module Biobase.Primary.Unknown where
import Control.Applicative ((<$>))
import Control.Arrow ((***),first)
import Data.Hashable
import Data.Ix (Ix(..))
import Data.Map.Strict (Map)
import Data.Primitive.Types
import Data.Tuple (swap)
import Data.Vector.Unboxed.Deriving
import Debug.Trace
import GHC.Base (remInt,quotInt)
import GHC.Generics (Generic)
import GHC.Read
import qualified Data.Bijection.Map as B
import qualified Data.ByteString.Char8 as BS
import qualified Data.ByteString.Lazy.Char8 as BSL
import qualified Data.Map.Strict as M
import qualified Data.Text as T
import qualified Data.Vector.Generic as VG
import qualified Data.Vector.Generic.Mutable as VGM
import qualified Data.Vector.Unboxed as VU
import qualified Text.ParserCombinators.ReadPrec as RP
import qualified Text.Read.Lex as Lex
import Biobase.Primary.Letter
data Unknown
unk :: Int -> Letter Unknown
unk = Letter
instance Show (Letter Unknown) where
show (Letter i) = "U " ++ show i
instance Read (Letter Unknown) where
readPrec = parens $ do
Lex.Ident u <- lexP
case u of
"U" -> unk <$> readPrec
_ -> RP.pfail
instance Enum (Letter Unknown) where
succ (Letter x) = Letter $ x+1
pred (Letter x) = Letter $ x1
toEnum = Letter
fromEnum = getLetter
instance MkPrimary (VU.Vector Int) Unknown where
primary = VU.map Letter