/****
DIAMOND protein sequence aligner
Copyright (C) 2012-2026 Benjamin J. Buchfink

This program 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.

This program 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 this program.  If not, see <http://www.gnu.org/licenses/>.
****/
// SPDX-License-Identifier: GPL-3.0-or-later

#pragma once
#include "query_mapper.h"
#include "dp/dp.h"

namespace ExtensionPipeline {
	namespace BandedSwipe {
		struct Target;
		struct Pipeline : public QueryMapper
		{
			Pipeline(size_t query_id, Search::Hit* begin, Search::Hit* end, DpStat& dp_stat, const Search::Config& cfg) :
				QueryMapper(query_id, begin, end, cfg),
				dp_stat(dp_stat)
			{}
			Target& target(size_t i);
			virtual void run(Statistics& stat, const Search::Config& cfg) override;
			void run_swipe(bool score_only);
			void range_ranking(const int64_t max_target_seqs);
			DpStat& dp_stat;
		};
	}
}
