module Biobase.Primary.Nuc.DNA where
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.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 Control.Category ((>>>))
import Biobase.Primary.Bounds
import Biobase.Primary.Letter
data DNA
pattern A = Letter 0 :: Letter DNA
pattern C = Letter 1 :: Letter DNA
pattern G = Letter 2 :: Letter DNA
pattern T = Letter 3 :: Letter DNA
pattern N = Letter 4 :: Letter DNA
instance Enum (Letter DNA) where
succ N = error "succ/N:DNA"
succ (Letter x) = Letter $ x+1
pred A = error "pred/A:DNA"
pred (Letter x) = Letter $ x1
toEnum k | k>=0 && k<=4 = Letter k
toEnum k = error $ "toEnum/Letter DNA " ++ show k
fromEnum (Letter k) = k
instance LetterChar DNA where
letterChar = dnaChar
charLetter = charDNA
instance (LetterChar DNA) => ToJSON (Primary DNA) where
toJSON = toJSON . VU.toList . VU.map letterChar
instance (MkPrimary (VU.Vector Char) DNA) => FromJSON (Primary DNA) where
parseJSON = fmap (primary :: String -> Primary DNA) . parseJSON
acgt :: [Letter DNA]
acgt = [A .. T]
charDNA = toUpper >>> \case
'A' -> A
'C' -> C
'G' -> G
'T' -> T
_ -> N
dnaChar = \case
A -> 'A'
C -> 'C'
G -> 'G'
T -> 'T'
N -> 'N'
instance Show (Letter DNA) where
show c = [dnaChar c]
instance Read (Letter DNA) where
readsPrec p [] = []
readsPrec p (x:xs)
| x==' ' = readsPrec p xs
| otherwise = [(charDNA x, xs)]
dnaSeq :: MkPrimary n DNA => n -> Primary DNA
dnaSeq = primary
instance Bounded (Letter DNA) where
minBound = A
maxBound = N
instance MkPrimary (VU.Vector Char) DNA where
primary = VU.map charDNA
instance IsString [Letter DNA] where
fromString = map charDNA