module Biobase.Primary.Nuc.RNA where
import Control.Category ((>>>))
import Control.Lens (Iso', iso)
import Data.Aeson
import Data.Char (toUpper)
import Data.Ix (Ix(..))
import Data.Primitive.Types
import Data.String
import Data.Tuple (swap)
import qualified Data.ByteString.Builder as BB
import qualified Data.ByteString.Char8 as BS
import qualified Data.ByteString.Lazy.Char8 as BSL
import qualified Data.Text as T
import qualified Data.Text.Lazy as TL
import qualified Data.Vector.Generic as VG
import qualified Data.Vector.Generic.Mutable as VGM
import qualified Data.Vector.Unboxed as VU
import Biobase.Primary.Bounds
import Biobase.Primary.Letter
data RNA
pattern A = Letter 0 :: Letter RNA
pattern C = Letter 1 :: Letter RNA
pattern G = Letter 2 :: Letter RNA
pattern U = Letter 3 :: Letter RNA
pattern N = Letter 4 :: Letter RNA
instance Bounded (Letter RNA) where
minBound = A
maxBound = N
instance Enum (Letter RNA) where
succ N = error "succ/N:RNA"
succ (Letter x) = Letter $ x+1
pred A = error "pred/A:RNA"
pred (Letter x) = Letter $ x1
toEnum k | k>=0 && k<=4 = Letter k
toEnum k = error $ "toEnum/Letter RNA " ++ show k
fromEnum (Letter k) = k
instance LetterChar RNA where
letterChar = rnaChar
charLetter = charRNA
instance ToJSON (Letter RNA) where
toJSON = toJSON . letterChar
instance FromJSON (Letter RNA) where
parseJSON = fmap charLetter . parseJSON
acgu :: [Letter RNA]
acgu = [A .. U]
charRNA = toUpper >>> \case
'A' -> A
'C' -> C
'G' -> G
'U' -> U
_ -> N
rnaChar = \case
A -> 'A'
C -> 'C'
G -> 'G'
U -> 'U'
N -> 'N'
crna ∷ Iso' Char (Letter RNA)
crna = iso charRNA rnaChar
instance Show (Letter RNA) where
show c = [rnaChar c]
instance Read (Letter RNA) where
readsPrec p [] = []
readsPrec p (x:xs)
| x==' ' = readsPrec p xs
| otherwise = [(charRNA x, xs)]
rnaSeq :: MkPrimary n RNA => n -> Primary RNA
rnaSeq = primary
instance MkPrimary (VU.Vector Char) RNA where
primary = VU.map charRNA
instance IsString [Letter RNA] where
fromString = map charRNA