SequenceData.hpp

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/*******************************************************************************
 *
 * Copyright (c) 2010-2015   Edans Sandes
 *
 * This file is part of MASA-Core.
 * 
 * MASA-Core 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 3 of the License, or
 * (at your option) any later version.
 * 
 * MASA-Core 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 MASA-Core.  If not, see <http://www.gnu.org/licenses/>.
 *
 ******************************************************************************/

#ifndef SEQUENCEDATA_HPP_
#define SEQUENCEDATA_HPP_

#include <string>
using namespace std;

#include "SequenceModifiers.hpp"

class SequenceData {
public:
        //SequenceData(char* data, int size, SequenceModifiers* modifiers);
        SequenceData(string filename, SequenceModifiers* modifiers);
        virtual ~SequenceData();
        string getDescription() const;
        char* getForwardData() const;
        char* getReverseData() const;
        int getSize() const;
        int getOriginalSize() const;

private:
        void loadFile(string filename);
        char* createReverseData(char* forwardData, int size);
        SequenceModifiers* modifiers;
        string description;
        char* forwardData;
        char* reverseData;
        int size;
        int originalSize;
};

#endif /* SEQUENCEDATA_HPP_ */