/**
 * 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 <QObject>
#include <QString>

#include <U2Core/DNAAlphabet.h>
#include <U2Core/Task.h>

struct plan7_s;
struct msa_struct;

namespace U2 {

class TaskStateInfo;
class IOAdapterFactory;

class HMMIO : public QObject {
    Q_OBJECT
public:
    static void writeHMM2(IOAdapterFactory* iof, const QString& url, TaskStateInfo& si, plan7_s* hmm);

    static void readHMM2(IOAdapterFactory* iof, const QString& url, TaskStateInfo& si, plan7_s** ret_hmm);

    static plan7_s* cloneHMM(plan7_s* src);

    // utility methods, TODO: move to a separate class

    static const QString HMM_ID;
    static const QString HMM_EXT;
    static QString getHMMFileFilter();

    static DNAAlphabetType convertHMMAlphabet(int hmmAtype);
};

class HMMReadTask : public Task {
    Q_OBJECT
public:
    HMMReadTask(const QString& url);
    ~HMMReadTask();
    void run();
    plan7_s* getHMM() const {
        return hmm;
    }
    const QString& getURL() const {
        return url;
    }

private:
    plan7_s* hmm;
    QString url;
};

class HMMWriteTask : public Task {
    Q_OBJECT
public:
    HMMWriteTask(const QString& url, plan7_s* s, uint = 0);
    virtual void run();

private:
    QString url;
    plan7_s* hmm;
    uint fileMode;
};

}  // namespace U2
