/**
 * UGENE - Integrated Bioinformatics Tools.
 * Copyright (C) 2008-2025 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 <QMap>
#include <QMutex>

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

#include <U2Core/AnnotationData.h>
#include <U2Core/AppResources.h>
#include <U2Core/DNASequence.h>
#include <U2Core/GObjectReference.h>
#include <U2Core/SequenceWalkerTask.h>
#include <U2Core/Task.h>

#include "RFBase.h"
#include "RF_SuffixArray.h"

namespace U2 {

namespace TSConstants {
enum TSAlgo { AlgoSuffix = 0,
              AlgoSuffixBinary = 1 };
enum TSPreset { PresetAll = 0,
                PresetMicro = 1,
                PresetMini = 2,
                PresetBigPeriod = 3,
                PresetCustom = 4 };
}  // namespace TSConstants

class FindTandemsTaskSettings {
public:
    static const int DEFAULT_MIN_TANDEM_SIZE;
    static const int DEFAULT_MIN_REPEAT_COUNT;
    static const TSConstants::TSAlgo DEFAULT_ALGO = TSConstants::AlgoSuffixBinary;

public:
    FindTandemsTaskSettings()
        : minPeriod(1), maxPeriod(INT_MAX), minTandemSize(DEFAULT_MIN_TANDEM_SIZE), minRepeatCount(DEFAULT_MIN_REPEAT_COUNT),
          accuracy(0), maxResults(10 * 1000 * 100), reportSeqShift(0), showOverlappedTandems(false), algo(DEFAULT_ALGO), nThreads(MAX_PARALLEL_SUBTASKS_AUTO) {
    }

    int minPeriod;
    int maxPeriod;
    int minTandemSize;
    int minRepeatCount;
    int accuracy;
    int maxResults;
    qint64 reportSeqShift;
    U2Region seqRegion;
    bool showOverlappedTandems;

    TSConstants::TSAlgo algo;
    int nThreads;
};

class FindTandemsToAnnotationsTask : public Task {
    Q_OBJECT
public:
    FindTandemsToAnnotationsTask(const FindTandemsTaskSettings& s, const DNASequence& seq, const QString& annName, const QString& groupName, const QString& annDescription, const GObjectReference& annObjRef);
    FindTandemsToAnnotationsTask(const FindTandemsTaskSettings& s, const DNASequence& seq);

    QList<Task*> onSubTaskFinished(Task* subTask);
    QList<SharedAnnotationData> importTandemAnnotations(const QList<Tandem>& tandems, qint64 seqStart, const bool showOverlapped);

    QList<SharedAnnotationData> getResult() const {
        return result;
    }

private:
    bool saveAnns;
    DNASequence mainSeq;
    QString annName;
    QString annGroup;
    const QString annDescription;
    GObjectReference annObjRef;

    QList<SharedAnnotationData> result;
    const FindTandemsTaskSettings s;
};

class TandemFinder : public Task, public SequenceWalkerCallback {
    Q_OBJECT
public:
    TandemFinder(const FindTandemsTaskSettings& s, const DNASequence& seq);
    void prepare();
    void run();
    const QList<Tandem>& getResults() {
        return foundTandems;
    }
    const FindTandemsTaskSettings& getSettings() const {
        return settings;
    }
    const static quint32 maxCheckPeriod = 1024;  // max period is 1k
protected:
    // main sequence
    char* sequence;
    FindTandemsTaskSettings settings;
    QMutex tandemsAccessMutex;
    QList<Tandem> foundTandems;
    QList<Task*> onSubTaskFinished(Task* subTask);
    void onRegion(SequenceWalkerSubtask* t, TaskStateInfo& ti);

private:
    QMutex subtasksQueue;
    quint32 regionCount;
    quint64 startTime;
    QList<Task*> regionTasks;
};

class TandemFinder_Region : public Task {
    Q_OBJECT
public:
    TandemFinder_Region(const int regionId, const char* _sequence, const quint32 _seqSize, const quint64 _regionOffset, const FindTandemsTaskSettings& _settings)
        : Task(tr("Find tandems in %1 region").arg(regionId), TaskFlags_NR_FOSCOE),
          sequence(_sequence), seqSize(_seqSize), id(regionId), regionOffset(_regionOffset), settings(_settings) {
    }

    ~TandemFinder_Region();

    const QList<Tandem> getResult() {
        QMutexLocker tandemsAccessLocker(&tandemsAccessMutex);
        return foundTandems;
    };
    quint64 getRegionId() const {
        return id;
    }
    quint64 getRegionOffset() const {
        return regionOffset;
    }
    void prepare();

protected:
    // main sequence
    const char* sequence;
    const long seqSize;

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

private:
    const int id;
    const quint64 regionOffset;

    const FindTandemsTaskSettings& settings;
    QList<Tandem> foundTandems;
    QMutex tandemsAccessMutex;
    friend class ExactSizedTandemFinder;
    friend class LargeSizedTandemFinder;
    void addResult(const Tandem& tandem);
    void addResults(const QMap<Tandem, Tandem>& tandems);
};

class ConcreteTandemFinder : public Task {
    Q_OBJECT
public:
    ConcreteTandemFinder(QString taskName, const char* _sequence, const long _seqSize, const FindTandemsTaskSettings& _settings, const int _analysisSize);
    ~ConcreteTandemFinder() {};

    void prepare();
    void cleanup();

protected:
    // main sequence
    const char* sequence;
    const int seqSize;

    SArrayIndex* index;
    SuffixArray* suffixArray;
    const FindTandemsTaskSettings& settings;
    const int prefixLength;

    const quint32 suffArrSize;
    QList<Task*> onSubTaskFinished(Task* subTask);

private:
    const BitsTable bitsTable;

protected:
    QMap<Tandem, Tandem> rawTandems;
};

class ExactSizedTandemFinder : public ConcreteTandemFinder {
    Q_OBJECT
public:
    ExactSizedTandemFinder(const char* _sequence, const long _seqSize, const FindTandemsTaskSettings& _settings, const int _analysisSize);
    ~ExactSizedTandemFinder();

    void run();

private:
    quint32* checkAndSpreadTandem(const quint32* tandemStart, const quint32* tandemLast, quint32 repeatLen);
    quint32* checkAndSpreadTandem_bv(const quint32* tandemStart, const quint32* tandemLast, quint32 repeatLen);
    bool comparePrefixChars(const char*, const char*);
};

class LargeSizedTandemFinder : public ConcreteTandemFinder {
    Q_OBJECT
public:
    LargeSizedTandemFinder(const char* _sequence, const long _seqSize, const FindTandemsTaskSettings& _settings, const int _analysisSize);
    ~LargeSizedTandemFinder();

    void run();

private:
    quint32* checkAndSpreadTandem(const quint32* tandemStart, const quint32* tandemLast, const unsigned repeatLen);
    quint32* checkAndSpreadTandem_bv(const quint32* tandemStart, const quint32* tandemLast, const unsigned repeatLen);
    bool comparePrefixChars(const char*, const char*);
};

}  // namespace U2
