AminoAcidS.hs

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

-- |
-- Module      :  ELynx.Data.AminoAcid
-- Description :  Amino acid related types and functions
-- 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'.
--
-- Amino acids with gaps and translation stops.
--
-- @
-- Amino Acid Code:  Three letter Code:  Amino Acid:
-- ----------------  ------------------  -----------
-- A                 Ala                 Alanine
-- C                 Cys                 Cysteine
-- D                 Asp                 Aspartic Acid
-- E                 Glu                 Glutamic Acid
-- F                 Phe                 Phenylalanine
-- G                 Gly                 Glycine
-- H                 His                 Histidine
-- I                 Ile                 Isoleucine
-- K                 Lys                 Lysine
-- L                 Leu                 Leucine
-- M                 Met                 Methionine
-- N                 Asn                 Asparagine
-- P                 Pro                 Proline
-- Q                 Gln                 Glutamine
-- R                 Arg                 Arginine
-- S                 Ser                 Serine
-- T                 Thr                 Threonine
-- V                 Val                 Valine
-- W                 Trp                 Tryptophan
-- Y                 Tyr                 Tyrosine
-- ----------------  ------------------  -----------
-- *                 Stp                 No amino acid
-- ----------------  ------------------  -----------
-- -                 Gap                 No amino acid (preferred)
-- .                 Gap                 No amino acid
-- @
module ELynx.Data.Character.AminoAcidS
  ( AminoAcidS (..),
  )
where

import Data.ByteString.Internal (c2w, w2c)
import Data.Vector.Unboxed.Deriving
import Data.Word8
import qualified ELynx.Data.Character.Character as C

-- | Amino acids.
data AminoAcidS
  = A
  | C
  | D
  | E
  | F
  | G
  | H
  | I
  | K
  | L
  | M
  | N
  | P
  | Q
  | R
  | S
  | T
  | V
  | W
  | Y
  | Stop
  | Gap
  deriving (Show, Read, Eq, Ord, Enum, Bounded)

toWord :: AminoAcidS -> Word8
toWord A = c2w 'A'
toWord C = c2w 'C'
toWord D = c2w 'D'
toWord E = c2w 'E'
toWord F = c2w 'F'
toWord G = c2w 'G'
toWord H = c2w 'H'
toWord I = c2w 'I'
toWord K = c2w 'K'
toWord L = c2w 'L'
toWord M = c2w 'M'
toWord N = c2w 'N'
toWord P = c2w 'P'
toWord Q = c2w 'Q'
toWord R = c2w 'R'
toWord S = c2w 'S'
toWord T = c2w 'T'
toWord V = c2w 'V'
toWord W = c2w 'W'
toWord Y = c2w 'Y'
toWord Stop = c2w '*'
toWord Gap = c2w '-'

fromWord :: Word8 -> AminoAcidS
fromWord w = case w2c w of
  'A' -> A
  'C' -> C
  'D' -> D
  'E' -> E
  'F' -> F
  'G' -> G
  'H' -> H
  'I' -> I
  'K' -> K
  'L' -> L
  'M' -> M
  'N' -> N
  'P' -> P
  'Q' -> Q
  'R' -> R
  'S' -> S
  'T' -> T
  'V' -> V
  'W' -> W
  'Y' -> Y
  '*' -> Stop
  '-' -> Gap
  '.' -> Gap
  _ -> error "fromWord: Cannot convert to AminoAcidS."

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

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

instance C.CharacterX AminoAcidS where
  gap = Gap