genetics.cuh

Go to the documentation of this file.

 
#pragma once
 
#include "BitString.cuh"
#include "nucleotide.hpp"
 
#include <filesystem>
#include <istream>
#include <string>
#include <vector>
 
typedef BitString<Nucleotide, 2> Gene;
 
namespace genetics
{
    static const std::string GENETIC_DIRECTORY = "genetic/";
    
    static const std::string VIRUS_DIRECTORY = GENETIC_DIRECTORY + "virus/";
    
    static const std::string ABC_HUMI_DIRECTORY = GENETIC_DIRECTORY + "ABC-HuMi/";
    
    static const std::string DNA_EXTENSION = ".dna";
    
    static const std::string DNA_BIN_EXTENSION = ".dna.bin";
    
    static const std::string DNA_BIN_COMBINED_EXTENSION = ".dna.bin.combined";
    
    static const std::string DNA_BIN_SIZES_EXTENSION = ".dna.bin.sizes";
    
    static const std::string GBK_EXTENSION = ".gbk";
    
    static const std::string FNA_EXTENSION = ".fna";
 
    enum class FileType
    {
        GBK,            
        FNA,            
        DNA,            
        DNA_BIN,        
        DNA_BIN_COMBINED, 
        UNKNOWN         
    };
 
    Gene from_gbk(const std::string& filename);
    
    Gene from_fna(const std::string& filename);
    
    Gene from_dna(const std::string& filename);
    
    Gene from_file(const std::string& filename);
    
    Gene from_file(const std::filesystem::path& path);
    
    Gene from_file(const std::filesystem::directory_entry& entry);
    
    void to_dna(const Gene& gene, const std::string& filename);
    
    std::vector<Gene> from_directory(const std::string& dirname);
    
    std::vector<Gene> from_directory(const std::string& dirname, FileType type);
    
    std::vector<std::string> get_dna_strings_from_directory(const std::string& dirname);
    
    FileType get_file_type(const std::string& filename);
    
    FileType get_file_type(const std::filesystem::path& path);
    
    FileType get_file_type(const std::filesystem::directory_entry& entry);
    
    Gene from_stream(std::istream& stream);
    
    std::vector<std::filesystem::path> get_virus_nucleotide_paths();
    
    void combine_dna_bin_files(const std::string& dirname, const std::string& combined_filename);
 
    struct GeneManager
    {
    public:
        GeneManager(const std::string& path);
        
        ~GeneManager();
 
        std::vector<Gene> all_genes() const;
        
        std::vector<Gene> get_random_genes(size_t count) const;
    private:
        struct GeneInfo
        {
            std::string name;     
            std::streampos position; 
            size_t size;          
        };
 
        std::string m_path;       
        mutable std::ifstream m_file; 
        std::vector<GeneInfo> m_gene_infos; 
 
        void save_sizes();
        
        void load_sizes();
    };
};