/**
* UGENE - Integrated Bioinformatics Tools.
* Copyright (C) 2008-2020 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.
*/
#include "seqboot.h"
#include "cons.h"

#include <U2Core/MultipleSequenceAlignment.h>
#include <U2Core/PhyTree.h>
#include <U2Algorithm/CreatePhyTreeSettings.h>
#include <QVector>
#include <iostream>


namespace U2{

typedef QVector<float> matrixrow;
typedef QVector<matrixrow> matrix;

class SeqBoot{
private:
    MultipleSequenceAlignment malignment;
    QVector<MultipleSequenceAlignment> generatedSeq;
    int seqLen;
    int seqRowCount;

   
public:
    QString getTmpFileTemplate();
    void clearGenratedSequences(); //to free memory
    void generateSequencesFromAlignment( const MultipleSequenceAlignment& ma, const CreatePhyTreeSettings& settings );

    const MultipleSequenceAlignment& getMSA(int pos) const;

    void initGenerSeq(int reps, int rowC, int seqLen);

    SeqBoot();
    ~SeqBoot();
};


}
