bpp-seq  2.2.0
DNA.h
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1 //
2 // File: DNA.h
3 // Created by: Guillaume Deuchst
4 // Julien Dutheil
5 // Created on: Tue Jul 22 2003
6 //
7 
8 /*
9  Copyright or © or Copr. Bio++ Development Team, (November 17, 2004)
10 
11  This software is a computer program whose purpose is to provide classes
12  for sequences analysis.
13 
14  This software is governed by the CeCILL license under French law and
15  abiding by the rules of distribution of free software. You can use,
16  modify and/ or redistribute the software under the terms of the CeCILL
17  license as circulated by CEA, CNRS and INRIA at the following URL
18  "http://www.cecill.info".
19 
20  As a counterpart to the access to the source code and rights to copy,
21  modify and redistribute granted by the license, users are provided only
22  with a limited warranty and the software's author, the holder of the
23  economic rights, and the successive licensors have only limited
24  liability.
25 
26  In this respect, the user's attention is drawn to the risks associated
27  with loading, using, modifying and/or developing or reproducing the
28  software by the user in light of its specific status of free software,
29  that may mean that it is complicated to manipulate, and that also
30  therefore means that it is reserved for developers and experienced
31  professionals having in-depth computer knowledge. Users are therefore
32  encouraged to load and test the software's suitability as regards their
33  requirements in conditions enabling the security of their systems and/or
34  data to be ensured and, more generally, to use and operate it in the
35  same conditions as regards security.
36 
37  The fact that you are presently reading this means that you have had
38  knowledge of the CeCILL license and that you accept its terms.
39 */
40 
41 #ifndef _DNA_H_
42 #define _DNA_H_
43 
44 #include "NucleicAlphabet.h"
45 
46 //From the STL:
47 #include <string>
48 #include <vector>
49 
50 namespace bpp
51 {
52 
60  class DNA:
61  public NucleicAlphabet
62  {
63  public:
68  DNA(bool exclamationMarkCountsAsGap = false);
69 
70  DNA(const DNA& bia) : NucleicAlphabet(bia) {}
71 
72  DNA& operator=(const DNA& bia)
73  {
75  return *this;
76  }
77 
78  DNA* clone() const
79  {
80  return new DNA(*this);
81  }
82 
83  virtual ~DNA() {}
84 
85  public:
86  std::vector<int> getAlias(int state) const throw (BadIntException);
87  std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
88  int getGeneric(const std::vector<int>& states) const throw (BadIntException);
89  std::string getGeneric(const std::vector<std::string>& states) const throw (BadCharException);
90  std::string getAlphabetType() const { return "DNA alphabet"; }
91  };
92 
93 } //end of namespace bpp.
94 
95 #endif // _DNA_H_
96 
DNA(bool exclamationMarkCountsAsGap=false)
Definition: DNA.cpp:57
An alphabet exception thrown when trying to specify a bad char to the alphabet.
int getGeneric(const std::vector< int > &states) const
Get the generic state that match a set of states.
Definition: DNA.cpp:124
NucleicAlphabet & operator=(const NucleicAlphabet &bia)
This alphabet is used to deal NumericAlphabet.
std::string getAlphabetType() const
Identification method.
Definition: DNA.h:90
DNA * clone() const
Definition: DNA.h:78
DNA & operator=(const DNA &bia)
Definition: DNA.h:72
This alphabet is used to deal with DNA sequences.
Definition: DNA.h:60
virtual ~DNA()
Definition: DNA.h:83
An alphabet exception thrown when trying to specify a bad int to the alphabet.
std::vector< int > getAlias(int state) const
Get all resolved states that match a generic state.
Definition: DNA.cpp:89
DNA(const DNA &bia)
Definition: DNA.h:70
The abstract base class for nucleic alphabets.