/****
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 <sstream>
#include <set>
#include <string.h>
#include <algorithm>
#include <iostream>
#include <functional>
#include <map>
#include "basic/match.h"
#include "output_format.h"
#include "util/sequence/sequence.h"
#include "data/sequence_file.h"
#include "data/taxonomy_nodes.h"
#include "util/system/system.h"

using namespace Output;
using std::array;
using std::endl;
using std::set;
using std::string;
using std::transform;
using std::back_inserter;
using std::vector;
using std::runtime_error;
using std::map;
using std::pair;

map<FieldId, OutputField> TabularFormat::field_def = {
{ FieldId::QSeqId, { FieldId::QSeqId, "qseqid", "cseqid", "Query Seq - id", HspValues::NONE, Flags::IS_STRING } },
{ FieldId::QLen, { FieldId::QLen, "qlen", "clen", "Query sequence length", HspValues::NONE, Flags::NONE } },
{ FieldId::SSeqId, { FieldId::SSeqId, "sseqid",    "mseqid", "Subject Seq - id", HspValues::NONE, Flags::IS_STRING | Flags::SSEQID } },
{ FieldId::SAllSeqId, { FieldId::SAllSeqId, "sallseqid", "", "All subject Seq - id(s), separated by a ';'", HspValues::NONE, Flags::ALL_SEQIDS | Flags::IS_ARRAY | Flags::SSEQID } },
{ FieldId::SLen, { FieldId::SLen, "slen", "mlen", "Subject sequence length", HspValues::NONE, Flags::NONE } },
{ FieldId::QStart, { FieldId::QStart, "qstart", "cstart", "Start of alignment in query", HspValues::QUERY_START, Flags::NONE } },
{ FieldId::QEnd, { FieldId::QEnd, "qend", "cend", "End of alignment in query", HspValues::QUERY_END, Flags::NONE } },
{ FieldId::SStart, { FieldId::SStart, "sstart", "mstart", "Start of alignment in subject", HspValues::TARGET_START, Flags::NONE } },
{ FieldId::SEnd, { FieldId::SEnd, "send", "mend", "End of alignment in subject", HspValues::TARGET_END, Flags::NONE } },
{ FieldId::QSeq, { FieldId::QSeq, "qseq", "", "Aligned part of query sequence", HspValues::QUERY_COORDS, Flags::IS_STRING | Flags::NO_REALIGN } },
{ FieldId::SSeq, { FieldId::SSeq, "sseq", "", "Aligned part of subject sequence", HspValues::TRANSCRIPT, Flags::IS_STRING | Flags::NO_REALIGN } },
{ FieldId::EValue, { FieldId::EValue, "evalue", "evalue", "Expect value", HspValues::NONE, Flags::NONE } },
{ FieldId::BitScore, { FieldId::BitScore, "bitscore", "Bitscore", "Bit score", HspValues::NONE, Flags::NONE } },
{ FieldId::Score, { FieldId::Score, "score", "score", "Raw score", HspValues::NONE, Flags::NONE } },
{ FieldId::Length, { FieldId::Length, "length", "length", "Alignment length", HspValues::LENGTH, Flags::NONE } },
{ FieldId::PIdent, { FieldId::PIdent, "pident", "pident" ,"Percentage of identical matches", HspValues::IDENT | HspValues::LENGTH, Flags::NONE } },
{ FieldId::NIdent, { FieldId::NIdent, "nident", "nident", "Number of identical matches", HspValues::IDENT, Flags::NONE } },
{ FieldId::Mismatch, { FieldId::Mismatch, "mismatch", "mismatch", "Number of mismatches", HspValues::MISMATCHES, Flags::NONE } },
{ FieldId::Positive, { FieldId::Positive, "positive", "positive", "Number of positive - scoring matches", HspValues::TRANSCRIPT, Flags::NONE } },
{ FieldId::GapOpen, { FieldId::GapOpen, "gapopen", "gapopen", "Number of gap openings", HspValues::GAP_OPENINGS, Flags::NONE } },
{ FieldId::Gaps, { FieldId::Gaps, "gaps", "gaps", "Total number of gaps", HspValues::GAPS, Flags::NONE } },
{ FieldId::PPos, { FieldId::PPos, "ppos", "ppos", "Percentage of positive - scoring matches", HspValues::TRANSCRIPT, Flags::NONE } },
{ FieldId::QFrame, { FieldId::QFrame, "qframe", "", "Query frame", HspValues::NONE, Flags::NO_REALIGN  } },
{ FieldId::BTop, { FieldId::BTop, "btop", "", "Blast traceback operations (BTOP)", HspValues::TRANSCRIPT, Flags::IS_STRING | Flags::NO_REALIGN  } },
{ FieldId::STaxIds, { FieldId::STaxIds, "staxids", "", "Unique Subject Taxonomy ID(s), separated by a ';' (in numerical order)", HspValues::NONE, Flags::IS_ARRAY | Flags::NO_REALIGN  } },
{ FieldId::SSciNames, { FieldId::SSciNames, "sscinames", "", "Unique Subject Scientific Name(s), separated by a ';'", HspValues::NONE, Flags::IS_ARRAY | Flags::NO_REALIGN  } },
{ FieldId::SSKingdoms, { FieldId::SSKingdoms, "sskingdoms",    "", "Unique Subject Super Kingdom(s), separated by a ';'", HspValues::NONE, Flags::IS_ARRAY | Flags::NO_REALIGN  } },
{ FieldId::STitle, { FieldId::STitle, "stitle", "", "Subject Title", HspValues::NONE, Flags::FULL_TITLES | Flags::IS_STRING  | Flags::SSEQID } },
{ FieldId::SAllTitles, { FieldId::SAllTitles, "salltitles", "", "All Subject Title(s), separated by a '<>'", HspValues::NONE, Flags::ALL_SEQIDS | Flags::FULL_TITLES | Flags::IS_ARRAY | Flags::SSEQID } },
{ FieldId::QCovHsp, { FieldId::QCovHsp, "qcovhsp", "ccovhsp", "Query coverage per HSP", HspValues::QUERY_COORDS, Flags::NONE } },
{ FieldId::QTitle, { FieldId::QTitle, "qtitle", "", "Query title", HspValues::NONE, Flags::IS_STRING } },
{ FieldId::FullSSeq, { FieldId::FullSSeq, "full_sseq", "", "Subject sequence", HspValues::NONE, Flags::IS_STRING | Flags::NO_REALIGN } },
{ FieldId::QQual, { FieldId::QQual, "qqual", "", "Query quality values for the aligned part of the query", HspValues::QUERY_COORDS, Flags::IS_STRING | Flags::NO_REALIGN } },
{ FieldId::QNum, { FieldId::QNum, "qnum", "", "Query ordinal id", HspValues::NONE, Flags::NONE } },
{ FieldId::SNum, { FieldId::SNum, "snum", "", "Subject ordinal id", HspValues::NONE, Flags::NONE } },
{ FieldId::SCovHsp, { FieldId::SCovHsp, "scovhsp", "mcovhsp", "Subject coverage per HSP", HspValues::TARGET_COORDS, Flags::NONE } },
{ FieldId::FullQQual, { FieldId::FullQQual, "full_qqual", "", "Query quality values", HspValues::NONE, Flags::IS_STRING | Flags::NO_REALIGN } },
{ FieldId::FullQSeq, { FieldId::FullQSeq, "full_qseq", "", "Query sequence", HspValues::NONE, Flags::IS_STRING | Flags::NO_REALIGN } },
{ FieldId::QSeqGapped, { FieldId::QSeqGapped, "qseq_gapped", "", "Aligned part of query sequence (with gaps)", HspValues::TRANSCRIPT, Flags::IS_STRING | Flags::NO_REALIGN } },
{ FieldId::SSeqGapped, { FieldId::SSeqGapped, "sseq_gapped", "", "Aligned part of subject sequence (with gaps)", HspValues::TRANSCRIPT, Flags::IS_STRING | Flags::NO_REALIGN } },
{ FieldId::QStrand, { FieldId::QStrand, "qstrand", "", "Query strand", HspValues::NONE, Flags::IS_STRING | Flags::NO_REALIGN } },
{ FieldId::Cigar, { FieldId::Cigar, "cigar", "", "CIGAR string", HspValues::TRANSCRIPT, Flags::IS_STRING | Flags::NO_REALIGN } },
{ FieldId::SKingdoms, { FieldId::SKingdoms, "skingdoms", "", "Unique Subject Kingdom(s), separated by a ';'", HspValues::NONE, Flags::IS_ARRAY | Flags::NO_REALIGN } },
{ FieldId::SPhylums, { FieldId::SPhylums, "sphylums", "", "Unique Subject Phylum(s), separated by a ';'", HspValues::NONE, Flags::IS_ARRAY | Flags::NO_REALIGN } },
{ FieldId::FullQSeqMate, { FieldId::FullQSeqMate, "full_qseq_mate", "", "Query sequence of the mate", HspValues::NONE, Flags::IS_STRING | Flags::NO_REALIGN } },
{ FieldId::QSeqTranslated, { FieldId::QSeqTranslated, "qseq_translated", "", "Aligned part of query sequence (translated)", HspValues::TRANSCRIPT, Flags::IS_STRING | Flags::NO_REALIGN } },
{ FieldId::HspNum, { FieldId::HspNum, "hspnum", "", "Number of HSP within the subject", HspValues::NONE, Flags::NONE } },
{ FieldId::NormalizedBitscore, { FieldId::NormalizedBitscore, "normalized_bitscore", "", "Bitscore normalized by maximum self alignment score", HspValues::NONE, Flags::SELF_ALN_SCORES | Flags::NO_REALIGN } },
{ FieldId::NormalizedBitscoreQuery, { FieldId::NormalizedBitscoreQuery, "normalized_bitscore_query", "", "Bitscore normalized by maximum self alignment score of query", HspValues::NONE, Flags::SELF_ALN_SCORES | Flags::NO_REALIGN } },
{ FieldId::NORMALIZED_NIDENT, { FieldId::NORMALIZED_NIDENT, "normalized_nident", "normalized_nident", "Number of identical matches normalized by maximum length", HspValues::IDENT | HspValues::LENGTH, Flags::NONE } },
{ FieldId::ApproxPIdent, { FieldId::ApproxPIdent, "approx_pident", "approx_pident", "Approximate percentage of identical matches", HspValues::COORDS, Flags::NONE } },
{ FieldId::CorrectedBitScore, { FieldId::CorrectedBitScore, "corrected_bitscore", "corrected_bitscore", "Bit score corrected for edge effects", HspValues::NONE, Flags::NONE } },
{ FieldId::SLineages, { FieldId::SLineages, "slineages", "", "Unique Subject Lineage(s), separated by a '<>'", HspValues::NONE, Flags::NO_REALIGN } }
#ifdef DP_STAT
{ FieldId::Reserved1, { FieldId::Reserved1, "reserved1", "reserved1", "", HspValues::NONE, Flags::NO_REALIGN } },
{ FieldId::Reserved2, { FieldId::Reserved2, "reserved2", "reserved2", "", HspValues::NONE, Flags::NO_REALIGN } }
#endif
};

template<>
struct EnumTraits<Header> {
	static const SEMap<Header> from_string;
};

const SEMap<Header> EnumTraits<Header>::from_string = { {"0", Header::NONE}, {"simple", Header::SIMPLE}, {"verbose", Header::VERBOSE} };

static std::function<void(const TabularFormat&, const HspContext&, Output::Info&)> make_invalid_match_handler(const string& key)
{
    return [key](const TabularFormat&, const HspContext&, Output::Info&) {
        throw runtime_error(string("Invalid output field: ") + key);
        };
}

static std::function<void(const TabularFormat&, Output::Info&)> make_invalid_intro_handler(const string& key)
{
    return [key](const TabularFormat&, Output::Info&) {
        throw runtime_error(string("Invalid output field: ") + key);
        };
}

static void print_staxids(TextBuffer& out, int64_t subject_global_id, const SequenceFile& db, bool json = false)
{
    out.print(db.taxids(subject_global_id), json ? ',' : ';');
}

static vector<TaxId> lineage(TaxId taxid, SequenceFile& db) {
    vector<TaxId> l;
    TaxId i = taxid;
    int n = 0;
    while (true) {
        if (i <= 0)
            return {};
        if (i == 1)
            break;
        l.push_back(i);
        i = db.get_parent(i);
        if (l.size() >= MAX_LINEAGE)
            throw runtime_error("Lineage too long for taxid " + std::to_string(taxid));
    }
    return l;
}

static void print_lineage(int64_t target_oid, SequenceFile& db, TextBuffer& out, bool json = false) {
    const vector<TaxId> taxids = db.taxids(target_oid);
    if (taxids.empty()) {
        out << (json ? " []" : "N/A");
        return;
    }
    set<vector<TaxId>> lineages;
    for (TaxId i : taxids) {
        const vector<TaxId> l = lineage(i, db);
        if (!l.empty())
            lineages.insert(l);
    }
    if (lineages.empty()) {
        out << (json ? " []" : "N/A");
        return;
    }
    if (json) {
        out << " [" DEFAULT_LINE_DELIMITER;
    }
    for (auto i = lineages.begin(); i != lineages.end(); ++i) {
        if (i != lineages.begin())
            out << (json ? "," DEFAULT_LINE_DELIMITER : "<>");
        if (json) {
            out << "\t\t[";
        }
        const vector<TaxId>& lin = *i;
        for (auto j = lin.rbegin(); j != lin.rend(); ++j) {
            if (j != lin.rbegin())
                out << (json ? ", " : "; ");
            if (json)
                out << '\"';
            out << db.taxon_scientific_name(*j);
            if (json)
                out << '\"';
        }
        if (json) {
            out << ']';
        }
    }
    if (json) {
        out << DEFAULT_LINE_DELIMITER "\t]";
    }
}

map<FieldId, FieldCallbacks> TabularFormat::field_callbacks = [] {
    map<FieldId, FieldCallbacks> callbacks;
    for (const auto& f : TabularFormat::field_def) {
        callbacks.emplace(f.first, FieldCallbacks{ make_invalid_match_handler(f.second.key), make_invalid_intro_handler(f.second.key) });
    }

    callbacks[FieldId::QSeqId].match = [](const TabularFormat&, const HspContext& r, Output::Info& info) {
        info.out.write_until(r.query_title.c_str(), Util::Seq::id_delimiters);
        };
    callbacks[FieldId::QSeqId].query_intro = [](const TabularFormat&, Output::Info& info) {
        info.out.write_until(info.query.title, Util::Seq::id_delimiters);
        };

    callbacks[FieldId::QLen].match = [](const TabularFormat&, const HspContext& r, Output::Info& info) {
        info.out << r.query_len;
        };
    callbacks[FieldId::QLen].query_intro = [](const TabularFormat&, Output::Info& info) {
        info.out << info.query.len;
        };

    callbacks[FieldId::SSeqId].match = [](const TabularFormat&, const HspContext& r, Output::Info& info) {
        OutputFormat::print_title(info.out, r.target_title.c_str(), false, false, "");
        };
    callbacks[FieldId::SSeqId].query_intro = [](const TabularFormat&, Output::Info& info) {
        info.out << '*';
        };

    callbacks[FieldId::SAllSeqId].match = [](const TabularFormat& format, const HspContext& r, Output::Info& info) {
        OutputFormat::print_title(info.out, r.target_title.c_str(), false, true, format.is_json ? "," : ";", 0, format.is_json);
        };
    callbacks[FieldId::SAllSeqId].query_intro = [](const TabularFormat&, Output::Info& info) {
        info.out << '*';
        };

    callbacks[FieldId::SLen].match = [](const TabularFormat&, const HspContext& r, Output::Info& info) {
        info.out << r.subject_len;
        };
    callbacks[FieldId::SLen].query_intro = [](const TabularFormat&, Output::Info& info) {
        info.out << "-1";
        };

    callbacks[FieldId::QStart].match = [](const TabularFormat&, const HspContext& r, Output::Info& info) {
        info.out << r.oriented_query_range().begin_ + 1;
        };
    callbacks[FieldId::QStart].query_intro = [](const TabularFormat&, Output::Info& info) {
        info.out << "-1";
        };

    callbacks[FieldId::QEnd].match = [](const TabularFormat&, const HspContext& r, Output::Info& info) {
        info.out << r.oriented_query_range().end_ + 1;
        };
    callbacks[FieldId::QEnd].query_intro = [](const TabularFormat&, Output::Info& info) {
        info.out << "-1";
        };

    callbacks[FieldId::SStart].match = [](const TabularFormat&, const HspContext& r, Output::Info& info) {
        info.out << r.subject_source_range().begin_ + 1;
        };
    callbacks[FieldId::SStart].query_intro = [](const TabularFormat&, Output::Info& info) {
        info.out << "-1";
        };

    callbacks[FieldId::SEnd].match = [](const TabularFormat&, const HspContext& r, Output::Info& info) {
        info.out << r.subject_source_range().end_;
        };
    callbacks[FieldId::SEnd].query_intro = [](const TabularFormat&, Output::Info& info) {
        info.out << "-1";
        };

    callbacks[FieldId::QSeq].match = [](const TabularFormat&, const HspContext& r, Output::Info& info) {
        r.query.source().print(info.out, r.query_source_range().begin_, r.query_source_range().end_, input_value_traits);
        };
    callbacks[FieldId::QSeq].query_intro = [](const TabularFormat&, Output::Info& info) {
        info.out << '*';
        };

    callbacks[FieldId::SSeq].match = [](const TabularFormat&, const HspContext& r, Output::Info& info) {
        vector<Letter> seq;
        seq.reserve(r.subject_range().length());
        for (HspContext::Iterator j = r.begin(); j.good(); ++j)
            if (!(j.op() == op_insertion))
                seq.push_back(j.subject());
        info.out << Sequence(seq);
        };
    callbacks[FieldId::SSeq].query_intro = [](const TabularFormat&, Output::Info& info) {
        info.out << '*';
        };

    callbacks[FieldId::EValue].match = [](const TabularFormat&, const HspContext& r, Output::Info& info) {
        info.out.print_e(r.evalue());
        };
    callbacks[FieldId::EValue].query_intro = [](const TabularFormat&, Output::Info& info) {
        info.out << "-1";
        };

    callbacks[FieldId::BitScore].match = [](const TabularFormat&, const HspContext& r, Output::Info& info) {
        info.out << r.bit_score();
        };
    callbacks[FieldId::BitScore].query_intro = [](const TabularFormat&, Output::Info& info) {
        info.out << "-1";
        };

    callbacks[FieldId::Score].match = [](const TabularFormat&, const HspContext& r, Output::Info& info) {
        info.out << r.score();
        };
    callbacks[FieldId::Score].query_intro = [](const TabularFormat&, Output::Info& info) {
        info.out << "-1";
        };

    callbacks[FieldId::Length].match = [](const TabularFormat&, const HspContext& r, Output::Info& info) {
        info.out << r.length();
        };
    callbacks[FieldId::Length].query_intro = [](const TabularFormat&, Output::Info& info) {
        info.out << "-1";
        };

    callbacks[FieldId::PIdent].match = [](const TabularFormat&, const HspContext& r, Output::Info& info) {
        info.out << r.id_percent();
        };
    callbacks[FieldId::PIdent].query_intro = [](const TabularFormat&, Output::Info& info) {
        info.out << "-1";
        };

    callbacks[FieldId::NIdent].match = [](const TabularFormat&, const HspContext& r, Output::Info& info) {
        info.out << r.identities();
        };
    callbacks[FieldId::NIdent].query_intro = [](const TabularFormat&, Output::Info& info) {
        info.out << "-1";
        };

    callbacks[FieldId::Mismatch].match = [](const TabularFormat&, const HspContext& r, Output::Info& info) {
        info.out << r.mismatches();
        };
    callbacks[FieldId::Mismatch].query_intro = [](const TabularFormat&, Output::Info& info) {
        info.out << "-1";
        };

    callbacks[FieldId::Positive].match = [](const TabularFormat&, const HspContext& r, Output::Info& info) {
        info.out << r.positives();
        };
    callbacks[FieldId::Positive].query_intro = [](const TabularFormat&, Output::Info& info) {
        info.out << "-1";
        };

    callbacks[FieldId::GapOpen].match = [](const TabularFormat&, const HspContext& r, Output::Info& info) {
        info.out << r.gap_openings();
        };
    callbacks[FieldId::GapOpen].query_intro = [](const TabularFormat&, Output::Info& info) {
        info.out << "-1";
        };

    callbacks[FieldId::Gaps].match = [](const TabularFormat&, const HspContext& r, Output::Info& info) {
        info.out << r.gaps();
        };
    callbacks[FieldId::Gaps].query_intro = [](const TabularFormat&, Output::Info& info) {
        info.out << "-1";
        };

    callbacks[FieldId::PPos].match = [](const TabularFormat&, const HspContext& r, Output::Info& info) {
        info.out << (double)r.positives() * 100.0 / r.length();
        };
    callbacks[FieldId::PPos].query_intro = [](const TabularFormat&, Output::Info& info) {
        info.out << "-1";
        };

    callbacks[FieldId::QFrame].match = [](const TabularFormat&, const HspContext& r, Output::Info& info) {
        info.out << r.blast_query_frame();
        };
    callbacks[FieldId::QFrame].query_intro = [](const TabularFormat&, Output::Info& info) {
        info.out << '0';
        };

    callbacks[FieldId::BTop].match = [](const TabularFormat&, const HspContext& r, Output::Info& info) {
        unsigned n_matches = 0;
        for (HspContext::Iterator i = r.begin(); i.good(); ++i) {
            switch (i.op()) {
            case op_match:
                ++n_matches;
                break;
            case op_substitution:
            case op_frameshift_forward:
            case op_frameshift_reverse:
                if (n_matches > 0) {
                    info.out << n_matches;
                    n_matches = 0;
                }
                info.out << i.query_char() << i.subject_char();
                break;
            case op_insertion:
                if (n_matches > 0) {
                    info.out << n_matches;
                    n_matches = 0;
                }
                info.out << i.query_char() << '-';
                break;
            case op_deletion:
                if (n_matches > 0) {
                    info.out << n_matches;
                    n_matches = 0;
                }
                info.out << '-' << i.subject_char();
                break;
            }
        }
        if (n_matches > 0)
            info.out << n_matches;
        };
    callbacks[FieldId::BTop].query_intro = [](const TabularFormat&, Output::Info& info) {
        info.out << '*';
        };

    callbacks[FieldId::STaxIds].match = [](const TabularFormat& format, const HspContext& r, Output::Info& info) {
        print_staxids(info.out, r.subject_oid, *info.db, format.is_json);
        };
    callbacks[FieldId::STaxIds].query_intro = [](const TabularFormat&, Output::Info& info) {
        info.out << '*';
        };

    callbacks[FieldId::SSciNames].match = [](const TabularFormat& format, const HspContext& r, Output::Info& info) {
        const vector<TaxId> tax_id = info.db->taxids(r.subject_oid);
        print_taxon_names(tax_id.begin(), tax_id.end(), *info.db, info.out, format.is_json);
        };
    callbacks[FieldId::SSciNames].query_intro = [](const TabularFormat&, Output::Info& info) {
        info.out << '*';
        };

    callbacks[FieldId::SSKingdoms].match = [](const TabularFormat& format, const HspContext& r, Output::Info& info) {
        const set<TaxId> tax_id = info.db->rank_taxid(info.db->taxids(r.subject_oid), Rank::superkingdom);
        print_taxon_names(tax_id.begin(), tax_id.end(), *info.db, info.out, format.is_json);
        };
    callbacks[FieldId::SSKingdoms].query_intro = [](const TabularFormat&, Output::Info& info) {
        info.out << '*';
        };

    callbacks[FieldId::STitle].match = [](const TabularFormat& format, const HspContext& r, Output::Info& info) {
        OutputFormat::print_title(info.out, r.target_title.c_str(), true, false, format.is_json ? "," : "<>", 0, false);
        };
    callbacks[FieldId::STitle].query_intro = [](const TabularFormat&, Output::Info& info) {
        info.out << '*';
        };

    callbacks[FieldId::SAllTitles].match = [](const TabularFormat& format, const HspContext& r, Output::Info& info) {
        OutputFormat::print_title(info.out, r.target_title.c_str(), true, true, format.is_json ? "," : "<>", 0, format.is_json);
        };
    callbacks[FieldId::SAllTitles].query_intro = [](const TabularFormat&, Output::Info& info) {
        info.out << '*';
        };

    callbacks[FieldId::QCovHsp].match = [](const TabularFormat&, const HspContext& r, Output::Info& info) {
        info.out << r.qcovhsp();
        };
    callbacks[FieldId::QCovHsp].query_intro = [](const TabularFormat&, Output::Info& info) {
        info.out << "-1";
        };

    callbacks[FieldId::QTitle].match = [](const TabularFormat&, const HspContext& r, Output::Info& info) {
        info.out << r.query_title;
        };
    callbacks[FieldId::QTitle].query_intro = [](const TabularFormat&, Output::Info& info) {
        info.out << info.query.title;
        };

    callbacks[FieldId::FullSSeq].match = [](const TabularFormat&, const HspContext& r, Output::Info& info) {
        info.out << r.subject_seq;
        };
    callbacks[FieldId::FullSSeq].query_intro = [](const TabularFormat&, Output::Info& info) {
        info.out << '*';
        };

    callbacks[FieldId::QQual].match = [](const TabularFormat&, const HspContext& r, Output::Info& info) {
        if (strlen(info.query.qual) == 0) {
            info.out << '*';
            return;
        }
        info.out << string(info.query.qual + r.query_source_range().begin_, info.query.qual + r.query_source_range().end_).c_str();
        };
    callbacks[FieldId::QQual].query_intro = [](const TabularFormat&, Output::Info& info) {
        info.out << '*';
        };

    callbacks[FieldId::QNum].match = [](const TabularFormat&, const HspContext& r, Output::Info& info) {
        info.out << r.query_oid;
        };
    callbacks[FieldId::QNum].query_intro = [](const TabularFormat&, Output::Info& info) {
        info.out << "-1";
        };

    callbacks[FieldId::SNum].match = [](const TabularFormat&, const HspContext& r, Output::Info& info) {
        info.out << r.subject_oid;
        };
    callbacks[FieldId::SNum].query_intro = [](const TabularFormat&, Output::Info& info) {
        info.out << "-1";
        };

    callbacks[FieldId::SCovHsp].match = [](const TabularFormat&, const HspContext& r, Output::Info& info) {
        info.out << r.scovhsp();
        };
    callbacks[FieldId::SCovHsp].query_intro = [](const TabularFormat&, Output::Info& info) {
        info.out << "-1";
        };

    callbacks[FieldId::FullQQual].match = [](const TabularFormat&, const HspContext&, Output::Info& info) {
        info.out << (strlen(info.query.qual) ? info.query.qual : "*");
        };
    callbacks[FieldId::FullQQual].query_intro = [](const TabularFormat&, Output::Info& info) {
        info.out << (strlen(info.query.qual) ? info.query.qual : "*");
        };

    callbacks[FieldId::FullQSeq].match = [](const TabularFormat&, const HspContext& r, Output::Info& info) {
        r.query.source().print(info.out, input_value_traits);
        };
    callbacks[FieldId::FullQSeq].query_intro = [](const TabularFormat&, Output::Info& info) {
        info.query.source_seq.print(info.out, input_value_traits);
        };

    callbacks[FieldId::QSeqGapped].match = [](const TabularFormat&, const HspContext& r, Output::Info& info) {
        for (HspContext::Iterator i = r.begin(); i.good(); ++i)
            info.out << i.query_char();
        };
    callbacks[FieldId::QSeqGapped].query_intro = [](const TabularFormat&, Output::Info& info) {
        info.out << '*';
        };

    callbacks[FieldId::SSeqGapped].match = [](const TabularFormat&, const HspContext& r, Output::Info& info) {
        for (HspContext::Iterator i = r.begin(); i.good(); ++i)
            info.out << i.subject_char();
        };
    callbacks[FieldId::SSeqGapped].query_intro = [](const TabularFormat&, Output::Info& info) {
        info.out << '*';
        };

    callbacks[FieldId::QStrand].match = [](const TabularFormat&, const HspContext& r, Output::Info& info) {
        if (align_mode.query_translated)
            info.out << ((r.blast_query_frame() > 0) ? '+' : '-');
        else
            info.out << '+';
        };
    callbacks[FieldId::QStrand].query_intro = [](const TabularFormat&, Output::Info& info) {
        info.out << '*';
        };

    callbacks[FieldId::Cigar].match = [](const TabularFormat&, const HspContext& r, Output::Info& info) {
        print_cigar(r, info.out);
        };
    callbacks[FieldId::Cigar].query_intro = [](const TabularFormat&, Output::Info& info) {
        info.out << '*';
        };

    callbacks[FieldId::SKingdoms].match = [](const TabularFormat&, const HspContext& r, Output::Info& info) {
        const set<TaxId> tax_id = info.db->rank_taxid(info.db->taxids(r.subject_oid), Rank::kingdom);
        print_taxon_names(tax_id.begin(), tax_id.end(), *info.db, info.out);
        };
    callbacks[FieldId::SKingdoms].query_intro = [](const TabularFormat&, Output::Info& info) {
        info.out << '*';
        };

    callbacks[FieldId::SPhylums].match = [](const TabularFormat&, const HspContext& r, Output::Info& info) {
        const set<TaxId> tax_id = info.db->rank_taxid(info.db->taxids(r.subject_oid), Rank::phylum);
        print_taxon_names(tax_id.begin(), tax_id.end(), *info.db, info.out);
        };
    callbacks[FieldId::SPhylums].query_intro = [](const TabularFormat&, Output::Info& info) {
        info.out << '*';
        };

    callbacks[FieldId::FullQSeqMate].match = [](const TabularFormat&, const HspContext& r, Output::Info& info) {
        if (config.query_file.size() == 2) {
            info.query.mate_seq.print(info.out, input_value_traits);
            return;
        }
        info.out << '*';
        };

    callbacks[FieldId::QSeqTranslated].match = [](const TabularFormat&, const HspContext& r, Output::Info& info) {
        if (config.frame_shift) {
            vector<Letter> seq;
            seq.reserve(r.query_range().length());
            for (HspContext::Iterator j = r.begin(); j.good(); ++j)
                if (j.op() != op_deletion && j.op() != op_frameshift_forward && j.op() != op_frameshift_reverse)
                    seq.push_back(j.query());
            info.out << Sequence(seq);
            return;
        }
        r.query.index(r.frame()).print(info.out, r.query_range().begin_, r.query_range().end_, amino_acid_traits);
        };
    callbacks[FieldId::QSeqTranslated].query_intro = [](const TabularFormat&, Output::Info& info) {
        info.out << '*';
        };

    callbacks[FieldId::ApproxPIdent].match = [](const TabularFormat&, const HspContext& r, Output::Info& info) {
        info.out << r.approx_id();
        };
    callbacks[FieldId::ApproxPIdent].query_intro = [](const TabularFormat&, Output::Info& info) {
        info.out << "-1";
        };

    callbacks[FieldId::CorrectedBitScore].match = [](const TabularFormat&, const HspContext& r, Output::Info& info) {
        info.out << r.corrected_bit_score();
        };

    callbacks[FieldId::SLineages].match = [](const TabularFormat& format, const HspContext& r, Output::Info& info) {
        print_lineage(r.subject_oid, *info.db, info.out, format.is_json);
        };
    callbacks[FieldId::SLineages].query_intro = [](const TabularFormat&, Output::Info& info) {
        info.out << '*';
        };

    callbacks[FieldId::HspNum].match = [](const TabularFormat&, const HspContext& r, Output::Info& info) {
        info.out << r.hsp_num;
        };

    callbacks[FieldId::NormalizedBitscore].match = [](const TabularFormat&, const HspContext& r, Output::Info& info) {
        info.out.print_d(r.bit_score() / std::max(r.query_self_aln_score, r.target_self_aln_score));
        };

    callbacks[FieldId::NormalizedBitscoreQuery].match = [](const TabularFormat&, const HspContext& r, Output::Info& info) {
        info.out.print_d(r.bit_score() / r.query_self_aln_score);
        };

    callbacks[FieldId::NORMALIZED_NIDENT].match = [](const TabularFormat&, const HspContext& r, Output::Info& info) {
        info.out.print_d((double)r.identities() / std::max(r.query.index(r.frame()).length(), r.subject_len));
        };

#ifdef DP_STAT
    callbacks[FieldId::Reserved1].match = [](const TabularFormat&, const HspContext& r, Output::Info& info) {
        info.out << r.reserved1();
        };
    callbacks[FieldId::Reserved2].match = [](const TabularFormat&, const HspContext& r, Output::Info& info) {
        info.out << r.reserved2();
        };
#endif

    return callbacks;
    }();

Header TabularFormat::header_format(unsigned workflow) {
    const bool cluster = workflow == Config::cluster || workflow == Config::DEEPCLUST || workflow == Config::LINCLUST;
	if (workflow != Config::blastp && !cluster)
		throw runtime_error("header_format");
	if (!config.output_header.present())
		return Header::NONE;
	if (config.output_header.empty())
		return cluster ? Header::SIMPLE : Header::VERBOSE;
	if (config.output_header.size() > 1)
		throw runtime_error("Invalid header format: " + join(" ", config.output_header.cbegin(), config.output_header.cend()));
	const Header h = from_string<Header>(config.output_header.front());
	if (h == Header::VERBOSE && cluster)
		throw runtime_error("Verbose header format is not supported for cluster workflow.");
	return h;
}

TabularFormat::TabularFormat(bool json) :
    OutputFormat((json ? OutputFormat::json : OutputFormat::blast_tab), HspValues::NONE, Flags::NONE, json ? ',' : '\0'),
    is_json(json)
{
    static const FieldId stdf[] = { FieldId::QSeqId, FieldId::SSeqId, FieldId::PIdent, FieldId::Length, FieldId::Mismatch, FieldId::GapOpen, FieldId::QStart, FieldId::QEnd, FieldId::SStart, FieldId::SEnd, FieldId::EValue, FieldId::BitScore };
    const vector<string>& f = config.output_format;
    if (f.size() <= 1) {
        fields = vector<FieldId>(stdf, stdf + 12);
        if (config.frame_shift == 0)
            hsp_values = HspValues::QUERY_COORDS | HspValues::TARGET_COORDS | HspValues::LENGTH | HspValues::IDENT | HspValues::MISMATCHES | HspValues::GAP_OPENINGS;
        else
            hsp_values = HspValues::TRANSCRIPT;
        flags |= Output::Flags::SSEQID;
        return;
    }
    for (vector<string>::const_iterator i = f.begin() + 1; i != f.end(); ++i) {
        auto it = std::find_if(field_def.begin(), field_def.end(), [i](const pair<FieldId, OutputField>& f) {return f.second.key == *i; });
        if (it == field_def.end())
            throw std::runtime_error(string("Invalid output field: ") + *i);
        const FieldId id = it->first;
        if (id == FieldId::STaxIds)
            needs_taxon_id_lists = true;
        if (id == FieldId::SSciNames || id == FieldId::SSKingdoms || id == FieldId::SKingdoms || id == FieldId::SPhylums || id == FieldId::SLineages || id >= FieldId::COUNT) {
            needs_taxon_scientific_names = true;
            needs_taxon_id_lists = true;
        }
        if (id == FieldId::SSKingdoms || id == FieldId::SKingdoms || id == FieldId::SPhylums || id >= FieldId::COUNT) {
            needs_taxon_nodes = true;
            needs_taxon_ranks = true;
        }
        if (id == FieldId::SLineages) {
            needs_taxon_nodes = true;
        }
        fields.push_back(id);
        if (id == FieldId::FullSSeq || id == FieldId::ApproxPIdent)
            flags |= Flags::TARGET_SEQS;
        if (id == FieldId::QQual || id == FieldId::FullQQual)
            config.store_query_quality = true;
        if (id == FieldId::FullQSeqMate)
            needs_paired_end_info = true;
        if (id == FieldId::ApproxPIdent && score_matrix.name() != "BLOSUM62")
            throw std::runtime_error("Approximate identity is only supported for the BLOSUM62 scoring matrix.");
        if ((id == FieldId::FullQSeqMate || id == FieldId::QSeqTranslated) && !align_mode.query_translated)
            throw std::runtime_error("Output field only supported for translated search.");
        hsp_values |= field_def.at(id).hsp_values;
        flags |= field_def.at(id).flags;
    }
    //if (config.traceback_mode == TracebackMode::NONE && config.max_hsps == 1 && !needs_transcript && !needs_stats && !config.query_range_culling && config.min_id == 0.0 && config.query_cover == 0.0 && config.subject_cover == 0.0)
        //config.traceback_mode = TracebackMode::SCORE_ONLY;
}

void TabularFormat::print_match(const HspContext& r, Output::Info& info)
{
    TextBuffer& out = info.out;
    const char* prepos = "\t";
    const auto seed_only_field_available = [](const FieldId id) {
        switch (id) {
        case FieldId::QSeqId:
        case FieldId::QLen:
        case FieldId::SSeqId:
        case FieldId::SAllSeqId:
        case FieldId::SLen:
        case FieldId::QStart:
        case FieldId::QEnd:
        case FieldId::SStart:
        case FieldId::SEnd:
        case FieldId::Score:
        case FieldId::QFrame:
        case FieldId::STaxIds:
        case FieldId::SSciNames:
        case FieldId::SSKingdoms:
        case FieldId::STitle:
        case FieldId::SAllTitles:
        case FieldId::QTitle:
        case FieldId::FullSSeq:
        case FieldId::QNum:
        case FieldId::SNum:
        case FieldId::FullQQual:
        case FieldId::FullQSeq:
        case FieldId::QStrand:
        case FieldId::SKingdoms:
        case FieldId::SPhylums:
        case FieldId::FullQSeqMate:
        case FieldId::HspNum:
        case FieldId::SLineages:
        case FieldId::QCovHsp: // TODO
        case FieldId::SCovHsp:
        case FieldId::CorrectedBitScore:
            return true;
        default:
            return false;
        }
    };
    const auto print_seed_only_blank = [&](const OutputField& field) {
        if (is_json && !flag_any(field.flags, Flags::IS_STRING) && !flag_any(field.flags, Flags::IS_ARRAY))
            out << "N/A";
    };
    if (is_json) {
        if (r.hit_num != 0)
            out << ",";
        out << "\n\t{\n";
    }
    for (auto i = fields.cbegin(); i != fields.cend(); ++i) {
        const OutputField& field = field_def.at(*i);
        if (is_json) {
            out << prepos << "\"" << field.key << "\":";
            if (flag_any(field.flags, Flags::IS_STRING))
                out << "\"";
            if (flag_any(field.flags, Flags::IS_ARRAY))
                out << "[";
        }
        if (r.seed_only() && !seed_only_field_available(*i))
            print_seed_only_blank(field);
        else {
            const FieldCallbacks& callbacks = field_callbacks.at(*i);
            callbacks.match(*this, r, info);
        }
        if (is_json) {
            if (flag_any(field.flags, Flags::IS_STRING))
                out << "\"";
            if (flag_any(field.flags, Flags::IS_ARRAY))
                out << "]";
            if (i < fields.end() - 1)
                out << ",\n";
            else
                out << "\n";
        }
        else if (i < fields.end() - 1)
            out << '\t';
    }
    out << (is_json ? "\t}" : "\n");
}

void TabularFormat::print_query_intro(Output::Info& info) const
{
    TextBuffer& out = info.out;
    if (info.unaligned && config.report_unaligned == 1) {
        for (auto i = fields.cbegin(); i != fields.cend(); ++i) {
            const FieldCallbacks& callbacks = field_callbacks.at(*i);
            callbacks.query_intro(*this, info);
            if (i < fields.end() - 1)
                out << '\t';
        }
        out << '\n';
    }
}

void TabularFormat::output_header(File& f, bool cluster) const {
    vector<string> headers;
    transform(fields.begin(), fields.end(), back_inserter(headers), [cluster](FieldId i) {
        const OutputField& field = TabularFormat::field_def.at(i);
        const string& key = cluster ? field.clust_key : field.key;
        if (cluster && key.empty())
            throw runtime_error("Output field not supported for clustering: " + field.key);
        return key;
        });
    const string s = join("\t", headers.begin(), headers.end()) + '\n';
    f.write(s.data(), s.length());
    return;
}

void TabularFormat::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 {
    const Header h = header_format(Config::blastp);
    if (h == Header::VERBOSE) {
        std::ostringstream ss;
        ss << "# DIAMOND v" << Const::version_string << ". http://github.com/bbuchfink/diamond" << endl;
        ss << "# Invocation: " << config.invocation << endl;
        ss << "# Fields: ";
		for (auto i = fields.begin(); i != fields.end(); ++i) {
            if(i != fields.begin())
				ss << ", ";
            ss << field_def.at(*i).description;
        }
        ss << std::endl;
        const string s(ss.str());
        f.write(s.data(), s.length());
    }
    else if (h == Header::SIMPLE) {
        output_header(f, false);
    }
    if (is_json) {
        const char* hdr = "[";
        f.write(hdr, strlen(hdr));
    }
}

void TabularFormat::print_footer(File &f) const {
    if(is_json) {
        const char* s = "\n]";
		f.write(s, strlen(s));
    }
}
