/****
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 "output_format.h"
#include "util/util.h"
#include "stats/score_matrix.h"

void PairwiseFormat::print_match(const HspContext& r, Output::Info &info)
{
    static const unsigned width = 60;
    TextBuffer& out = info.out;
    const int dna_len = (int)r.query.source().length();
    out << '>';
    const Strand strand = (config.command == ::Config::blastn) ? (r.frame() ? FORWARD : REVERSE) : (r.frame() < 3 ? FORWARD : REVERSE);
    OutputFormat::print_title(out, r.target_title.c_str(), true, true, " ");
    out << "\nLength=" << r.subject_len << "\n\n";
    out << " Score = " << r.bit_score() << " bits (" << r.score() << "),  Expect = ";
    out.print_e(r.evalue());
    out << '\n';
    out << " Identities = " << r.identities() << '/' << r.length() << " (" << percentage<unsigned,unsigned>(r.identities(), r.length()) << "%), Positives = " << r.positives() << '/' << r.length() << " (" << percentage<unsigned, unsigned>(r.positives(), r.length())
        << "%), Gaps = " << r.gaps() << '/' << r.length() << " (" << percentage<unsigned, unsigned>(r.gaps(), r.length()) << "%)\n";
    if (align_mode.query_translated)
        out << " Frame = " << r.blast_query_frame() << '\n';

#ifdef WITH_DNA
    if(config.command == ::Config::blastn) {
        out << " Strand = " ;
        if(r.frame()) out << "Plus/"; else out<< "Minus/";
        out << "Plus" << '\n';
    }

#endif
    out << '\n';
    const unsigned digits = (unsigned)std::max(ceil(log10(r.subject_range().end_)), ceil(log10(r.query_source_range().end_)));

    HspContext::Iterator qi = r.begin(), mi = r.begin(), si = r.begin();
    while (qi.good()) {
        out << "Query  ";
        out.print(qi.query_pos.absolute(dna_len) + 1, digits);
        out << "  ";
        for (unsigned i = 0; i < width && qi.good(); ++i, ++qi)
            out << qi.query_char();
        out << " ";
        out << TranslatedPosition::oriented_position(qi.query_pos.in_strand() - 1, strand, dna_len) + 1;
        out << '\n';

        for (unsigned i = 0; i < digits + 9; ++i)
            out << ' ';
        for (unsigned i = 0; i < width && mi.good(); ++i, ++mi)
            out << mi.midline_char(score_matrix(mi.query(), mi.subject()));
        out << '\n';

        out << "Sbjct  ";
        out.print(si.subject_pos+1, digits);
        out << "  ";
        for (unsigned i = 0; i < width && si.good(); ++i, ++si)
            out << si.subject_char();
        out << " ";
        out << si.subject_pos;
        out << "\n\n";
    }
}

void PairwiseFormat::print_footer(File &out) const
{

}

void PairwiseFormat::print_query_epilog(Output::Info &info) const
{
}

void PairwiseFormat::print_query_intro(Output::Info &info) const
{
	info.out << "Query= " << info.query.title << "\n\nLength=" << info.query.len << "\n\n";
	if (info.unaligned) {
		info.out << "\n***** No hits found *****\n\n\n";
	}
}

void PairwiseFormat::print_header(File &f, int mode, const char *matrix, int gap_open, int gap_extend, double evalue, const char *first_query_name, unsigned first_query_len) const
{
	static const char* header = "BLASTP 2.3.0+\n\n\n";
	f.write(header, strlen(header));
}
