bpp-seq  2.2.0
DefaultAlphabet.cpp
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1 //
2 // File: DefaultAlphabet.cpp
3 // Authors: Julien Dutheil
4 // Sylvain Gaillard
5 // Created on: 2005
6 //
7 
8 /*
9 Copyright or © or Copr. Bio++ Development Team, (November 17, 2004)
10 
11 This software is a computer program whose purpose is to provide classes
12 for sequences analysis.
13 
14 This software is governed by the CeCILL license under French law and
15 abiding by the rules of distribution of free software. You can use,
16 modify and/ or redistribute the software under the terms of the CeCILL
17 license as circulated by CEA, CNRS and INRIA at the following URL
18 "http://www.cecill.info".
19 
20 As a counterpart to the access to the source code and rights to copy,
21 modify and redistribute granted by the license, users are provided only
22 with a limited warranty and the software's author, the holder of the
23 economic rights, and the successive licensors have only limited
24 liability.
25 
26 In this respect, the user's attention is drawn to the risks associated
27 with loading, using, modifying and/or developing or reproducing the
28 software by the user in light of its specific status of free software,
29 that may mean that it is complicated to manipulate, and that also
30 therefore means that it is reserved for developers and experienced
31 professionals having in-depth computer knowledge. Users are therefore
32 encouraged to load and test the software's suitability as regards their
33 requirements in conditions enabling the security of their systems and/or
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35 same conditions as regards security.
36 
37 The fact that you are presently reading this means that you have had
38 knowledge of the CeCILL license and that you accept its terms.
39 */
40 
41 
42 #include "DefaultAlphabet.h"
43 #include "AlphabetState.h"
44 #include <Bpp/Text/TextTools.h>
45 
46 using namespace bpp;
47 
49  chars_("ABCDEFGHIJKLMNOPQRSTUVWXYZ1234567890.?")
50 {
51  // Alphabet content definition
52  registerState(new AlphabetState(-1, "-", "Gap"));
53 
54  for (size_t i = 0; i < chars_.size(); i++)
55  {
56  registerState(new AlphabetState(static_cast<int>(i), TextTools::toString(chars_[i]), ""));
57  }
58 }
59 
This is the base class to describe states in an Alphabet.
Definition: AlphabetState.h:54
This alphabet is used to deal NumericAlphabet.
void registerState(AlphabetState *st)
Add a state to the Alphabet.