/**
 * 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_ALIGN_SEQUENCES_TO_ALIGNMENT_TASK_H_
#define _U2_ALIGN_SEQUENCES_TO_ALIGNMENT_TASK_H_

#include <QPointer>

#include <U2Algorithm/AlignSequencesToAlignmentTaskSettings.h>

#include <U2Core/BaseDocumentFormats.h>
#include <U2Core/DNASequenceObject.h>
#include <U2Core/DocumentProviderTask.h>
#include <U2Core/MultipleSequenceAlignmentObject.h>
#include <U2Core/Task.h>
#include <U2Core/U2AlphabetUtils.h>

namespace U2 {

class StateLock;
class MSAEditor;

class SequenceObjectsExtractor {
public:
    SequenceObjectsExtractor();

    void setAlphabet(const DNAAlphabet *newAlphabet);

    void extractSequencesFromDocuments(const QList<Document *> &documentsList);

    void extractSequencesFromDocument(Document *doc);

    void extractSequencesFromObjects(const QList<GObject *> &objects);

    const QStringList &getErrorList() const;

    const DNAAlphabet *getAlphabet() const;

    const QList<U2EntityRef> &getSequenceRefs() const;

    const QStringList &getSequenceNames() const;

    qint64 getMaxSequencesLength() const;

    const QList<Document *> &getUsedDocuments() const;

    const DNAAlphabet *resultingAlphabet() const;

private:
    void checkAlphabet(const DNAAlphabet *alphabet, const QString &objectName);

    QList<U2EntityRef> sequenceRefs;
    QStringList errorList;
    const DNAAlphabet *seqsAlphabet;
    bool extractFromMsa;
    QStringList sequenceNames;
    qint64 sequencesMaxLength;
    QList<Document *> usedDocuments;
};

class LoadSequencesTask : public Task {
    Q_OBJECT
public:
    LoadSequencesTask(const DNAAlphabet *msaAlphabet, const QStringList &filesWithSequences);
    void prepare();

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

    ReportResult report();

    const SequenceObjectsExtractor &getExtractor() const;

private:
    const DNAAlphabet *msaAlphabet;
    QStringList urls;

    SequenceObjectsExtractor extractor;

    static const int maxErrorListSize;

private:
    void setupError();
};

class AlignSequencesToAlignmentTask : public Task {
    Q_OBJECT
public:
    AlignSequencesToAlignmentTask(MultipleSequenceAlignmentObject *obj, const SequenceObjectsExtractor &extractor, bool forceUseUgeneNativeAligner = false);
    void prepare();
    ReportResult report();

private:
    void fillSettingsByDefault();

    QPointer<MultipleSequenceAlignmentObject> maObjPointer;
    QStringList urls;
    StateLock *stateLock;
    StateLock *docStateLock;
    qint64 sequencesMaxLength;
    AlignSequencesToAlignmentTaskSettings settings;
    QList<Document *> usedDocuments;
    const DNAAlphabet *initialMsaAlphabet;
    SequenceObjectsExtractor extr;
};

class LoadSequencesAndAlignToAlignmentTask : public Task {
    Q_OBJECT
public:
    LoadSequencesAndAlignToAlignmentTask(MultipleSequenceAlignmentObject *obj, const QStringList &urls, bool forceUseUgeneNativeAligner = false);

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

private:
    QStringList urls;
    QPointer<MultipleSequenceAlignmentObject> maObjPointer;
    LoadSequencesTask *loadSequencesTask;
    bool forceUseUgeneNativeAligner;
};

}    // namespace U2

#endif    //_U2_ALIGN_SEQUENCES_TO_ALIGNMENT_TASK_H_
