bpp-seq  2.2.0
GranthamAAChemicalDistance.h
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1 //
2 // File: GranthamAAChemicalDistance.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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38  */
39 
40 #ifndef _GRANTHAMAACHEMICALDISTANCE_H_
41 #define _GRANTHAMAACHEMICALDISTANCE_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 {
97  public virtual AlphabetIndex2
98 {
99 private:
100  LinearMatrix<double> distanceMatrix_;
101  LinearMatrix<double> signMatrix_;
103  short int sign_;
104 
105 public:
107 
111  alpha_(gd.alpha_),
112  sign_(gd.sign_)
113  {}
114 
116  {
119  alpha_ = gd.alpha_;
120  sign_ = gd.sign_;
121  return *this;
122  }
123 
124  virtual ~GranthamAAChemicalDistance();
125 
126 public:
132  double getIndex(int state1, int state2) const throw (BadIntException);
133  double getIndex(const std::string& state1, const std::string& state2) const throw (BadCharException);
134  const Alphabet* getAlphabet() const { return alpha_; }
136  Matrix<double>* getIndexMatrix() const;
139 public:
140  void setSymmetric(bool yn) { sign_ = (yn ? SIGN_NONE : SIGN_ARBITRARY); }
141  bool isSymmetric() const { return sign_ == SIGN_NONE; }
149  void setPC1Sign(bool yn) { sign_ = (yn ? SIGN_PC1 : SIGN_ARBITRARY); }
150 
151  static short int SIGN_ARBITRARY;
152  static short int SIGN_PC1;
153  static short int SIGN_NONE;
154 };
155 } // end of namespace bpp.
156 
157 #endif // _GRANTHAMAACHEMICALDISTANCE_H_
158 
An alphabet exception thrown when trying to specify a bad char to the alphabet.
This alphabet is used to deal NumericAlphabet.
GranthamAAChemicalDistance & operator=(const GranthamAAChemicalDistance &gd)
The Alphabet interface.
Definition: Alphabet.h:130
Grantham (1974) Amino-Acid chemical distance.
This alphabet is used to deal with proteins.
GranthamAAChemicalDistance(const GranthamAAChemicalDistance &gd)
const Alphabet * getAlphabet() const
Get the alphabet associated to this index.
GranthamAAChemicalDistance * clone() const
Two dimensionnal alphabet index interface.
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.
void setPC1Sign(bool yn)
The sign of the distance is computed using the coordinate on the first axis of a principal component ...