bpp-seq  2.2.0
Dcse.h
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1 //
2 // File: DCSE.h
3 // Created by: Julien Dutheil
4 // Created on: Wed Mar 3 2004
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
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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 _DCSE_H_
41 #define _DCSE_H_
42 
43 #include "AbstractIAlignment.h"
44 #include "../Sequence.h"
45 #include "../Container/SequenceContainer.h"
46 #include "../Container/AlignedSequenceContainer.h"
47 
48 namespace bpp
49 {
50 
60 class DCSE :
61  public AbstractIAlignment,
62  public virtual ISequence
63 {
64 
65  public:
66  DCSE() {};
67  virtual ~DCSE() {};
68 
69  public:
70 
76  void appendAlignmentFromStream(std::istream& input, SiteContainer& sc) const throw (Exception);
87  virtual SequenceContainer* readSequences(std::istream& input, const Alphabet* alpha) const throw (Exception) {
88  return readAlignment(input, alpha);
89  }
90  virtual SequenceContainer* readSequences(const std::string& path, const Alphabet* alpha) const throw (Exception) {
91  return readAlignment(path, alpha);
92  }
101  const std::string getFormatName() const;
102  const std::string getFormatDescription() const;
104 };
105 
106 } //end of namespace bpp.
107 
108 #endif // _DCSE_H_
109 
The SiteContainer interface.
Definition: SiteContainer.h:63
void appendAlignmentFromStream(std::istream &input, SiteContainer &sc) const
Append sequences to a container from a stream.
Definition: Dcse.cpp:52
virtual SequenceContainer * readSequences(std::istream &input, const Alphabet *alpha) const
Create a new container from a stream.
Definition: Dcse.h:87
This alphabet is used to deal NumericAlphabet.
Partial implementation of the IAlignment interface, dedicated to alignment readers.
The Alphabet interface.
Definition: Alphabet.h:130
virtual SequenceContainer * readSequences(const std::string &path, const Alphabet *alpha) const
Create a new container from a file.
Definition: Dcse.h:90
DCSE()
Definition: Dcse.h:66
Support for the Dedicated Comparative Sequence Editor format.
Definition: Dcse.h:60
const std::string getFormatName() const
Definition: Dcse.cpp:94
const std::string getFormatDescription() const
Definition: Dcse.cpp:96
virtual ~DCSE()
Definition: Dcse.h:67
The SequenceContainer interface.
virtual void readAlignment(std::istream &input, SiteContainer &sc) const
Add sequences to a container from a stream.
The ISequence interface.
Definition: ISequence.h:64