Ss2Input.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 __Ss2Input_H__
#define __Ss2Input_H__

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

namespace Victor { namespace Align2{

    class Ss2Input {
    public:

        // CONSTRUCTORS:

        Ss2Input();

        Ss2Input(istream &is);

        Ss2Input(const Ss2Input &orig);

        virtual ~Ss2Input();


        // OPERATORS:

        Ss2Input& operator =(const Ss2Input &orig);

        friend ostream& operator <<(ostream &os, const Ss2Input &object);

        friend istream& operator >>(istream &is, Ss2Input &object);


        // PREDICATES:

        double score(int i, int j);

        virtual unsigned int size() const;


        // MODIFIERS:

        virtual void copy(const Ss2Input& orig);

        virtual Ss2Input* newCopy();


        // HELPERS:

        template<class T> static void pWriteDoubleVector(ostream &os,
                vector< vector<T> > data);

        template<class T> static void pReadDoubleVector(istream &is,
                vector< vector<T> > &data);


    protected:


    private:

        // ATTRIBUTES:

        vector< vector<double> > residuescores; 

    };

    // -----------------------------------------------------------------------------
    //                                  Ss2Input
    // -----------------------------------------------------------------------------

    // PREDICATES:

    inline double
    Ss2Input::score(int i, int j) {
        return residuescores[i][j];
    }

    inline unsigned int
    Ss2Input::size() const {
        return residuescores.size();
    }

}} // namespace

#endif