SeqConstructor.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 _SIDECHAIN_CONSTRUCTOR_H_
#define _SIDECHAIN_CONSTRUCTOR_H_

// Includes:
#include <Spacer.h>
#include <AminoAcid.h>
#include <Debug.h>
#include <string>
#include <vector>

// Global constants, typedefs, etc. (to avoid):

namespace Victor { namespace Biopool { 

    class SeqConstructor {
    public:

        // CONSTRUCTORS/DESTRUCTOR:

        SeqConstructor(istream& _refInput = cin) :
        refInput(_refInput), loaded(false), refAmino() {
        }

        virtual ~SeqConstructor() {
            PRINT_NAME;
        }

        // MODIFIERS:
        virtual Spacer& makeSpacer(string type, unsigned int n);
        // make spacer by concatenating code n-times 

    protected:
        // HELPERS:
        virtual void loadReference();
        void searchReference(AminoAcid& aa, string type);
        void buildAminoAcid(AminoAcid& aa, AminoAcid* prev);

    private:
        istream& refInput; // reference stream
        bool loaded; // is reference loaded yet?
        vector<AminoAcid> refAmino; // reference types
    };

}} //namespace
#endif //_SEQ_CONSTRUCTOR_H_