bpp-seq  2.2.0
AscidianMitochondrialGeneticCode.h
Go to the documentation of this file.
1 //
2 // File: AscidianMitochondrialGeneticCode.h
3 // Created by: Fidel Botero and Julien Dutheil
4 // Created on: Thu Jun 13 11:32:00 CET 2013
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 #ifndef _ASCIDIANMITOCHONDRIALGENETICCODE_H_
41 #define _ASCIDIANMITOCHONDRIALGENETICCODE_H_
42 
43 #include "GeneticCode.h"
44 #include "../Alphabet/NucleicAlphabet.h"
45 
46 namespace bpp
47 {
48 
54  public virtual GeneticCode
55 {
56  public:
58 
60 
62  return new AscidianMitochondrialGeneticCode(*this);
63  }
64 
65  public:
66  size_t getNumberOfStopCodons() const { return 2.; }
67 
68  std::vector<int> getStopCodonsAsInt() const {
69  std::vector<int> v(4);
70  v[0] = 8;
71  v[1] = 10;
72  v[2] = 48;
73  v[3] = 50;
74  return v;
75  }
76 
77  std::vector<std::string> getStopCodonsAsChar() const {
78  std::vector<std::string> v(4);
79  v[0] = "AGA";
80  v[1] = "AGG";
81  v[2] = "TAA";
82  v[4] = "TAG";
83  return v;
84  }
85 
86  bool isStop(int state) const throw (BadIntException) {
87  //Test:
88  codonAlphabet_.intToChar(state); //throw exception if invalid state!
89  return (state == 48 || state == 50);
90  }
91 
92  bool isStop(const std::string& state) const throw (BadCharException) {
93  int i = codonAlphabet_.charToInt(state);
94  return (i == 48 || i == 50);
95  }
96 
97  bool isAltStart(int state) const throw (BadIntException) {
98  //Test:
99  codonAlphabet_.intToChar(state); //throw exception if invalid state!
100  return (state == 12 || state == 46 || state == 62);
101  }
102 
103  bool isAltStart(const std::string& state) const throw (BadCharException) {
104  int i = codonAlphabet_.charToInt(state);
105  return (i == 12 || i == 46 || i == 62);
106  }
107 
108 };
109 
110 } //end of namespace bpp.
111 
112 #endif //_ASCIDIANMITOCHONDRIALGENETICCODE_H_
113 
bool isAltStart(int state) const
Tells is a particular codon is an alternative start codon.
bool isStop(const std::string &state) const
Tells is a particular codon is a stop codon.
An alphabet exception thrown when trying to specify a bad char to the alphabet.
int charToInt(const std::string &state) const
Give the int description of a state given its string description.
Definition: WordAlphabet.h:127
bool isStop(int state) const
Tells is a particular codon is a stop codon.
This alphabet is used to deal NumericAlphabet.
AscidianMitochondrialGeneticCode(const NucleicAlphabet *alphabet)
std::vector< std::string > getStopCodonsAsChar() const
This class implements the ascidian mitochondrial genetic code as describe on the NCBI web site: http:...
CodonAlphabet codonAlphabet_
Definition: GeneticCode.h:84
bool isAltStart(const std::string &state) const
Tells is a particular codon is an alternative start codon.
virtual AscidianMitochondrialGeneticCode * clone() const
An alphabet exception thrown when trying to specify a bad int to the alphabet.
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.