/**
 * 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_ENZYMES_TESTS_H_
#define _U2_ENZYMES_TESTS_H_

#include <QDomElement>
#include <QMultiMap>

#include <U2Core/AnnotationTableObject.h>
#include <U2Core/GObject.h>
#include <U2Core/U2Region.h>

#include <U2Test/XMLTestUtils.h>

#include "DNAFragment.h"

namespace U2 {

class LoadEnzymeFileTask;
class U2SequenceObject;

//cppcheck-suppress noConstructor
class GTest_FindEnzymes : public XmlTest {
    Q_OBJECT
    SIMPLE_XML_TEST_BODY_WITH_FACTORY(GTest_FindEnzymes, "find-enzymes");

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

private:
    int minHits;
    int maxHits;
    QString enzymesUrl;
    QString seqObjCtx;
    QString aObjName;
    U2SequenceObject *seqObj;
    QVector<U2Region> excludedRegions;
    QStringList enzymeNames;
    AnnotationTableObject *aObj;
    LoadEnzymeFileTask *loadTask;
    bool contextIsAdded;
    QMultiMap<QString, U2Region> resultsPerEnzyme;
};

//cppcheck-suppress noConstructor
class GTest_DigestIntoFragments : public XmlTest {
    Q_OBJECT
    SIMPLE_XML_TEST_BODY_WITH_FACTORY(GTest_DigestIntoFragments, "digest-into-fragments");

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

private:
    QString seqObjCtx;
    QString aObjCtx;
    QString enzymesUrl;
    QStringList enzymeNames;
    bool searchForEnzymes;
    bool isCircular;
    AnnotationTableObject *aObj;
    U2SequenceObject *seqObj;
    LoadEnzymeFileTask *loadTask;
};

class LigateFragmentsTask;

//cppcheck-suppress noConstructor
class GTest_LigateFragments : public XmlTest {
    Q_OBJECT
    SIMPLE_XML_TEST_BODY_WITH_FACTORY(GTest_LigateFragments, "ligate-fragments");

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

private:
    QStringList seqObjNames;
    QStringList annObjNames;
    QStringList fragmentNames;
    QString resultDocName;
    QList<GObject *> sObjs, aObjs;
    QList<DNAFragment> targetFragments;
    bool makeCircular;
    bool checkOverhangs;
    bool contextAdded;
    LigateFragmentsTask *ligateTask;
};

class EnzymeTests {
public:
    static QList<XMLTestFactory *> createTestFactories();
};

}    // namespace U2

#endif
