Implements modification for suffix arrays. More...
#include <OpenMS/CHEMISTRY/ModifierRep.h>
| Public Member Functions | |
| ModifierRep () | |
| Constructor.  More... | |
| ModifierRep (const ModifierRep &source) | |
| copy constructor  More... | |
| virtual | ~ModifierRep () | 
| destructor  More... | |
| void | setNumberOfModifications (Size i) | 
| setter for number of modifications  More... | |
| Size | getNumberOfModifications () const | 
| getter for number of modifications  More... | |
| const std::vector< std::vector < double > > & | getModificationTable () | 
| getter for the modification table  More... | |
| void | refreshModificationList (std::map< double, SignedSize > &mod_map, const char &c) | 
| updates the modifications list if with the modifications of a new amino acid  More... | |
| Size | getMaxModificationMasses () | 
| calculates the maximal number unique masses of combinations of modifications (maximal possible size of the modification map)  More... | |
| std::vector< String > | getModificationsForMass (double &m) | 
| gets all modification possibilities for a given mass  More... | |
| std::vector< String > | getModificationsForMass (double &m, const String &seq) | 
| gets all modification possibilities for a given mass and for the given peptide  More... | |
| Protected Attributes | |
| std::vector< std::vector < double > > | modification_table_ | 
| all possible modifications  More... | |
| Size | number_of_modifications_ | 
| number of maximal modifications  More... | |
| std::map< String, std::vector < String > > | mass_mapping_ | 
| maps a mass to the combination of modifications  More... | |
Implements modification for suffix arrays.
| ModifierRep | ( | ) | 
Constructor.
| ModifierRep | ( | const ModifierRep & | source | ) | 
copy constructor
| 
 | virtual | 
destructor
| Size getMaxModificationMasses | ( | ) | 
calculates the maximal number unique masses of combinations of modifications (maximal possible size of the modification map)
gets all modification possibilities for a given mass
| m | masse | 
gets all modification possibilities for a given mass and for the given peptide
| m | masse | 
| seq | peptide sequence | 
| const std::vector<std::vector<double> >& getModificationTable | ( | ) | 
getter for the modification table
| Size getNumberOfModifications | ( | ) | const | 
getter for number of modifications
| void refreshModificationList | ( | std::map< double, SignedSize > & | mod_map, | 
| const char & | c | ||
| ) | 
updates the modifications list if with the modifications of a new amino acid
| mod_map | reference to the map holding the possible modifications | 
| c | const character for the amino acid | 
all modification for the given amino acid are added to the map. The key is the mass, the value is the number of modifications for that mass. So the advantage of using a map is that a value will occure only once. the mass of the modification is added to all elements in the map whose number of modifications is smaller than the maximal number of modifications.
| void setNumberOfModifications | ( | Size | i | ) | 
setter for number of modifications
| i | number of modifications | 
maps a mass to the combination of modifications
| 
 | protected | 
all possible modifications
| 
 | protected | 
number of maximal modifications
| OpenMS / TOPP release 1.11.1 | Documentation generated on Thu Nov 14 2013 11:19:27 using doxygen 1.8.5 |