nucleotide.hpp File Reference

Defines nucleotide representation and related utility functions. More...

#include <array>
#include <cstdint>
#include <stdexcept>
#include <fstream>

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Enumerations
enum class	Nucleotide : uint8_t {   A = 0 , C = 1 , G = 2 , T = 3 ,   INVALID }
	Enumerates the four nucleotides of DNA. More...

Functions
bool	is_valid_nucleotide (char nucleotide)
	Checks if a character represents a valid nucleotide.
std::ostream &	operator<< (std::ostream &os, const Nucleotide &nucleotide)
	Inserts a textual representation of a nucleotide into an output stream.

Variables
static constexpr std::array< Nucleotide, 256 >	char_to_nucleotide
	Lookup table for converting characters to nucleotides.
static constexpr std::array< char, 4 >	nucleotide_to_char
	Lookup table for converting nucleotides to characters.

Detailed Description

Defines nucleotide representation and related utility functions.

This file provides a type-safe representation of DNA nucleotides and utility functions for converting between character and nucleotide formats. It supports case-insensitive conversion and implements streaming operators for convenient output. This is used primarily for genetic sequence processing in the trie data structures.

See also

genetics.hpp

BitString.cuh

Definition in file nucleotide.hpp.

Enumeration Type Documentation

Nucleotide

enum class Nucleotide : uint8_t

strong

Enumerates the four nucleotides of DNA.

This enumeration provides a type-safe way of representing the four nucleotides in DNA: Adenine (A), Cytosine (C), Guanine (G), and Thymine (T). It also includes an INVALID value for error handling.

Enumerator
A	Adenine.
C	Cytosine.
G	Guanine.
T	Thymine.
INVALID	Invalid nucleotide.

Definition at line 29 of file nucleotide.hpp.

{
    A = 0, 
    C = 1, 
    G = 2, 
    T = 3,  
    INVALID 
};

Function Documentation

is_valid_nucleotide()

bool is_valid_nucleotide

(

char

nucleotide

)

Checks if a character represents a valid nucleotide.

Determines whether the provided character is a valid nucleotide representation (A, C, G, T in either uppercase or lowercase).

Parameters

nucleotide

The character to check.

Returns

true if the character is a valid nucleotide representation, false otherwise.

See also

char_to_nucleotide

Definition at line 14 of file nucleotide.cpp.

{
    // 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;
}

operator<<()

std::ostream & operator<<	(	std::ostream &	os,
		const Nucleotide &	nucleotide
	)

Inserts a textual representation of a nucleotide into an output stream.

Converts the Nucleotide enum value to its character representation and inserts it into the provided output stream. Uses a switch statement to handle each nucleotide type explicitly and throws an std::invalid_argument exception for Nucleotide::INVALID rather than silently outputting a placeholder. This allows Nucleotide objects to be used directly with stream operators.

Parameters

os	The output stream to insert into.
nucleotide	The nucleotide to insert.

Returns

Reference to the output stream for chaining.

Exceptions

std::invalid_argument

if nucleotide is Nucleotide::INVALID.

See also

nucleotide_to_char

Definition at line 21 of file nucleotide.cpp.

{
    // 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;
}

Variable Documentation

char_to_nucleotide

constexpr std::array<Nucleotide, 256> char_to_nucleotide

staticconstexpr

Initial value:

= []() {
    std::array<Nucleotide, 256> result;
    result.fill(Nucleotide::INVALID);
 
    
    result['A'] = Nucleotide::A;
    result['a'] = Nucleotide::A;
    result['C'] = Nucleotide::C;
    result['c'] = Nucleotide::C;
    result['G'] = Nucleotide::G;
    result['g'] = Nucleotide::G;
    result['T'] = Nucleotide::T;
    result['t'] = Nucleotide::T;
 
    return result;
}()

Lookup table for converting characters to nucleotides.

This constexpr array provides O(1) conversion from ASCII characters to Nucleotide enum values. It supports both uppercase and lowercase letters (A/a, C/c, G/g, T/t) and marks all other characters as INVALID. Using a lookup table avoids branching in critical code paths.

Definition at line 44 of file nucleotide.hpp.

                                                                     {
    std::array<Nucleotide, 256> result;
    result.fill(Nucleotide::INVALID);
 
    // Initialize valid nucleotide mappings
    result['A'] = Nucleotide::A;
    result['a'] = Nucleotide::A;
    result['C'] = Nucleotide::C;
    result['c'] = Nucleotide::C;
    result['G'] = Nucleotide::G;
    result['g'] = Nucleotide::G;
    result['T'] = Nucleotide::T;
    result['t'] = Nucleotide::T;
 
    return result;
}();

nucleotide_to_char

constexpr std::array<char, 4> nucleotide_to_char

staticconstexpr

Initial value:

= {
    'A', 'C', 'G', 'T'
}

Lookup table for converting nucleotides to characters.

This array provides O(1) conversion from Nucleotide enum values to their corresponding ASCII character representation. The array is indexed by the underlying uint8_t value of the Nucleotide enum, so Nucleotide::A (0) maps to 'A', etc. Note that this array doesn't include a mapping for Nucleotide::INVALID.

See also

Nucleotide

Definition at line 69 of file nucleotide.hpp.

                                                        {
    'A', 'C', 'G', 'T'
};