bpp-seq  2.2.0
UserAlphabetIndex1.h
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1 //
2 // File: UserAlphabetIndex1.h
3 // Created by: Laurent Guéguen
4 // Created on: vendredi 29 mars 2013, à 13h 05
5 //
6 
7 /*
8  Copyright or © or Copr. CNRS, (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
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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 _USERALPHABETINDEX1_H_
41 #define _USERALPHABETINDEX1_H_
42 
43 #include "AlphabetIndex1.h"
44 
45 // From the STL:
46 #include <vector>
47 
48 namespace bpp
49 {
55  public virtual AlphabetIndex1
56 {
57 private:
58  const Alphabet* alph_;
59  std::vector<double> index_;
60 
61 public:
63  alph_(alph),
64  index_(alph->getSize(),0)
65  {}
66 
68  alph_(uAlph.alph_),//->clone()),
69  index_(uAlph.index_)
70  {}
71 
73  {
74  alph_ = uAlph.alph_;//->clone();
75  index_ = uAlph.index_;
76  return *this;
77  }
78 
79  virtual ~UserAlphabetIndex1() {}
80 
81  UserAlphabetIndex1* clone() const { return new UserAlphabetIndex1(*this); }
82 
83 public:
84  double getIndex(int state) const
85  {
86  return index_[alph_->getStateIndex(state)];
87  }
88 
89  void setIndex(int state, double val)
90  {
91  index_[alph_->getStateIndex(state)] = val;
92  }
93 
94  double getIndex(const std::string& state) const
95  {
96  return index_[alph_->getStateIndex(state)];
97  }
98 
99  void setIndex(const std::string& state, double val)
100  {
101  index_[alph_->getStateIndex(state)] = val;
102  }
103 
104  std::vector<double>* getIndexVector() const { return new std::vector<double>(index_); }
105 
106  const Alphabet* getAlphabet() const { return alph_; }
107 };
108 } // end of namespace bpp.
109 
110 #endif // _USERALPHABETINDEX1_H_
111 
std::vector< double > index_
double getIndex(int state) const
Get the index associated to a state.
std::vector< double > * getIndexVector() const
UserAlphabetIndex1(const Alphabet *alph)
This alphabet is used to deal NumericAlphabet.
The Alphabet interface.
Definition: Alphabet.h:130
double getIndex(const std::string &state) const
Get the index associated to a state.
UserAlphabetIndex1 * clone() const
One dimensionnal alphabet index interface.
virtual size_t getStateIndex(int state) const =0
UserAlphabetIndex1 & operator=(const UserAlphabetIndex1 &uAlph)
UserAlphabetIndex1(const UserAlphabetIndex1 &uAlph)
const Alphabet * getAlphabet() const
Get the alphabet associated to this index.
Alphabet index given by user.
void setIndex(int state, double val)
void setIndex(const std::string &state, double val)