1 /**** 2 DIAMOND protein aligner 3 Copyright (C) 2013-2021 Max Planck Society for the Advancement of Science e.V. 4 Benjamin Buchfink 5 Eberhard Karls Universitaet Tuebingen 6 7 This program is free software: you can redistribute it and/or modify 8 it under the terms of the GNU General Public License as published by 9 the Free Software Foundation, either version 3 of the License, or 10 (at your option) any later version. 11 12 This program is distributed in the hope that it will be useful, 13 but WITHOUT ANY WARRANTY; without even the implied warranty of 14 MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the 15 GNU General Public License for more details. 16 17 You should have received a copy of the GNU General Public License 18 along with this program. If not, see <http://www.gnu.org/licenses/>. 19 ****/ 20 21 #pragma once 22 #include "../basic/value.h" 23 #include "../basic/diagonal_segment.h" 24 #include "../stats/hauser_correction.h" 25 26 //int xdrop_ungapped(const Letter *query, const Letter *subject, unsigned seed_len, unsigned &delta, unsigned &len); 27 //int xdrop_ungapped(const Letter *query, const Letter *subject, unsigned &delta, unsigned &len); 28 int xdrop_ungapped_right(const Letter *query, const Letter *subject, int &len); 29 int ungapped_window(const Letter* query, const Letter* subject, int window); 30 Diagonal_segment xdrop_ungapped(const Sequence &query, const Bias_correction &query_bc, const Sequence &subject, int qa, int sa); 31 Diagonal_segment xdrop_ungapped(const Sequence &query, const Sequence &subject, int qa, int sa); 32 int score_range(Sequence query, Sequence subject, int i, int j, int j_end); 33 int self_score(const Sequence& seq);