/**
 * UGENE - Integrated Bioinformatics Tools.
 * Copyright (C) 2008-2023 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 <QVector>

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

#include "RFBase.h"

namespace U2 {

class SArrayIndex;
class RFSArrayWKSubtask;
class RFRollingArray;

class RFSArrayWKAlgorithm : public RFAlgorithmBase {
    Q_OBJECT
    friend class RFSArrayWKSubtask;

public:
    RFSArrayWKAlgorithm(RFResultsListener* rl, const char* seqX, int sizeX, const char* seqY, int sizeY, DNAAlphabetType seqType, int w, int k);

    ~RFSArrayWKAlgorithm() {
        cleanup();
    }

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

    void cleanup();

private:
    void addResult(int a, int s, int l, int c);
    void calculate(RFSArrayWKSubtask* t);

public:
    QVector<int> diagOffsets;  // holds start position for the last checked window
    int ARRAY_SIZE;
    int SEARCH_SIZE;

    const char* arraySeq;
    const char* searchSeq;
    bool arrayIsX;

    quint32 q;

    CreateSArrayIndexTask* indexTask;
    int nThreads;
};

class RFSArrayWKSubtask : public Task, public SArrayIndex::SAISearchContext {
    Q_OBJECT
    friend class RFSArrayWKAlgorithm;

public:
    RFSArrayWKSubtask(RFSArrayWKAlgorithm* owner, int _tid);
    virtual ~RFSArrayWKSubtask() {
    }
    void run();

    RFSArrayWKAlgorithm* owner;

    const int tid;
};

}  // namespace U2
