Expressor.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/Expressor.h"
#include "bio/genetic/Plasmid.h"
#include "bio/genetic/common/Codes.h"
 
namespace bio {
namespace genetic {
 
Expressor::~Expressor()
{
 
}
 
Code Expressor::Activate(StandardDimension proteinId)
{
    Code ret = code::Success();
    molecular::Protein* toActivate = GetById< molecular::Protein* >(proteinId);
    BIO_SANITIZE(toActivate, ,
        return false);
    return toActivate->Activate();
}
 
Code Expressor::Activate(Name proteinName)
{
    return Activate(molecular::ProteinPerspective::Instance().GetIdWithoutCreation(proteinName));
}
 
Code Expressor::ExpressGenes()
{
    Plasmid* plasmidBuffer;
    Code ret = code::Success();
    for (
        SmartIterator dna = GetAll< Plasmid* >()->Begin();
        !dna.IsAtEnd();
        ++dna
        )
    {
        plasmidBuffer = dna;
        if (AddToTranscriptome(plasmidBuffer->TranscribeFor(this)) != code::Success() && ret == code::Success())
        {
            ret = code::TranscriptionError();
        }
    }
    for (
        Transcriptome::const_iterator rna = m_transcriptome.begin();
        rna != m_transcriptome.end();
        ++rna
        )
    {
        if (Translate(*rna) != code::Success() && ret == code::Success())
        {
            ret = code::TranslationError();
        }
    }
    return ret;
}
 
Code Expressor::AddToTranscriptome(const RNA* toExpress)
{
    BIO_SANITIZE(toExpress, ,
        return code::BadArgument1());
    m_transcriptome.push_back(toExpress);
    return code::Success();
}
 
Code Expressor::Translate(const RNA* mRNA)
{
    BIO_SANITIZE(mRNA, ,
        code::BadArgument1());
 
    Code ret = code::Success();
 
    Gene* geneBuffer;
    for (
        Transcriptome::const_iterator rna = m_transcriptome.begin();
        rna != m_transcriptome.end();
        ++rna
        )
    {
        for (
            SmartIterator gen = (*rna)->GetAll< Gene* >()->Begin();
            !gen.IsAtEnd();
            ++gen
            )
        {
            geneBuffer = gen;
            if (!geneBuffer->m_insertion.Seek(this))
            {
                ret = code::UnknownError();
            }
        }
    }
    return ret;
}
 
} //molecular namespace
} //bio namespace