/**
 * 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_MSA_UTILS_H_
#define _U2_MSA_UTILS_H_

#include <QSet>

#include <U2Core/DocumentModel.h>
#include <U2Core/MultipleSequenceAlignmentObject.h>

namespace U2 {

class U2CORE_EXPORT MSAUtils : public QObject {
    Q_OBJECT
public:
    static bool equalsIgnoreGaps(const MultipleAlignmentRow &row, int startPos, const QByteArray &pattern, int &alternateLen);

    static int getPatternSimilarityIgnoreGaps(const MultipleSequenceAlignmentRow &row, int startPos, const QByteArray &pattern, int &alternateLen);

    static MultipleSequenceAlignment seq2ma(const QList<GObject *> &dnas, U2OpStatus &os, bool useGenbankHeader = false, bool recheckAlphabetFromDataIfRaw = false);

    static MultipleSequenceAlignment seq2ma(const QList<DNASequence> &dnas, U2OpStatus &os, bool recheckAlphabetFromDataIfRaw = false);

    static QList<DNASequence> ma2seq(const MultipleSequenceAlignment &ma, bool trimGaps);

    static QList<DNASequence> ma2seq(const MultipleSequenceAlignment &ma, bool trimGaps, const QSet<qint64> &rowIds);

    // Returns common alphabet for the sequences in the list. Returns RAW is the list is empty.
    static const DNAAlphabet *deriveCommonAlphabet(const QList<DNASequence> &sequenceList, bool recheckAlphabetFromDataIfRaw);
    static const DNAAlphabet *deriveCommonAlphabet(const QList<U2SequenceObject *> &sequenceList, bool recheckAlphabetFromDataIfRaw, U2OpStatus &os);
    // Returns common alphabet for all in the list. Returns RAW is the list is empty.
    static const DNAAlphabet *deriveCommonAlphabet(const QList<const DNAAlphabet *> &alphabetList);

    // Returns row index or -1 if name is not present
    static int getRowIndexByName(const MultipleSequenceAlignment &ma, const QString &name);

    //checks that alignment is not empty and all packed sequence parts has equal length
    static bool checkPackedModelSymmetry(const MultipleSequenceAlignment &ali, U2OpStatus &ti);

    static MultipleSequenceAlignmentObject *seqDocs2msaObj(QList<Document *> doc, const QVariantMap &hints, U2OpStatus &os, bool recheckAlphabetFromDataIfRaw = false);
    static MultipleSequenceAlignmentObject *seqObjs2msaObj(const QList<GObject *> &objects, const QVariantMap &hints, U2OpStatus &os, bool shallowCopy = false, bool recheckAlphabetFromDataIfRaw = false);

    /**
     * Compares rows in the 'origMsa' and 'newMsa' by names of the sequences.
     * It is assumed that:
     *   1) All rows in 'newMsa' are present in 'origMsa';
     *   2) Corresponding sequences are the same (however, only their length are verified);
     * The method modifies 'newMsa' to contain original rows and sequences IDs (from 'origMsa') and
     * returns the list of rows IDs in the order of 'newMsa'.
     * Note, that 'newMsa' may contain less rows than 'origMsa'
     * (e.g. ClustalO may decrease the number of sequences after the alignment).
     */
    static QList<qint64> compareRowsAfterAlignment(const MultipleSequenceAlignment &origMsa, MultipleSequenceAlignment &newMsa, U2OpStatus &os);
    static void copyRowFromSequence(MultipleSequenceAlignmentObject *msaObj, U2SequenceObject *seqObj, U2OpStatus &os);
    static U2MsaRow copyRowFromSequence(U2SequenceObject *seqObj, const U2DbiRef &dstDbi, U2OpStatus &os);
    static U2MsaRow copyRowFromSequence(DNASequence seq, const U2DbiRef &dstDbi, U2OpStatus &os);

    static MultipleSequenceAlignment setUniqueRowNames(const MultipleSequenceAlignment &ma);

    /** Returns unique MSA row name. Uses rowName as is if it can't be found in the currentlyUsedNamesSet or rolls the suffix of rowName. */
    static QString rollMsaRowName(const QString &rowName, const QSet<QString> &usedRowNamesSet, const QString& suffixSeparator = "_");

    /**
      * Renames rows in the 'ma' to 'names' according to the following assumptions:
      *   1) 'ma' row names are integers from [0..n - 1] interval,
      *      where n is equal to row number of 'ma';
      *   2) Row name 'i' will be renamed to 'names[i]' value;
      **/
    static bool restoreRowNames(MultipleSequenceAlignment &ma, const QStringList &names);

    static QList<U2Region> getColumnsWithGaps(const U2MsaListGapModel &maGapModel, int length, int requiredGapsCount = -1);
    static void removeColumnsWithGaps(MultipleSequenceAlignment &msa, int requiredGapsCount = -1);
};

}    // namespace U2

#endif
