/**
 * UGENE - Integrated Bioinformatics Tools.
 * Copyright (C) 2008-2024 UniPro <ugene@unipro.ru>
 * http://ugene.net
 *
 * 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 2
 * 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, write to the Free Software
 * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
 * MA 02110-1301, USA.
 */

#pragma once

#include <QList>
#include <QObject>

#include <U2Algorithm/EnzymeModel.h>

#include <U2Core/AppContext.h>
#include <U2Core/DNAAlphabet.h>
#include <U2Core/DNASequence.h>
#include <U2Core/DNATranslation.h>
#include <U2Core/Task.h>
#include <U2Core/TextUtils.h>
#include <U2Core/U2Region.h>
#include <U2Core/U2SafePoints.h>
#include <U2Core/U2Type.h>

namespace U2 {

class FindEnzymesAlgListener {
public:
    ~FindEnzymesAlgListener() {
    }
    /*
     * Callback, which handle FindEnzymesAlgorithm::run(...) result finding.
     *
     * \param pos Start position of enzyme, which was found.
     * \param enzyme The enzyme, which was found.
     * \param strand Strand (direct of reverse-complement) the enzyme was found on.
     * \param stop This argument signals to FindEnzymesAlgorithm::run(...) to stop enzymes searching (without errors or cancels).
    **/
    virtual void onResult(int pos, const SEnzymeData& enzyme, const U2Strand& strand, bool& stop) = 0;
};

template<typename CompareFN>
class FindEnzymesAlgorithm {
public:
    void run(const DNASequence& sequence, const U2Region& region, const SEnzymeData& enzyme, FindEnzymesAlgListener* resultListener, TaskStateInfo& stateInfo, int resultPosShift = 0) {
        SAFE_POINT(enzyme->alphabet != nullptr, "No enzyme alphabet", );

        QByteArray enzymeSequence = enzyme->seq;
        int leadingNsNumber = 0;
        int trailingNsNumber = 0;
        enzyme->calculateLeadingAndTrailingLengths(leadingNsNumber, trailingNsNumber);
        if (leadingNsNumber != 0) {
            enzymeSequence.insert(0, QByteArray(leadingNsNumber, EnzymeData::UNDEFINED_BASE));
        }
        if (trailingNsNumber != 0) {
            enzymeSequence.append(QByteArray(trailingNsNumber, EnzymeData::UNDEFINED_BASE));
        }

        // look for results in direct strand
        run(sequence, region, enzyme, enzymeSequence, leadingNsNumber, U2Strand::Direct, resultListener, stateInfo, resultPosShift);
        CHECK_OP(stateInfo, );

        // if enzyme is not symmetric - look in complementary strand too
        DNATranslation* tt = AppContext::getDNATranslationRegistry()->lookupComplementTranslation(enzyme->alphabet);
        if (tt == nullptr) {
            return;
        }
        QByteArray revCompl = enzymeSequence;
        tt->translate(revCompl.data(), revCompl.size());
        TextUtils::reverse(revCompl.data(), revCompl.size());
        if (revCompl == enzymeSequence) {
            return;
        }
        run(sequence, region, enzyme, revCompl, trailingNsNumber, U2Strand::Complementary, resultListener, stateInfo, resultPosShift);
    }

    void run(const DNASequence& sequence, const U2Region& region, const SEnzymeData& enzyme, const QByteArray& byteArrayPattern, int leftShift, U2Strand stand, FindEnzymesAlgListener* resultListener, TaskStateInfo& ti, int resultPosShift = 0) {
        const char* pattern = byteArrayPattern.constData();
        CompareFN fn(sequence.alphabet, enzyme->alphabet);
        const char* seq = sequence.constData();
        char unknownChar = sequence.alphabet->getDefaultSymbol();
        int plen = byteArrayPattern.length();
        for (int pos = region.startPos, endPos = region.endPos() - plen + 1; pos < endPos; pos++) {
            bool match = matchSite(seq + pos, pattern, plen, unknownChar, fn);
            if (match) {
                bool stop = false;
                resultListener->onResult(resultPosShift + pos + leftShift, enzyme, stand, stop);
                CHECK(!stop, );
            }
            CHECK_OP(ti, );
        }
    }

    bool matchSite(const char* seq, const char* pattern, int plen, char unknownChar, const CompareFN& fn) const {
        bool match = true;
        for (int p = 0; p < plen && match; p++) {
            char c1 = seq[p];
            char c2 = pattern[p];
            bool seqUnknown = c1 == unknownChar;
            bool patternUnknown = c2 == unknownChar;
            if (seqUnknown && patternUnknown) {
                match = true;
            } else if (seqUnknown && !patternUnknown) {
                match = false;
            } else if (!seqUnknown && patternUnknown) {
                match = true;
            } else if (!seqUnknown && !patternUnknown) {
                match = fn.equals(c2, c1);
            }
        }
        return match;
    }
};

}  // namespace U2
