bpp-seq  2.2.0
SimpleScore.h
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1 //
2 // File: SimpleScore.h
3 // Created by: Julien Dutheil
4 // Created on: Fri May 04 09:35 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 
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
33  data to be ensured and, more generally, to use and operate it in the
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 _SIMPLESCORE_H_
41 #define _SIMPLESCORE_H_
42 
43 // from the STL:
44 #include <string>
45 
46 #include "AlphabetIndex2.h"
47 #include "../Alphabet/Alphabet.h"
48 #include "../Alphabet/AlphabetExceptions.h"
49 #include <Bpp/Exceptions.h>
50 #include <Bpp/Numeric/Matrix/Matrix.h>
51 
52 namespace bpp
53 {
57 class SimpleScore :
58  public virtual AlphabetIndex2
59 {
60 private:
61  LinearMatrix<double> distanceMatrix_;
63 
64 public:
72  SimpleScore(const Alphabet* alphabet, double match, double mismatch);
73 
74  SimpleScore(const SimpleScore& sc) :
77  {}
78 
80  {
82  alphabet_ = sc.alphabet_;
83  return *this;
84  }
85 
86  virtual ~SimpleScore() {}
87 
88  SimpleScore* clone() const { return new SimpleScore(*this); }
89 
90 public:
96  double getIndex(int state1, int state2) const throw (BadIntException);
97  double getIndex(const std::string& state1, const std::string& state2) const throw (BadCharException);
98  const Alphabet* getAlphabet() const { return alphabet_; }
99  LinearMatrix<double>* getIndexMatrix() const;
100  bool isSymmetric() const { return true; }
102 };
103 } // end of namespace bpp.
104 
105 #endif // _SIMPLESCORE_H_
106 
virtual ~SimpleScore()
Definition: SimpleScore.h:86
An alphabet exception thrown when trying to specify a bad char to the alphabet.
const Alphabet * getAlphabet() const
Get the alphabet associated to this index.
Definition: SimpleScore.h:98
LinearMatrix< double > * getIndexMatrix() const
Definition: SimpleScore.cpp:80
This alphabet is used to deal NumericAlphabet.
SimpleScore(const Alphabet *alphabet, double match, double mismatch)
Build a new simpleScore object.
Definition: SimpleScore.cpp:49
const Alphabet * alphabet_
Definition: SimpleScore.h:62
The Alphabet interface.
Definition: Alphabet.h:130
SimpleScore * clone() const
Definition: SimpleScore.h:88
SimpleScore & operator=(const SimpleScore &sc)
Definition: SimpleScore.h:79
Two dimensionnal alphabet index interface.
bool isSymmetric() const
Definition: SimpleScore.h:100
Simple Substitution Matrix, with match and mismatch penalties.
Definition: SimpleScore.h:57
An alphabet exception thrown when trying to specify a bad int to the alphabet.
SimpleScore(const SimpleScore &sc)
Definition: SimpleScore.h:74
double getIndex(int state1, int state2) const
Get the index associated to a pair of states.
Definition: SimpleScore.cpp:64
LinearMatrix< double > distanceMatrix_
Definition: SimpleScore.h:61