/**
 * UGENE - Integrated Bioinformatics Tools.
 * Copyright (C) 2008-2021 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.
 */

#ifndef _U2_SEQUENCE_DBI_WALKER_TASK_H_
#define _U2_SEQUENCE_DBI_WALKER_TASK_H_

#include <U2Core/Task.h>
#include <U2Core/U2Type.h>

#include "SequenceWalkerTask.h"

namespace U2 {

class DNATranslation;
class SequenceDbiWalkerSubtask;

class U2CORE_EXPORT SequenceDbiWalkerConfig : public SequenceWalkerConfig {
public:
    U2EntityRef seqRef;
};

class U2CORE_EXPORT SequenceDbiWalkerCallback {
public:
    virtual ~SequenceDbiWalkerCallback() {
    }

    virtual void onRegion(SequenceDbiWalkerSubtask *t, TaskStateInfo &ti) = 0;

    /* implement this to give SequenceDbiWalkerSubtask required resources
     * here are resources for ONE(!) SequenceDbiWalkerSubtask execution e.g. for one execution of onRegion function
     */
    virtual QList<TaskResourceUsage> getResources(SequenceDbiWalkerSubtask *t) {
        Q_UNUSED(t);
        return QList<TaskResourceUsage>();
    }
};

class U2CORE_EXPORT SequenceDbiWalkerTask : public Task {
    Q_OBJECT
public:
    SequenceDbiWalkerTask(const SequenceDbiWalkerConfig &config, SequenceDbiWalkerCallback *callback, const QString &name, TaskFlags tf = TaskFlags_NR_FOSE_COSC);

    SequenceDbiWalkerCallback *getCallback() const {
        return callback;
    }
    const SequenceDbiWalkerConfig &getConfig() const {
        return config;
    }

    // reverseMode - start splitting from the end of the range
    static QVector<U2Region> splitRange(const U2Region &range, int chunkSize, int overlapSize, int lastChunkExtraLen, bool reverseMode);

    void setError(const QString &err) {
        stateInfo.setError(err);
    }

private:
    QList<SequenceDbiWalkerSubtask *> prepareSubtasks();
    QList<SequenceDbiWalkerSubtask *> createSubs(const QVector<U2Region> &chunks, bool doCompl, bool doAmino);

    SequenceDbiWalkerConfig config;
    SequenceDbiWalkerCallback *callback;
};

class U2CORE_EXPORT SequenceDbiWalkerSubtask : public Task {
    Q_OBJECT
public:
    SequenceDbiWalkerSubtask(SequenceDbiWalkerTask *t, const U2Region &globalReg, bool lo, bool ro, const U2EntityRef &seqRef, int localLen, bool doCompl, bool doAmino);

    void run();

    const char *getRegionSequence();

    int getRegionSequenceLen();

    bool isDNAComplemented() const {
        return doCompl;
    }

    bool isAminoTranslated() const {
        return doAmino;
    }

    U2Region getGlobalRegion() const {
        return globalRegion;
    }

    const SequenceDbiWalkerConfig &getGlobalConfig() const {
        return t->getConfig();
    }

    bool intersectsWithOverlaps(const U2Region &globalReg) const;
    bool hasLeftOverlap() const {
        return leftOverlap;
    }
    bool hasRightOverlap() const {
        return rightOverlap;
    }

private:
    bool needLocalRegionProcessing() const {
        return (doAmino || doCompl) && processedSeqImage.isEmpty();
    }
    void prepareLocalRegion();

    SequenceDbiWalkerTask *t;
    U2Region globalRegion;
    U2EntityRef seqRef;
    const char *localSeq;
    const char *originalLocalSeq;
    int localLen;
    int originalLocalLen;
    bool doCompl;
    bool doAmino;
    bool leftOverlap;
    bool rightOverlap;

    QByteArray processedSeqImage;
};

}    // namespace U2

#endif
