bpp-seq  2.2.0
SimpleIndexDistance.h
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1 //
2 // File: SimpleIndexDistance.h
3 // Created by: Julien Dutheil
4 // Created on: Tue Apr 21 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
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
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31  encouraged to load and test the software's suitability as regards their
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34  same conditions as regards security.
35 
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38  */
39 
40 #ifndef _SIMPLEINDEXDISTANCE_H_
41 #define _SIMPLEINDEXDISTANCE_H_
42 
43 // from the STL:
44 #include <string>
45 
46 #include "AlphabetIndex1.h"
47 #include "AlphabetIndex2.h"
48 #include "../Alphabet/ProteicAlphabet.h"
49 #include "../Alphabet/AlphabetExceptions.h"
50 #include <Bpp/Exceptions.h>
51 #include <Bpp/Numeric/Matrix/Matrix.h>
52 
53 namespace bpp
54 {
62  public virtual AlphabetIndex2
63 {
64 private:
65  std::auto_ptr<AlphabetIndex1> index_;
66  bool sym_;
67 
68 public:
70  index_(index),
71  sym_(false)
72  {}
73 
75  index_(dynamic_cast<AlphabetIndex1*>(sid.index_->clone())),
76  sym_(sid.sym_)
77  {}
78 
80  {
81  index_.reset(dynamic_cast<AlphabetIndex1*>(sid.index_->clone()));
82  sym_ = sid.sym_;
83  return *this;
84  }
85 
86  virtual ~SimpleIndexDistance() {}
87 
88 public:
89  double getIndex(int state1, int state2) const throw (BadIntException)
90  {
91  double d = index_->getIndex(state2) - index_->getIndex(state1);
92  return sym_ ? NumTools::abs<double>(d) : d;
93  }
94 
95  double getIndex(const std::string& state1, const std::string& state2) const throw (BadCharException)
96  {
97  double d = index_->getIndex(state2) - index_->getIndex(state1);
98  return sym_ ? NumTools::abs<double>(d) : d;
99  }
100 
101  const Alphabet* getAlphabet() const { return index_->getAlphabet(); }
102 
103  SimpleIndexDistance* clone() const { return new SimpleIndexDistance(*this); }
104 
105  Matrix<double>* getIndexMatrix() const
106  {
107  size_t n = index_->getAlphabet()->getSize(); //We should change to "supported ints" there...
108  RowMatrix<double>* m = new RowMatrix<double>(n, n);
109  for (size_t i = 0; i < n; ++i)
110  {
111  for (size_t j = 0; j < n; ++j)
112  {
113  (*m)(i, j) = getIndex(static_cast<int>(i), static_cast<int>(j));
114  }
115  }
116  return m;
117  }
118 
119 public:
120  void setSymmetric(bool yn) { sym_ = yn; }
121  bool isSymmetric() const { return sym_; }
125  const AlphabetIndex1& getAlphabetIndex1() const { return *index_; }
130 };
131 } // end of namespace bpp.
132 
133 #endif // _SIMPLEINDEXDISTANCE_H_
134 
AlphabetIndex1 & getAlphabetIndex1()
An alphabet exception thrown when trying to specify a bad char to the alphabet.
SimpleIndexDistance * clone() const
SimpleIndexDistance(const SimpleIndexDistance &sid)
This alphabet is used to deal NumericAlphabet.
SimpleIndexDistance(AlphabetIndex1 *index)
std::auto_ptr< AlphabetIndex1 > index_
The Alphabet interface.
Definition: Alphabet.h:130
const Alphabet * getAlphabet() const
Get the alphabet associated to this index.
SimpleIndexDistance & operator=(const SimpleIndexDistance &sid)
const AlphabetIndex1 & getAlphabetIndex1() const
One dimensionnal alphabet index interface.
double getIndex(const std::string &state1, const std::string &state2) const
Get the index associated to a pair of states.
Two dimensionnal alphabet index interface.
Simple dissimilarity distance.
Matrix< double > * getIndexMatrix() const
An alphabet exception thrown when trying to specify a bad int to the alphabet.
double getIndex(int state1, int state2) const
Get the index associated to a pair of states.