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ModificationsDB.h
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34 
35 #ifndef OPENMS_CHEMISTRY_MODIFICATIONSDB_H
36 #define OPENMS_CHEMISTRY_MODIFICATIONSDB_H
37 
41 
42 #include <set>
43 
44 namespace OpenMS
45 {
46  // forward declarations
47  class ResidueModification;
48  class Residue;
49 
69  class OPENMS_DLLAPI ModificationsDB
70  {
71 public:
72 
73  inline static ModificationsDB * getInstance()
74  {
75  static ModificationsDB * db_ = 0;
76  if (db_ == 0)
77  {
78  db_ = new ModificationsDB;
79  }
80  return db_;
81  }
82 
84  Size getNumberOfModifications() const;
85 
87  const ResidueModification & getModification(Size index) const;
88 
90  void searchTerminalModifications(std::set<const ResidueModification *> & mods, const String & name, ResidueModification::Term_Specificity term_spec) const;
91 
93  void searchModifications(std::set<const ResidueModification *> & mods, const String & orgin, const String & mod_name, ResidueModification::Term_Specificity term_spec) const;
94 
96  void searchModifications(std::set<const ResidueModification *> & mods, const String & mod_name, ResidueModification::Term_Specificity term_spec) const;
97 
107  const ResidueModification & getTerminalModification(const String & name, ResidueModification::Term_Specificity term_spec) const;
108 
110  const ResidueModification & getModification(const String & residue_name, const String & mod_name, ResidueModification::Term_Specificity term_spec) const;
111 
112  const ResidueModification & getModification(const String & modification) const;
113 
115  Size findModificationIndex(const String & mod_name) const;
116 
118  void getTerminalModificationsByDiffMonoMass(std::vector<String> & mods, double mass, double error, ResidueModification::Term_Specificity term_spec);
119 
121  void getModificationsByDiffMonoMass(std::vector<String> & mods, double mass, double error = 0.0);
122 
124  void getModificationsByDiffMonoMass(std::vector<String> & mods, const String & residue, double mass, double error = 0.0);
125 
145  const ResidueModification * getBestModificationsByMonoMass(const String & residue, double mass, double max_error = 0.0);
146 
166  const ResidueModification * getBestModificationsByDiffMonoMass(const String & residue, double mass, double max_error = 0.0);
167 
169  void readFromOBOFile(const String & filename);
170 
172  void readFromUnimodXMLFile(const String & filename);
173 
175  void getAllSearchModifications(std::vector<String> & modifications);
176 
177 protected:
178 
180  std::vector<ResidueModification *> mods_;
181 
184 
185 
186 private:
187 
191  ModificationsDB();
193 
195  ModificationsDB(const ModificationsDB & residue_db);
196 
198  virtual ~ModificationsDB();
200 
204  ModificationsDB & operator=(const ModificationsDB & aa);
207  };
208 }
209 #endif
A more convenient string class.
Definition: String.h:57
Representation of a modification.
Definition: ResidueModification.h:65
std::vector< ResidueModification * > mods_
stores the modifications
Definition: ModificationsDB.h:180
static ModificationsDB * getInstance()
Definition: ModificationsDB.h:73
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
database which holds all residue modifications from UniMod
Definition: ModificationsDB.h:69
Term_Specificity
Position where the modification is allowed to occur.
Definition: ResidueModification.h:85
Map class based on the STL map (containing several convenience functions)
Definition: Map.h:51
Map< String, std::set< const ResidueModification * > > modification_names_
stores the mappings of (unique) names to the modifications
Definition: ModificationsDB.h:183

OpenMS / TOPP release 2.0.0 Documentation generated on Sat May 16 2015 16:13:25 using doxygen 1.8.9.1