Expressor.h

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/*
 * This file is a part of the Biology project by eons LLC.
 * Biology (aka Develop Biology) is a framework for approaching software
 * development from a natural sciences perspective.
 *
 * Copyright (C) 2021 Séon O'Shannon & eons LLC
 *
 * This program is free software: you can redistribute it and/or modify
 * it under the terms of the GNU Affero General Public License as
 * published by the Free Software Foundation, either version 3 of the
 * License, or (at your option) any later version.
 *
 * This program 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 Affero General Public License for more details.
 *
 * You should have received a copy of the GNU Affero General Public License
 * along with this program.  If not, see <https://www.gnu.org/licenses/>.
 */
 
#pragma once
 
#include "bio/molecular/Vesicle.h"
#include "bio/molecular/Protein.h"
#include "bio/genetic/common/Types.h"
#include "bio/genetic/common/Filters.h"
#include "bio/genetic/macros/Macros.h"
#include "RNA.h"
 
namespace bio {
namespace genetic {
 
class Plasmid;
 
class Expressor :
    public genetic::Class< Expressor >,
    public chemical::UnorderedMotif< TranscriptionFactor >,
    public chemical::LinearMotif< Plasmid* >,
    public chemical::LinearMotif< molecular::Protein* >,
    virtual public molecular::Vesicle
{
public:
 
    BIO_DISAMBIGUATE_ALL_CLASS_METHODS(genetic,
        Expressor)
 
     BIO_DEFAULT_IDENTIFIABLE_CONSTRUCTORS(genetic,
        Expressor,
        &molecular::VesiclePerspective::Instance(),
        filter::Genetic())
 
    
    virtual ~Expressor();
 
    virtual void CacheProteins()
    {
        //   YOUR CODE HERE
    }
 
    Code Activate(StandardDimension proteinId);
 
    Code Activate(Name proteinName);
 
    template < typename T >
    Code Activate()
    {
        return Activate(TypeName< T >);
    }
 
 
    virtual Code Translate(const RNA* mRNA);
 
    virtual Code ExpressGenes();
 
    virtual Code AddToTranscriptome(const RNA* toExpress);
 
protected:
    Transcriptome m_transcriptome;
};
 
} //molecular namespace
} //bio namespace