RNAPolymerase.cpp

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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/>.
 */
 
#include "bio/genetic/proteins/RNAPolymerase.h"
#include "bio/genetic/Expressor.h"
#include "bio/genetic/Plasmid.h"
#include "bio/genetic/RNA.h"
#include "bio/common/TypeName.h"
 
namespace bio {
namespace genetic {
 
RNAPolymerase::RNAPolymerase(Plasmid* toTranscribe)
    :
    molecular::Protein(chemical::PeriodicTable::Instance().GetNameFromType(*this))
{
    SetSource(toTranscribe);
    mc_rna = Define("RNA Binding Site");
}
 
RNAPolymerase::~RNAPolymerase()
{
 
}
 
Code RNAPolymerase::Activate()
{
    Expressor* expressor = ChemicalCast< Expressor* >(GetEnvironment());
    BIO_SANITIZE(expressor, ,
        return code::BadArgument1());
    RNA* boundRNA = RotateTo< RNA* >(mc_rna);
    BIO_SANITIZE(mc_rna, ,
        return code::BadArgument2());
 
    Gene* geneBuffer;
    bool shouldTranscribe = false;
    for (
        SmartIterator gen = m_source->GetAll< Gene* >()->Begin();
        !gen.IsAtEnd();
        ++gen
        )
    {
        geneBuffer = gen;
        shouldTranscribe = expressor->HasAll< TranscriptionFactor >(
            geneBuffer->GetAll< TranscriptionFactor >());
        if (!shouldTranscribe)
        {
            continue;
        }
        boundRNA->Add< Gene* >(geneBuffer);
    }
    return code::Success();
}
} //genetic namespace
} //bio namespace