💿🐜 Antkeeper source code
https://antkeeper.com
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74 lines
2.5 KiB
74 lines
2.5 KiB
/*
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* Copyright (C) 2021 Christopher J. Howard
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*
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* This file is part of Antkeeper source code.
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*
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* Antkeeper source code is free software: you can redistribute it and/or modify
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* it under the terms of the GNU General Public License as published by
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* the Free Software Foundation, either version 3 of the License, or
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* (at your option) any later version.
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*
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* Antkeeper source code is distributed in the hope that it will be useful,
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* but WITHOUT ANY WARRANTY; without even the implied warranty of
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* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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* GNU General Public License for more details.
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*
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* You should have received a copy of the GNU General Public License
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* along with Antkeeper source code. If not, see <http://www.gnu.org/licenses/>.
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*/
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#include "entity/systems/proteome.hpp"
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#include "entity/components/proteome.hpp"
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#include "genetics/sequence.hpp"
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#include "genetics/standard-code.hpp"
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namespace entity {
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namespace system {
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proteome::proteome(entity::registry& registry):
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updatable(registry)
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{
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registry.on_construct<entity::component::genome>().connect<&proteome::on_genome_construct>(this);
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registry.on_replace<entity::component::genome>().connect<&proteome::on_genome_replace>(this);
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}
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void proteome::update(double t, double dt)
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{}
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void proteome::on_genome_construct(entity::registry& registry, entity::id entity_id, entity::component::genome& genome)
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{
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on_genome_replace(registry, entity_id, genome);
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}
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void proteome::on_genome_replace(entity::registry& registry, entity::id entity_id, entity::component::genome& genome)
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{
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// Allocate a proteome component
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entity::component::proteome proteome_component;
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// For each chromosome in the genome
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for (const std::string& chromosome: genome.chromosomes)
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{
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// Find the first ORF in the chromosome
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auto orf = genetics::sequence::find_orf(chromosome.begin(), chromosome.end(), genetics::standard_code);
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// While the ORF is valid
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while (orf.start != chromosome.end())
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{
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// Translate the base sequence into an amino acid sequence (protein)
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std::string protein;
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genetics::sequence::translate(orf.start, orf.stop, std::back_inserter(protein), genetics::standard_code);
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// Append protein to the proteome
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proteome_component.proteins.push_back(protein);
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// Find the next ORF
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orf = genetics::sequence::find_orf(orf.stop, chromosome.end(), genetics::standard_code);
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}
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}
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// Assign or replace the entity's proteome component
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registry.assign_or_replace<entity::component::proteome>(entity_id, proteome_component);
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}
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} // namespace system
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} // namespace entity
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