OpenMS  2.4.0
ModificationsDB.h
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32 // $Authors: Andreas Bertsch $
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34 
35 #pragma once
36 
40 
41 #include <set>
42 
43 namespace OpenMS
44 {
45  // forward declarations
46  class ResidueModification;
47  class Residue;
48 
72  class OPENMS_DLLAPI ModificationsDB
73  {
74 public:
75 
77  inline static ModificationsDB* getInstance(OpenMS::String unimod_file = "CHEMISTRY/unimod.xml", OpenMS::String psimod_file = "CHEMISTRY/PSI-MOD.obo", OpenMS::String xlmod_file = "CHEMISTRY/XLMOD.obo")
78  {
79  static ModificationsDB* db_ = nullptr;
80  if (db_ == nullptr)
81  {
82  db_ = new ModificationsDB(unimod_file, psimod_file, xlmod_file);
83  }
84  return db_;
85  }
86 
88  static bool isInstantiated();
89 
90  friend class CrossLinksDB;
91 
93  Size getNumberOfModifications() const;
94 
100  const ResidueModification& getModification(Size index) const;
101 
112  void searchModifications(std::set<const ResidueModification*>& mods, const String& mod_name, const String& residue = "", ResidueModification::TermSpecificity term_spec = ResidueModification::NUMBER_OF_TERM_SPECIFICITY) const;
113 
125  const ResidueModification& getModification(const String& mod_name, const String& residue = "", ResidueModification::TermSpecificity term_spec = ResidueModification::NUMBER_OF_TERM_SPECIFICITY) const;
126 
128  bool has(String modification) const;
129 
134  void addModification(ResidueModification * new_mod);
135 
142  Size findModificationIndex(const String& mod_name) const;
143 
150  void searchModificationsByDiffMonoMass(std::vector<String>& mods, double mass, double max_error, const String& residue = "", ResidueModification::TermSpecificity term_spec = ResidueModification::NUMBER_OF_TERM_SPECIFICITY);
151 
170  const ResidueModification* getBestModificationByMonoMass(double mass, double max_error, const String& residue = "", ResidueModification::TermSpecificity term_spec = ResidueModification::NUMBER_OF_TERM_SPECIFICITY);
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 
206 
208  bool residuesMatch_(const String& residue, char origin) const;
209 
210 private:
211 
220  ModificationsDB(OpenMS::String unimod_file = "CHEMISTRY/unimod.xml", OpenMS::String psimod_file = "CHEMISTRY/PSI-MOD.obo", OpenMS::String xlmod_file = "CHEMISTRY/XLMOD.obo");
222 
224  ModificationsDB(const ModificationsDB& residue_db);
225 
227  virtual ~ModificationsDB();
229 
233  ModificationsDB & operator=(const ModificationsDB& aa);
236 
242  void readFromOBOFile(const String& filename);
243 
245  void readFromUnimodXMLFile(const String& filename);
246 
247  };
248 }
A more convenient string class.
Definition: String.h:57
Definition: ResidueModification.h:102
Definition: CrossLinksDB.h:41
Representation of a modification.
Definition: ResidueModification.h:76
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
static ModificationsDB * getInstance(OpenMS::String unimod_file="CHEMISTRY/unimod.xml", OpenMS::String psimod_file="CHEMISTRY/PSI-MOD.obo", OpenMS::String xlmod_file="CHEMISTRY/XLMOD.obo")
Returns a pointer to the modifications DB (singleton)
Definition: ModificationsDB.h:77
static bool is_instantiated_
Stores whether ModificationsDB was instantiated before.
Definition: ModificationsDB.h:199
database which holds all residue modifications from UniMod
Definition: ModificationsDB.h:72
TermSpecificity
Position where the modification is allowed to occur.
Definition: ResidueModification.h:95
Map< String, std::set< const ResidueModification * > > modification_names_
Stores the mappings of (unique) names to the modifications.
Definition: ModificationsDB.h:205
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
std::vector< ResidueModification * > mods_
Stores the modifications.
Definition: ModificationsDB.h:202
Map class based on the STL map (containing several convenience functions)
Definition: Map.h:50