bpp-seq  2.2.0
GranthamAAChemicalDistance.cpp
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1 //
2 // File: GranthamAAChemicalDistance.cpp
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
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 // from the STL:
41 #include <string>
42 
44 #include "../Alphabet/AlphabetTools.h"
45 #include <Bpp/Numeric/NumTools.h>
46 
47 using namespace bpp;
48 
52 
54  distanceMatrix_(20, 20),
55  signMatrix_(20, 20),
56  alpha_(&AlphabetTools::PROTEIN_ALPHABET),
57  sign_(0)
58 {
59  // Load the matrix:
60  #include "__GranthamMatrixCode"
61 }
63 
64 double GranthamAAChemicalDistance::getIndex(int state1, int state2) const
65 throw (BadIntException)
66 {
67  size_t stateIndex1 = alpha_->getStateIndex(state1);
68  size_t stateIndex2 = alpha_->getStateIndex(state2);
69  double d = distanceMatrix_(stateIndex1, stateIndex2);
70  if (sign_ == SIGN_NONE)
71  return NumTools::abs<double>(d);
72  if (sign_ == SIGN_PC1)
73  return signMatrix_(stateIndex1, stateIndex2) * NumTools::abs<double>(d);
74  return d;
75 }
76 
77 double GranthamAAChemicalDistance::getIndex(const std::string& state1, const std::string& state2) const
78 throw (BadCharException)
79 {
80  return getIndex(alpha_->charToInt(state1), alpha_->charToInt(state2));
81 }
82 
84 {
85  RowMatrix<double>* m = new RowMatrix<double>(distanceMatrix_);
86  if (sign_ == SIGN_NONE)
87  {
88  for (size_t i = 0; i < 20; ++i)
89  {
90  for (size_t j = 0; j < 20; ++j)
91  {
92  (*m)(i, j) = NumTools::abs<double>((*m)(i, j));
93  }
94  }
95  }
96  else if (sign_ == SIGN_PC1)
97  {
98  for (size_t i = 0; i < 20; ++i)
99  {
100  for (size_t j = 0; j < 20; ++j)
101  {
102  (*m)(i, j) = signMatrix_(i, j) * NumTools::abs<double>((*m)(i, j));
103  }
104  }
105  }
106  return m;
107 }
108 
An alphabet exception thrown when trying to specify a bad char to the alphabet.
This alphabet is used to deal NumericAlphabet.
Utilitary functions dealing with alphabets.
Definition: AlphabetTools.h:59
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.