OpenMS
PepXMLFile::AminoAcidModification Struct Reference
Collaboration diagram for PepXMLFile::AminoAcidModification:
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Public Member Functions

 AminoAcidModification ()=delete
 
 AminoAcidModification (const String &aminoacid, const String &massdiff, const String &mass, String variable, const String &description, String terminus, const 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
 
AminoAcidModificationoperator= (const AminoAcidModification &rhs)=default
 
String toUnimodLikeString () const
 
const StringgetDescription () const
 
bool isVariable () const
 
const ResidueModificationgetRegisteredMod () const
 
double getMassDiff () const
 
double getMass () const
 
const StringgetTerminus () const
 
const StringgetAminoAcid () const
 
const std::vector< String > & getErrors () const
 

Private Member Functions

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

Private Attributes

String aminoacid_
 
double massdiff_
 
double mass_
 
bool is_variable_
 
String description_
 
String terminus_
 
bool is_protein_terminus_
 
ResidueModification::TermSpecificity term_spec_
 
std::vector< Stringerrors_
 
const ResidueModificationregistered_mod_
 

Constructor & Destructor Documentation

◆ AminoAcidModification() [1/3]

◆ AminoAcidModification() [2/3]

AminoAcidModification ( const String aminoacid,
const String massdiff,
const String mass,
String  variable,
const String description,
String  terminus,
const 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 String& getAminoAcid ( ) const

◆ getDescription()

const String& getDescription ( ) const

◆ getErrors()

const std::vector<String>& getErrors ( ) const

◆ getMass()

double getMass ( ) const

◆ getMassDiff()

double getMassDiff ( ) const

◆ getRegisteredMod()

const ResidueModification* getRegisteredMod ( ) const

◆ getTerminus()

const String& getTerminus ( ) const

◆ isVariable()

bool isVariable ( ) const

◆ lookupModInPreferredMods_()

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

◆ operator=()

AminoAcidModification& operator= ( const AminoAcidModification rhs)
default

◆ toUnimodLikeString()

String toUnimodLikeString ( ) const

Member Data Documentation

◆ aminoacid_

String aminoacid_
private

◆ description_

String description_
private

◆ errors_

std::vector<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_

◆ terminus_

String terminus_
private