/**
 * 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 <U2Core/AnnotationData.h>
#include <U2Core/DNASequenceObject.h>
#include <U2Core/DocumentProviderTask.h>

namespace U2 {

class DNAAlphabet;
class DNATranslation;
class U2Sequence;

/** An item to export sequence. Contains unprocessed sequence + annotations + info about required transformations */
class ExportSequenceItem {
public:
    ExportSequenceItem();
    ExportSequenceItem(const ExportSequenceItem& other);

    ~ExportSequenceItem();

    void setOwnershipOverSeq(const U2Sequence& seq, const U2DbiRef& dbiRef);
    void setSequenceInfo(U2SequenceObject* seqObj);

    // after calling this method the client code takes responsibility for correct release the sequence from the database
    U2SequenceObject* takeOwnedSeq();
    bool ownsSeq() const;
    bool isEmpty() const;

    ExportSequenceItem& operator=(const ExportSequenceItem& other);
    bool operator==(const ExportSequenceItem& other) const;

    U2EntityRef seqRef;  // sequence to copy
    QString name;
    bool circular;
    const DNAAlphabet* alphabet;
    qint64 length;

    // Annotations to copy. Key is the annotations group path, value - the list of the corresponding annotations
    QMap<QString, QList<SharedAnnotationData>> annotations;
    const DNATranslation* complTT;  // complement translations for a sequence. Used only if 'strand' is 'compl' or 'both'
    const DNATranslation* aminoTT;  // amino translation for a sequence. If not NULL -> sequence is translated
    const DNATranslation* backTT;  // nucleic translation for a sequence. If not NULL -> sequence is back translated

private:
    void startSeqOwnership();
    int incrementSeqRefCount() const;
    int decrementSeqRefCount() const;
    void stopSeqOwnership();

    void releaseOwnedSeq();

    static QMap<U2EntityRef, int> sequencesRefCounts;
};

class ExportSequenceTaskSettings {
public:
    ExportSequenceTaskSettings();

    QList<ExportSequenceItem> items;  // sequences to export

    QString fileName;  // result file name
    bool merge;  // if true -> multiple sequences are merged
    int mergeGap;  // the gap between sequences if merged

    TriState strand;  // Yes -> direct, No -> complement, Unknown -> Both
    bool allAminoFrames;  // for every sequence and (every complement if needed) generates 3-frame amino translations

    bool mostProbable;  // True - use most probable codon, False - use distribution according to frequency

    bool saveAnnotations;  // Store available annotations for sequences into result file too

    DocumentFormatId formatId;

    QString sequenceName;  // custom sequence name

    qint64 sequenceLength;  // length of the sequence if there is the only source sequence
};

/** Exports sequences a file */
class ExportSequenceTask : public DocumentProviderTask {
    Q_OBJECT
public:
    ExportSequenceTask(const ExportSequenceTaskSettings& s);

    void run() override;

    static ExportSequenceItem mergedCircularItem(const ExportSequenceItem& first,
                                                 const ExportSequenceItem& second,
                                                 U2OpStatus& os);

private:
    ExportSequenceTaskSettings config;
};

//////////////////////////////////////////////////////////////////////////
// Task to export sequences under annotations

class ExportSequenceAItem {
public:
    ExportSequenceAItem();

    QPointer<U2SequenceObject> sequence;  // sequence
    QList<SharedAnnotationData> annotations;  // annotated regions to be exported
    const DNATranslation* aminoTT;  // if not null -> sequence regions will be translated (0-frame only)
    const DNATranslation* complTT;  // if not null & annotation location is on complement strand - it will be rev-complemented
};

class ExportAnnotationSequenceTaskSettings {
public:
    QList<ExportSequenceAItem> items;  // data to export
    ExportSequenceTaskSettings exportSequenceSettings;  // extra configuration for ExportSequenceTask
};

class ExportAnnotationSequenceSubTask : public Task {
    Q_OBJECT
public:
    ExportAnnotationSequenceSubTask(ExportAnnotationSequenceTaskSettings& s);

    void run() override;

private:
    U2Sequence importAnnotatedSeq2Dbi(const SharedAnnotationData& ad, const ExportSequenceAItem& ei, const U2DbiRef& resultDbiRef, QVector<U2Region>& resultRegions, U2OpStatus& os);
    ExportAnnotationSequenceTaskSettings& config;
};

class ExportAnnotationSequenceTask : public DocumentProviderTask {
    Q_OBJECT
public:
    ExportAnnotationSequenceTask(const ExportAnnotationSequenceTaskSettings& s);

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

private:
    ExportAnnotationSequenceTaskSettings config;
    ExportAnnotationSequenceSubTask* extractSubTask;
    ExportSequenceTask* exportSubTask;
};

}  // namespace U2
