ProForma Class Reference

#include <OpenMS/CHEMISTRY/ProForma.h>

Collaboration diagram for ProForma:

Public Member Functions
	ProForma (const AASequence &seq)
AASequence	fromProFormaString (const std::string &proforma_str)
std::string	toProFormaString () const
void	addModification (size_t start_pos, size_t end_pos, const std::string &mod_id, double mass_shift)
void	removeModification (size_t position)

Private Member Functions
void	parseCVModificationNames (const std::string &modString, size_t &pos, size_t residue_pos)
void	parseStandardModification (const std::string &modString, size_t &pos, size_t residue_pos)
void	parseDeltaMassNotation (const std::string &modString, size_t &pos, size_t residue_pos)
void	parseNTerminalModification (const std::string &modString, size_t &pos)
void	parseCTerminalModification (const std::string &modString, size_t &pos)
void	parseRangeModification (const std::string &modString, size_t &pos)
void	throwParseError (const std::string &message) const
void	validateCVModification (const std::string &modification)

Private Attributes
AASequence	sequence_
std::unordered_map< size_t, ModificationAttributes >	modifications_
std::unordered_set< std::string >	supported_cvs_ {"UNIMOD", "MOD", "RESID", "XLMOD", "GNO"}

Constructor & Destructor Documentation

ProForma()

ProForma ( const AASequence &  seq )

explicit

Member Function Documentation

addModification()

void addModification	(	size_t	start_pos,
		size_t	end_pos,
		const std::string &	mod_id,
		double	mass_shift
	)

fromProFormaString()

AASequence fromProFormaString

(

const std::string &

proforma_str

)

parseCTerminalModification()

void parseCTerminalModification ( const std::string &  modString, size_t &  pos  )

private

parseCVModificationNames()

void parseCVModificationNames ( const std::string &  modString, size_t &  pos, size_t  residue_pos  )

private

parseDeltaMassNotation()

void parseDeltaMassNotation ( const std::string &  modString, size_t &  pos, size_t  residue_pos  )

private

parseNTerminalModification()

void parseNTerminalModification ( const std::string &  modString, size_t &  pos  )

private

parseRangeModification()

void parseRangeModification ( const std::string &  modString, size_t &  pos  )

private

parseStandardModification()

void parseStandardModification ( const std::string &  modString, size_t &  pos, size_t  residue_pos  )

private

removeModification()

void removeModification

(

size_t

position

)

throwParseError()

void throwParseError ( const std::string &  message ) const

private

toProFormaString()

std::string toProFormaString

(

)

const

validateCVModification()

void validateCVModification ( const std::string &  modification )

private

Member Data Documentation

modifications_

std::unordered_map<size_t, ModificationAttributes> modifications_

private

sequence_

AASequence sequence_

private

supported_cvs_

std::unordered_set<std::string> supported_cvs_ {"UNIMOD", "MOD", "RESID", "XLMOD", "GNO"}

private