{-# OPTIONS_GHC -fno-warn-orphans #-}

module Bio.NucleicAcid.Chain where

import           Bio.Chain                  as C
import           Bio.NucleicAcid.Nucleotide
import           Control.Lens
import           Data.Array                 (Ix (..))
import           Data.String                (IsString (..))

newtype NucleicAcidChain i a = NucleicAcidChain { forall i a. NucleicAcidChain i a -> Chain i a
getChain :: Chain i a }
  deriving (Int -> NucleicAcidChain i a -> ShowS
forall a.
(Int -> a -> ShowS) -> (a -> String) -> ([a] -> ShowS) -> Show a
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(Ix i, Show i, Show a) =>
Int -> NucleicAcidChain i a -> ShowS
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(Ix i, Show i, Show a) =>
[NucleicAcidChain i a] -> ShowS
forall i a.
(Ix i, Show i, Show a) =>
NucleicAcidChain i a -> String
showList :: [NucleicAcidChain i a] -> ShowS
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(Ix i, Show i, Show a) =>
[NucleicAcidChain i a] -> ShowS
show :: NucleicAcidChain i a -> String
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(Ix i, Show i, Show a) =>
NucleicAcidChain i a -> String
showsPrec :: Int -> NucleicAcidChain i a -> ShowS
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Int -> NucleicAcidChain i a -> ShowS
Show, NucleicAcidChain i a -> NucleicAcidChain i a -> Bool
forall a. (a -> a -> Bool) -> (a -> a -> Bool) -> Eq a
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/= :: NucleicAcidChain i a -> NucleicAcidChain i a -> Bool
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(Ix i, Eq a) =>
NucleicAcidChain i a -> NucleicAcidChain i a -> Bool
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(a -> b) -> NucleicAcidChain i a -> NucleicAcidChain i b
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forall a. Num a => NucleicAcidChain i a -> a
forall a. Ord a => NucleicAcidChain i a -> a
forall m. Monoid m => NucleicAcidChain i m -> m
forall a. NucleicAcidChain i a -> Bool
forall a. NucleicAcidChain i a -> Int
forall a. NucleicAcidChain i a -> [a]
forall a. (a -> a -> a) -> NucleicAcidChain i a -> a
forall i a. Eq a => a -> NucleicAcidChain i a -> Bool
forall i a. Num a => NucleicAcidChain i a -> a
forall i a. Ord a => NucleicAcidChain i a -> a
forall m a. Monoid m => (a -> m) -> NucleicAcidChain i a -> m
forall i m. Monoid m => NucleicAcidChain i m -> m
forall i a. NucleicAcidChain i a -> Bool
forall i a. NucleicAcidChain i a -> Int
forall i a. NucleicAcidChain i a -> [a]
forall b a. (b -> a -> b) -> b -> NucleicAcidChain i a -> b
forall a b. (a -> b -> b) -> b -> NucleicAcidChain i a -> b
forall i a. (a -> a -> a) -> NucleicAcidChain i a -> a
forall i m a. Monoid m => (a -> m) -> NucleicAcidChain i a -> m
forall i b a. (b -> a -> b) -> b -> NucleicAcidChain i a -> b
forall i a b. (a -> b -> b) -> b -> NucleicAcidChain i a -> b
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product :: forall a. Num a => NucleicAcidChain i a -> a
$cproduct :: forall i a. Num a => NucleicAcidChain i a -> a
sum :: forall a. Num a => NucleicAcidChain i a -> a
$csum :: forall i a. Num a => NucleicAcidChain i a -> a
minimum :: forall a. Ord a => NucleicAcidChain i a -> a
$cminimum :: forall i a. Ord a => NucleicAcidChain i a -> a
maximum :: forall a. Ord a => NucleicAcidChain i a -> a
$cmaximum :: forall i a. Ord a => NucleicAcidChain i a -> a
elem :: forall a. Eq a => a -> NucleicAcidChain i a -> Bool
$celem :: forall i a. Eq a => a -> NucleicAcidChain i a -> Bool
length :: forall a. NucleicAcidChain i a -> Int
$clength :: forall i a. NucleicAcidChain i a -> Int
null :: forall a. NucleicAcidChain i a -> Bool
$cnull :: forall i a. NucleicAcidChain i a -> Bool
toList :: forall a. NucleicAcidChain i a -> [a]
$ctoList :: forall i a. NucleicAcidChain i a -> [a]
foldl1 :: forall a. (a -> a -> a) -> NucleicAcidChain i a -> a
$cfoldl1 :: forall i a. (a -> a -> a) -> NucleicAcidChain i a -> a
foldr1 :: forall a. (a -> a -> a) -> NucleicAcidChain i a -> a
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foldl' :: forall b a. (b -> a -> b) -> b -> NucleicAcidChain i a -> b
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foldl :: forall b a. (b -> a -> b) -> b -> NucleicAcidChain i a -> b
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foldr' :: forall a b. (a -> b -> b) -> b -> NucleicAcidChain i a -> b
$cfoldr' :: forall i a b. (a -> b -> b) -> b -> NucleicAcidChain i a -> b
foldr :: forall a b. (a -> b -> b) -> b -> NucleicAcidChain i a -> b
$cfoldr :: forall i a b. (a -> b -> b) -> b -> NucleicAcidChain i a -> b
foldMap' :: forall m a. Monoid m => (a -> m) -> NucleicAcidChain i a -> m
$cfoldMap' :: forall i m a. Monoid m => (a -> m) -> NucleicAcidChain i a -> m
foldMap :: forall m a. Monoid m => (a -> m) -> NucleicAcidChain i a -> m
$cfoldMap :: forall i m a. Monoid m => (a -> m) -> NucleicAcidChain i a -> m
fold :: forall m. Monoid m => NucleicAcidChain i m -> m
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Foldable, forall {i}. Ix i => Functor (NucleicAcidChain i)
forall {i}. Ix i => Foldable (NucleicAcidChain i)
forall i (m :: * -> *) a.
(Ix i, Monad m) =>
NucleicAcidChain i (m a) -> m (NucleicAcidChain i a)
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NucleicAcidChain i (f a) -> f (NucleicAcidChain i a)
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(a -> m b) -> NucleicAcidChain i a -> m (NucleicAcidChain i b)
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-> Traversable t
forall (f :: * -> *) a b.
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(a -> f b) -> NucleicAcidChain i a -> f (NucleicAcidChain i b)
sequence :: forall (m :: * -> *) a.
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NucleicAcidChain i (m a) -> m (NucleicAcidChain i a)
$csequence :: forall i (m :: * -> *) a.
(Ix i, Monad m) =>
NucleicAcidChain i (m a) -> m (NucleicAcidChain i a)
mapM :: forall (m :: * -> *) a b.
Monad m =>
(a -> m b) -> NucleicAcidChain i a -> m (NucleicAcidChain i b)
$cmapM :: forall i (m :: * -> *) a b.
(Ix i, Monad m) =>
(a -> m b) -> NucleicAcidChain i a -> m (NucleicAcidChain i b)
sequenceA :: forall (f :: * -> *) a.
Applicative f =>
NucleicAcidChain i (f a) -> f (NucleicAcidChain i a)
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(Ix i, Applicative f) =>
NucleicAcidChain i (f a) -> f (NucleicAcidChain i a)
traverse :: forall (f :: * -> *) a b.
Applicative f =>
(a -> f b) -> NucleicAcidChain i a -> f (NucleicAcidChain i b)
$ctraverse :: forall i (f :: * -> *) a b.
(Ix i, Applicative f) =>
(a -> f b) -> NucleicAcidChain i a -> f (NucleicAcidChain i b)
Traversable, Index (NucleicAcidChain i a)
-> (IxValue (NucleicAcidChain i a)
    -> IxValue (NucleicAcidChain i a))
-> NucleicAcidChain i a
-> NucleicAcidChain i a
NucleicAcidChain i a
-> [(Index (NucleicAcidChain i a), IxValue (NucleicAcidChain i a))]
NucleicAcidChain i a
-> (Index (NucleicAcidChain i a), Index (NucleicAcidChain i a))
NucleicAcidChain i a
-> Index (NucleicAcidChain i a) -> IxValue (NucleicAcidChain i a)
forall m.
Ixed m
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forall {i} {a}.
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forall {i} {a}. (Ix i, Enum i) => Ixed (NucleicAcidChain i a)
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(Ix i, Enum i) =>
NucleicAcidChain i a
-> Index (NucleicAcidChain i a) -> IxValue (NucleicAcidChain i a)
unsafeRead :: NucleicAcidChain i a
-> Index (NucleicAcidChain i a) -> IxValue (NucleicAcidChain i a)
$cunsafeRead :: forall i a.
(Ix i, Enum i) =>
NucleicAcidChain i a
-> Index (NucleicAcidChain i a) -> IxValue (NucleicAcidChain i a)
modifyAfter :: Index (NucleicAcidChain i a)
-> (IxValue (NucleicAcidChain i a)
    -> IxValue (NucleicAcidChain i a))
-> NucleicAcidChain i a
-> NucleicAcidChain i a
$cmodifyAfter :: forall i a.
(Ix i, Enum i) =>
Index (NucleicAcidChain i a)
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    -> IxValue (NucleicAcidChain i a))
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-> NucleicAcidChain i a
modifyBefore :: Index (NucleicAcidChain i a)
-> (IxValue (NucleicAcidChain i a)
    -> IxValue (NucleicAcidChain i a))
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-> NucleicAcidChain i a
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(Ix i, Enum i) =>
Index (NucleicAcidChain i a)
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    -> IxValue (NucleicAcidChain i a))
-> NucleicAcidChain i a
-> NucleicAcidChain i a
modify :: Index (NucleicAcidChain i a)
-> (IxValue (NucleicAcidChain i a)
    -> IxValue (NucleicAcidChain i a))
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-> NucleicAcidChain i a
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(Ix i, Enum i) =>
Index (NucleicAcidChain i a)
-> (IxValue (NucleicAcidChain i a)
    -> IxValue (NucleicAcidChain i a))
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-> NucleicAcidChain i a
assocs :: NucleicAcidChain i a
-> [(Index (NucleicAcidChain i a), IxValue (NucleicAcidChain i a))]
$cassocs :: forall i a.
(Ix i, Enum i) =>
NucleicAcidChain i a
-> [(Index (NucleicAcidChain i a), IxValue (NucleicAcidChain i a))]
bounds :: NucleicAcidChain i a
-> (Index (NucleicAcidChain i a), Index (NucleicAcidChain i a))
$cbounds :: forall i a.
(Ix i, Enum i) =>
NucleicAcidChain i a
-> (Index (NucleicAcidChain i a), Index (NucleicAcidChain i a))
ChainLike)

type instance Index (NucleicAcidChain i a) = i
type instance IxValue (NucleicAcidChain i a) = a

instance Ix i => Ixed (NucleicAcidChain i a) where
    ix :: Index (NucleicAcidChain i a)
-> Traversal'
     (NucleicAcidChain i a) (IxValue (NucleicAcidChain i a))
ix Index (NucleicAcidChain i a)
i' = forall s t a b. (Coercible s a, Coercible t b) => Iso s t a b
coerced forall b c a. (b -> c) -> (a -> b) -> a -> c
. forall m. Ixed m => Index m -> Traversal' m (IxValue m)
ix @(Chain i a) Index (NucleicAcidChain i a)
i'

instance IsString (NucleicAcidChain Int DNA) where
  fromString :: String -> NucleicAcidChain Int DNA
fromString = forall i a. Chain i a -> NucleicAcidChain i a
NucleicAcidChain forall b c a. (b -> c) -> (a -> b) -> a -> c
. forall a. IsString a => String -> a
fromString

instance IsString (NucleicAcidChain Int RNA) where
  fromString :: String -> NucleicAcidChain Int RNA
fromString = forall i a. Chain i a -> NucleicAcidChain i a
NucleicAcidChain forall b c a. (b -> c) -> (a -> b) -> a -> c
. forall a. IsString a => String -> a
fromString