bpp-seq  2.2.0
AlphabetIndex2.h
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1 //
2 // File: AlphabetIndex2.h
3 // Created by: Julien Dutheil
4 // Created on: Mon Feb 21 17:42 2005
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
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17  "http://www.cecill.info".
18 
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22  economic rights, and the successive licensors have only limited
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27  software by the user in light of its specific status of free software,
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38  */
39 
40 #ifndef _ALPHABETINDEX2_H_
41 #define _ALPHABETINDEX2_H_
42 
43 #include "../Alphabet/Alphabet.h"
44 #include <Bpp/Clonable.h>
45 #include <Bpp/Numeric/Matrix/Matrix.h>
46 
47 // From the STL:
48 #include <string>
49 
50 namespace bpp
51 {
57 class AlphabetIndex2 : public Clonable
58 {
59 public:
61  virtual ~AlphabetIndex2() {}
62 
63 public:
64  virtual AlphabetIndex2* clone() const = 0;
65 
73  virtual double getIndex(int state1, int state2) const = 0;
74 
82  virtual double getIndex(const std::string& state1, const std::string& state2) const = 0;
83 
89  virtual const Alphabet* getAlphabet() const = 0;
90 
94  virtual Matrix<double>* getIndexMatrix() const = 0;
95 
99  virtual bool isSymmetric() const = 0;
100 };
101 } // end of namespace bpp.
102 
103 #endif // _ALPHABETINDEX2_H_
104 
virtual Matrix< double > * getIndexMatrix() const =0
virtual AlphabetIndex2 * clone() const =0
This alphabet is used to deal NumericAlphabet.
virtual bool isSymmetric() const =0
The Alphabet interface.
Definition: Alphabet.h:130
virtual ~AlphabetIndex2()
Two dimensionnal alphabet index interface.
virtual double getIndex(int state1, int state2) const =0
Get the index associated to a pair of states.
virtual const Alphabet * getAlphabet() const =0
Get the alphabet associated to this index.