTheFlyDecoys, int &targetProteins, int &decoyProteins, int &onTheFlyDecoyProteins ) : int
proteomeDatabase	System.IO.FileStream
onTheFlyDecoys	bool
targetProteins	int
decoyProteins	int
onTheFlyDecoyProteins	int
return	int

HasDecoyProteins() public static method

public static HasDecoyProteins ( string fastaProteomeDatabaseFilepath ) : bool
fastaProteomeDatabaseFilepath	string
return	bool

ReadProteins() public static method

public static ReadProteins ( FileStream proteomeDatabase, bool onTheFlyDecoys, Modification>.IDictionary knownVariableModifications ) : IEnumerable
proteomeDatabase	System.IO.FileStream
onTheFlyDecoys	bool
knownVariableModifications	Modification>.IDictionary
return	IEnumerable

ReadUniProtXmlModifications() public static method

public static ReadUniProtXmlModifications ( string uniProtXmlProteomeDatabaseFilepath ) : Modification>.Dictionary
uniProtXmlProteomeDatabaseFilepath	string
return	Modification>.Dictionary