/**
 * 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 <QMutex>
#include <QVector>

#include <U2Algorithm/SArrayBasedFindTask.h>
#include <U2Algorithm/SArrayIndex.h>

#include "RFBase.h"

namespace U2 {

class RFSArrayWSubtask;

// finds exact matches using SArray index
class RFSArrayWAlgorithm : public RFAlgorithmBase {
    Q_OBJECT
    friend class RFSArrayWSubtask;

public:
    RFSArrayWAlgorithm(RFResultsListener* rl, const char* seqX, int sizeX, const char* seqY, int sizeY, const DNAAlphabet* al, int w);

    void prepare();

    QList<Task*> onSubTaskFinished(Task* subTask);

    void run();

    /** 8x/GAP mem usage (GAP~=W/2)*/
    void calculate(RFSArrayWSubtask* t);

private:
    void run(RFSArrayWSubtask* t);
    void addResult(int a, int s, int l, int c, RFSArrayWSubtask* t);
    void processBoundaryResults();

    static int getWGap(int w);

    const char* arraySeq;
    const char* searchSeq;
    int ARRAY_SIZE;
    int SEARCH_SIZE;
    bool arrayIsX;
    int arrayPercent;

    QMutex boundaryMutex;

    quint32 bitMaskCharBitsNum;
    const quint32* bitMask;
    BitsTable bt;

    /** boundary results */
    QVector<RFResult> bresults;

    CreateSArrayIndexTask* indexTask;
    int nThreads;
};

class RFSArrayWSubtask : public Task, public SArrayIndex::SAISearchContext {
    Q_OBJECT
    friend class RFSArrayWAlgorithm;

public:
    RFSArrayWSubtask(RFSArrayWAlgorithm* owner, int sStart, int sEnd, int _tid);

    void run();

    RFSArrayWAlgorithm* owner;
    const int sStart;
    const int sEnd;
    const int tid;
};

class CheckEdge {
public:
    CheckEdge(const char* _posS = nullptr, const char* _lastS = nullptr, qint32 _diag = 0)
        : posS(_posS), lastS(_lastS), diag(_diag) {
        next = this;
        prev = this;
    }

    void fromChain() {
        prev->next = next;
        next->prev = prev;
    }

    void toChain(CheckEdge* chain) {
        next = chain;
        prev = chain->prev;
        chain->prev->next = this;
        chain->prev = this;
    }

    const char* posS;
    const char* lastS;
    CheckEdge* next;
    CheckEdge* prev;
    int diag;
};

class EdgePool {
public:
    EdgePool(int size) {
        pool.resize(size);
        for (int i = 0; i < size; i++) {
            pool[i] = new CheckEdge();
        }
        nAvailable = size;
    }
    ~EdgePool() {
        qDeleteAll(pool);
    }

    CheckEdge* allocEdge(const char* posS, const char* lastS, int diag) {
        if (nAvailable != 0) {
            assert(nAvailable > 0);
            CheckEdge* edge = pool[--nAvailable];
            edge->posS = posS;
            edge->lastS = lastS;
            edge->diag = diag;
            edge->next = nullptr;
            edge->prev = edge;
            pool[nAvailable] = nullptr;
            return edge;
        }
        return new CheckEdge(posS, lastS, diag);
    }

    void returnEdge(CheckEdge* e) {
        if (nAvailable != pool.size()) {
            assert(nAvailable < pool.size() && nAvailable >= 0);
            assert(pool[nAvailable] == nullptr);
            pool[nAvailable++] = e;
        } else {
            delete e;
        }
    }

    int nAvailable;
    QVector<CheckEdge*> pool;
};

}  // namespace U2
