nucleotide.cpp

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#include "nucleotide.hpp"
 
#include <fstream>
 
bool is_valid_nucleotide(char nucleotide)
{
    // Use the lookup table approach for efficient character validation
    // This avoids multiple comparisons by directly indexing into the table
    return char_to_nucleotide[nucleotide] != Nucleotide::INVALID;
}
 
std::ostream& operator<<(std::ostream& os, const Nucleotide& nucleotide)
{
    // Handle each nucleotide case explicitly in the switch statement
    // Note: We could use the nucleotide_to_char array directly for valid nucleotides,
    // but the switch approach provides clearer error handling for invalid values
    switch (nucleotide)
    {
    case Nucleotide::A:
        os << 'A';
        break;
    case Nucleotide::C:
        os << 'C';
        break;
    case Nucleotide::G:
        os << 'G';
        break;
    case Nucleotide::T:
        os << 'T';
        break;
    default:
        // Throw an exception for invalid nucleotides rather than silently outputting a placeholder
        // This helps catch programming errors early
        throw std::invalid_argument("Invalid nucleotide");
    }
 
    return os;
}