bpp-seq  2.2.0
OSequence.h
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1 //
2 // File: OSequence.h
3 // Created by: Guillaume Deuchst
4 // Julien Dutheil
5 // Created on: Tue Aug 21 2003
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
34 data to be ensured and, more generally, to use and operate it in the
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 #ifndef _OSEQUENCE_H_
42 #define _OSEQUENCE_H_
43 
44 #include "../Container/SequenceContainer.h"
45 #include "../Container/SiteContainer.h"
46 #include "IoSequence.h"
47 
48 #include <Bpp/Exceptions.h>
49 
50 namespace bpp
51 {
52 
58  class OSequence:
59  public virtual IOSequence
60  {
61  public:
62  OSequence() {}
63  virtual ~OSequence() {}
64 
65  public:
66 
74  virtual void writeSequences(std::ostream& output, const SequenceContainer& sc) const throw (Exception) = 0;
75 
85  virtual void writeSequences(const std::string& path, const SequenceContainer & sc, bool overwrite) const throw (Exception) = 0;
86 
87  };
88 
89 
95  class OAlignment:
96  public virtual IOSequence
97  {
98  public:
100  virtual ~OAlignment() {}
101 
102  public:
103 
111  virtual void writeAlignment(std::ostream& output, const SiteContainer& sc) const throw (Exception) = 0;
112 
122  virtual void writeAlignment(const std::string& path, const SiteContainer& sc, bool overwrite) const throw (Exception) = 0;
123 
124  };
125 } //end of namespace bpp.
126 
127 #endif // _OSEQUENCE_H_
128 
The OAlignment interface.
Definition: OSequence.h:95
The OSequence interface.
Definition: OSequence.h:58
The SiteContainer interface.
Definition: SiteContainer.h:63
This alphabet is used to deal NumericAlphabet.
virtual ~OSequence()
Definition: OSequence.h:63
virtual void writeAlignment(std::ostream &output, const SiteContainer &sc) const =0
Write a container to a stream.
virtual void writeSequences(std::ostream &output, const SequenceContainer &sc) const =0
Write a container to a stream.
virtual ~OAlignment()
Definition: OSequence.h:100
The SequenceContainer interface.
The IOSequence interface.
Definition: IoSequence.h:57