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ResidueModification Class Reference

#include <OpenMS/CHEMISTRY/ResidueModification.h>

List of all members.


Detailed Description

Representation of a modification.

Public Member Functions

Constructors and Destructors
 ResidueModification ()
 default constructor
 ResidueModification (const ResidueModification &modification)
 copy constructor
virtual ~ResidueModification ()
 destructor
Assignment
ResidueModificationoperator= (const ResidueModification &modification)
 assignment operator
Accessors
void setName (const String &name)
 sets the name of the modification
const StringgetName () const
 returns the name of the modification
void setShortName (const String &name)
 sets the short name of the modification, this name is used in PeptideSequence as output
const StringgetShortName () const
 returns the short name of the modification
void setNamePrefix (const String &name_prefix)
 sets the naming prefix of modified residues
const StringgetNamePrefix () const
 returns the naming prefix of modified residues
void setSynonyms (const std::set< String > &synonyms)
 sets the synonyms of the modification
void addSynonym (const String &synonym)
 adds a synonym to the modification
const std::set< String > & getSynonyms () const
 returns the synonym names of the modifications
void setAddFormula (const EmpiricalFormula &formula)
 sets the formula, which is added to the original residue
const EmpiricalFormulagetAddFormula () const
 returns the formula, which is added to the original residue
void setAddAverageWeight (DoubleReal weight)
 sets the average weight of the added formula
DoubleReal getAddAverageWeight () const
 returns the weight of the added formula
void setAddMonoWeight (DoubleReal weight)
 sets the mono isotopic weight of the added formula
DoubleReal getAddMonoWeight () const
 returns the mono isotopic weight of the added formula
void setDelFormula (const EmpiricalFormula &formula)
 sets the formula which is deleted from the residue
const EmpiricalFormulagetDelFormula () const
 returns the formula which is deleted from the residue
void setDelAverageWeight (DoubleReal weight)
 sets the average weight of the deletion
DoubleReal getDelAverageWeight () const
 returns the average weight of the deletion
void setDelMonoWeight (DoubleReal weight)
 sets the mono isotopic weight of the deletion
DoubleReal getDelMonoWeight () const
 returns the mono isotopic weight of the deletion
void setValidResidues (const std::set< Residue * > &valid_residues)
 sets the residues where the modification can be applied to
void addValidResidue (Residue *valid_residue)
 adds a valid residue
const std::set< Residue * > & getValidResidues () const
 returns the residues where the modifications can be applied to
Predicates
bool operator== (const ResidueModification &modification) const
 equality operator
bool operator!= (const ResidueModification &modification) const
 inequality operator

Protected Attributes

String name_
String short_name_
String name_prefix_
std::set< Stringsynonyms_
EmpiricalFormula add_formula_
DoubleReal add_average_weight_
DoubleReal add_mono_weight_
EmpiricalFormula del_formula_
DoubleReal del_average_weight_
DoubleReal del_mono_weight_
std::set< Residue * > valid_residues_

Constructor & Destructor Documentation

ResidueModification (  ) 

default constructor

ResidueModification ( const ResidueModification modification  ) 

copy constructor

virtual ~ResidueModification (  )  [virtual]

destructor


Member Function Documentation

ResidueModification& operator= ( const ResidueModification modification  ) 

assignment operator

void setName ( const String name  ) 

sets the name of the modification

const String& getName (  )  const

returns the name of the modification

void setShortName ( const String name  ) 

sets the short name of the modification, this name is used in PeptideSequence as output

const String& getShortName (  )  const

returns the short name of the modification

void setNamePrefix ( const String name_prefix  ) 

sets the naming prefix of modified residues

const String& getNamePrefix (  )  const

returns the naming prefix of modified residues

void setSynonyms ( const std::set< String > &  synonyms  ) 

sets the synonyms of the modification

void addSynonym ( const String synonym  ) 

adds a synonym to the modification

const std::set<String>& getSynonyms (  )  const

returns the synonym names of the modifications

void setAddFormula ( const EmpiricalFormula formula  ) 

sets the formula, which is added to the original residue

const EmpiricalFormula& getAddFormula (  )  const

returns the formula, which is added to the original residue

void setAddAverageWeight ( DoubleReal  weight  ) 

sets the average weight of the added formula

DoubleReal getAddAverageWeight (  )  const

returns the weight of the added formula

void setAddMonoWeight ( DoubleReal  weight  ) 

sets the mono isotopic weight of the added formula

DoubleReal getAddMonoWeight (  )  const

returns the mono isotopic weight of the added formula

void setDelFormula ( const EmpiricalFormula formula  ) 

sets the formula which is deleted from the residue

const EmpiricalFormula& getDelFormula (  )  const

returns the formula which is deleted from the residue

void setDelAverageWeight ( DoubleReal  weight  ) 

sets the average weight of the deletion

DoubleReal getDelAverageWeight (  )  const

returns the average weight of the deletion

void setDelMonoWeight ( DoubleReal  weight  ) 

sets the mono isotopic weight of the deletion

DoubleReal getDelMonoWeight (  )  const

returns the mono isotopic weight of the deletion

void setValidResidues ( const std::set< Residue * > &  valid_residues  ) 

sets the residues where the modification can be applied to

void addValidResidue ( Residue valid_residue  ) 

adds a valid residue

const std::set<Residue*>& getValidResidues (  )  const

returns the residues where the modifications can be applied to

bool operator== ( const ResidueModification modification  )  const

equality operator

bool operator!= ( const ResidueModification modification  )  const

inequality operator


Member Data Documentation

String name_ [protected]

String short_name_ [protected]

String name_prefix_ [protected]

std::set<String> synonyms_ [protected]

EmpiricalFormula add_formula_ [protected]

DoubleReal add_average_weight_ [protected]

DoubleReal add_mono_weight_ [protected]

EmpiricalFormula del_formula_ [protected]

DoubleReal del_average_weight_ [protected]

DoubleReal del_mono_weight_ [protected]

std::set<Residue*> valid_residues_ [protected]


The documentation for this class was generated from the following file:
Generated Tue Apr 1 15:36:43 2008 -- using doxygen 1.5.4 OpenMS / TOPP 1.1