| OpenMS 2.5.0

ResidueDB.h
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2 // OpenMS -- Open-Source Mass Spectrometry
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4 // Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
5 // ETH Zurich, and Freie Universitaet Berlin 2002-2020.
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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 <boost/unordered_map.hpp>
39 #include <OpenMS/DATASTRUCTURES/String.h>
40
41 #include <set>
42
43 namespace OpenMS
44 {
45 // forward declarations
46 class ResidueModification;
47 class Residue;
48
60 class OPENMS_DLLAPI ResidueDB
61 {
62 public:
63
67 typedef std::set<Residue*>::iterator ResidueIterator;
68 typedef std::set<const Residue*>::const_iterator ResidueConstIterator;
70
72 static ResidueDB* getInstance();
73
77 virtual ~ResidueDB();
80
84 Size getNumberOfResidues() const;
86
88 Size getNumberOfModifiedResidues() const;
89
91 const Residue* getResidue(const String& name) const;
92
94 const Residue* getResidue(const unsigned char& one_letter_code) const;
95
102 const Residue* getModifiedResidue(const String& name);
103
112 const Residue* getModifiedResidue(const Residue* residue, const String& name);
113
130 const std::set<const Residue*> getResidues(const String& residue_set = "All") const;
131
133 const std::set<String> getResidueSets() const;
134
136
140 bool hasResidue(const String& name) const;
142
144 bool hasResidue(const Residue* residue) const;
146
150 inline ResidueIterator beginResidue() { return residues_.begin(); }
151
152 inline ResidueIterator endResidue() { return residues_.end(); }
153
154 inline ResidueConstIterator beginResidue() const { return const_residues_.begin(); }
155
156 inline ResidueConstIterator endResidue() const { return const_residues_.end(); }
158
159 protected:
161 void setResidues_(const String& filename);
162
166 ResidueDB();
168
170 ResidueDB(const ResidueDB& residue_db);
172
176 ResidueDB& operator=(const ResidueDB& aa);
179
185 void readResiduesFromFile_(const String& filename);
186
188 Residue* parseResidue_(Map<String, String>& values);
189
191 void clear_();
192
194 void clearResidues_();
195
197 void clearResidueModifications_();
198
200 void buildResidueNames_();
201
202 void addResidue_(Residue* residue);
203
204 boost::unordered_map<String, Residue*> residue_names_;
205
206 // fast lookup table for residues
207 Residue* residue_by_one_letter_code_[256];
208
209 Map<String, Map<String, Residue*> > residue_mod_names_;
210
211 std::set<Residue*> residues_;
212
213 std::set<const Residue*> const_residues_;
214
215 std::set<Residue*> modified_residues_;
216
217 std::set<const Residue*> const_modified_residues_;
218
219 Map<String, std::set<const Residue*> > residues_by_set_;
220
221 std::set<String> residue_sets_;
222 };
223 }
OpenMS::String
A more convenient string class.
Definition: String.h:58
OpenMS::ResidueDB::modified_residues_
std::set< Residue * > modified_residues_
Definition: ResidueDB.h:215
OpenMS::ResidueDB::ResidueConstIterator
std::set< const Residue * >::const_iterator ResidueConstIterator
Definition: ResidueDB.h:68
OpenMS::ResidueDB::residue_names_
boost::unordered_map< String, Residue * > residue_names_
Definition: ResidueDB.h:204
OpenMS::ResidueDB::const_residues_
std::set< const Residue * > const_residues_
Definition: ResidueDB.h:213
OpenMS::ResidueDB::endResidue
ResidueConstIterator endResidue() const
Definition: ResidueDB.h:156
OpenMS::Residue
Representation of a residue.
Definition: Residue.h:61
OpenMS::ResidueDB::residue_sets_
std::set< String > residue_sets_
Definition: ResidueDB.h:221
OpenMS::ResidueDB::beginResidue
ResidueConstIterator beginResidue() const
Definition: ResidueDB.h:154
OpenMS::ResidueDB
residue data base which holds residues
Definition: ResidueDB.h:60
OpenMS::ResidueDB::const_modified_residues_
std::set< const Residue * > const_modified_residues_
Definition: ResidueDB.h:217
String.h
OpenMS::Map
Map class based on the STL map (containing several convenience functions)
Definition: Map.h:50
OpenMS::ResidueDB::ResidueIterator
std::set< Residue * >::iterator ResidueIterator
Definition: ResidueDB.h:67
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
Map.h
OpenMS::ResidueDB::endResidue
ResidueIterator endResidue()
Definition: ResidueDB.h:152
OpenMS::ResidueDB::beginResidue
ResidueIterator beginResidue()
Definition: ResidueDB.h:150
OpenMS::ResidueDB::residues_
std::set< Residue * > residues_
Definition: ResidueDB.h:211
OpenMS::ResidueDB::residues_by_set_
Map< String, std::set< const Residue * > > residues_by_set_
Definition: ResidueDB.h:219
OpenMS::ResidueDB::residue_mod_names_
Map< String, Map< String, Residue * > > residue_mod_names_
Definition: ResidueDB.h:209
OpenMS::Size
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127