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CaseMaskedAlphabet.h
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1 //
2 // File: CaseMaskedAlphabet.h
3 // Created by: Julien Dutheil
4 // Created on: Sun Sep 05 2010
5 //
6 
7 /*
8 Copyright or © or Copr. CNRS, (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 
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 #ifndef _CASEMASKEDALPHABET_H_
41 #define _CASEMASKEDALPHABET_H_
42 
43 #include "LetterAlphabet.h"
44 
45 //From the STL:
46 #include <string>
47 
48 namespace bpp
49 {
50 
59 class CaseMaskedAlphabet :
60  public LetterAlphabet
61 {
62  public:
63  const LetterAlphabet* nocaseAlphabet_;
64 
65  public:
66  CaseMaskedAlphabet(const LetterAlphabet* nocaseAlphabet);
67  CaseMaskedAlphabet(const CaseMaskedAlphabet& cma) :
68  LetterAlphabet(cma), nocaseAlphabet_(cma.nocaseAlphabet_) {}
69  CaseMaskedAlphabet& operator=(const CaseMaskedAlphabet& cma) {
70  LetterAlphabet::operator=(cma);
71  nocaseAlphabet_ = cma.nocaseAlphabet_;
72  return *this;
73  }
74 
75  public:
76  unsigned int getSize() const { return nocaseAlphabet_->getSize(); }
77  unsigned int getNumberOfTypes() const { return nocaseAlphabet_->getNumberOfTypes(); }
78  std::string getAlphabetType() const { return "Default alphabet"; }
79  int getUnknownCharacterCode() const { return nocaseAlphabet_->getUnknownCharacterCode(); }
80  bool isUnresolved(int state) const { return nocaseAlphabet_->isUnresolved(state); }
81  bool isUnresolved(const std::string& state) const { return nocaseAlphabet_->isUnresolved(state); }
82 
83  const Alphabet* getUnmaskedAlphabet() const { return nocaseAlphabet_; }
84 
85  bool isMasked(int state) const { return state >= 100; }
86  bool isMasked(const std::string& state) const {
87  char c = state.c_str()[0];
88  return isMasked(c);
89  }
90  bool isMasked(char state) const {
91  return isalpha(state) && !isupper(state);
92  }
93 
101  int getMaskedEquivalentState(int state) const throw (BadIntException);
110  const std::string getMaskedEquivalentState(const std::string& state) const throw (BadCharException, BadIntException);
111 
112 };
113 
114 } // end of namespace bpp
115 
116 #endif //_CASEMASKEDALPHABET_H_
117