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ISequence.h
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1 //
2 // File: ISequence.h
3 // Created by: Guillaume Deuchst
4 // Julien Dutheil
5 // Created on: Wed Jul 30 2003
6 //
7 
8 
9 /*
10 Copyright or © or Copr. Bio++ Development Team, (November 17, 2004)
11 
12 This software is a computer program whose purpose is to provide classes
13 for sequences analysis.
14 
15 This software is governed by the CeCILL license under French law and
16 abiding by the rules of distribution of free software. You can use,
17 modify and/ or redistribute the software under the terms of the CeCILL
18 license as circulated by CEA, CNRS and INRIA at the following URL
19 "http://www.cecill.info".
20 
21 As a counterpart to the access to the source code and rights to copy,
22 modify and redistribute granted by the license, users are provided only
23 with a limited warranty and the software's author, the holder of the
24 economic rights, and the successive licensors have only limited
25 liability.
26 
27 In this respect, the user's attention is drawn to the risks associated
28 with loading, using, modifying and/or developing or reproducing the
29 software by the user in light of its specific status of free software,
30 that may mean that it is complicated to manipulate, and that also
31 therefore means that it is reserved for developers and experienced
32 professionals having in-depth computer knowledge. Users are therefore
33 encouraged to load and test the software's suitability as regards their
34 requirements in conditions enabling the security of their systems and/or
35 data to be ensured and, more generally, to use and operate it in the
36 same conditions as regards security.
37 
38 The fact that you are presently reading this means that you have had
39 knowledge of the CeCILL license and that you accept its terms.
40 */
41 
42 #ifndef _ISEQUENCE_H_
43 #define _ISEQUENCE_H_
44 
45 #include "IoSequence.h"
46 #include "../Sequence.h"
47 #include "../Container/SequenceContainer.h"
48 #include "../Container/SiteContainer.h"
49 #include <Bpp/Exceptions.h>
50 
51 //From the STL:
52 #include <iostream>
53 #include <string>
54 
55 namespace bpp
56 {
57 
64 class ISequence :
65  public virtual IOSequence
66 {
67  public:
68  ISequence() {}
69  virtual ~ISequence() {}
70 
71  public:
72 
81  virtual SequenceContainer* readSequences(std::istream& input, const Alphabet* alpha) const throw (Exception) = 0;
90  virtual SequenceContainer* readSequences(const std::string& path, const Alphabet* alpha) const throw (Exception) = 0;
91 
92 };
93 
99 class IAlignment:
100  public virtual IOSequence
101 {
102  public:
103  IAlignment() {}
104  virtual ~IAlignment() {}
105 
106  public:
107 
116  virtual SiteContainer* readAlignment(std::istream& input, const Alphabet* alpha) const throw (Exception) = 0;
125  virtual SiteContainer* readAlignment(const std::string& path, const Alphabet* alpha) const throw (Exception) = 0;
126 
127 };
128 
129 } //end of namespace bpp.
130 
131 #endif // _ISEQUENCE_H_
132