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- /*
- * Copyright (C) 2021 Christopher J. Howard
- *
- * This file is part of Antkeeper source code.
- *
- * Antkeeper source code is free software: you can redistribute it and/or modify
- * it under the terms of the GNU General Public License as published by
- * the Free Software Foundation, either version 3 of the License, or
- * (at your option) any later version.
- *
- * Antkeeper source code 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 General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with Antkeeper source code. If not, see <http://www.gnu.org/licenses/>.
- */
-
- #include "entity/systems/proteome.hpp"
- #include "entity/components/proteome.hpp"
- #include "genetics/sequence.hpp"
- #include "genetics/standard-code.hpp"
-
- namespace entity {
- namespace system {
-
- proteome::proteome(entity::registry& registry):
- updatable(registry)
- {
- registry.on_construct<entity::component::genome>().connect<&proteome::on_genome_construct>(this);
- registry.on_replace<entity::component::genome>().connect<&proteome::on_genome_replace>(this);
- }
-
- void proteome::update(double t, double dt)
- {}
-
- void proteome::on_genome_construct(entity::registry& registry, entity::id entity_id, entity::component::genome& genome)
- {
- on_genome_replace(registry, entity_id, genome);
- }
-
- void proteome::on_genome_replace(entity::registry& registry, entity::id entity_id, entity::component::genome& genome)
- {
- // Allocate a proteome component
- entity::component::proteome proteome_component;
-
- // For each chromosome in the genome
- for (const std::string& chromosome: genome.chromosomes)
- {
- // Find the first ORF in the chromosome
- auto orf = genetics::sequence::find_orf(chromosome.begin(), chromosome.end(), genetics::standard_code);
-
- // While the ORF is valid
- while (orf.start != chromosome.end())
- {
- // Translate the base sequence into an amino acid sequence (protein)
- std::string protein;
- genetics::sequence::translate(orf.start, orf.stop, std::back_inserter(protein), genetics::standard_code);
-
- // Append protein to the proteome
- proteome_component.proteins.push_back(protein);
-
- // Find the next ORF
- orf = genetics::sequence::find_orf(orf.stop, chromosome.end(), genetics::standard_code);
- }
- }
-
- // Assign or replace the entity's proteome component
- registry.assign_or_replace<entity::component::proteome>(entity_id, proteome_component);
- }
-
- } // namespace system
- } // namespace entity
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