/**
 * 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 <U2Core/Task.h>
#include <U2Core/U2Region.h>

namespace U2 {

class DNATranslation;
class SequenceWalkerSubtask;

enum StrandOption {
    StrandOption_DirectOnly,
    StrandOption_ComplementOnly,
    StrandOption_Both
};
class U2CORE_EXPORT SequenceWalkerConfig {
public:
    // TODO: allow select custom strand only!

    SequenceWalkerConfig();

    const char* seq;  //  sequence to split
    quint64 seqSize;  //  size of the sequence to split
    U2Region range;  //  if not empty -> only this region is processed
    DNATranslation* complTrans;
    DNATranslation* aminoTrans;

    quint64 chunkSize;  // optimal chunk size, used by default for all regions except last one
    int lastChunkExtraLen;  // extra length allowed to be added to the last chunk
    int overlapSize;  // overlap for 2 neighbor regions
    int nThreads;
    StrandOption strandToWalk;

    bool walkCircular;
    quint64 walkCircularDistance;
};

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

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

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

class U2CORE_EXPORT SequenceWalkerTask : public Task {
    Q_OBJECT
public:
    SequenceWalkerTask(const SequenceWalkerConfig& config, SequenceWalkerCallback* callback, const QString& name, TaskFlags tf = TaskFlags_NR_FOSE_COSC);

    SequenceWalkerCallback* getCallback() const {
        return callback;
    }
    const SequenceWalkerConfig& 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<SequenceWalkerSubtask*> prepareSubtasks();
    QList<SequenceWalkerSubtask*> createSubs(const QVector<U2Region>& chunks, bool doCompl, bool doAmino);

    SequenceWalkerConfig config;
    SequenceWalkerCallback* callback;

    QByteArray tempBuffer;
};

class U2CORE_EXPORT SequenceWalkerSubtask : public Task {
    Q_OBJECT
public:
    SequenceWalkerSubtask(SequenceWalkerTask* t, const U2Region& globalReg, bool lo, bool ro, const char* localSeq, int localLen, bool doCompl, bool doAmino);

    void run() override;

    const char* getRegionSequence();

    int getRegionSequenceLen();

    bool isDNAComplemented() const {
        return doCompl;
    }

    bool isAminoTranslated() const {
        return doAmino;
    }

    U2Region getGlobalRegion() const {
        return globalRegion;
    }

    const SequenceWalkerConfig& 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();

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

    QByteArray processedSeqImage;
};

}  // namespace U2
