#include <OpenMS/CHEMISTRY/ResidueModification.h>
Public Member Functions | |
Constructors and Destructors | |
ResidueModification () | |
default constructor | |
ResidueModification (const ResidueModification &modification) | |
copy constructor | |
virtual | ~ResidueModification () |
destructor | |
Assignment | |
ResidueModification & | operator= (const ResidueModification &modification) |
assignment operator | |
Accessors | |
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 | |
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< String > | synonyms_ |
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_ |
default constructor
ResidueModification | ( | const ResidueModification & | modification | ) |
copy constructor
virtual ~ResidueModification | ( | ) | [virtual] |
destructor
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
String short_name_ [protected] |
String name_prefix_ [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] |
Generated Tue Apr 1 15:36:43 2008 -- using doxygen 1.5.4 | OpenMS / TOPP 1.1 |