bpp-seq  2.2.0
StandardGeneticCode.h
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1 //
2 // File: StandardGeneticCode.h
3 // Created by: Julien Dutheil
4 // Created on: Mon Oct 13 15:39:17 2003
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 
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17 "http://www.cecill.info".
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39 
40 #ifndef _STANDARDGENETICCODE_H_
41 #define _STANDARDGENETICCODE_H_
42 
43 #include "GeneticCode.h"
44 #include "../Alphabet/NucleicAlphabet.h"
45 
46 namespace bpp
47 {
48 
54  public virtual GeneticCode
55 {
56  public:
57  StandardGeneticCode(const NucleicAlphabet* alphabet);
58 
59  virtual ~StandardGeneticCode() {}
60 
61  virtual StandardGeneticCode* clone() const {
62  return new StandardGeneticCode(*this);
63  }
64 
65  public:
66  size_t getNumberOfStopCodons() const { return 3.; }
67 
68  std::vector<int> getStopCodonsAsInt() const {
69  std::vector<int> v(3);
70  v[0] = 48;
71  v[1] = 50;
72  v[02] = 56;
73  return v;
74  }
75 
76  std::vector<std::string> getStopCodonsAsChar() const {
77  std::vector<std::string> v(3);
78  v[0] = "TAA";
79  v[1] = "TAG";
80  v[2] = "TGA";
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 || state == 56);
88  }
89 
90  bool isStop(const std::string& state) const throw (BadCharException) {
91  int i = codonAlphabet_.charToInt(state);
92  return (i == 48 || i == 50 || i == 56);
93  }
94 
95  bool isAltStart(int state) const throw (BadIntException) {
96  //Test:
97  codonAlphabet_.intToChar(state); //throw exception if invalid state!
98  return (state == 62 || state == 30);
99  }
100 
101  bool isAltStart(const std::string& state) const throw (BadCharException) {
102  int i = codonAlphabet_.charToInt(state);
103  return (i == 62 || i == 30);
104  }
105 
106 };
107 
108 } //end of namespace bpp.
109 
110 #endif //_STANDARDGENETICCODE_H_
111 
std::vector< int > getStopCodonsAsInt() const
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 isAltStart(int state) const
Tells is a particular codon is an alternative start codon.
This alphabet is used to deal NumericAlphabet.
std::vector< std::string > getStopCodonsAsChar() const
StandardGeneticCode(const NucleicAlphabet *alphabet)
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.
virtual StandardGeneticCode * clone() const
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 int to the alphabet.
size_t getNumberOfStopCodons() const
Partial implementation of the Transliterator interface for genetic code object.
Definition: GeneticCode.h:79
This class implements the standard genetic code as describe on the NCBI web site: http://www...
The abstract base class for nucleic alphabets.
std::string intToChar(int state) const
Give the string description of a state given its int description.