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comparison egglib/egglib-2.1.5/include/egglib-cpp/CharMatrix.hpp @ 1:420b57c3c185 draft

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author dereeper
date Fri, 10 Jul 2015 04:39:30 -0400
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0:3e19d0dfcf3e 1:420b57c3c185
1 /*
2 Copyright 2009 Stéphane De Mita, Mathieu Siol
3
4 This file is part of the EggLib library.
5
6 EggLib is free software: you can redistribute it and/or modify
7 it under the terms of the GNU General Public License as published by
8 the Free Software Foundation, either version 3 of the License, or
9 (at your option) any later version.
10
11 EggLib is distributed in the hope that it will be useful,
12 but WITHOUT ANY WARRANTY; without even the implied warranty of
13 MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
14 GNU General Public License for more details.
15
16 You should have received a copy of the GNU General Public License
17 along with EggLib. If not, see <http://www.gnu.org/licenses/>.
18 */
19
20 #ifndef EGGLIB_CHARMATRIX_HPP
21 #define EGGLIB_CHARMATRIX_HPP
22
23
24 namespace egglib {
25
26 /** \brief Interface for classes usable as a square matrix of characters
27 *
28 * \ingroup core
29 *
30 */
31 class CharMatrix {
32
33 public:
34
35 /** \brief Gets number of rows or sequences
36 *
37 */
38 virtual unsigned int numberOfSequences() const = 0;
39
40
41 /** \brief Gets number of columns or sites
42 *
43 */
44 virtual unsigned int numberOfSites() const = 0;
45
46
47 /** \brief Gets the character at a given position
48 *
49 * The accessor should be "fast" and does not guarantee to
50 * perform out-of-bounds checks
51 *
52 */
53 virtual char character(unsigned int sequence, unsigned int site) const = 0;
54
55
56 /** \brief Gets population index
57 *
58 */
59 virtual unsigned int populationLabel(unsigned int row) const = 0;
60
61
62 /** \brief Get site position
63 *
64 */
65 virtual double sitePosition(unsigned int column) const = 0;
66
67 };
68 }
69
70 #endif