/**
 * 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 <U2Core/GUrl.h>
#include <U2Core/Task.h>
#include <U2Core/U2Assembly.h>
#include <U2Core/U2AssemblyDbi.h>
#include <U2Core/U2OpStatusUtils.h>

#include "ace/AceImportUtils.h"

namespace U2 {

class ConvertAceToSqliteTask : public Task {
    Q_OBJECT
public:
    ConvertAceToSqliteTask(const GUrl& sourceUrl, const U2DbiRef& dstDbiRef);

    virtual void run();
    virtual ReportResult report();

    GUrl getDestinationUrl() const;
    QMap<U2Sequence, U2Assembly> getImportedObjects() const;

private:
    qint64 importAssemblies(IOAdapter& ioAdapter);
    qint64 packReads();
    void updateAttributeDbi();

    const GUrl sourceUrl;

    U2DbiRef dstDbiRef;
    U2Dbi* dbi;

    bool databaseWasCreated;
    int countImportedAssembly;
    QMap<int, Assembly::Sequence> referencesData;
    QMap<int, U2Assembly> assemblies;
    QMap<int, U2AssemblyReadsImportInfo> importInfos;
    QMap<int, U2Sequence> importedReferences;
};

}  // namespace U2
