Sequence.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 _SEQUENCE_HPP
#define _SEQUENCE_HPP

#include <vector>
#include <string>
using namespace std;

#include "Constants.hpp"
#include "SequenceInfo.hpp"
#include "SequenceData.hpp"
#include "SequenceModifiers.hpp"

class Sequence {
public:
        Sequence( SequenceInfo* info, SequenceModifiers* modifiers );
        Sequence ( const Sequence* orig );
        virtual ~Sequence();

        void copyData( const Sequence* orig );
        //void setFlags( const int flags );
        //void setFileName ( const string filename );
        //void loadFile ( );
        void trim (int delta0, int delta1);
        //void setPadding(int lenth, char c);
        //void setBoundaries (int trimStart, int trimEnd);
        //void restore();

        void reverse();
        int getAbsolutePos(int relativePos) const;

        int getLen() const;
        int getTrimStart() const;
        int getTrimEnd() const;
        //int getType() const;
        //string getAccession() const;
        //string getDescription() const;

        //void setDescription(string description);
        //int getFlags() const;
        //int getOriginalLen() const;
        SequenceInfo* getInfo() const;
        void setInfo(SequenceInfo* info);
        SequenceModifiers* getModifiers() const;
        const char* getData(bool reverse = false) const;
        const char* getForwardData() const;
        const char* getReverseData() const;
        //char getPaddingChar() const;
        //int getPaddingLenght() const;
        bool isReversed() const;

        //char* data;
private:
        SequenceInfo* info;
        SequenceModifiers* modifiers;
        SequenceData* data;
        //char* original_forward_data;
        //char* original_reverse_data;
        int reverseData;
        int offset0;
        int offset1;
        int len;

        bool dataOwner;
        //int paddingLenght;
        //char paddingChar;
        //vector<char> data_vector;
        //void updateData();
        void setBoundaries(int trimStart, int trimEnd);
};

#endif  /* _SEQUENCE_HPP */