bpp-seq  2.2.0
BLOSUM50.h
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1 //
2 // File: BLOSUM50.h
3 // Created by: Julien Dutheil
4 // Created on: Tue Jan 18 10:28 2007
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 
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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
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34  same conditions as regards security.
35 
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38  */
39 
40 #ifndef _BLOSUM50_H_
41 #define _BLOSUM50_H_
42 
43 // from the STL:
44 #include <string>
45 
46 #include "AlphabetIndex2.h"
47 #include "../Alphabet/ProteicAlphabet.h"
48 #include "../Alphabet/AlphabetExceptions.h"
49 #include <Bpp/Exceptions.h>
50 #include <Bpp/Numeric/Matrix/Matrix.h>
51 
52 namespace bpp
53 {
64 class BLOSUM50 :
65  public virtual AlphabetIndex2
66 {
67 private:
68  LinearMatrix<double> distanceMatrix_;
70 
71 public:
72  BLOSUM50();
73 
74  BLOSUM50(const BLOSUM50& blosum) :
76  alpha_(blosum.alpha_)
77  {}
78 
79  BLOSUM50& operator=(const BLOSUM50& blosum)
80  {
82  alpha_ = blosum.alpha_;
83  return *this;
84  }
85 
86  virtual ~BLOSUM50() {}
87 
88 public:
94  double getIndex(int state1, int state2) const throw (BadIntException);
95  double getIndex(const std::string& state1, const std::string& state2) const throw (BadCharException);
96  const Alphabet* getAlphabet() const { return alpha_; }
97  BLOSUM50* clone() const { return new BLOSUM50(); }
98  LinearMatrix<double>* getIndexMatrix() const;
99  bool isSymmetric() const { return true; }
101 };
102 } // end of namespace bpp.
103 
104 #endif // _BLOSUM50_H_
105 
bool isSymmetric() const
Definition: BLOSUM50.h:99
An alphabet exception thrown when trying to specify a bad char to the alphabet.
virtual ~BLOSUM50()
Definition: BLOSUM50.h:86
This alphabet is used to deal NumericAlphabet.
BLOSUM50 & operator=(const BLOSUM50 &blosum)
Definition: BLOSUM50.h:79
double getIndex(int state1, int state2) const
Get the index associated to a pair of states.
Definition: BLOSUM50.cpp:58
The Alphabet interface.
Definition: Alphabet.h:130
const Alphabet * getAlphabet() const
Get the alphabet associated to this index.
Definition: BLOSUM50.h:96
This alphabet is used to deal with proteins.
LinearMatrix< double > distanceMatrix_
Definition: BLOSUM50.h:68
const ProteicAlphabet * alpha_
Definition: BLOSUM50.h:69
Two dimensionnal alphabet index interface.
BLOSUM 50 Substitution Matrix.
Definition: BLOSUM50.h:64
BLOSUM50 * clone() const
Definition: BLOSUM50.h:97
An alphabet exception thrown when trying to specify a bad int to the alphabet.
BLOSUM50(const BLOSUM50 &blosum)
Definition: BLOSUM50.h:74
LinearMatrix< double > * getIndexMatrix() const
Definition: BLOSUM50.cpp:74