/****
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 <memory>
#include <thread>
#include "basic/config.h"
#include "util/io/file.h"
#include "util/text_buffer.h"
#include "daa_file.h"
#include "util/binary_buffer.h"
#include "output/output_format.h"
#include "legacy/util/task_queue.h"
#include "stats/score_matrix.h"
#include "data/taxonomy.h"
#include "daa_write.h"
#include "run/config.h"
#include "daa_record.h"
#include "util/log_stream.h"

using std::thread;
using std::unique_ptr;
using std::vector;
using std::endl;

const unsigned view_buf_size = 32;

struct ViewWriter
{
	ViewWriter() :
		f_(new File(config.output_file, "wb", File::Flags::TREAT_BLANK_AS_STDOUT, config.compressor()))
	{ }
	void operator()(TextBuffer &buf)
	{
		f_->write(buf.data(), buf.size());
		buf.clear();
	}
	~ViewWriter()
	{
		f_->close();
	}
	unique_ptr<File> f_;
};

struct ViewFetcher
{
	ViewFetcher(DAAFile &daa) :
		daa(daa)
	{ }
	bool operator()()
	{
		n = 0;
		for (unsigned i = 0; i<view_buf_size; ++i)
			if (!daa.read_query_buffer(buf[i], query_num)) {
				query_num -= n - 1;
				return false;
			}
			else
				++n;
		query_num -= n - 1;
		return true;
	}
	BinaryBuffer buf[view_buf_size];
	unsigned n;
	size_t query_num;
	DAAFile &daa;
};

void view_query(DAA_query_record &r, TextBuffer &out, OutputFormat &format, const Search::Config& cfg)
{
	unique_ptr<OutputFormat> f(format.clone());
	size_t seek_pos;
	Output::Info info{ SeqInfo { (BlockId)r.query_num, (OId)r.query_num, r.query_name.c_str(), "", (Loc)r.query_len(), r.query_seq.source(), Sequence() },
		false, nullptr, out, Util::Seq::AccessionParsing(), r.file().db_seqs(), r.file().db_letters() };
	if (format == OutputFormat::daa)
		seek_pos = write_daa_query_record(out, r.query_name.c_str(), r.query_seq.source());
	else
		f->print_query_intro(info);
	
	DAA_query_record::Match_iterator i = r.begin();
	const unsigned top_score = i.good() ? i->score : 0;
	for (; i.good(); ++i) {
		if (i->frame > 2 && config.forwardonly)
			continue;
		if (!config.output_range(i->hit_num, i->score, top_score, cfg.max_target_seqs))
			break;
		if (format == OutputFormat::daa)
			write_daa_record(out, *i, i->subject_id);
		else
			f->print_match(i->context(), info);
	}
	if (format == OutputFormat::daa)
		finish_daa_query_record(out, seek_pos);
	else
		f->print_query_epilog(info);
	
}

void view_worker(DAAFile *daa, ViewWriter *writer, TaskQueue<TextBuffer, ViewWriter> *queue, OutputFormat *format, Search::Config* cfg)
{
	
	try {
		size_t n;
		ViewFetcher query_buf(*daa);
		TextBuffer *buffer = 0;
		while (queue->get(n, buffer, query_buf)) {
			for (unsigned j = 0; j < query_buf.n; ++j) {
				DAA_query_record r(*daa, query_buf.buf[j], query_buf.query_num + j);
				view_query(r, *buffer, *format, *cfg);
			}
			queue->push(n);
		}
	}
	catch (std::exception &e) {
		printf("%s\n", e.what());
		std::terminate();
	}
}

void view_daa()
{
	TaskTimer timer("Loading subject IDs");
	DAAFile daa(config.daa_file);
	if (align_mode.input_sequence_type == SequenceType::nucleotide)
		input_value_traits = nucleotide_traits;
	score_matrix = ScoreMatrix(daa.score_matrix(), daa.gap_open_penalty(), daa.gap_extension_penalty(), 0, 1, daa.db_letters());
	timer.finish();

	*message_stream << "Scoring parameters: " << score_matrix << endl;
	*log_stream << "Build version = " << daa.diamond_build() << endl;
	*message_stream << "DB sequences = " << daa.db_seqs() << endl;
	*message_stream << "DB sequences used = " << daa.db_seqs_used() << endl;
	*message_stream << "DB letters = " << daa.db_letters() << endl;

	std::unique_ptr<std::vector<BitVector>> target_seed_hits;
	Search::Config cfg(target_seed_hits);
	cfg.db_seqs = daa.db_seqs();
	cfg.db_letters = daa.db_letters();
	taxonomy.init();

	timer.go("Generating output");
	ViewWriter writer;
	if (*cfg.output_format == OutputFormat::daa)
		init_daa(*writer.f_);

	BinaryBuffer buf;
	size_t query_num;
	if (daa.read_query_buffer(buf, query_num)) {
		DAA_query_record r(daa, buf, query_num);
		TextBuffer out;
		view_query(r, out, *cfg.output_format, cfg);

		cfg.output_format->print_header(*writer.f_, daa.mode(), daa.score_matrix(), daa.gap_open_penalty(), daa.gap_extension_penalty(), daa.evalue(), r.query_name.c_str(), (unsigned)r.query_len());
		writer(out);

		vector<thread> threads;
		TaskQueue<TextBuffer, ViewWriter> queue(3 * config.threads_, writer);
		for (int i = 0; i < config.threads_; ++i)
			threads.emplace_back(view_worker, &daa, &writer, &queue, cfg.output_format.get(), &cfg);
		for (auto &t : threads)
			t.join();
	}
	else {
		TextBuffer out;
		cfg.output_format->print_header(*writer.f_, daa.mode(), daa.score_matrix(), daa.gap_open_penalty(), daa.gap_extension_penalty(), daa.evalue(), "", 0);
		writer(out);
	}

	if (*cfg.output_format == OutputFormat::daa)
		finish_daa(*writer.f_, daa);
	else
		cfg.output_format->print_footer(*writer.f_);
}