/**
 * UGENE - Integrated Bioinformatics Tools.
 * Copyright (C) 2008-2025 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/U2FeatureType.h>
#include <U2Core/U2Region.h>
#include <U2Core/U2Type.h>

namespace U2 {

class U2CORE_EXPORT U2AnnotationTable : public U2Object {
public:
    U2AnnotationTable()
        : U2Object() {
    }
    U2AnnotationTable(const U2DataId& id, const QString& dbId, qint64 version)
        : U2Object(id, dbId, version) {
    }

    /** Root feature's id */
    U2DataId rootFeature;

    U2DataType getType() const override {
        return U2Type::AnnotationTable;
    }
};

/** Feature location */
class U2CORE_EXPORT U2FeatureLocation {
public:
    U2FeatureLocation() {
    }

    U2FeatureLocation(const U2Strand& strand_, const U2Region& region_)
        : strand(strand_), region(region_) {
    }

    /**  Strand of the location. */
    U2Strand strand;

    /** Sequence region */
    U2Region region;

    bool operator==(const U2FeatureLocation& l) const;

    bool operator!=(const U2FeatureLocation& l) const {
        return !(*this == l);
    }
};

inline bool U2FeatureLocation::operator==(const U2FeatureLocation& l) const {
    bool res = region == l.region && strand == l.strand;
    return res;
}

/**
 * The flags specify whether the group operation has to be applied to the parent feature
 * besides its child features.
 */
enum SubfeatureSelectionMode {
    SelectParentFeature,
    NotSelectParentFeature
};

/**
 * Sequence annotation. Used to annotate set of sequence regions
 */
class U2CORE_EXPORT U2Feature : public U2Entity {
public:
    enum FeatureClass {
        Invalid,
        Annotation,
        Group
    };

    U2Feature()
        : featureClass(Annotation),
          featureType(U2FeatureTypes::Invalid) {
    }

    bool operator==(const U2Feature& f) const {
        return f.id == id;
    }
    bool operator!=(const U2Feature& f) const {
        return !(*this == f);
    }
    /**
     * Sequence this annotation is related to
     */
    U2DataId sequenceId;
    /**
     * Parent feature id
     */
    U2DataId parentFeatureId;
    /**
     * Id of the feature that represents the root of the annotation tree
     */
    U2DataId rootFeatureId;
    /**
     * Name of the feature. Not a FeatureKey, because in that case can be features with no name
     */
    QString name;
    /**
     * Annotation location
     */
    U2FeatureLocation location;
    /**
     * Type of feature
     */
    FeatureClass featureClass;
    U2FeatureType featureType;
};

typedef QFlags<U2Feature::FeatureClass> FeatureFlags;

/**
 * Feature key
 */
class U2CORE_EXPORT U2FeatureKey {
public:
    U2FeatureKey() {
    }
    /**
     * Constructs new feature key instance with key and value set
     */
    U2FeatureKey(const QString& _name, const QString& _value)
        : name(_name), value(_value) {
    }
    /**
     * Feature key is valid if  its name is not empty
     */
    bool isValid() const {
        return !name.isEmpty();
    }
    /**
     * Any two keys are equal if their names & values are equal
     */
    bool operator==(const U2FeatureKey& k) const {
        return k.name == name && k.value == value;
    }
    /**
     * Any two keys are not equal if either their names or values are  not equal
     */
    bool operator!=(const U2FeatureKey& k) const {
        return !(*this == k);
    }

    /**
     * Feature key name
     */
    QString name;
    /**
     * Feature key value
     */
    QString value;
};

}  // namespace U2
