bpp-seq  2.2.0
YeastMitochondrialGeneticCode.h
Go to the documentation of this file.
1 //
2 // File: YeastbrateMitochondrialGeneticCode.h
3 // Created by: Benoit Nabholz
4 // Created on: Sun Oct 10 14:33 CET 2010
5 //
6 
7 /*
8 Copyright or © or Copr. Bio++ Development Team, (November 17, 2004)
9 
10 This software is a computer program whose purpose is to provide classes
11 for sequences analysis.
12 
13 This software is governed by the CeCILL license under French law and
14 abiding by the rules of distribution of free software. You can use,
15 modify and/ or redistribute the software under the terms of the CeCILL
16 license as circulated by CEA, CNRS and INRIA at the following URL
17 "http://www.cecill.info".
18 
19 As a counterpart to the access to the source code and rights to copy,
20 modify and redistribute granted by the license, users are provided only
21 with a limited warranty and the software's author, the holder of the
22 economic rights, and the successive licensors have only limited
23 liability.
24 
25 In this respect, the user's attention is drawn to the risks associated
26 with loading, using, modifying and/or developing or reproducing the
27 software by the user in light of its specific status of free software,
28 that may mean that it is complicated to manipulate, and that also
29 therefore means that it is reserved for developers and experienced
30 professionals having in-depth computer knowledge. Users are therefore
31 encouraged to load and test the software's suitability as regards their
32 requirements in conditions enabling the security of their systems and/or
33 data to be ensured and, more generally, to use and operate it in the
34 same conditions as regards security.
35 
36 The fact that you are presently reading this means that you have had
37 knowledge of the CeCILL license and that you accept its terms.
38 */
39 
40 
41 #ifndef _YEASTMITOCHONDRIALGENETICCODE_H_
42 #define _YEASTMITOCHONDRIALGENETICCODE_H_
43 
44 #include "GeneticCode.h"
45 #include "../Alphabet/NucleicAlphabet.h"
46 
47 namespace bpp
48 {
49 
56  public virtual GeneticCode
57 {
58  public:
60 
62 
64  return new YeastMitochondrialGeneticCode(*this);
65  }
66 
67  public:
68  size_t getNumberOfStopCodons() const { return 2.; }
69 
70  std::vector<int> getStopCodonsAsInt() const {
71  std::vector<int> v(2);
72  v[1] = 48;
73  v[2] = 50;
74  return v;
75  }
76 
77  std::vector<std::string> getStopCodonsAsChar() const {
78  std::vector<std::string> v(2);
79  v[1] = "TAA";
80  v[2] = "TAG";
81  return v;
82  }
83 
84  bool isStop(int state) const throw (BadIntException) {
85  //Test:
86  codonAlphabet_.intToChar(state); //throw exception if invalid state!
87  return (state == 48 || state == 50);
88  }
89 
90  bool isStop(const std::string& state) const throw (BadCharException) {
91  int i = codonAlphabet_.charToInt(state);
92  return (i == 48 || i == 50);
93  }
94 
95  bool isAltStart(int state) const throw (BadIntException) {
96  //Test:
97  codonAlphabet_.intToChar(state); //throw exception if invalid state!
98  return (state == 12);
99  }
100 
101  bool isAltStart(const std::string& state) const throw (BadCharException) {
102  int i = codonAlphabet_.charToInt(state);
103  return (i == 12);
104  }
105 
106 
107 };
108 
109 } //end of namespace bpp.
110 
111 #endif //_YEASTMITOCHONDRIALGENETICCODE_H_
112 
std::vector< std::string > getStopCodonsAsChar() const
An alphabet exception thrown when trying to specify a bad char to the alphabet.
This class implements the Invertebrate Mitochondrial genetic code as describe on the NCBI website: ht...
int charToInt(const std::string &state) const
Give the int description of a state given its string description.
Definition: WordAlphabet.h:127
This alphabet is used to deal NumericAlphabet.
virtual YeastMitochondrialGeneticCode * clone() const
bool isStop(const std::string &state) const
Tells is a particular codon is a stop codon.
bool isAltStart(const std::string &state) const
Tells is a particular codon is an alternative start codon.
CodonAlphabet codonAlphabet_
Definition: GeneticCode.h:84
bool isStop(int state) const
Tells is a particular codon is a stop codon.
An alphabet exception thrown when trying to specify a bad int to the alphabet.
YeastMitochondrialGeneticCode(const NucleicAlphabet *alphaibet)
bool isAltStart(int state) const
Tells is a particular codon is an alternative start codon.
Partial implementation of the Transliterator interface for genetic code object.
Definition: GeneticCode.h:79
The abstract base class for nucleic alphabets.
std::string intToChar(int state) const
Give the string description of a state given its int description.