/****
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 <algorithm>
#include <thread>
#include <utility>
#include <numeric>
#include <atomic>
#include "../dp.h"
#include "swipe.h"
#include "target_iterator.h"
#include "util/data_structures/mem_buffer.h"
#include "util/simd/dispatch.h"
#include "../score_vector_int16.h"
#include "../score_vector_int8.h"

using std::list;
using std::thread;
using std::atomic;
using std::pair;
using std::vector;
using std::runtime_error;

namespace DISPATCH_ARCH {

template<typename Sv>
struct Banded3FrameSwipeMatrix
{

	struct ColumnIterator
	{
		ColumnIterator(Sv* hgap_front, Sv* score_front) :
			hgap_ptr_(hgap_front),
			score_ptr_(score_front)
		{
			sm4 = ScoreTraits<Sv>::zero();
			sm3 = *score_ptr_;
			sm2 = *(score_ptr_ + 1);
		}
		inline void operator++()
		{
			++hgap_ptr_; ++score_ptr_;
			sm4 = sm3;
			sm3 = sm2;
			sm2 = *(score_ptr_ + 1);
		}
		inline Sv hgap() const
		{
			return *(hgap_ptr_ + 3);
		}
		inline void set_hgap(const Sv& x)
		{
			*hgap_ptr_ = x;
		}
		inline void set_score(const Sv& x)
		{
			*score_ptr_ = x;
		}
		void set_zero()
		{
			*(score_ptr_ - 1) = ScoreTraits<Sv>::zero();
			*(score_ptr_ - 2) = ScoreTraits<Sv>::zero();
			*(score_ptr_ - 3) = ScoreTraits<Sv>::zero();
		}
		Sv *hgap_ptr_, *score_ptr_;
		Sv sm4, sm3, sm2;
	};

	Banded3FrameSwipeMatrix(size_t band, size_t cols) :
		band_(band)
	{
		hgap_.resize(band + 3);
		score_.resize(band + 1);
		std::fill(hgap_.begin(), hgap_.end(), Sv());
		std::fill(score_.begin(), score_.end(), Sv());
	}

	inline ColumnIterator begin(size_t offset, size_t col)
	{
		return ColumnIterator(&hgap_[offset], &score_[offset]);
	}

	size_t band() const
	{
		return band_;
	}

private:
	const size_t band_;
	MemBuffer<Sv> hgap_, score_;

};

template<typename Sv>
struct Banded3FrameSwipeTracebackMatrix
{

	typedef typename ScoreTraits<Sv>::Score Score;

	struct ColumnIterator
	{
		ColumnIterator(Sv* hgap_front, Sv* score_front, Sv* score_front1) :
			hgap_ptr_(hgap_front),
			score_ptr_(score_front),
			score_ptr1_(score_front1)
		{
			sm4 = ScoreTraits<Sv>::zero();
			sm3 = *(score_ptr_++);
			sm2 = *(score_ptr_);
		}
		inline void operator++()
		{
			++hgap_ptr_; ++score_ptr_; ++score_ptr1_;
			sm4 = sm3;
			sm3 = sm2;
			sm2 = *score_ptr_;
		}
		inline Sv hgap() const
		{
			return *(hgap_ptr_ + 3);
		}
		inline void set_hgap(const Sv& x)
		{
			*hgap_ptr_ = x;
		}
		inline void set_score(const Sv& x)
		{
			*score_ptr1_ = x;
		}
		void set_zero()
		{
			*(score_ptr1_ - 1) = ScoreTraits<Sv>::zero();
			*(score_ptr1_ - 2) = ScoreTraits<Sv>::zero();
			*(score_ptr1_ - 3) = ScoreTraits<Sv>::zero();
		}
		Sv* hgap_ptr_, *score_ptr_, *score_ptr1_;
		Sv sm4, sm3, sm2;
	};

	struct TracebackIterator
	{
		TracebackIterator(const Score *score, size_t band, int frame, int i, int j) :
			band_(band),
			score_(score),
			frame(frame),
			i(i),
			j(j)
		{
			assert(i >= 0 && j >= 0);
		}
		Score score() const
		{
			return *score_;
		}
		Score sm3() const
		{
			return *(score_ - (band_ + 1) * ScoreTraits<Sv>::CHANNELS);
		}
		Score sm4() const
		{
			return *(score_ - (band_ + 2) * ScoreTraits<Sv>::CHANNELS);
		}
		Score sm2() const
		{
			return *(score_ - band_ * ScoreTraits<Sv>::CHANNELS);
		}
		void walk_diagonal()
		{
			score_ -= (band_ + 1) * ScoreTraits<Sv>::CHANNELS;
			--i;
			--j;
			assert(i >= -1 && j >= -1);
		}
		void walk_forward_shift()
		{
			score_ -= (band_ + 2) * ScoreTraits<Sv>::CHANNELS;
			--i;
			--j;
			--frame;
			if (frame == -1) {
				frame = 2;
				--i;
			}
			assert(i >= -1 && j >= -1);
		}
		void walk_reverse_shift()
		{
			score_ -= band_ * ScoreTraits<Sv>::CHANNELS;
			--i;
			--j;
			++frame;
			if (frame == 3) {
				frame = 0;
				++i;
			}
			assert(i >= -1 && j >= -1);
		}
		pair<EditOperation, int> walk_gap(int d0, int d1)
		{
			const int i0 = std::max(d0 + j, 0), j0 = std::max(i - d1, -1);
			const Score *h = score_ - (band_ - 2) * ScoreTraits<Sv>::CHANNELS, *h0 = score_ - (j - j0) * (band_ - 2) * ScoreTraits<Sv>::CHANNELS;
			const Score *v = score_ - 3 * ScoreTraits<Sv>::CHANNELS, *v0 = score_ - (i - i0 + 1) * 3 * ScoreTraits<Sv>::CHANNELS;
			const Score score = this->score();
			const Score e = score_matrix.gap_extend();
			Score g = score_matrix.gap_open() + e;
			int l = 1;
			while (v > v0 && h > h0) {
				if (score + g == *h) {
					walk_hgap(h, l);
					return std::make_pair(op_deletion, l);
				}
				else if (score + g == *v) {
					walk_vgap(v, l);
					return std::make_pair(op_insertion, l);
				}
				h -= (band_ - 2) * ScoreTraits<Sv>::CHANNELS;
				v -= 3 * ScoreTraits<Sv>::CHANNELS;
				++l;
				g += e;
			}
			while (v > v0) {
				if (score + g == *v) {
					walk_vgap(v, l);
					return std::make_pair(op_insertion, l);
				}
				v -= 3 * ScoreTraits<Sv>::CHANNELS;
				++l;
				g += e;
			}
			while (h > h0) {
				if (score + g == *h) {
					walk_hgap(h, l);
					return std::make_pair(op_deletion, l);
				}
				h -= (band_ - 2) * ScoreTraits<Sv>::CHANNELS;
				++l;
				g += e;
			}
			throw runtime_error("Traceback error.");
		}
		void walk_hgap(const Score *h, int l)
		{
			score_ = h;
			j -= l;
			assert(i >= -1 && j >= -1);
		}
		void walk_vgap(const Score *v, int l)
		{
			score_ = v;
			i -= l;
			assert(i >= -1 && j >= -1);
		}
		const size_t band_;
		const Score *score_;
		int frame, i, j;
	};

	TracebackIterator traceback(size_t col, int i0, int j, int dna_len, size_t channel, Score score) const
	{
		const int i_ = std::max(-i0, 0) * 3,
			i1 = (int)std::min(band_, size_t(dna_len - 2 - i0 * 3));
		const Score *s = (Score*)(&score_[col*(band_ + 1) + i_]) + channel;
		for (int i = i_; i < i1; ++i, s += ScoreTraits<Sv>::CHANNELS)
			if (*s == score)
				return TracebackIterator(s, band_, i % 3, i0 + i / 3, j);
		throw runtime_error("Trackback error.");
	}

	Banded3FrameSwipeTracebackMatrix(size_t band, size_t cols) :
		band_(band)
	{
		hgap_.resize(band + 3);
		score_.resize((band + 1) * (cols + 1));
		const Sv z = Sv();
		std::fill(hgap_.begin(), hgap_.end(), z);
		std::fill(score_.begin(), score_.begin() + band + 1, z);
		for (size_t i = 0; i < cols; ++i)
			score_[i*(band + 1) + band] = z;
	}

	inline ColumnIterator begin(size_t offset, size_t col)
	{
		return ColumnIterator(&hgap_[offset], &score_[col*(band_ + 1) + offset], &score_[(col + 1)*(band_ + 1) + offset]);
	}

	size_t band() const
	{
		return band_;
	}

private:
	const size_t band_;
	MemBuffer<Sv> hgap_;
	MemBuffer<Sv> score_;

};

template<typename Sv, typename Traceback>
struct Banded3FrameSwipeMatrixRef
{
};

template<typename Sv>
struct Banded3FrameSwipeMatrixRef<Sv, DP::Traceback>
{
	typedef Banded3FrameSwipeTracebackMatrix<Sv> type;
};

template<typename Sv>
struct Banded3FrameSwipeMatrixRef<Sv, DP::ScoreOnly>
{
	typedef Banded3FrameSwipeMatrix<Sv> type;
};

template<typename Sv>
Hsp traceback(Sequence *query, Strand strand, int dna_len, const Banded3FrameSwipeTracebackMatrix<Sv> &dp, const DpTarget &target, int d_begin,
	typename ScoreTraits<Sv	>::Score max_score, double evalue, int max_col, int channel, int i0, int i1)
{
	typedef typename ScoreTraits<Sv>::Score Score;
	const int j0 = i1 - (target.d_end - 1), d1 = target.d_end;
	typename Banded3FrameSwipeTracebackMatrix<Sv>::TracebackIterator it(dp.traceback(max_col + 1, i0 + max_col, j0 + max_col, dna_len, channel, max_score));
	
	Hsp out(true);
	out.swipe_target = target.target_idx;
	out.score = ScoreTraits<Sv>::int_score(max_score) * config.cbs_matrix_scale;
	out.bit_score = score_matrix.bitscore(out.score);
	out.evalue = evalue;
	out.transcript.reserve(size_t(out.score * config.transcript_len_estimate));

	out.set_end(it.i + 1, it.j + 1, Frame(strand, it.frame), dna_len);

	while (it.score() > ScoreTraits<Sv>::zero_score()) {
		const Letter q = query[it.frame][it.i], s = target.seq[it.j];
		const Score m = score_matrix(q, s), score = it.score();
		if (score == it.sm3() + m) {
			out.push_match(q, s, m > (Score)0);
			it.walk_diagonal();
		}
		else if (score == it.sm4() + m - score_matrix.frame_shift()) {
			out.push_match(q, s, m > (Score)0);
			out.transcript.push_back(op_frameshift_forward);
			it.walk_forward_shift();
		}
		else if (score == it.sm2() + m - score_matrix.frame_shift()) {
			out.push_match(q, s, m > (Score)0);
			out.transcript.push_back(op_frameshift_reverse);
			it.walk_reverse_shift();
		}
		else {
			const pair<EditOperation, int> g(it.walk_gap(d_begin, d1));
			out.push_gap(g.first, g.second, target.seq.data() + it.j + g.second);
		}
	}

	out.set_begin(it.i + 1, it.j + 1, Frame(strand, it.frame), dna_len);
	out.transcript.reverse();
	out.transcript.push_terminator();
	out.subject_source_range = out.subject_range;
	return out;
}

template<typename Sv>
Hsp traceback(Sequence *query, Strand strand, int dna_len, const Banded3FrameSwipeMatrix<Sv> &dp, const DpTarget &target, int d_begin,
	typename ScoreTraits<Sv>::Score max_score, double evalue, int max_col, int channel, int i0, int i1)
{
	Hsp out(false);
	const int j0 = i1 - (target.d_end - 1);
	out.swipe_target = target.target_idx;
	out.score = ScoreTraits<Sv>::int_score(max_score) * config.cbs_matrix_scale;
	out.bit_score = score_matrix.bitscore(out.score);
	out.evalue = evalue;
	out.query_range.end_ = std::min(i0 + max_col + (int)dp.band() / 3 / 2, (int)query[0].length());
	out.query_range.begin_ = std::max(out.query_range.end_ - (j0 + max_col), 0);
	out.frame = strand == FORWARD ? 0 : 3;
	out.query_source_range = TranslatedPosition::absolute_interval(TranslatedPosition(out.query_range.begin_, Frame(out.frame)), TranslatedPosition(out.query_range.end_, Frame(out.frame)), dna_len);
	return out;
}

template<typename Sv, typename Traceback>
list<Hsp> banded_3frame_swipe(
	const TranslatedSequence& query,
	Strand strand, std::vector<DpTarget>::const_iterator subject_begin,
	std::vector<DpTarget>::const_iterator subject_end,
	DpStat &stat,
	bool parallel,
	std::vector<DpTarget> &overflow)
{
	typedef typename Banded3FrameSwipeMatrixRef<Sv, Traceback>::type Matrix;
	typedef typename ScoreTraits<Sv>::Score Score;

	assert(subject_end - subject_begin <= ScoreTraits<Sv>::CHANNELS);
	Sequence q[3];
	query.get_strand(strand, q);
	const int qlen = (int)q[0].length(), qlen2 = (int)q[1].length(), qlen3 = (int)q[2].length();

	int band = 0;
	for (vector<DpTarget>::const_iterator j = subject_begin; j < subject_end; ++j)
		band = std::max(band, j->d_end - j->d_begin);

	int i0 = INT_MAX, i1 = INT_MAX, d_begin[ScoreTraits<Sv>::CHANNELS];
	for (vector<DpTarget>::const_iterator j = subject_begin; j < subject_end; ++j) {
		d_begin[j - subject_begin] = j->d_end - band;
		int i2 = std::max(j->d_end - 1, 0);
		i1 = std::min(i1, i2);
		i0 = std::min(i0, i2 + 1 - band);
	}

	TargetIterator<Sv> targets(subject_begin, subject_end, false, i1, qlen, d_begin);
	Matrix dp(band * 3, targets.cols);

	const Sv open_penalty(score_matrix.gap_open() + score_matrix.gap_extend()),
		extend_penalty(score_matrix.gap_extend()),
		frameshift_penalty(score_matrix.frame_shift());
	
	SwipeProfile<Sv> profile;
#ifndef __SSSE3__
	std::array<const int8_t*, 32> target_scores;
#endif
	Score best[ScoreTraits<Sv>::CHANNELS];
	int max_col[ScoreTraits<Sv>::CHANNELS];
	for (int i = 0; i < ScoreTraits<Sv>::CHANNELS; ++i) {
		best[i] = ScoreTraits<Sv>::zero_score();
		max_col[i] = 0;
	}

	int j = 0;
	while (targets.active.size() > 0) {
		const int i0_ = std::max(i0, 0), i1_ = std::min(i1, qlen - 1);
		if (i0_ > i1_)
			break;
		typename Matrix::ColumnIterator it(dp.begin((i0_ - i0) * 3, j));
		if (i0_ - i0 > 0)
			it.set_zero();
		Sv vgap0, vgap1, vgap2, hgap, col_best;
		vgap0 = vgap1 = vgap2 = col_best = ScoreTraits<Sv>::zero();

#ifdef __SSSE3__
		profile.set(targets.get());
#else
		profile.set(targets.get(target_scores.data()));
#endif
		for (int i = i0_; i <= i1_; ++i) {
			hgap = it.hgap();
			Sv next = cell_update<Sv>(it.sm3, it.sm4, it.sm2, profile.get(q[0][i]), extend_penalty, open_penalty, frameshift_penalty, hgap, vgap0, col_best);
			it.set_hgap(hgap);
			it.set_score(next);
			++it;

			if (i >= qlen2)
				break;
			hgap = it.hgap();
			next = cell_update<Sv>(it.sm3, it.sm4, it.sm2, profile.get(q[1][i]), extend_penalty, open_penalty, frameshift_penalty, hgap, vgap1, col_best);
			it.set_hgap(hgap);
			it.set_score(next);
			++it;

			if (i >= qlen3)
				break;
			hgap = it.hgap();
			next = cell_update<Sv>(it.sm3, it.sm4, it.sm2, profile.get(q[2][i]), extend_penalty, open_penalty, frameshift_penalty, hgap, vgap2, col_best);
			it.set_hgap(hgap);
			it.set_score(next);
			++it;
		}

#ifdef DP_STAT
		//stat.net_cells += targets.live * (i1_ - i0_ + 1) * 3;
		//stat.gross_cells += ScoreTraits<_sv>::CHANNELS * (i1_ - i0_ + 1) * 3;
#endif

		Score col_best_[ScoreTraits<Sv>::CHANNELS];
		store_sv(col_best, col_best_);
		for (int i = 0; i < targets.active.size();) {
			int channel = targets.active[i];
			if (!targets.inc(channel))
				targets.active.erase(i);
			else
				++i;
			if (col_best_[channel] > best[channel]) {
				best[channel] = col_best_[channel];
				max_col[channel] = j;
			}
		}
		++i0;
		++i1;
		++j;
	}
	
	list<Hsp> out;
	for (int i = 0; i < targets.n_targets; ++i) {
		if (best[i] < ScoreTraits<Sv>::max_score()) {
			const int score = ScoreTraits<Sv>::int_score(best[i]) * config.cbs_matrix_scale;
			const double evalue = score_matrix.evalue(score, qlen, (unsigned)subject_begin[i].seq.length());
			if (score_matrix.report_cutoff(score, evalue))
				out.push_back(traceback<Sv>(q, strand, (int)query.source().length(), dp, subject_begin[i], d_begin[i], best[i], evalue, max_col[i], i, i0 - j, i1 - j));
		}
		else
			overflow.push_back(subject_begin[i]);
	}
	return out;
}

template<typename Sv>
list<Hsp> banded_3frame_swipe_targets(std::vector<DpTarget>::const_iterator begin,
	vector<DpTarget>::const_iterator end,
	bool score_only,
	const TranslatedSequence &query,
	Strand strand,
	DpStat &stat,
	bool parallel,
	std::vector<DpTarget> &overflow)
{
	list<Hsp> out;
	for (vector<DpTarget>::const_iterator i = begin; i < end; i += std::min((ptrdiff_t)ScoreTraits<Sv>::CHANNELS, end - i)) {
		if (score_only)
			out.splice(out.end(), banded_3frame_swipe<Sv, DP::ScoreOnly>(query, strand, i, i + std::min(ptrdiff_t(ScoreTraits<Sv>::CHANNELS), end - i), stat, parallel, overflow));
		else
			out.splice(out.end(), banded_3frame_swipe<Sv, DP::Traceback>(query, strand, i, i + std::min(ptrdiff_t(ScoreTraits<Sv>::CHANNELS), end - i), stat, parallel, overflow));
	}
	return out;
}

void banded_3frame_swipe_worker(std::vector<DpTarget>::const_iterator begin,
	std::vector<DpTarget>::const_iterator end,
	atomic<size_t> *next,
	bool score_only,
	const TranslatedSequence *query,
	Strand strand,
	list<Hsp> *out,
	vector<DpTarget> *overflow)
{
	DpStat stat;
	size_t pos;
	vector<DpTarget> of;
	while (begin + (pos = next->fetch_add(config.swipe_chunk_size, std::memory_order_relaxed)) < end)
#if defined(__SSE2__) | defined(__ARM_NEON)
		if(score_only)
			out->splice(out->end(), banded_3frame_swipe_targets<ScoreVector<int16_t, SHRT_MIN>>(begin + pos, min(begin + pos + config.swipe_chunk_size, end), score_only, *query, strand, stat, true, of));
		else
			out->splice(out->end(), banded_3frame_swipe_targets<int32_t>(begin + pos, min(begin + pos + config.swipe_chunk_size, end), score_only, *query, strand, stat, true, of));
#else
		out->splice(out->end(), banded_3frame_swipe_targets<int32_t>(begin + pos, min(begin + pos + config.swipe_chunk_size, end), score_only, *query, strand, stat, true, of));
#endif
	*overflow = std::move(of);
}

list<Hsp> banded_3frame_swipe(const TranslatedSequence &query, Strand strand, vector<DpTarget>::iterator target_begin, vector<DpTarget>::iterator target_end, DpStat &stat, bool score_only, bool parallel)
{
	vector<DpTarget> overflow16, overflow32;
#if defined (__SSE2__) | defined(__ARM_NEON)
	TaskTimer timer("Banded 3frame swipe (sort)", parallel ? 3 : UINT_MAX);
	std::stable_sort(target_begin, target_end);
	list<Hsp> out;
	if (parallel) {
		timer.go("Banded 3frame swipe (run)");
		vector<thread> threads;
		vector<list<Hsp>*> thread_out;
		vector<vector<DpTarget>> thread_overflow(config.threads_);
		atomic<size_t> next(0);
		for (int i = 0; i < config.threads_; ++i) {
			thread_out.push_back(new list<Hsp>);
			threads.emplace_back(banded_3frame_swipe_worker,
				target_begin,
				target_end,
				&next,
				score_only,
				&query,
				strand,
				thread_out.back(),
				&thread_overflow[i]);
		}
		for (auto &t : threads)
			t.join();
		timer.go("Banded 3frame swipe (merge)");
		for (list<Hsp>* l : thread_out) {
			out.splice(out.end(), *l);
			delete l;
		}
		overflow16.reserve(std::accumulate(thread_overflow.begin(), thread_overflow.end(), (size_t)0, [](size_t n, const vector<DpTarget> &v) { return n + v.size(); }));
		for (const vector<DpTarget> &v : thread_overflow)
			overflow16.insert(overflow16.end(), v.begin(), v.end());
	}
	else {
		if(score_only)
			out = banded_3frame_swipe_targets<ScoreVector<int16_t, SHRT_MIN>>(target_begin, target_end, score_only, query, strand, stat, false, overflow16);
		else
			out = banded_3frame_swipe_targets<int32_t>(target_begin, target_end, score_only, query, strand, stat, false, overflow16);
	}

	out.splice(out.end(), banded_3frame_swipe_targets<int32_t>(overflow16.begin(), overflow16.end(), score_only, query, strand, stat, false, overflow32));
	return out;
#else
	return banded_3frame_swipe_targets<int32_t>(target_begin, target_end, score_only, query, strand, stat, false, overflow32);
#endif
}

}

DISPATCH_7(std::list<Hsp>, banded_3frame_swipe, const TranslatedSequence&, query, Strand, strand, std::vector<DpTarget>::iterator, target_begin, std::vector<DpTarget>::iterator, target_end, DpStat&, stat, bool, score_only, bool, parallel)