Genome.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) 2022 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/Genome.h"
#include "bio/genetic/Plasmid.h"
#include "bio/genetic/common/TranscriptionFactors.h"
 
namespace bio {
namespace genetic {
 
GenomeImplementation::GenomeImplementation()
    :
    genetic::Class< GenomeImplementation >(
        this,
        "Genome",
        NULL,
        filter::Genetic())
{
    Add< TranscriptionFactor >(transcription_factor::Genome());
}
 
GenomeImplementation::~GenomeImplementation()
{
 
}
 
void GenomeImplementation::CacheProteins()
{
    mc_registerPlasmid = RotateTo< molecular::Protein* >("RegisterPlasmid");
    mc_fetchPlasmid = RotateTo< molecular::Protein* >("FetchPlasmid");
    mc_registrationSite = mc_registerPlasmid->GetIdWithoutCreation("Plasmid Binding Site");
    mc_nameSite = mc_fetchPlasmid->GetIdWithoutCreation("Name Binding Site");
    mc_idSite = mc_fetchPlasmid->GetIdWithoutCreation("Id Binding Site");
    mc_fetchSite = mc_fetchPlasmid->GetIdWithoutCreation("Return Site");
}
 
StandardDimension GenomeImplementation::RegisterPlasmid(Plasmid* toRegister)
{
    BIO_SANITIZE(toRegister, ,
        return PlasmidPerspective::InvalidId())
    StandardDimension ret = PlasmidPerspective::InvalidId();
    LockThread();
    mc_registerPlasmid->RotateTo(mc_registrationSite)->Bind(ChemicalCast< chemical::Substance* >(toRegister));
    if (mc_registerPlasmid->Activate() == code::Success())
    {
        ret = toRegister->GetId();
    }
    UnlockThread();
    return ret;
}
 
Plasmid* GenomeImplementation::FetchPlasmid(StandardDimension plasmidId)
{
    Plasmid* ret = NULL;
    LockThread();
    mc_fetchPlasmid->RotateTo(mc_idSite)->Bind(plasmidId);
    mc_fetchPlasmid->Activate();
    ret = mc_fetchPlasmid->RotateTo< Plasmid* >(mc_fetchSite);
    UnlockThread();
    return ret;
 
}
 
Plasmid* GenomeImplementation::FetchPlasmid(Name plasmidName)
{
    Plasmid* ret = NULL;
    LockThread();
    mc_fetchPlasmid->RotateTo(mc_nameSite)->Bind(plasmidName);
    mc_fetchPlasmid->Activate();
    ret = mc_fetchPlasmid->RotateTo< Plasmid* >(mc_fetchSite);
    UnlockThread();
    return ret;
}
 
} //genetic namespace
} //bio namespace