/**
 * 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 <QMutex>

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

#include "RFBase.h"

namespace U2 {

class FindRepeatsTaskSettings {
public:
    FindRepeatsTaskSettings()
        : minLen(2),
          mismatches(0),
          minDist(0),
          maxDist(0),
          inverted(false),
          reportReflected(false),
          maxResults(10 * 1000 * 100),
          reportSeqShift(0),
          reportSeq2Shift(0),
          algo(RFAlgorithm_Auto),
          filter(DisjointRepeats),
          nThreads(MAX_PARALLEL_SUBTASKS_AUTO),
          excludeTandems(false) {
    }

    int minLen;
    int mismatches;
    int minDist;
    int maxDist;
    bool inverted;
    bool reportReflected;
    int maxResults;
    U2Region seqRegion;
    U2Region seq2Region;
    qint64 reportSeqShift;
    qint64 reportSeq2Shift;

    // all these regions are in global sequence coordinates
    QVector<U2Region> midRegionsToInclude;  // reported repeat must contain one of these regions
    QVector<U2Region> midRegionsToExclude;  // reported repeat must not contain none of these regions
    QVector<U2Region> allowedRegions;  // reported repeat must fit one of these regions

    RFAlgorithm algo;
    RepeatsFilterAlgorithm filter;
    int nThreads;
    bool excludeTandems;

    void setIdentity(int percent) {
        mismatches = int((minLen / 100.0) * (100 - percent));
    }
    int getIdentity(int mismatch = -1) const {
        return qBound(50, int(100.0 - (mismatch == -1 ? mismatches : mismatch) * 100. / minLen), 100);
    }
    bool hasRegionFilters() const {
        return !midRegionsToInclude.isEmpty() || !midRegionsToExclude.isEmpty() || !allowedRegions.isEmpty();
    }

    static int getIdentity(int mismatch, int len) {
        return qBound(50, int(100.0 - (mismatch * 100. / len)), 100);
    }
};

// WARNING: this task is suitable only for a single sequence processing -> check addResults x/y sorting
class RevComplSequenceTask;
class FindTandemsToAnnotationsTask;
class FindRepeatsTask : public Task, public RFResultsListener {
    Q_OBJECT
public:
    FindRepeatsTask(const FindRepeatsTaskSettings& s, const DNASequence& seq, const DNASequence& seq2);

    void prepare();
    void run();
    ReportResult report();
    void cleanup();

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

    virtual void onResult(const RFResult& r);
    virtual void onResults(const QVector<RFResult>& v);

    QVector<RFResult> getResults() const {
        return results;
    }  // used if createAnnotations == false
    const FindRepeatsTaskSettings& getSettings() const {
        return settings;
    }

protected:
    void addResult(const RFResult& r);
    void _addResult(int x, int y, int l, int c);
    bool isFilteredByRegions(const RFResult& r);
    RFAlgorithmBase* createRFTask();
    void filterNestedRepeats();
    void filterUniqueRepeats();
    Task* createRepeatFinderTask();
    void filterTandems(const QList<SharedAnnotationData>& tandems, DNASequence& se);

    bool oneSequence;
    FindRepeatsTaskSettings settings;
    DNASequence seq1, seq2;
    QVector<RFResult> results;
    QMutex resultsLock;
    RevComplSequenceTask* revComplTask;
    RFAlgorithmBase* rfTask;
    quint64 startTime;
    FindTandemsToAnnotationsTask* tandemTask1;
    FindTandemsToAnnotationsTask* tandemTask2;
};

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

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

private:
    QString annName;
    QString annGroup;
    const QString annDescription;
    GObjectReference annObjRef;
    FindRepeatsTask* findTask;
    FindRepeatsTaskSettings settings;
};

class RevComplSequenceTask : public Task {
    Q_OBJECT
public:
    RevComplSequenceTask(const DNASequence& s, const U2Region& reg);

    void run();
    void cleanup();

    DNASequence sequence;
    U2Region region;
    DNASequence complementSequence;
};

}  // namespace U2
