{-# 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 { NucleicAcidChain i a -> Chain i a
getChain :: Chain i a }
  deriving (Int -> NucleicAcidChain i a -> ShowS
[NucleicAcidChain i a] -> ShowS
NucleicAcidChain i a -> String
(Int -> NucleicAcidChain i a -> ShowS)
-> (NucleicAcidChain i a -> String)
-> ([NucleicAcidChain i a] -> ShowS)
-> Show (NucleicAcidChain i a)
forall a.
(Int -> a -> ShowS) -> (a -> String) -> ([a] -> ShowS) -> Show a
forall i a.
(Ix i, Show i, Show a) =>
Int -> NucleicAcidChain i a -> ShowS
forall i a.
(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
$cshowList :: forall i a.
(Ix i, Show i, Show a) =>
[NucleicAcidChain i a] -> ShowS
show :: NucleicAcidChain i a -> String
$cshow :: forall i a.
(Ix i, Show i, Show a) =>
NucleicAcidChain i a -> String
showsPrec :: Int -> NucleicAcidChain i a -> ShowS
$cshowsPrec :: forall i a.
(Ix i, Show i, Show a) =>
Int -> NucleicAcidChain i a -> ShowS
Show, NucleicAcidChain i a -> NucleicAcidChain i a -> Bool
(NucleicAcidChain i a -> NucleicAcidChain i a -> Bool)
-> (NucleicAcidChain i a -> NucleicAcidChain i a -> Bool)
-> Eq (NucleicAcidChain i a)
forall a. (a -> a -> Bool) -> (a -> a -> Bool) -> Eq a
forall i a.
(Ix i, Eq a) =>
NucleicAcidChain i a -> NucleicAcidChain i a -> Bool
/= :: NucleicAcidChain i a -> NucleicAcidChain i a -> Bool
$c/= :: forall i a.
(Ix i, Eq a) =>
NucleicAcidChain i a -> NucleicAcidChain i a -> Bool
== :: NucleicAcidChain i a -> NucleicAcidChain i a -> Bool
$c== :: forall i a.
(Ix i, Eq a) =>
NucleicAcidChain i a -> NucleicAcidChain i a -> Bool
Eq, a -> NucleicAcidChain i b -> NucleicAcidChain i a
(a -> b) -> NucleicAcidChain i a -> NucleicAcidChain i b
(forall a b.
 (a -> b) -> NucleicAcidChain i a -> NucleicAcidChain i b)
-> (forall a b. a -> NucleicAcidChain i b -> NucleicAcidChain i a)
-> Functor (NucleicAcidChain i)
forall a b. a -> NucleicAcidChain i b -> NucleicAcidChain i a
forall a b.
(a -> b) -> NucleicAcidChain i a -> NucleicAcidChain i b
forall i a b. a -> NucleicAcidChain i b -> NucleicAcidChain i a
forall i a b.
(a -> b) -> NucleicAcidChain i a -> NucleicAcidChain i b
forall (f :: * -> *).
(forall a b. (a -> b) -> f a -> f b)
-> (forall a b. a -> f b -> f a) -> Functor f
<$ :: a -> NucleicAcidChain i b -> NucleicAcidChain i a
$c<$ :: forall i a b. a -> NucleicAcidChain i b -> NucleicAcidChain i a
fmap :: (a -> b) -> NucleicAcidChain i a -> NucleicAcidChain i b
$cfmap :: forall i a b.
(a -> b) -> NucleicAcidChain i a -> NucleicAcidChain i b
Functor, a -> NucleicAcidChain i a -> Bool
NucleicAcidChain i m -> m
NucleicAcidChain i a -> [a]
NucleicAcidChain i a -> Bool
NucleicAcidChain i a -> Int
NucleicAcidChain i a -> a
NucleicAcidChain i a -> a
NucleicAcidChain i a -> a
NucleicAcidChain i a -> a
(a -> m) -> NucleicAcidChain i a -> m
(a -> m) -> NucleicAcidChain i a -> m
(a -> b -> b) -> b -> NucleicAcidChain i a -> b
(a -> b -> b) -> b -> NucleicAcidChain i a -> b
(b -> a -> b) -> b -> NucleicAcidChain i a -> b
(b -> a -> b) -> b -> NucleicAcidChain i a -> b
(a -> a -> a) -> NucleicAcidChain i a -> a
(a -> a -> a) -> NucleicAcidChain i a -> a
(forall m. Monoid m => NucleicAcidChain i m -> m)
-> (forall m a. Monoid m => (a -> m) -> NucleicAcidChain i a -> m)
-> (forall m a. Monoid m => (a -> m) -> NucleicAcidChain i a -> m)
-> (forall a b. (a -> b -> b) -> b -> NucleicAcidChain i a -> b)
-> (forall a b. (a -> b -> b) -> b -> NucleicAcidChain i a -> b)
-> (forall b a. (b -> a -> b) -> b -> NucleicAcidChain i a -> b)
-> (forall b a. (b -> a -> b) -> b -> NucleicAcidChain i a -> b)
-> (forall a. (a -> a -> a) -> NucleicAcidChain i a -> a)
-> (forall a. (a -> a -> a) -> NucleicAcidChain i a -> a)
-> (forall a. NucleicAcidChain i a -> [a])
-> (forall a. NucleicAcidChain i a -> Bool)
-> (forall a. NucleicAcidChain i a -> Int)
-> (forall a. Eq a => a -> NucleicAcidChain i a -> Bool)
-> (forall a. Ord a => NucleicAcidChain i a -> a)
-> (forall a. Ord a => NucleicAcidChain i a -> a)
-> (forall a. Num a => NucleicAcidChain i a -> a)
-> (forall a. Num a => NucleicAcidChain i a -> a)
-> Foldable (NucleicAcidChain i)
forall a. Eq a => a -> NucleicAcidChain i a -> Bool
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
forall (t :: * -> *).
(forall m. Monoid m => t m -> m)
-> (forall m a. Monoid m => (a -> m) -> t a -> m)
-> (forall m a. Monoid m => (a -> m) -> t a -> m)
-> (forall a b. (a -> b -> b) -> b -> t a -> b)
-> (forall a b. (a -> b -> b) -> b -> t a -> b)
-> (forall b a. (b -> a -> b) -> b -> t a -> b)
-> (forall b a. (b -> a -> b) -> b -> t a -> b)
-> (forall a. (a -> a -> a) -> t a -> a)
-> (forall a. (a -> a -> a) -> t a -> a)
-> (forall a. t a -> [a])
-> (forall a. t a -> Bool)
-> (forall a. t a -> Int)
-> (forall a. Eq a => a -> t a -> Bool)
-> (forall a. Ord a => t a -> a)
-> (forall a. Ord a => t a -> a)
-> (forall a. Num a => t a -> a)
-> (forall a. Num a => t a -> a)
-> Foldable t
product :: NucleicAcidChain i a -> a
$cproduct :: forall i a. Num a => NucleicAcidChain i a -> a
sum :: NucleicAcidChain i a -> a
$csum :: forall i a. Num a => NucleicAcidChain i a -> a
minimum :: NucleicAcidChain i a -> a
$cminimum :: forall i a. Ord a => NucleicAcidChain i a -> a
maximum :: NucleicAcidChain i a -> a
$cmaximum :: forall i a. Ord a => NucleicAcidChain i a -> a
elem :: a -> NucleicAcidChain i a -> Bool
$celem :: forall i a. Eq a => a -> NucleicAcidChain i a -> Bool
length :: NucleicAcidChain i a -> Int
$clength :: forall i a. NucleicAcidChain i a -> Int
null :: NucleicAcidChain i a -> Bool
$cnull :: forall i a. NucleicAcidChain i a -> Bool
toList :: NucleicAcidChain i a -> [a]
$ctoList :: forall i a. NucleicAcidChain i a -> [a]
foldl1 :: (a -> a -> a) -> NucleicAcidChain i a -> a
$cfoldl1 :: forall i a. (a -> a -> a) -> NucleicAcidChain i a -> a
foldr1 :: (a -> a -> a) -> NucleicAcidChain i a -> a
$cfoldr1 :: forall i a. (a -> a -> a) -> NucleicAcidChain i a -> a
foldl' :: (b -> a -> b) -> b -> NucleicAcidChain i a -> b
$cfoldl' :: forall i b a. (b -> a -> b) -> b -> NucleicAcidChain i a -> b
foldl :: (b -> a -> b) -> b -> NucleicAcidChain i a -> b
$cfoldl :: forall i b a. (b -> a -> b) -> b -> NucleicAcidChain i a -> b
foldr' :: (a -> b -> b) -> b -> NucleicAcidChain i a -> b
$cfoldr' :: forall i a b. (a -> b -> b) -> b -> NucleicAcidChain i a -> b
foldr :: (a -> b -> b) -> b -> NucleicAcidChain i a -> b
$cfoldr :: forall i a b. (a -> b -> b) -> b -> NucleicAcidChain i a -> b
foldMap' :: (a -> m) -> NucleicAcidChain i a -> m
$cfoldMap' :: forall i m a. Monoid m => (a -> m) -> NucleicAcidChain i a -> m
foldMap :: (a -> m) -> NucleicAcidChain i a -> m
$cfoldMap :: forall i m a. Monoid m => (a -> m) -> NucleicAcidChain i a -> m
fold :: NucleicAcidChain i m -> m
$cfold :: forall i m. Monoid m => NucleicAcidChain i m -> m
Foldable, Functor (NucleicAcidChain i)
Foldable (NucleicAcidChain i)
Functor (NucleicAcidChain i)
-> Foldable (NucleicAcidChain i)
-> (forall (f :: * -> *) a b.
    Applicative f =>
    (a -> f b) -> NucleicAcidChain i a -> f (NucleicAcidChain i b))
-> (forall (f :: * -> *) a.
    Applicative f =>
    NucleicAcidChain i (f a) -> f (NucleicAcidChain i a))
-> (forall (m :: * -> *) a b.
    Monad m =>
    (a -> m b) -> NucleicAcidChain i a -> m (NucleicAcidChain i b))
-> (forall (m :: * -> *) a.
    Monad m =>
    NucleicAcidChain i (m a) -> m (NucleicAcidChain i a))
-> Traversable (NucleicAcidChain i)
(a -> f b) -> NucleicAcidChain i a -> f (NucleicAcidChain i b)
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)
forall i (f :: * -> *) a.
(Ix i, Applicative f) =>
NucleicAcidChain i (f a) -> f (NucleicAcidChain i a)
forall i (m :: * -> *) a b.
(Ix i, Monad m) =>
(a -> m b) -> NucleicAcidChain i a -> m (NucleicAcidChain i b)
forall i (f :: * -> *) a b.
(Ix i, Applicative f) =>
(a -> f b) -> NucleicAcidChain i a -> f (NucleicAcidChain i b)
forall (t :: * -> *).
Functor t
-> Foldable t
-> (forall (f :: * -> *) a b.
    Applicative f =>
    (a -> f b) -> t a -> f (t b))
-> (forall (f :: * -> *) a. Applicative f => t (f a) -> f (t a))
-> (forall (m :: * -> *) a b.
    Monad m =>
    (a -> m b) -> t a -> m (t b))
-> (forall (m :: * -> *) a. Monad m => t (m a) -> m (t a))
-> Traversable t
forall (m :: * -> *) a.
Monad m =>
NucleicAcidChain i (m a) -> m (NucleicAcidChain i a)
forall (f :: * -> *) a.
Applicative f =>
NucleicAcidChain i (f a) -> f (NucleicAcidChain i a)
forall (m :: * -> *) a b.
Monad m =>
(a -> m b) -> NucleicAcidChain i a -> m (NucleicAcidChain i b)
forall (f :: * -> *) a b.
Applicative f =>
(a -> f b) -> NucleicAcidChain i a -> f (NucleicAcidChain i b)
sequence :: 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 :: (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 :: NucleicAcidChain i (f a) -> f (NucleicAcidChain i a)
$csequenceA :: forall i (f :: * -> *) a.
(Ix i, Applicative f) =>
NucleicAcidChain i (f a) -> f (NucleicAcidChain i a)
traverse :: (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)
$cp2Traversable :: forall i. Ix i => Foldable (NucleicAcidChain i)
$cp1Traversable :: forall i. Ix i => Functor (NucleicAcidChain i)
Traversable, Enum (Index (NucleicAcidChain i a))
Ixed (NucleicAcidChain i a)
Index (NucleicAcidChain i a)
-> (IxValue (NucleicAcidChain i a)
    -> IxValue (NucleicAcidChain i a))
-> NucleicAcidChain i a
-> NucleicAcidChain i a
Ixed (NucleicAcidChain i a)
-> Enum (Index (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))])
-> (Index (NucleicAcidChain i a)
    -> (IxValue (NucleicAcidChain i a)
        -> IxValue (NucleicAcidChain i a))
    -> NucleicAcidChain i a
    -> NucleicAcidChain i a)
-> (Index (NucleicAcidChain i a)
    -> (IxValue (NucleicAcidChain i a)
        -> IxValue (NucleicAcidChain i a))
    -> NucleicAcidChain i a
    -> NucleicAcidChain i a)
-> (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))
-> ChainLike (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
-> Enum (Index m)
-> (m -> (Index m, Index m))
-> (m -> [(Index m, IxValue m)])
-> (Index m -> (IxValue m -> IxValue m) -> m -> m)
-> (Index m -> (IxValue m -> IxValue m) -> m -> m)
-> (Index m -> (IxValue m -> IxValue m) -> m -> m)
-> (m -> Index m -> IxValue m)
-> ChainLike m
forall i a. (Ix i, Enum i) => Enum (Index (NucleicAcidChain i a))
forall i a. (Ix i, Enum i) => Ixed (NucleicAcidChain i a)
forall i a.
(Ix i, Enum i) =>
Index (NucleicAcidChain i a)
-> (IxValue (NucleicAcidChain i a)
    -> IxValue (NucleicAcidChain i a))
-> NucleicAcidChain i a
-> NucleicAcidChain i a
forall i a.
(Ix i, Enum i) =>
NucleicAcidChain i a
-> [(Index (NucleicAcidChain i a), IxValue (NucleicAcidChain i a))]
forall i a.
(Ix i, Enum i) =>
NucleicAcidChain i a
-> (Index (NucleicAcidChain i a), Index (NucleicAcidChain i a))
forall i a.
(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)
-> (IxValue (NucleicAcidChain i a)
    -> IxValue (NucleicAcidChain i a))
-> NucleicAcidChain i a
-> NucleicAcidChain i a
modifyBefore :: Index (NucleicAcidChain i a)
-> (IxValue (NucleicAcidChain i a)
    -> IxValue (NucleicAcidChain i a))
-> NucleicAcidChain i a
-> NucleicAcidChain i a
$cmodifyBefore :: forall i a.
(Ix i, Enum i) =>
Index (NucleicAcidChain i a)
-> (IxValue (NucleicAcidChain i a)
    -> IxValue (NucleicAcidChain i a))
-> NucleicAcidChain i a
-> NucleicAcidChain i a
modify :: Index (NucleicAcidChain i a)
-> (IxValue (NucleicAcidChain i a)
    -> IxValue (NucleicAcidChain i a))
-> NucleicAcidChain i a
-> NucleicAcidChain i a
$cmodify :: forall i a.
(Ix i, Enum i) =>
Index (NucleicAcidChain i a)
-> (IxValue (NucleicAcidChain i a)
    -> IxValue (NucleicAcidChain i a))
-> NucleicAcidChain i a
-> 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))
$cp2ChainLike :: forall i a. (Ix i, Enum i) => Enum (Index (NucleicAcidChain i a))
$cp1ChainLike :: forall i a. (Ix i, Enum i) => Ixed (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' = (Chain i a -> f (Chain i a))
-> NucleicAcidChain i a -> f (NucleicAcidChain i a)
forall s t a b. (Coercible s a, Coercible t b) => Iso s t a b
coerced ((Chain i a -> f (Chain i a))
 -> NucleicAcidChain i a -> f (NucleicAcidChain i a))
-> ((a -> f a) -> Chain i a -> f (Chain i a))
-> (a -> f a)
-> NucleicAcidChain i a
-> f (NucleicAcidChain i a)
forall b c a. (b -> c) -> (a -> b) -> a -> c
. Index (Chain i a) -> Traversal' (Chain i a) (IxValue (Chain i a))
forall m. Ixed m => Index m -> Traversal' m (IxValue m)
ix @(Chain i a) Index (Chain i a)
Index (NucleicAcidChain i a)
i'

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

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