OpenMS  2.5.0
ModificationsDB.h
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34 
35 #pragma once
36 
40 
41 #include <set>
42 #include <unordered_map>
43 
44 namespace OpenMS
45 {
46  // forward declarations
47  class ResidueModification;
48  class Residue;
49 
74  class OPENMS_DLLAPI ModificationsDB
75  {
76 public:
77 
79  static ModificationsDB* getInstance();
80 
82  static ModificationsDB* initializeModificationsDB(OpenMS::String unimod_file = "CHEMISTRY/unimod.xml", OpenMS::String psimod_file = "CHEMISTRY/PSI-MOD.obo", OpenMS::String xlmod_file = "CHEMISTRY/XLMOD.obo");
83 
85  static bool isInstantiated();
86 
87  friend class CrossLinksDB;
88 
90  Size getNumberOfModifications() const;
91 
96  const ResidueModification* getModification(Size index) const;
97 
105  void searchModifications(std::set<const ResidueModification*>& mods,
106  const String& mod_name,
107  const String& residue = "",
109 
124  const ResidueModification* searchModificationsFast(const String& mod_name,
125  bool& multiple_matches,
126  const String& residue = "",
128 
142  const ResidueModification* getModification(const String& mod_name, const String& residue = "", ResidueModification::TermSpecificity term_spec = ResidueModification::NUMBER_OF_TERM_SPECIFICITY) const;
143 
145  bool has(String modification) const;
146 
151  void addModification(ResidueModification * new_mod);
152 
161  Size findModificationIndex(const String& mod_name) const;
162 
169  void searchModificationsByDiffMonoMass(std::vector<String>& mods, double mass, double max_error, const String& residue = "", ResidueModification::TermSpecificity term_spec = ResidueModification::NUMBER_OF_TERM_SPECIFICITY);
170 
171 
191  const ResidueModification* getBestModificationByDiffMonoMass(double mass, double max_error, const String& residue = "", ResidueModification::TermSpecificity term_spec = ResidueModification::NUMBER_OF_TERM_SPECIFICITY);
192 
194  void getAllSearchModifications(std::vector<String>& modifications) const;
195 
196 protected:
197 
199  static bool is_instantiated_;
200 
202  std::vector<ResidueModification*> mods_;
203 
205  std::unordered_map<String, std::set<const ResidueModification*> > modification_names_;
206 
221  bool residuesMatch_(const char residue, const ResidueModification* curr_mod) const;
222 
223 private:
224 
233  ModificationsDB(OpenMS::String unimod_file = "CHEMISTRY/unimod.xml", OpenMS::String psimod_file = "CHEMISTRY/PSI-MOD.obo", OpenMS::String xlmod_file = "CHEMISTRY/XLMOD.obo");
235 
237  ModificationsDB(const ModificationsDB& residue_db);
238 
240  virtual ~ModificationsDB();
242 
246  ModificationsDB & operator=(const ModificationsDB& aa);
249 
255  void readFromOBOFile(const String& filename);
256 
258  void readFromUnimodXMLFile(const String& filename);
259 
260  };
261 }
OpenMS::ModificationsDB::modification_names_
std::unordered_map< String, std::set< const ResidueModification * > > modification_names_
Stores the mappings of (unique) names to the modifications.
Definition: ModificationsDB.h:205
OpenMS::ResidueModification
Representation of a modification.
Definition: ResidueModification.h:76
OpenMS::String
A more convenient string class.
Definition: String.h:58
OpenMS::Size
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
OpenMS::ModificationsDB::is_instantiated_
static bool is_instantiated_
Stores whether ModificationsDB was instantiated before.
Definition: ModificationsDB.h:199
OpenMS::ModificationsDB
database which holds all residue modifications from UniMod
Definition: ModificationsDB.h:74
Map.h
OpenMS::ResidueModification::NUMBER_OF_TERM_SPECIFICITY
Definition: ResidueModification.h:102
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
OpenMS::ResidueModification::TermSpecificity
TermSpecificity
Position where the modification is allowed to occur.
Definition: ResidueModification.h:95
String.h
ResidueModification.h
OpenMS::CrossLinksDB
Definition: CrossLinksDB.h:41
OpenMS::ModificationsDB::mods_
std::vector< ResidueModification * > mods_
Stores the modifications.
Definition: ModificationsDB.h:202