/**
 * 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 <U2Test/GTest.h>
#include <U2Test/XMLTestFormat.h>
#include <U2Test/XMLTestUtils.h>

#include "HmmerBuildTask.h"

namespace U2 {

/*****************************************
 * Builds hmm profile from input file
 *****************************************/
class GTest_UHMMER3Build : public XmlTest {
    Q_OBJECT
public:
    static const QString INPUT_FILE_TAG;
    static const QString OUTPUT_FILE_TAG;
    static const QString OUTPUT_DIR_TAG;
    static const QString DEL_OUTPUT_TAG;

    static const QString RELATIVE_WEIGHTING_OPTION_TAG; /* --wgsc, --wblosum, --wpb, --wnone, --wgiven */

    static const QString EFFECTIVE_WEIGHTING_OPTION_TAG; /* --eent, --eclust, --enone, --eset */

    static const QString E_VALUE_CALIBRATION_OPTION_TAG; /*  */

    static const QString MODEL_CONSTRUCTION_OPTION_TAG; /* --fast + symfrac and
                                                        --hand ( requires RF annotation )*/
    static const QString SEED_OPTION_TAG;

    static void setBuildSettings(HmmerBuildSettings& settings, const QDomElement& el, TaskStateInfo& ti);

public:
    SIMPLE_XML_TEST_BODY_WITH_FACTORY(GTest_UHMMER3Build, "uhmmer3-build")

    virtual void prepare();
    ReportResult report();
    void cleanup();

private:
    void setAndCheckArgs();

private:
    QString inFile;
    QString outFile;
    QString outputDir;
    bool delOutFile;
    HmmerBuildSettings bldSettings;
    HmmerBuildTask* buildTask;

};  // GTest_UHMMER3Build

/*****************************************
 * Totally compares two hmm files
 *****************************************/
class GTest_CompareHmmFiles : public XmlTest {
    Q_OBJECT
public:
    static const QString FILE1_NAME_TAG;
    static const QString FILE2_NAME_TAG;
    static const QString FILE1_TMP_TAG;
    static const QString FILE2_TMP_TAG;

public:
    SIMPLE_XML_TEST_BODY_WITH_FACTORY(GTest_CompareHmmFiles, "hmm3-compare-files");
    ReportResult report();

private:
    void setAndCheckArgs();

private:
    QString filename1;
    QString filename2;
    bool file1Tmp;
    bool file2Tmp;

};  // GTest_CompareHmmFiles

}  // namespace U2
