Nucleotide.hs

{-# LANGUAGE MultiParamTypeClasses #-}
{-# LANGUAGE TemplateHaskell #-}
{-# LANGUAGE TypeFamilies #-}

-- |
-- Module      :  ELynx.Data.Nucleotide
-- Description :  Nucleotides
-- Copyright   :  (c) Dominik Schrempf 2018
-- License     :  GPL-3.0-or-later
--
-- Maintainer  :  dominik.schrempf@gmail.com
-- Stability   :  unstable
-- Portability :  portable
--
-- Creation date: Thu Oct  4 18:26:35 2018.
--
-- See header of 'ELynx.Data.Alphabet.Alphabet'.
--
-- @
-- Symbol  Description  Bases represented  Complement
-- ------  -----------  -----------------  ----------
-- A       Adenine      A                  T
-- C       Cytosine        C               G
-- G       Guanine            G            C
-- T       Thymine               T         A
-- @
module ELynx.Data.Character.Nucleotide
  ( Nucleotide (..),
  )
where

import Data.Vector.Unboxed.Deriving
import Data.Word8
import qualified ELynx.Data.Character.Character as C
import ELynx.Tools

-- | Nucleotides.
data Nucleotide = A | C | G | T
  deriving (Show, Read, Eq, Ord, Enum, Bounded)

-- See https://stackoverflow.com/a/31527024; apparently, pattern matching (and
-- case statements) are fast because they are compiled to lookup tables. Hence,
-- they are faster than guards (because equality has to be checked), and faster
-- than lookups with sets.
toWord :: Nucleotide -> Word8
toWord A = c2w 'A'
toWord C = c2w 'C'
toWord G = c2w 'G'
toWord T = c2w 'T'

fromWord :: Word8 -> Nucleotide
fromWord w = case w2c w of
  'A' -> A
  'C' -> C
  'G' -> G
  'T' -> T
  c -> error $ "fromWord: Cannot convert " ++ show c ++ " to Nucleotide."

derivingUnbox
  "Nucleotide"
  [t|Nucleotide -> Word8|]
  [|toWord|]
  [|fromWord|]

instance C.Character Nucleotide where
  toWord = toWord
  fromWord = fromWord