/**
 * 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 <U2Algorithm/FindAlgorithm.h>

#include <U2Core/AbstractProjectFilterTask.h>

namespace U2 {

class U2SequenceObject;

//////////////////////////////////////////////////////////////////////////
/// SequenceConentFilterTask
//////////////////////////////////////////////////////////////////////////

class SequenceContentFilterTask : public AbstractProjectFilterTask, public FindAlgorithmResultsListener {
    Q_OBJECT
public:
    SequenceContentFilterTask(const ProjectTreeControllerModeSettings& settings, const QList<QPointer<Document>>& docs);

    void onResult(const FindAlgorithmResult& r) override;

protected:
    bool filterAcceptsObject(GObject* obj) override;

private:
    bool sequenceContainsPattern(U2SequenceObject* seqObject, const QString& pattern, const FindAlgorithmSettings& findSettings);
    void searchThroughRegion(U2SequenceObject* seqObject, const U2Region& searchRegion, const QString& pattern, const FindAlgorithmSettings& findSettings);

    static bool patternFitsSequenceAlphabet(U2SequenceObject* seqObject, const QString& pattern);
    static bool initFindAlgorithmSettings(U2SequenceObject* seqObject, FindAlgorithmSettings& findSettings);

    int searchStopFlag;

    static const qint64 SEQUENCE_CHUNK_SIZE;
};

//////////////////////////////////////////////////////////////////////////
/// SequenceConentFilterTaskFactory
//////////////////////////////////////////////////////////////////////////

class U2ALGORITHM_EXPORT SequenceContentFilterTaskFactory : public ProjectFilterTaskFactory {
protected:
    AbstractProjectFilterTask* createNewTask(const ProjectTreeControllerModeSettings& settings,
                                             const QList<QPointer<Document>>& docs) const override;
};

}  // namespace U2
