Home  · Classes  · Annotated Classes  · Modules  · Members  · Namespaces  · Related Pages
ModificationsDB.h
Go to the documentation of this file.
1 // --------------------------------------------------------------------------
2 // OpenMS -- Open-Source Mass Spectrometry
3 // --------------------------------------------------------------------------
4 // Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
5 // ETH Zurich, and Freie Universitaet Berlin 2002-2017.
6 //
7 // This software is released under a three-clause BSD license:
8 // * Redistributions of source code must retain the above copyright
9 // notice, this list of conditions and the following disclaimer.
10 // * Redistributions in binary form must reproduce the above copyright
11 // notice, this list of conditions and the following disclaimer in the
12 // documentation and/or other materials provided with the distribution.
13 // * Neither the name of any author or any participating institution
14 // may be used to endorse or promote products derived from this software
15 // without specific prior written permission.
16 // For a full list of authors, refer to the file AUTHORS.
17 // --------------------------------------------------------------------------
18 // THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
19 // AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
20 // IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
21 // ARE DISCLAIMED. IN NO EVENT SHALL ANY OF THE AUTHORS OR THE CONTRIBUTING
22 // INSTITUTIONS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
23 // EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
24 // PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
25 // OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
26 // WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
27 // OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
28 // ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
29 //
30 // --------------------------------------------------------------------------
31 // $Maintainer: Timo Sachsenberg $
32 // $Authors: Andreas Bertsch $
33 // --------------------------------------------------------------------------
34 
35 #ifndef OPENMS_CHEMISTRY_MODIFICATIONSDB_H
36 #define OPENMS_CHEMISTRY_MODIFICATIONSDB_H
37 
41 
42 #include <set>
43 
44 namespace OpenMS
45 {
46  // forward declarations
47  class ResidueModification;
48  class Residue;
49 
69  class OPENMS_DLLAPI ModificationsDB
70  {
71 public:
72 
74  inline static ModificationsDB* getInstance()
75  {
76  static ModificationsDB* db_ = 0;
77  if (db_ == 0)
78  {
79  db_ = new ModificationsDB;
80  }
81  return db_;
82  }
83 
84  friend class CrossLinksDB;
85 
87  Size getNumberOfModifications() const;
88 
94  const ResidueModification& getModification(Size index) const;
95 
106  void searchModifications(std::set<const ResidueModification*>& mods, const String& mod_name, const String& residue = "", ResidueModification::TermSpecificity term_spec = ResidueModification::NUMBER_OF_TERM_SPECIFICITY) const;
107 
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 
136  Size findModificationIndex(const String& mod_name) const;
137 
144  void searchModificationsByDiffMonoMass(std::vector<String>& mods, double mass, double max_error, const String& residue = "", ResidueModification::TermSpecificity term_spec = ResidueModification::NUMBER_OF_TERM_SPECIFICITY);
145 
164  const ResidueModification* getBestModificationByMonoMass(double mass, double max_error, const String& residue = "", ResidueModification::TermSpecificity term_spec = ResidueModification::NUMBER_OF_TERM_SPECIFICITY);
165 
185  const ResidueModification* getBestModificationByDiffMonoMass(double mass, double max_error, const String& residue = "", ResidueModification::TermSpecificity term_spec = ResidueModification::NUMBER_OF_TERM_SPECIFICITY);
186 
192  void readFromOBOFile(const String& filename);
193 
195  void readFromUnimodXMLFile(const String& filename);
196 
198  void getAllSearchModifications(std::vector<String>& modifications) const;
199 
200 protected:
201 
203  std::vector<ResidueModification*> mods_;
204 
207 
209  bool residuesMatch_(const String& residue, char origin) const;
210 
211 private:
212 
216  ModificationsDB();
218 
220  ModificationsDB(const ModificationsDB& residue_db);
221 
223  virtual ~ModificationsDB();
225 
229  ModificationsDB & operator=(const ModificationsDB& aa);
232  };
233 }
234 #endif
A more convenient string class.
Definition: String.h:57
Definition: ResidueModification.h:103
Definition: CrossLinksDB.h:42
Representation of a modification.
Definition: ResidueModification.h:77
static ModificationsDB * getInstance()
Returns a pointer to the modifications DB (singleton)
Definition: ModificationsDB.h:74
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
database which holds all residue modifications from UniMod
Definition: ModificationsDB.h:69
TermSpecificity
Position where the modification is allowed to occur.
Definition: ResidueModification.h:96
Map< String, std::set< const ResidueModification * > > modification_names_
Stores the mappings of (unique) names to the modifications.
Definition: ModificationsDB.h:206
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:128
std::vector< ResidueModification * > mods_
Stores the modifications.
Definition: ModificationsDB.h:203
Map class based on the STL map (containing several convenience functions)
Definition: Map.h:51

OpenMS / TOPP release 2.3.0 Documentation generated on Tue Jan 9 2018 18:22:02 using doxygen 1.8.13