nucleotide.cpp File Reference

Implementation of nucleotide utility functions. More...

#include "nucleotide.hpp"
#include <fstream>

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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.

Detailed Description

Implementation of nucleotide utility functions.

This file implements the functions declared in nucleotide.hpp for nucleotide validation and stream output operations. It provides efficient implementations for handling nucleotide conversions and validation.

See also

nucleotide.hpp

Definition in file nucleotide.cpp.

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;
}