bpp-seq  2.2.0
AAIndex2Entry.h
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1 //
2 // File: AAIndex2Entry.h
3 // Created by: Julien Dutheil
4 // Created on: Fri Jan 19 17:07 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
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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 _AAINDEX2ENTRY_H_
41 #define _AAINDEX2ENTRY_H_
42 
43 #include "AlphabetIndex2.h"
44 #include "../Alphabet/ProteicAlphabet.h"
45 #include <Bpp/Numeric/Matrix/Matrix.h>
46 
47 namespace bpp
48 {
53  public virtual AlphabetIndex2
54 {
55 private:
56  LinearMatrix<double> property_;
58  bool sym_;
59 
60 public:
72  AAIndex2Entry(std::istream& input, bool sym = true) throw (IOException);
73 
74  AAIndex2Entry(const AAIndex2Entry& index) :
75  property_(index.property_),
76  alpha_(index.alpha_),
77  sym_(index.sym_)
78  {}
79 
81  {
82  property_ = index.property_;
83  alpha_ = index.alpha_;
84  sym_ = index.sym_;
85  return *this;
86  }
87 
88  virtual ~AAIndex2Entry() {}
89 
90 public:
91  const Alphabet* getAlphabet() const { return alpha_; }
92 
93  AAIndex2Entry* clone() const { return new AAIndex2Entry(*this); }
94 
95  double getIndex(int state1, int state2) const throw (BadIntException)
96  {
97  size_t stateIndex1 = alpha_->getStateIndex(state1);
98  size_t stateIndex2 = alpha_->getStateIndex(state2);
99  return property_(stateIndex1, stateIndex2);
100  }
101 
102  double getIndex(const std::string& state1, const std::string& state2) const throw (BadCharException)
103  {
104  size_t stateIndex1 = alpha_->getStateIndex(state1);
105  size_t stateIndex2 = alpha_->getStateIndex(state2);
106  return property_(stateIndex1, stateIndex2);
107  }
108 
109  LinearMatrix<double>* getIndexMatrix() const { return new LinearMatrix<double>(property_); }
110 
111  bool isSymmetric() const { return sym_; }
112 
113 };
114 } // end of namespace bpp.
115 
116 #endif // _AAINDEX2ENTRY_H_
117 
virtual ~AAIndex2Entry()
Definition: AAIndex2Entry.h:88
An alphabet exception thrown when trying to specify a bad char to the alphabet.
This alphabet is used to deal NumericAlphabet.
double getIndex(int state1, int state2) const
Get the index associated to a pair of states.
Definition: AAIndex2Entry.h:95
The Alphabet interface.
Definition: Alphabet.h:130
AAIndex2Entry(std::istream &input, bool sym=true)
Create a new AAIndex2Entry from an input stream.
const Alphabet * getAlphabet() const
Get the alphabet associated to this index.
Definition: AAIndex2Entry.h:91
This alphabet is used to deal with proteins.
Create a AlphabetIndex2 object from an AAIndex2 entry.
Definition: AAIndex2Entry.h:52
LinearMatrix< double > property_
Definition: AAIndex2Entry.h:56
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.
bool isSymmetric() const
LinearMatrix< double > * getIndexMatrix() const
An alphabet exception thrown when trying to specify a bad int to the alphabet.
AAIndex2Entry & operator=(const AAIndex2Entry &index)
Definition: AAIndex2Entry.h:80
size_t getStateIndex(int state) const
AAIndex2Entry * clone() const
Definition: AAIndex2Entry.h:93
const ProteicAlphabet * alpha_
Definition: AAIndex2Entry.h:57