bpp-seq  2.2.0
CaseMaskedAlphabet.h
Go to the documentation of this file.
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
30  professionals having in-depth computer knowledge. Users are therefore
31  encouraged to load and test the software's suitability as regards their
32  requirements in conditions enabling the security of their systems and/or
33  data to be ensured and, more generally, to use and operate it in the
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 
60  public LetterAlphabet
61  {
62  public:
64 
65  public:
66  CaseMaskedAlphabet(const LetterAlphabet* nocaseAlphabet);
67 
70 
74  return *this;
75  }
76 
78  {
79  return new CaseMaskedAlphabet(*this);
80  }
81 
82  public:
83  unsigned int getSize() const { return nocaseAlphabet_->getSize(); }
84  unsigned int getNumberOfTypes() const { return nocaseAlphabet_->getNumberOfTypes(); }
85  std::string getAlphabetType() const { return "Default alphabet"; }
87  bool isUnresolved(int state) const { return nocaseAlphabet_->isUnresolved(state); }
88  bool isUnresolved(const std::string& state) const { return nocaseAlphabet_->isUnresolved(state); }
89 
90  const Alphabet* getUnmaskedAlphabet() const { return nocaseAlphabet_; }
91 
92  bool isMasked(int state) const { return state >= 100; }
93  bool isMasked(const std::string& state) const {
94  char c = state.c_str()[0];
95  return isMasked(c);
96  }
97  bool isMasked(char state) const {
98  return isalpha(state) && !isupper(state);
99  }
100 
108  int getMaskedEquivalentState(int state) const throw (BadIntException);
117  const std::string getMaskedEquivalentState(const std::string& state) const throw (BadCharException, BadIntException);
118 
119  };
120 
121 } // end of namespace bpp
122 
123 #endif //_CASEMASKEDALPHABET_H_
124 
LetterAlphabet & operator=(const LetterAlphabet &bia)
An alphabet exception thrown when trying to specify a bad char to the alphabet.
unsigned int getNumberOfTypes() const
Get the number of distinct states in alphabet (e.g. return 15 for DNA alphabet). This is the number o...
This alphabet is used to deal NumericAlphabet.
const Alphabet * getUnmaskedAlphabet() const
virtual bool isUnresolved(int state) const =0
virtual unsigned int getSize() const =0
Get the number of resolved states in the alphabet (e.g. return 4 for DNA alphabet). This is the method you&#39;ll need in most cases.
The Alphabet interface.
Definition: Alphabet.h:130
CaseMaskedAlphabet(const CaseMaskedAlphabet &cma)
bool isMasked(int state) const
bool isUnresolved(const std::string &state) const
Specialized partial implementation of Alphabet using single letters.
std::string getAlphabetType() const
Identification method.
bool isUnresolved(int state) const
int getMaskedEquivalentState(int state) const
Get the masked state equivalent to the input one.
CaseMaskedAlphabet & operator=(const CaseMaskedAlphabet &cma)
unsigned int getSize() const
Get the number of resolved states in the alphabet (e.g. return 4 for DNA alphabet). This is the method you&#39;ll need in most cases.
CaseMaskedAlphabet * clone() const
bool isMasked(char state) const
An alphabet exception thrown when trying to specify a bad int to the alphabet.
bool isMasked(const std::string &state) const
const LetterAlphabet * nocaseAlphabet_
virtual unsigned int getNumberOfTypes() const =0
Get the number of distinct states in alphabet (e.g. return 15 for DNA alphabet). This is the number o...
CaseMaskedAlphabet(const LetterAlphabet *nocaseAlphabet)
Case-sensitive letter alphabet.
virtual int getUnknownCharacterCode() const =0