35 #ifndef OPENMS_CHEMISTRY_RESIDUEDB_H
36 #define OPENMS_CHEMISTRY_RESIDUEDB_H
39 #include <boost/unordered_map.hpp>
47 class ResidueModification;
93 Size getNumberOfResidues()
const;
96 Size getNumberOfModifiedResidues()
const;
102 const Residue * getResidue(
const unsigned char & one_letter_code)
const;
126 const std::set<const Residue *> getResidues(
const String & residue_set =
"All")
const;
129 const std::set<String> & getResidueSets()
const;
132 void setResidues(
const String & filename);
135 void addResidue(
const Residue & residue);
141 bool hasResidue(
const String & name)
const;
145 bool hasResidue(
const Residue * residue)
const;
153 inline ResidueIterator
endResidue() {
return residues_.end(); }
155 inline ResidueConstIterator
beginResidue()
const {
return const_residues_.begin(); }
157 inline ResidueConstIterator
endResidue()
const {
return const_residues_.end(); }
180 void readResiduesFromFile_(
const String & filename);
189 void clearResidues_();
192 void buildResidueNames_();
194 void addResidue_(
Residue * residue);
ResidueConstIterator beginResidue() const
Definition: ResidueDB.h:155
A more convenient string class.
Definition: String.h:57
Map< String, std::set< const Residue * > > residues_by_set_
Definition: ResidueDB.h:211
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
Representation of a residue.
Definition: Residue.h:62
std::set< const Residue * > const_residues_
Definition: ResidueDB.h:205
Map< String, Map< String, Residue * > > residue_mod_names_
Definition: ResidueDB.h:201
static ResidueDB * getInstance()
this member function serves as a replacement of the constructor
Definition: ResidueDB.h:73
std::set< Residue * > residues_
Definition: ResidueDB.h:203
std::set< const Residue * >::const_iterator ResidueConstIterator
Definition: ResidueDB.h:69
ResidueIterator endResidue()
Definition: ResidueDB.h:153
std::set< const Residue * > const_modified_residues_
Definition: ResidueDB.h:209
std::set< Residue * >::iterator ResidueIterator
Definition: ResidueDB.h:68
boost::unordered_map< String, Residue * > residue_names_
Definition: ResidueDB.h:196
residue data base which holds residues
Definition: ResidueDB.h:61
std::set< String > residue_sets_
Definition: ResidueDB.h:213
ResidueConstIterator endResidue() const
Definition: ResidueDB.h:157
std::set< Residue * > modified_residues_
Definition: ResidueDB.h:207
Map class based on the STL map (containing several convenience functions)
Definition: Map.h:51
ResidueIterator beginResidue()
Definition: ResidueDB.h:151