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