/**
 * UGENE - Integrated Bioinformatics Tools.
 * Copyright (C) 2008-2023 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 <QPointer>

#include <U2Algorithm/ORFAlgorithmTask.h>

#include <U2Core/AutoAnnotationsSupport.h>

namespace U2 {

class AnnotationTableObject;
class Settings;
class DNASequence;

struct ORFSettingsKeys {
public:
    static const QString STRAND;
    static const QString AMINO_TRANSL;
    static const QString SEARCH_REGION;
    static const QString MIN_LEN;
    static const QString MUST_FIT;
    static const QString MUST_INIT;
    static const QString ALLOW_ALT_START;
    static const QString ALLOW_OVERLAP;
    static const QString INCLUDE_STOP_CODON;
    static const QString CIRCULAR_SEARCH;
    static const QString MAX_RESULT;
    static const QString IS_RESULT_LIMITED;

    static void save(const ORFAlgorithmSettings& cfg, Settings* st);
    static void read(ORFAlgorithmSettings& cfg, const Settings* st);
};

class FindORFsToAnnotationsTask : public Task {
    Q_OBJECT
public:
    FindORFsToAnnotationsTask(AnnotationTableObject* aobj, const U2EntityRef& entityRef, const ORFAlgorithmSettings& settings, const QString& groupName = QString(), const QString& annDescription = "");

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

private:
    QPointer<AnnotationTableObject> annotationTableObject;
    ORFFindTask* fTask;
    ORFAlgorithmSettings cfg;
    QString groupName;
    const QString annDescription;
    U2EntityRef entityRef;
};

class ORFAutoAnnotationsUpdater : public AutoAnnotationsUpdater {
    Q_OBJECT
public:
    ORFAutoAnnotationsUpdater();
    Task* createAutoAnnotationsUpdateTask(const AutoAnnotationObject* aa);
    bool checkConstraints(const AutoAnnotationConstraints& constraints);
};

}  // namespace U2
