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/*
* Copyright (C) 2009-2012 Simon A. Berger
*
* This file is part of papara.
*
* papara is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
*
* papara is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with papara. If not, see <http://www.gnu.org/licenses/>.
*/
#ifndef __pairwise_seq_distance_h
#define __pairwise_seq_distance_h
// under certain circumstances gcc produces more consistent performance when the heavy-lifting is done in included code. maybe due to better optimization inside a compilation unit.
#ifdef PWDIST_INLINE
#define PSD_DECLARE_INLINE inline
#include "pairwise_seq_distance.cpp"
#else
#include <cstddef>
#include <vector>
#include <stdint.h>
#include "ivymike/tdmatrix.h"
namespace ivy_mike {
class scoring_matrix;
}
bool pairwise_seq_distance( const std::vector< std::vector<uint8_t> > &seq_raw1, const std::vector< std::vector<uint8_t> > &seq_raw2, bool identical, ivy_mike::tdmatrix<int> &out_scores, const ivy_mike::scoring_matrix &sm, const int gap_open, const int gap_extend, const size_t n_thread, const size_t block_size );
#endif
inline bool pairwise_seq_distance( const std::vector< std::vector<uint8_t> > &seq_raw, ivy_mike::tdmatrix<int> &out_scores, const ivy_mike::scoring_matrix &sm, const int gap_open, const int gap_extend, const size_t n_thread, const size_t block_size ) {
return pairwise_seq_distance( seq_raw, seq_raw, true, out_scores, sm, gap_open, gap_extend, n_thread, block_size );
}
#endif