98 lines
2.4 KiB
C++
98 lines
2.4 KiB
C++
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/** Implement the genetic code as a thread-safe GeneticCode.
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*
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* @see https://refactoring.guru/design-patterns/GeneticCode/cpp/example#example-1
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*/
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#pragma once
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#include <algorithm>
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#include <complex>
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#include <fstream>
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#include <sstream>
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#include <iostream>
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#include <stdexcept>
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#include <unordered_map>
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#include <vector>
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#include <mutex>
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#include "Sequence.hpp"
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#include "strutils.hpp"
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class GeneticCode {
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private:
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static GeneticCode *pinstance_;
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static std::mutex mutex_;
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protected:
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std::unordered_map<std::string, char> codon_table;
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GeneticCode(): GeneticCode("./resources/codons.txt") {}
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GeneticCode(std::string input_filename) {
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std::ifstream input(input_filename);
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if (!input.good()) {
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throw std::invalid_argument("Error: could not read codon table from " + input_filename + " file.");
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}
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load_genetic_code(input);
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}
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void load_genetic_code(std::ifstream &input) {
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if (!input.good()) {
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throw std::invalid_argument("Error: Could not read the codon table from the text file.");
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}
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std::string line;
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while(input.good()) {
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std::getline(input, line);
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std::vector<std::string> fields = split_string(line, '\t');
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std::string codon = fields.at(0);
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char amino_acid = fields.at(2)[0];
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GeneticCode::codon_table.insert({codon, amino_acid});
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}
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}
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public:
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GeneticCode(GeneticCode &other) = delete;
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void operator=(const GeneticCode &) = delete;
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static GeneticCode *GetInstance();
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static GeneticCode *GetInstance(std::string input_filename);
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char get_amino_acid(std::string codon) {
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replace_all(codon, 'U', 'T');
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if (codon_table.find(codon) != codon_table.end()) {
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return codon_table.at(codon);
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} else {
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throw std::invalid_argument("Error: codon '" + codon + "' not found in genetic code");
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}
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}
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};
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GeneticCode* GeneticCode::pinstance_{nullptr};
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std::mutex GeneticCode::mutex_;
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GeneticCode *GeneticCode::GetInstance()
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{
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std::lock_guard<std::mutex> lock(mutex_);
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if (pinstance_ == nullptr)
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{
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pinstance_ = new GeneticCode();
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}
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return pinstance_;
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}
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GeneticCode *GeneticCode::GetInstance(std::string input_filename)
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{
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std::lock_guard<std::mutex> lock(mutex_);
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if (pinstance_ == nullptr)
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{
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pinstance_ = new GeneticCode(input_filename);
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}
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return pinstance_;
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}
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