cusbf::ProteinAlphabet Struct Reference

An alphabet for encoding protein sequences, consisting of the 20 standard amino acids plus common ambiguous and rare residue symbols: More...

Static Public Member Functions
constexpr __host__ __device__ static __forceinline__ uint8_t	encode (const char *input)
	Maps one amino-acid letter to a 5-bit index, or invalidSymbol.

Static Public Attributes
static constexpr uint64_t	symbolWidth = 1
	Input bytes per encoded symbol.
static constexpr uint64_t	symbolCount = 26
	Number of letter symbols (A–Z).
static constexpr uint8_t	invalidSymbol = 0xFFu
	Sentinel returned by encode for invalid input bytes.
static constexpr uint8_t	separator = '*'
	Separator byte between concatenated records.
static constexpr char	validBytes [] = "ABCDEFGHIJKLMNOPQRSTUVWXYZ"
	Representative valid bytes for compile-time separator checks.

Detailed Description

An alphabet for encoding protein sequences, consisting of the 20 standard amino acids plus common ambiguous and rare residue symbols:

A through Z.

Each symbol is encoded as a unique 5-bit value from 0 to 25. Invalid bytes are encoded as 0xFF.

Definition at line 189 of file Alphabet.cuh.

Member Function Documentation

encode()

constexpr __host__ __device__ static __forceinline__ uint8_t cusbf::ProteinAlphabet::encode ( const char *  input )

inlinestaticconstexpr

Maps one amino-acid letter to a 5-bit index, or invalidSymbol.

Accepts A–Z in either case.

Parameters

input

Pointer to one raw byte.

Definition at line 208 of file Alphabet.cuh.

      {
        const auto byte = static_cast<uint8_t>(input[0]);
        const uint8_t upper = byte & 0xDFu;
        const uint8_t letterIndex = upper - 'A';
        const uint8_t valid = letterIndex < 26;
        const uint8_t mask = -valid;
        return (letterIndex & mask) | (invalidSymbol & ~mask);
    }

Member Data Documentation

invalidSymbol

constexpr uint8_t cusbf::ProteinAlphabet::invalidSymbol = 0xFFu

staticconstexpr

Sentinel returned by encode for invalid input bytes.

Definition at line 195 of file Alphabet.cuh.

separator

constexpr uint8_t cusbf::ProteinAlphabet::separator = '*'

staticconstexpr

Separator byte between concatenated records.

Definition at line 197 of file Alphabet.cuh.

symbolCount

constexpr uint64_t cusbf::ProteinAlphabet::symbolCount = 26

staticconstexpr

Number of letter symbols (A–Z).

Definition at line 193 of file Alphabet.cuh.

symbolWidth

constexpr uint64_t cusbf::ProteinAlphabet::symbolWidth = 1

staticconstexpr

Input bytes per encoded symbol.

Definition at line 191 of file Alphabet.cuh.

validBytes

constexpr char cusbf::ProteinAlphabet::validBytes[] = "ABCDEFGHIJKLMNOPQRSTUVWXYZ"

staticconstexpr

Representative valid bytes for compile-time separator checks.

Definition at line 199 of file Alphabet.cuh.

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The documentation for this struct was generated from the following file:

• Alphabet.cuh