PepXMLFile::AminoAcidModification Struct Reference

Collaboration diagram for PepXMLFile::AminoAcidModification:

Public Member Functions
	AminoAcidModification ()=delete
	AminoAcidModification (const std::string &aminoacid, const std::string &massdiff, const std::string &mass, std::string variable, const std::string &description, std::string terminus, const std::string &protein_terminus, const std::vector< const ResidueModification * > &preferred_fixed_mods, const std::vector< const ResidueModification * > &preferred_var_mods, double tolerance)
	AminoAcidModification (const AminoAcidModification &rhs)=default
virtual	~AminoAcidModification ()=default
AminoAcidModification &	operator= (const AminoAcidModification &rhs)=default
std::string	toUnimodLikeString () const
const std::string &	getDescription () const
bool	isVariable () const
const ResidueModification *	getRegisteredMod () const
double	getMassDiff () const
double	getMass () const
const std::string &	getTerminus () const
const std::string &	getAminoAcid () const
const std::vector< std::string > &	getErrors () const

Private Member Functions
const ResidueModification *	lookupModInPreferredMods_ (const std::vector< const ResidueModification * > &preferred_fixed_mods, const std::string &aminoacid, double massdiff, const std::string &description, const ResidueModification::TermSpecificity term_spec, double tolerance)

Private Attributes
std::string	aminoacid_
double	massdiff_
double	mass_
bool	is_variable_
std::string	description_
std::string	terminus_
bool	is_protein_terminus_
ResidueModification::TermSpecificity	term_spec_
std::vector< std::string >	errors_
const ResidueModification *	registered_mod_

Constructor & Destructor Documentation

AminoAcidModification() [1/3]

AminoAcidModification ( )

delete

AminoAcidModification() [2/3]

AminoAcidModification	(	const std::string &	aminoacid,
		const std::string &	massdiff,
		const std::string &	mass,
		std::string	variable,
		const std::string &	description,
		std::string	terminus,
		const std::string &	protein_terminus,
		const std::vector< const ResidueModification * > &	preferred_fixed_mods,
		const std::vector< const ResidueModification * > &	preferred_var_mods,
		double	tolerance
	)

Creates an AminoAcidModification object from the pepXML attributes in EITHER aminoacid_modification elements OR terminal_modification elements since we use them ambiguously

AminoAcidModification() [3/3]

AminoAcidModification ( const AminoAcidModification &  rhs )

default

~AminoAcidModification()

virtual ~AminoAcidModification ( )

virtualdefault

Member Function Documentation

getAminoAcid()

const std::string & getAminoAcid

(

)

const

getDescription()

const std::string & getDescription

(

)

const

getErrors()

const std::vector< std::string > & getErrors

(

)

const

getMass()

double getMass

(

)

const

getMassDiff()

double getMassDiff

(

)

const

getRegisteredMod()

const ResidueModification * getRegisteredMod

(

)

const

getTerminus()

const std::string & getTerminus

(

)

const

isVariable()

bool isVariable

(

)

const

lookupModInPreferredMods_()

const ResidueModification * lookupModInPreferredMods_ ( const std::vector< const ResidueModification * > &  preferred_fixed_mods, const std::string &  aminoacid, double  massdiff, const std::string &  description, const ResidueModification::TermSpecificity  term_spec, double  tolerance  )

private

operator=()

AminoAcidModification & operator= ( const AminoAcidModification &  rhs )

default

toUnimodLikeString()

std::string toUnimodLikeString

(

)

const

Member Data Documentation

aminoacid_

std::string aminoacid_

private

description_

std::string description_

private

errors_

std::vector<std::string> errors_

private

is_protein_terminus_

bool is_protein_terminus_

private

is_variable_

bool is_variable_

private

mass_

double mass_

private

massdiff_

double massdiff_

private

registered_mod_

const ResidueModification* registered_mod_

private

term_spec_

ResidueModification::TermSpecificity term_spec_

private

terminus_

std::string terminus_

private