/**
 * UGENE - Integrated Bioinformatics Tools.
 * Copyright (C) 2008-2021 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.
 */

#ifndef _U2_WEVOTE_TASK_H_
#define _U2_WEVOTE_TASK_H_

#include <U2Core/ExternalToolRunTask.h>

#include "../ngs_reads_classification/src/TaxonomySupport.h"

namespace U2 {

class PrepareWevoteTaxonomyDataTask;

struct WevoteTaskSettings {
    WevoteTaskSettings();

    int penalty;
    int numberOfAgreedTools;
    int scoreThreshold;
    int numberOfThreads;
    QString inputFileUrl;
    QString workingDir;
    QString outputFileUrl;
};

class WevoteTask : public ExternalToolSupportTask {
    Q_OBJECT
public:
    WevoteTask(const WevoteTaskSettings &settings, FileStorage::WorkflowProcess &workflowProcess);

    const QString &getClassificationUrl() const;
    const LocalWorkflow::TaxonomyClassificationResult &getClassification() const;

    static const QString SUFFIX;

private:
    void prepare();
    QList<Task *> onSubTaskFinished(Task *subTask);
    void run();

    void checkSettings();
    QStringList getArguments();
    void moveFile();
    void parseClassification();

    const WevoteTaskSettings settings;
    FileStorage::WorkflowProcess &workflowProcess;

    PrepareWevoteTaxonomyDataTask *prepareTaxonomyTask;
    QString wevotePrefix;
    LocalWorkflow::TaxonomyClassificationResult classification;
};

}    // namespace U2

#endif    // _U2_WEVOTE_TASK_H_
