/****
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

#include "../util/simd/dispatch.h"
#include "../stage2.h"
#include "kernel.h"
#include "kernel_self.h"
#include "kernel_mutual_cov.h"
#include "kernel_lin.h"

namespace Search { namespace DISPATCH_ARCH {

typedef void Stage1KernelPackedLoc(const ::PackedLoc*, ::uint_fast32_t, const ::PackedLoc*, ::uint_fast32_t, ::Search::WorkSet&);
typedef void Stage1KernelPackedLocId(const ::PackedLocId*, ::uint_fast32_t, const ::PackedLocId*, ::uint_fast32_t, ::Search::WorkSet&);

static Stage1KernelPackedLocId* stage1_dispatch(const Search::Config* cfg, PackedLocId) {
	if (config.lin_stage1_query) {
		return cfg->min_length_ratio > 0.0 ? stage1_mutual_cov_query_lin : stage1_query_lin_ranked;
	}
	if (cfg->lin_stage1_target) {
		return cfg->min_length_ratio > 0.0 ? stage1_mutual_cov_target_lin : stage1_target_lin<PackedLocId>;
	}
	if (cfg->min_length_ratio > 0.0) {
		return config.self && cfg->current_ref_block == 0 ? stage1_self_mutual_cov : stage1_mutual_cov;
	}
	if (config.self && cfg->current_ref_block == 0) {
		return stage1_self;
	}
	return stage1;
}

static Stage1KernelPackedLoc* stage1_dispatch(const Search::Config* cfg, PackedLoc) {
	return config.lin_stage1_query ? stage1_query_lin
		: (cfg->lin_stage1_target ? stage1_target_lin<PackedLoc>
			: (config.self && cfg->current_ref_block == 0 ? stage1_self<PackedLoc> : stage1<PackedLoc>));
}

void run_stage1(JoinIterator<PackedLoc>& it, Search::WorkSet* work_set, const Search::Config* cfg) {
	auto kernel = stage1_dispatch(cfg, PackedLoc());
	for (; it; ++it) {
		work_set->stats.inc(Statistics::SEEDS_HIT);
		kernel(it.r->begin(), (int32_t)it.r->size(), it.s->begin(), (int32_t)it.s->size(), *work_set);
	}
}

void run_stage1(JoinIterator<PackedLocId>& it, Search::WorkSet* work_set, const Search::Config* cfg) {
	auto kernel = stage1_dispatch(cfg, PackedLocId());
	for (; it; ++it) {
		work_set->stats.inc(Statistics::SEEDS_HIT);
		kernel(it.r->begin(), (int32_t)it.r->size(), it.s->begin(), (int32_t)it.s->size(), *work_set);
	}
}

}}

/*namespace Search {
	
DISPATCH_3V(run_stage1, JoinIterator<PackedLoc>&, it, Search::WorkSet*, work_set, const Search::Config*, cfg)
DISPATCH_3V(run_stage1, JoinIterator<PackedLocId>&, it, Search::WorkSet*, work_set, const Search::Config*, cfg)
DISPATCH_1(bool, keep_target_id, const Search::Config&, cfg)

}*/