/**
 * 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 <U2Core/AnnotationData.h>
#include <U2Core/GObject.h>

namespace U2 {

class U2SequenceObject;
class DNATranslation;
class DNASequence;
class GUrl;
class DNAAlphabet;

class U2CORE_EXPORT GObjectUtils {
public:
    static QList<GObject*> select(const QList<GObject*>& objects, const GObjectType& type, UnloadedObjectFilter f);

    static GObject* selectOne(const QList<GObject*>& objects, GObjectType type, UnloadedObjectFilter f);

    /**
     * Returns list of all objects from the active project that match the parameters.
     * 'objectType' may be empty. In this case any object type is matched.
     */
    static QList<GObject*> findAllObjects(const UnloadedObjectFilter& unloadedObjectFilter, const GObjectType& objectType = GObjectType(), bool writableOnly = false);

    /*
     * Select objects from @fromObjects that are referenced by relations stored in @obj with @relationRole and @type.
     */
    static QList<GObject*> selectRelations(GObject* obj, GObjectType type, GObjectRelationRole relationRole, const QList<GObject*>& fromObjects, UnloadedObjectFilter f);

    static QList<GObject*> selectRelationsFromParentDoc(const GObject* obj, const GObjectType& type, GObjectRelationRole relationRole);

    /*
     * Returns list of objects that references the @obj with @relationRole and have @resultObjType as well.
     * Result list is a sublist of @fromObjects list.
     */
    static QList<GObject*> findObjectsRelatedToObjectByRole(const GObject* obj, GObjectType resultObjType, GObjectRelationRole role, const QList<GObject*>& fromObjects, UnloadedObjectFilter f);

    static QList<GObject*> findObjectsRelatedToObjectByRole(const GObjectReference& obj, GObjectType resultObjType, GObjectRelationRole role, const QList<GObject*>& fromObjects, UnloadedObjectFilter f);

    /*
     * Selects objects from 'fromObjects' with filter 'f' that have relation(relationRole, type)
     * 'availableObjectsOnly'  -> check if the related object is in project
     */
    static QList<GObject*> selectObjectsWithRelation(const QList<GObject*>& fromObjects,
                                                     GObjectType type,
                                                     GObjectRelationRole relationRole,
                                                     UnloadedObjectFilter f,
                                                     bool availableObjectsOnly);

    static GObject* selectObjectByReference(const GObjectReference& r, const QList<GObject*>& fromObjects, UnloadedObjectFilter f);

    static GObject* selectObjectByReference(const GObjectReference& r, UnloadedObjectFilter f);

    static DNATranslation* findComplementTT(const DNAAlphabet* al);

    static DNATranslation* findAminoTT(U2SequenceObject* so, bool fromHintsOnly, const QString& table = nullptr);

    static DNATranslation* findBackTranslationTT(U2SequenceObject* so, const QString& table = nullptr);

    // checks object type for both loaded and unloaded states
    static bool hasType(GObject* obj, const GObjectType& type);

    static void updateRelationsURL(GObject* o, const QString& fromURL, const QString& toURL);

    static void updateRelationsURL(GObject* o, const GUrl& fromURL, const GUrl& toURL);

    static void replaceAnnotationQualfier(SharedAnnotationData& a, const QString& name, const QString& newVal, bool create = false);

    static GObject* createObject(const U2DbiRef& ref, const U2DataId& id, const QString& name);
};

}  // namespace U2
