/**
 * 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 "PhmmerSearchTask.h"

namespace U2 {

/*****************************************
 * Test for hmmer3 phmmer.
 * settings set by same tags from hmm3-search and hmm3-build tests + gaps probab. options and subst. matr
 * we test here 1<->1 queries
 *****************************************/
class GTest_UHMM3Phmmer : public XmlTest {
    Q_OBJECT
public:
    static const QString QUERY_FILENAME_TAG;
    static const QString DB_FILENAME_TAG;

    static const QString GAP_OPEN_PROBAB_OPTION_TAG;
    static const QString GAP_EXTEND_PROBAB_OPTION_TAG;

    static const QString OUTPUT_DIR_TAG;

public:
    SIMPLE_XML_TEST_BODY_WITH_FACTORY(GTest_UHMM3Phmmer, "hmm3-phmmer");

    void prepare();
    ReportResult report();
    QList<Task*> onSubTaskFinished(Task* subTask);

private:
    void setAndCheckArgs();

    static void setSearchTaskSettings(PhmmerSearchSettings& set, const QDomElement& el, TaskStateInfo& si);

private:
    PhmmerSearchSettings searchSettings;
    QString queryFilename;
    QString dbFilename;
    PhmmerSearchTask* phmmerTask;
    QString outputDir;
};  // GTest_UHMM3Phmmer

/*****************************************
 * Test compares original hmmer3 phmmer results with UHMM3SearchResults
 *
 * Note, that you should make original hmmer3 to show results in academic version (e.g. 1.01e-23)
 *****************************************/

class GTest_UHMM3PhmmerCompare : public XmlTest {
    Q_OBJECT
public:
    static const QString ACTUAL_OUT_FILE_TAG;
    static const QString TRUE_OUT_FILE_TAG;

public:
    SIMPLE_XML_TEST_BODY_WITH_FACTORY(GTest_UHMM3PhmmerCompare, "hmm3-phmmer-compare");
    ReportResult report();

private:
    void setAndCheckArgs();

private:
    QString actualOutFilename;
    QString trueOutFilename;
};  // GTest_UHMM3PhmmerCompare

}  // namespace U2
