| OpenMS 2.5.0

ModificationsDB.h
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2 // OpenMS -- Open-Source Mass Spectrometry
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30 // --------------------------------------------------------------------------
31 // $Maintainer: Timo Sachsenberg $
32 // $Authors: Andreas Bertsch $
33 // --------------------------------------------------------------------------
34
35 #pragma once
36
37 #include <OpenMS/DATASTRUCTURES/Map.h>
38 #include <OpenMS/DATASTRUCTURES/String.h>
39 #include <OpenMS/CHEMISTRY/ResidueModification.h>
40
41 #include <set>
42
43 namespace OpenMS
44 {
45 // forward declarations
46 class ResidueModification;
47 class Residue;
48
73 class OPENMS_DLLAPI ModificationsDB
74 {
75 public:
76
78 static ModificationsDB* getInstance();
79
81 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");
82
84 static bool isInstantiated();
85
86 friend class CrossLinksDB;
87
89 Size getNumberOfModifications() const;
90
95 const ResidueModification* getModification(Size index) const;
96
104 void searchModifications(std::set<const ResidueModification*>& mods, const String& mod_name, const String& residue = "", ResidueModification::TermSpecificity term_spec = ResidueModification::NUMBER_OF_TERM_SPECIFICITY) const;
105
119 const ResidueModification* getModification(const String& mod_name, const String& residue = "", ResidueModification::TermSpecificity term_spec = ResidueModification::NUMBER_OF_TERM_SPECIFICITY) const;
120
122 bool has(String modification) const;
123
128 void addModification(ResidueModification * new_mod);
129
138 Size findModificationIndex(const String& mod_name) const;
139
146 void searchModificationsByDiffMonoMass(std::vector<String>& mods, double mass, double max_error, const String& residue = "", ResidueModification::TermSpecificity term_spec = ResidueModification::NUMBER_OF_TERM_SPECIFICITY);
147
148
168 const ResidueModification* getBestModificationByDiffMonoMass(double mass, double max_error, const String& residue = "", ResidueModification::TermSpecificity term_spec = ResidueModification::NUMBER_OF_TERM_SPECIFICITY);
169
171 void getAllSearchModifications(std::vector<String>& modifications) const;
172
173 protected:
174
176 static bool is_instantiated_;
177
179 std::vector<ResidueModification*> mods_;
180
182 Map<String, std::set<const ResidueModification*> > modification_names_;
183
185 bool residuesMatch_(const String& residue, const ResidueModification* origin) const;
186
187 private:
188
197 ModificationsDB(OpenMS::String unimod_file = "CHEMISTRY/unimod.xml", OpenMS::String psimod_file = "CHEMISTRY/PSI-MOD.obo", OpenMS::String xlmod_file = "CHEMISTRY/XLMOD.obo");
199
201 ModificationsDB(const ModificationsDB& residue_db);
202
204 virtual ~ModificationsDB();
206
210 ModificationsDB & operator=(const ModificationsDB& aa);
213
219 void readFromOBOFile(const String& filename);
220
222 void readFromUnimodXMLFile(const String& filename);
223
224 };
225 }
OpenMS::String
A more convenient string class.
Definition: String.h:58
OpenMS::ResidueModification
Representation of a modification.
Definition: ResidueModification.h:76
OpenMS::CrossLinksDB
Definition: CrossLinksDB.h:41
String.h
OpenMS::Map
Map class based on the STL map (containing several convenience functions)
Definition: Map.h:50
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
OpenMS::ModificationsDB
database which holds all residue modifications from UniMod
Definition: ModificationsDB.h:73
Map.h
OpenMS::ModificationsDB::is_instantiated_
static bool is_instantiated_
Stores whether ModificationsDB was instantiated before.
Definition: ModificationsDB.h:176
OpenMS::ModificationsDB::mods_
std::vector< ResidueModification * > mods_
Stores the modifications.
Definition: ModificationsDB.h:179
OpenMS::ResidueModification::TermSpecificity
TermSpecificity
Position where the modification is allowed to occur.
Definition: ResidueModification.h:95
OpenMS::ModificationsDB::modification_names_
Map< String, std::set< const ResidueModification * > > modification_names_
Stores the mappings of (unique) names to the modifications.
Definition: ModificationsDB.h:182
OpenMS::ResidueModification::NUMBER_OF_TERM_SPECIFICITY
Definition: ResidueModification.h:102
OpenMS::Size
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
ResidueModification.h