| 1 | /* |
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| 2 | Copyright (c) 2006-2018 Elmar Pruesse <elmar.pruesse@ucdenver.edu> |
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| 3 | |
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| 4 | This file is part of SINA. |
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| 5 | SINA is free software: you can redistribute it and/or modify it under |
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| 6 | the terms of the GNU General Public License as published by the Free |
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| 7 | Software Foundation, either version 3 of the License, or (at your |
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| 8 | option) any later version. |
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| 9 | |
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| 10 | SINA is distributed in the hope that it will be useful, but WITHOUT ANY |
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| 11 | WARRANTY; without even the implied warranty of MERCHANTABILITY or |
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| 12 | FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License |
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| 13 | for more details. |
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| 14 | |
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| 15 | You should have received a copy of the GNU General Public License |
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| 16 | along with SINA. If not, see <http://www.gnu.org/licenses/>. |
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| 17 | |
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| 18 | Additional permission under GNU GPL version 3 section 7 |
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| 19 | |
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| 20 | If you modify SINA, or any covered work, by linking or combining it |
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| 21 | with components of ARB (or a modified version of that software), |
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| 22 | containing parts covered by the terms of the |
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| 23 | ARB-public-library-license, the licensors of SINA grant you additional |
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| 24 | permission to convey the resulting work. Corresponding Source for a |
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| 25 | non-source form of such a combination shall include the source code |
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| 26 | for the parts of ARB used as well as that of the covered work. |
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| 27 | */ |
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| 28 | |
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| 29 | #ifndef _ALIGNMENT_STATS_H_ |
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| 30 | #define _ALIGNMENT_STATS_H_ |
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| 31 | |
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| 32 | #include "aligned_base.h" |
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| 33 | |
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| 34 | #include <vector> |
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| 35 | #include <string> |
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| 36 | |
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| 37 | namespace sina { |
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| 38 | |
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| 39 | class alignment_stats { |
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| 40 | public: |
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| 41 | struct freqs { |
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| 42 | unsigned int num_a{0}; |
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| 43 | unsigned int num_g{0}; |
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| 44 | unsigned int num_c{0}; |
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| 45 | unsigned int num_u{0}; |
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| 46 | unsigned int num_mutations{0}; |
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| 47 | unsigned int num_transversions{0}; |
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| 48 | }; |
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| 49 | alignment_stats(); |
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| 50 | alignment_stats(std::string name_, |
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| 51 | unsigned int ntaxa, unsigned int alen, |
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| 52 | const unsigned int *na, const unsigned int *nc, const unsigned int *ng, |
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| 53 | const unsigned int *nu, const unsigned int *nM, const unsigned int *nT, |
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| 54 | std::vector<int> pairs_); |
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| 55 | |
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| 56 | const std::vector<float>& getWeights() const { return weights; } |
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| 57 | const std::vector<int>& getPairs() const { return pairs; } |
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| 58 | const aligned_base::matrix_type getSubstMatrix(double identity) const; |
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| 59 | int getWidth() const {return width;} |
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| 60 | std::string getName() const {return name;} |
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| 61 | private: |
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| 62 | std::string name; |
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| 63 | unsigned int num_taxa{0}; |
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| 64 | unsigned int width{0}; |
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| 65 | |
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| 66 | freqs global_freqs; |
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| 67 | std::vector<freqs> column_freqs; |
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| 68 | |
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| 69 | std::vector<int> pairs; |
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| 70 | |
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| 71 | std::vector<float> weights; |
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| 72 | float maxweight{0}, minweight{0}, sumweight{0}; |
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| 73 | int weighted_columns{0}; |
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| 74 | }; |
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| 75 | |
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| 76 | } // namespace sina |
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| 77 | #endif //_ALIGNMENT_STATS_H_ |
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| 78 | |
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| 79 | /* |
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| 80 | Local Variables: |
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| 81 | mode:c++ |
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| 82 | c-file-style:"stroustrup" |
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| 83 | c-file-offsets:((innamespace . 0)(inline-open . 0)(case-label . +)) |
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| 84 | indent-tabs-mode:nil |
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| 85 | fill-column:99 |
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| 86 | End: |
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| 87 | */ |
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| 88 | // vim: filetype=cpp:expandtab:shiftwidth=4:tabstop=8:softtabstop=4:encoding=utf-8:textwidth=99 : |
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