OpenMS  2.8.0
RibonucleotideDB.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 2002-2021.
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: Hendrik Weisser $
32 // $Authors: Hendrik Weisser $
33 // --------------------------------------------------------------------------
34 
35 #pragma once
36 
39 #include <unordered_map>
40 
41 namespace OpenMS
42 {
50  class OPENMS_DLLAPI RibonucleotideDB
51  {
52  public:
54 
56  typedef std::vector<ConstRibonucleotidePtr>::const_iterator ConstIterator;
57 
60 
62  virtual ~RibonucleotideDB();
63 
65  RibonucleotideDB(const RibonucleotideDB& other) = delete;
66 
68  RibonucleotideDB& operator=(const RibonucleotideDB& other) = delete;
69 
71  inline ConstIterator begin() const
72  {
73  return ribonucleotides_.begin();
74  }
75 
77  inline ConstIterator end() const
78  {
79  return ribonucleotides_.end();
80  }
81 
87  ConstRibonucleotidePtr getRibonucleotide(const std::string& code);
88 
95 
101  std::pair<ConstRibonucleotidePtr, ConstRibonucleotidePtr> getRibonucleotideAlternatives(const std::string& code);
102 
103 
104  protected:
107 
109  void readFromFile_(const std::string& path);
110 
112  ConstRibonucleotidePtr parseRow_(const std::string& row, Size line_count);
113 
115  std::vector<ConstRibonucleotidePtr> ribonucleotides_;
116 
118  std::unordered_map<std::string, Size> code_map_;
119 
121  std::map<std::string, std::pair<ConstRibonucleotidePtr, ConstRibonucleotidePtr>> ambiguity_map_;
122 
124  };
125 }
Database of ribonucleotides (modified and unmodified)
Definition: RibonucleotideDB.h:51
RibonucleotideDB()
default constructor
static RibonucleotideDB * getInstance()
replacement for constructor (singleton pattern)
ConstRibonucleotidePtr parseRow_(const std::string &row, Size line_count)
create a (modified) nucleotide from an input row
std::pair< ConstRibonucleotidePtr, ConstRibonucleotidePtr > getRibonucleotideAlternatives(const std::string &code)
Get the alternatives for an ambiguous modification code.
RibonucleotideDB & operator=(const RibonucleotideDB &other)=delete
assignment operator not available
virtual ~RibonucleotideDB()
destructor
RibonucleotideDB(const RibonucleotideDB &other)=delete
copy constructor not available
ConstRibonucleotidePtr getRibonucleotide(const std::string &code)
Get a ribonucleotide by its code (short name)
ConstIterator end() const
Const iterator to end of database.
Definition: RibonucleotideDB.h:77
std::unordered_map< std::string, Size > code_map_
mapping of codes (short names) to indexes into ribonucleotides_
Definition: RibonucleotideDB.h:118
std::vector< ConstRibonucleotidePtr >::const_iterator ConstIterator
const iterator type definition
Definition: RibonucleotideDB.h:56
Size max_code_length_
Definition: RibonucleotideDB.h:123
ConstIterator begin() const
Const iterator to beginning of database.
Definition: RibonucleotideDB.h:71
ConstRibonucleotidePtr getRibonucleotidePrefix(const std::string &seq)
Get the ribonucleotide with the longest code that matches a prefix of seq.
void readFromFile_(const std::string &path)
read (modified) nucleotides from input file
std::map< std::string, std::pair< ConstRibonucleotidePtr, ConstRibonucleotidePtr > > ambiguity_map_
mapping of ambiguity codes to the alternatives they represent
Definition: RibonucleotideDB.h:121
std::vector< ConstRibonucleotidePtr > ribonucleotides_
list of known (modified) nucleotides
Definition: RibonucleotideDB.h:115
Representation of a ribonucleotide (modified or unmodified)
Definition: Ribonucleotide.h:52
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47