ProfInput.h

/*  This file is part of Victor.

    Victor 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.

    Victor 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 Victor.  If not, see <http://www.gnu.org/licenses/>.
 */


#ifndef __ProfInput_H__
#define __ProfInput_H__

#include <IoTools.h>
#include <stringtools.h>
#include <Substitution.h>
#include <iostream>
#include <string>

namespace Victor { namespace Align2{

    class ProfInput {
    public:

        // CONSTRUCTORS:

        ProfInput();

        ProfInput(istream &is);

        ProfInput(const ProfInput &orig);

        virtual ~ProfInput();


        // OPERATORS:

        ProfInput& operator =(const ProfInput &orig);

        friend ostream& operator <<(ostream &os, const ProfInput &object);

        friend istream& operator >>(istream &is, ProfInput &object);


        // PREDICATES:

        char getProfSS(int i);

        char getProfBE(int i);

        char getProfMixSSBE(char ssChar, char beChar);

        virtual unsigned int size() const;


        // MODIFIERS:

        virtual void copy(const ProfInput &orig);

        virtual ProfInput* newCopy();


        // HELPERS:

        static void pWriteString(ostream &os, string data1, string data2,
                string data3);

        static void pReadString(istream &is, string &data1, string &data2,
                string &data3);


    protected:


    private:

        // ATTRIBUTES:

        string seq; 
        string profSSPred; 
        string profBEPred; 

    };

    // -----------------------------------------------------------------------------
    //                                  ProfInput
    // -----------------------------------------------------------------------------

    // PREDICATES:

    inline char
    ProfInput::getProfSS(int i) {
        return profSSPred[i];
    }

    inline char
    ProfInput::getProfBE(int i) {
        return profBEPred[i];
    }

    inline unsigned int
    ProfInput::size() const {
        return seq.size();
    }

}} // namespace

#endif