bpp-seq  2.2.0
AAChenGuHuangHydrophobicityIndex.h
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1 //
2 // File: AAChenGuHuangHydrophobicityIndex.h
3 // Created by: Bastien Boussau
4 // Created on: Fri Jan 14 10:31 2011
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 
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17  "http://www.cecill.info".
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39 
40 #ifndef _AACHENGUHUANGHYDROPHOBICITYINDEX_H_
41 #define _AACHENGUHUANGHYDROPHOBICITYINDEX_H_
42 
43 #include "AlphabetIndex1.h"
44 #include "../Alphabet/ProteicAlphabet.h"
45 #include "../Alphabet/AlphabetTools.h"
46 
47 namespace bpp
48 {
67  public AlphabetIndex1
68 {
69 private:
70  std::vector<double> hydrophobicity_;
71 
72 public:
75  {
76  hydrophobicity_.resize(20);
77  hydrophobicity_[ 0] = 0.87; // A
78  hydrophobicity_[ 1] = 0.85; // R
79  hydrophobicity_[ 2] = 0.09; // N
80  hydrophobicity_[ 3] = 0.66; // D
81  hydrophobicity_[ 4] = 1.52; // C
82  hydrophobicity_[ 5] = 0.00; // Q
83  hydrophobicity_[ 6] = 0.67; // E
84  hydrophobicity_[ 7] = 0.00; // G
85  hydrophobicity_[ 8] = 0.87; // H
86  hydrophobicity_[ 9] = 3.15; // I
87  hydrophobicity_[10] = 2.17; // L
88  hydrophobicity_[11] = 1.64; // K
89  hydrophobicity_[12] = 1.67; // M
90  hydrophobicity_[13] = 2.87; // F
91  hydrophobicity_[14] = 2.77; // P
92  hydrophobicity_[15] = 0.07; // S
93  hydrophobicity_[16] = 0.07; // T
94  hydrophobicity_[17] = 3.77; // W
95  hydrophobicity_[18] = 2.76; // Y
96  hydrophobicity_[19] = 1.87; // V
97  }
98 
100 
102 
103 public:
104  double getIndex(int state) const throw (BadIntException)
105  {
106  if (state < 0 || state > 19) throw BadIntException(state, "AAChenGuHuangHydrophobicityIndex::getIndex(). Invalid state.", &AlphabetTools::PROTEIN_ALPHABET);
107  return hydrophobicity_[static_cast<size_t>(state)];
108  }
109 
110  double getIndex(const std::string& state) const throw (BadCharException)
111  {
112  return hydrophobicity_[static_cast<size_t>(AlphabetTools::PROTEIN_ALPHABET.charToInt(state))];
113  }
114 
115  std::vector<double>* getIndexVector() const { return new std::vector<double>(hydrophobicity_); }
116 
118 };
119 } // end of namespace bpp.
120 
121 #endif // _AACHENGUHUANGHYDROPHOBICITYINDEX_H_
122 
An alphabet exception thrown when trying to specify a bad char to the alphabet.
This alphabet is used to deal NumericAlphabet.
double getIndex(int state) const
Get the index associated to a state.
The Alphabet interface.
Definition: Alphabet.h:130
const Alphabet * getAlphabet() const
Get the alphabet associated to this index.
One dimensionnal alphabet index interface.
AAChenGuHuangHydrophobicityIndex * clone() const
An alphabet exception thrown when trying to specify a bad int to the alphabet.
static const ProteicAlphabet PROTEIN_ALPHABET
Definition: AlphabetTools.h:64
Hydrophobicity of each amino acid, according to Table 1 in Chen, Gu and Huang, BMC Bioinformatics 200...
int charToInt(const std::string &state) const
Give the int description of a state given its string description.
double getIndex(const std::string &state) const
Get the index associated to a state.