bpp-seq  2.2.0
Transliterator.h
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1 //
2 // File: Transliterator.h
3 // Created by: Julien Dutheil
4 // Created on: Sun Oct 12 14:25:25 2003
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
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 _TRANSLITERATOR_H_
41 #define _TRANSLITERATOR_H_
42 
43 #include "Alphabet/Alphabet.h"
44 #include "Sequence.h"
45 
46 namespace bpp
47 {
48 
53 {
54  public:
56  virtual ~Transliterator() {}
57 
58  public:
59 
65  virtual const Alphabet * getSourceAlphabet() const = 0;
66 
72  virtual const Alphabet * getTargetAlphabet() const = 0;
73 
82  virtual int translate(int state) const throw (BadIntException, Exception) = 0;
83 
92  virtual std::string translate(const std::string & state) const throw (BadCharException, Exception) = 0;
93 
102  virtual Sequence * translate(const Sequence & sequence) const throw (AlphabetMismatchException, Exception) = 0;
103 };
104 
109  public virtual Transliterator
110 {
111  public:
114 
115  public:
116 
125  virtual int reverse(int state) const throw (BadIntException, Exception) = 0;
126 
135  virtual std::string reverse(const std::string & state) const throw (BadCharException, Exception) = 0;
136 
145  virtual Sequence * reverse(const Sequence & sequence) const throw (AlphabetMismatchException, Exception) = 0;
146 };
147 
152  public virtual Transliterator
153 {
154  public:
157 
158  public:
159  virtual int translate(int state) const throw (BadIntException, Exception) = 0;
160  virtual std::string translate(const std::string & state) const throw (BadCharException, Exception) = 0;
161  virtual Sequence * translate(const Sequence & sequence) const throw (AlphabetMismatchException, Exception);
162 };
163 
168  public ReverseTransliterator,
170 {
171  public:
174 
175  public:
176  //These two redeclarations must be here because of the multiple inheritance.
177  virtual const Alphabet * getSourceAlphabet() const = 0;
178  virtual const Alphabet * getTargetAlphabet() const = 0;
179  virtual int reverse(int state) const throw (BadIntException, Exception) = 0;
180  virtual std::string reverse(const std::string & state) const throw (BadCharException, Exception) = 0;
181  virtual Sequence * reverse(const Sequence & sequence) const throw (AlphabetMismatchException, Exception);
182 };
183 
184 } //end of namespace bpp.
185 
186 #endif //_TRANSLITERATOR_H_
187 
This interface is used when translating a sequence from an alphabet to another: it gives the translat...
virtual int reverse(int state) const =0
Translate a given state coded as a int from target alphabet to source alphabet.
An alphabet exception thrown when trying to specify a bad char to the alphabet.
This alphabet is used to deal NumericAlphabet.
Partial implementation of the Transliterator interface.
The Alphabet interface.
Definition: Alphabet.h:130
virtual const Alphabet * getSourceAlphabet() const =0
Get the source alphabet.
virtual int translate(int state) const =0
Translate a given state coded as a int from source alphabet to target alphabet.
virtual const Alphabet * getSourceAlphabet() const =0
Get the source alphabet.
virtual int translate(int state) const =0
Translate a given state coded as a int from source alphabet to target alphabet.
The sequence interface.
Definition: Sequence.h:74
virtual int reverse(int state) const =0
Translate a given state coded as a int from target alphabet to source alphabet.
virtual const Alphabet * getTargetAlphabet() const =0
Get the target alphabet.
An alphabet exception thrown when trying to specify a bad int to the alphabet.
Exception thrown when two alphabets do not match.
virtual const Alphabet * getTargetAlphabet() const =0
Get the target alphabet.
Partial implementation of the ReverseTransliterator interface.
The same as previous, but can perform the reverse translation, eg: RNA -> DNA and DNA -> RNA;...
virtual ~Transliterator()