module Biobase.SubstMatrix.Types where

import Control.Lens
import GHC.Generics (Generic)

import Algebra.Structure.Semiring
import Biobase.Types.BioSequence (AA,DNA)
import Biobase.Primary.AA (aaRange)
import Biobase.Primary.Letter
import Biobase.Primary.Nuc.DNA ()
import Data.PrimitiveArray
import Statistics.Odds
import Numeric.Discretized



-- | Denotes that we are dealing with a similarity score. Higher is more
-- similar.

data Similarity

-- | Denotes that we are dealing with a distance score. Lower is more
-- similar.

data Distance

-- An amino-acid substitution matrix. Tagged with the type of scoring used.

data AASubstMat t s a b = AASubstMat
  { AASubstMat t s a b -> Unboxed ((Z :. Letter AA a) :. Letter AA b) s
_aaSubstMat     :: !(Unboxed (Z:.Letter AA a:.Letter AA b) s)
  , AASubstMat t s a b -> Double
_aaSubstLambda  :: Double
  }
  deriving ((forall x. AASubstMat t s a b -> Rep (AASubstMat t s a b) x)
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makeLenses ''AASubstMat

--instance Binary    (AASubstMat t)
--instance Serialize (AASubstMat t)
--instance FromJSON  (AASubstMat t)
--instance (ToJSON s, VU.Unbox s, Generic s) ⇒ ToJSON    (AASubstMat t s)

--instance NFData (AASubstMat t s)

-- | @PAM@ matrices are similarity matrices.

type SubstPAM = AASubstMat Similarity (DiscLogOdds (RTyId 1))

-- | @BLOSUM@ matrices are distance matrices.

type SubstBLOSUM = AASubstMat Distance (DiscLogOdds (RTyId 1))

-- | Substitution matrix from amino acids to nucleotide triplets.

newtype ANuc3SubstMat t s a n = ANuc3SubstMat { ANuc3SubstMat t s a n
-> Unboxed
     ((((Z :. Letter AA a) :. Letter DNA n) :. Letter DNA n)
      :. Letter DNA n)
     s
_anuc3SubstMat :: Unboxed (Z:.Letter AA a:.Letter DNA n:.Letter DNA n:.Letter DNA n) s }
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makeLenses ''ANuc3SubstMat

--instance Binary    (ANuc3SubstMat t)
--instance Serialize (ANuc3SubstMat t)
--instance FromJSON  (ANuc3SubstMat t)
--instance ToJSON    (ANuc3SubstMat t)

--instance NFData (ANuc3SubstMat t)

-- | Substitution matrix from amino acids to degenerate nucleotide
-- 2-tuples. The third nucleotide letter is missing.

newtype ANuc2SubstMat t s a n = ANuc2SubstMat { ANuc2SubstMat t s a n
-> Unboxed (((Z :. Letter AA a) :. Letter DNA n) :. Letter DNA n) s
_anuc2SubstMat :: Unboxed (Z:.Letter AA a:.Letter DNA n:.Letter DNA n) s }
  deriving ((forall x. ANuc2SubstMat t s a n -> Rep (ANuc2SubstMat t s a n) x)
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makeLenses ''ANuc2SubstMat

--instance Binary    (ANuc2SubstMat t)
--instance Serialize (ANuc2SubstMat t)
--instance FromJSON  (ANuc2SubstMat t)
--instance ToJSON    (ANuc2SubstMat t)

--instance NFData (ANuc2SubstMat t)

-- | Substitution matrix from amino acids to degenerate nucleotide
-- 1-tuples. Two out of three nucleotides in a triplet are missing.

newtype ANuc1SubstMat t s a n = ANuc1SubstMat { ANuc1SubstMat t s a n
-> Unboxed ((Z :. Letter AA a) :. Letter DNA n) s
_anuc1SubstMat :: Unboxed (Z:.Letter AA a:.Letter DNA n) s }
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ReadS [ANuc1SubstMat t s a n]
readsPrec :: Int -> ReadS (ANuc1SubstMat t s a n)
$creadsPrec :: forall k (t :: k) s k (a :: k) k (n :: k).
(Read s, Unbox s) =>
Int -> ReadS (ANuc1SubstMat t s a n)
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[ANuc1SubstMat t s a n] -> ShowS
ANuc1SubstMat t s a n -> String
(Int -> ANuc1SubstMat t s a n -> ShowS)
-> (ANuc1SubstMat t s a n -> String)
-> ([ANuc1SubstMat t s a n] -> ShowS)
-> Show (ANuc1SubstMat t s a n)
forall a.
(Int -> a -> ShowS) -> (a -> String) -> ([a] -> ShowS) -> Show a
forall k (t :: k) s k (a :: k) k (n :: k).
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forall k (t :: k) s k (a :: k) k (n :: k).
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forall k (t :: k) s k (a :: k) k (n :: k).
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showList :: [ANuc1SubstMat t s a n] -> ShowS
$cshowList :: forall k (t :: k) s k (a :: k) k (n :: k).
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show :: ANuc1SubstMat t s a n -> String
$cshow :: forall k (t :: k) s k (a :: k) k (n :: k).
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makeLenses ''ANuc1SubstMat

--instance Binary    (ANuc1SubstMat t)
--instance Serialize (ANuc1SubstMat t)
--instance FromJSON  (ANuc1SubstMat t)
--instance ToJSON    (ANuc1SubstMat t)

--instance NFData (ANuc1SubstMat t)



data GapCost t = GapCost
  { GapCost t -> t
gcInit ∷ !t
  , GapCost t -> t
gcCont ∷ !t
  }