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ModificationsDB.h
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34 
35 #ifndef OPENMS_CHEMISTRY_MODIFICATIONSDB_H
36 #define OPENMS_CHEMISTRY_MODIFICATIONSDB_H
37 
40 
41 #include <set>
42 
43 namespace OpenMS
44 {
45  // forward declarations
46  class ResidueModification;
47  class Residue;
48 
68  class OPENMS_DLLAPI ModificationsDB
69  {
70 public:
71 
72  inline static ModificationsDB * getInstance()
73  {
74  static ModificationsDB * db_ = 0;
75  if (db_ == 0)
76  {
77  db_ = new ModificationsDB;
78  }
79  return db_;
80  }
81 
83  Size getNumberOfModifications() const;
84 
86  const ResidueModification & getModification(Size index) const;
87 
89  void searchTerminalModifications(std::set<const ResidueModification *> & mods, const String & name, ResidueModification::Term_Specificity term_spec) const;
90 
92  void searchModifications(std::set<const ResidueModification *> & mods, const String & orgin, const String & mod_name, ResidueModification::Term_Specificity term_spec) const;
93 
95  void searchModifications(std::set<const ResidueModification *> & mods, const String & mod_name, ResidueModification::Term_Specificity term_spec) const;
96 
106  const ResidueModification & getTerminalModification(const String & name, ResidueModification::Term_Specificity term_spec) const;
107 
109  const ResidueModification & getModification(const String & residue_name, const String & mod_name, ResidueModification::Term_Specificity term_spec) const;
110 
111  const ResidueModification & getModification(const String & modification) const;
112 
114  Size findModificationIndex(const String & mod_name) const;
115 
117  void getTerminalModificationsByDiffMonoMass(std::vector<String> & mods, DoubleReal mass, DoubleReal error, ResidueModification::Term_Specificity term_spec);
118 
120  void getModificationsByDiffMonoMass(std::vector<String> & mods, DoubleReal mass, DoubleReal error = 0.0);
121 
123  void getModificationsByDiffMonoMass(std::vector<String> & mods, const String & residue, DoubleReal mass, DoubleReal error = 0.0);
124 
126  void readFromOBOFile(const String & filename);
127 
129  void readFromUnimodXMLFile(const String & filename);
130 
132  void getAllSearchModifications(std::vector<String> & modifications);
133 
134 protected:
135 
137  std::vector<ResidueModification *> mods_;
138 
141 
142 
143 private:
144 
148  ModificationsDB();
150 
152  ModificationsDB(const ModificationsDB & residue_db);
153 
155  virtual ~ModificationsDB();
157 
161  ModificationsDB & operator=(const ModificationsDB & aa);
164  };
165 }
166 #endif
A more convenient string class.
Definition: String.h:56
Representation of a modification.
Definition: ResidueModification.h:58
std::vector< ResidueModification * > mods_
stores the modifications
Definition: ModificationsDB.h:137
static ModificationsDB * getInstance()
Definition: ModificationsDB.h:72
database which holds all residue modifications from UniMod
Definition: ModificationsDB.h:68
Term_Specificity
Position where the modification is allowed to occur.
Definition: ResidueModification.h:78
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:144
Map class based on the STL map (containing serveral convenience functions)
Definition: Map.h:50
Map< String, std::set< const ResidueModification * > > modification_names_
stores the mappings of (unique) names to the modifications
Definition: ModificationsDB.h:140

OpenMS / TOPP release 1.11.1 Documentation generated on Thu Nov 14 2013 11:19:17 using doxygen 1.8.5