OpenMS  3.0.0
ModificationsDB.h
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34 
35 #pragma once
36 
40 
41 #include <set>
42 #include <memory> // unique_ptr
43 #include <unordered_map>
44 
45 namespace OpenMS
46 {
47  // forward declarations
48  class ResidueModification;
49  class Residue;
50 
75  class OPENMS_DLLAPI ModificationsDB
76  {
77 public:
78 
80  static ModificationsDB* getInstance();
81 
83  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");
84 
86  static bool isInstantiated();
87 
88  friend class CrossLinksDB;
89  // for access to addNewModification_ (without checking presence)
90  friend class Residue;
91  friend class AASequence;
92 
94  Size getNumberOfModifications() const;
95 
100  const ResidueModification* getModification(Size index) const;
101 
110  void searchModifications(std::set<const ResidueModification*>& mods,
111  const String& mod_name,
112  const String& residue = "",
114 
124  const ResidueModification* searchModification(const ResidueModification& mod_in) const;
125 
140  const ResidueModification* searchModificationsFast(const String& mod_name,
141  bool& multiple_matches,
142  const String& residue = "",
144 
158  const ResidueModification* getModification(const String& mod_name, const String& residue = "", ResidueModification::TermSpecificity term_spec = ResidueModification::NUMBER_OF_TERM_SPECIFICITY) const;
159 
161  bool has(const String& modification) const;
162 
170  const ResidueModification* addModification(std::unique_ptr<ResidueModification> new_mod);
171 
179  const ResidueModification* addModification(const ResidueModification& new_mod);
180 
189  Size findModificationIndex(const String& mod_name) const;
190 
198  void searchModificationsByDiffMonoMass(std::vector<String>& mods, double mass, double max_error, const String& residue = "", ResidueModification::TermSpecificity term_spec = ResidueModification::NUMBER_OF_TERM_SPECIFICITY);
199  void searchModificationsByDiffMonoMass(std::vector<const ResidueModification*>& mods, double mass, double max_error, const String& residue = "", ResidueModification::TermSpecificity term_spec = ResidueModification::NUMBER_OF_TERM_SPECIFICITY);
200 
208  void searchModificationsByDiffMonoMassSorted(std::vector<String>& mods, double mass, double max_error, const String& residue = "", ResidueModification::TermSpecificity term_spec = ResidueModification::NUMBER_OF_TERM_SPECIFICITY);
209  void searchModificationsByDiffMonoMassSorted(std::vector<const ResidueModification*>& mods, double mass, double max_error, const String& residue = "", ResidueModification::TermSpecificity term_spec = ResidueModification::NUMBER_OF_TERM_SPECIFICITY);
210 
211 
231  const ResidueModification* getBestModificationByDiffMonoMass(double mass, double max_error, const String& residue = "", ResidueModification::TermSpecificity term_spec = ResidueModification::NUMBER_OF_TERM_SPECIFICITY);
232 
234  void getAllSearchModifications(std::vector<String>& modifications) const;
235 
237  void writeTSV(const String& filename);
238 
239  protected:
240 
242  static bool is_instantiated_;
243 
245  std::vector<ResidueModification*> mods_;
246 
248  std::unordered_map<String, std::set<const ResidueModification*> > modification_names_;
249 
264  bool residuesMatch_(const char residue, const ResidueModification* curr_mod) const;
265 
266 private:
267 
276  explicit ModificationsDB(OpenMS::String unimod_file = "CHEMISTRY/unimod.xml", OpenMS::String psimod_file = "CHEMISTRY/PSI-MOD.obo", OpenMS::String xlmod_file = "CHEMISTRY/XLMOD.obo");
277 
279  ModificationsDB(const ModificationsDB& residue_db);
280 
282  virtual ~ModificationsDB();
284 
288  ModificationsDB & operator=(const ModificationsDB& aa);
291 
297  const ResidueModification* addNewModification_(const ResidueModification& new_mod);
298 
304  void readFromOBOFile(const String& filename);
305 
307  void readFromUnimodXMLFile(const String& filename);
308  };
309 }
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:248
OpenMS::ResidueModification
Representation of a modification on an amino acid residue.
Definition: ResidueModification.h:78
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
ResidueModification
sets the modification of AA at index by providing a pointer to a
OpenMS::ModificationsDB::is_instantiated_
static bool is_instantiated_
Stores whether ModificationsDB was instantiated before.
Definition: ModificationsDB.h:242
OpenMS::ModificationsDB
database which holds all residue modifications from UniMod
Definition: ModificationsDB.h:75
OpenMS::ResidueModification::NUMBER_OF_TERM_SPECIFICITY
Definition: ResidueModification.h:104
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
OpenMS::Residue
Representation of an amino acid residue.
Definition: Residue.h:62
OpenMS::ResidueModification::TermSpecificity
TermSpecificity
Position where the modification is allowed to occur.
Definition: ResidueModification.h:97
AASequence.h
OpenMS::StringUtils::has
static bool has(const String &this_s, Byte byte)
Definition: StringUtilsSimple.h:142
String.h
OpenMS::AASequence
Representation of a peptide/protein sequence.
Definition: AASequence.h:111
ResidueModification.h
OpenMS::CrossLinksDB
Definition: CrossLinksDB.h:41
OpenMS::ModificationsDB::mods_
std::vector< ResidueModification * > mods_
Stores the modifications.
Definition: ModificationsDB.h:245