Conversion.hs

--  {-# Language CPP #-}
--  
--  #if __GLASGOW_HASKELL__ < 710
--  {-# LANGUAGE OverlappingInstances #-}
--  #endif

-- | Convert between different nucleotide representations

module Biobase.Primary.Nuc.Conversion where

import           Control.Lens (iso, from)
import qualified Data.Vector.Unboxed as VU

import           Biobase.Types.BioSequence (Transcribe(..),RNA,DNA)

import           Biobase.Primary.Letter (Letter(..), Primary)
import qualified Biobase.Primary.Nuc.DNA as D
import qualified Biobase.Primary.Nuc.RNA as R
import qualified Biobase.Primary.Nuc.XNA as X



-- * Single-character translations.

-- | Transform RNA to DNA. That means change @U@ to @T@ and keep the other
-- characters as is.

rnaTdna = \case
  R.A -> D.A
  R.C -> D.C
  R.G -> D.G
  R.U -> D.T
  _   -> D.N
{-# INLINE rnaTdna #-}

-- | Transform DNA to RNA. That means change @T@ to @U@ and keep the other
-- characters as is.

dnaTrna = \case
  D.A -> R.A
  D.C -> R.C
  D.G -> R.G
  D.T -> R.U
  _   -> R.N
{-# INLINE dnaTrna #-}

-- | Generalize an RNA character to a XNA character.

rnaGxna = \case
  R.A -> X.A
  R.C -> X.C
  R.G -> X.G
  R.U -> X.U
  _   -> X.N
{-# INLINE rnaGxna #-}

-- | Generalize a DNA character to a XNA character.

dnaGxna = \case
  D.A -> X.A
  D.C -> X.C
  D.G -> X.G
  D.T -> X.T
  _   -> X.N
{-# INLINE dnaGxna #-}

-- | Specialize XNA to RNA, @T@ becomes @N@.

xnaSrna = \case
  X.A -> R.A
  X.C -> R.C
  X.G -> R.G
  X.U -> R.U
  _   -> R.N
{-# INLINE xnaSrna #-}

-- | Specialize XNA to DNA, @U@ becomes @N@.

xnaSdna = \case
  X.A -> D.A
  X.C -> D.C
  X.G -> D.G
  X.T -> D.T
  _   -> D.N
{-# INLINE xnaSdna #-}



-- ** Transcription between RNA and DNA. Both on the individual sequence level,
-- and on the level of primary sequence data.

instance Transcribe (Letter RNA n) where
  type TranscribeTo (Letter RNA n) = Letter DNA n
  transcribe = iso rnaTdna dnaTrna
  {-# Inline transcribe #-}

instance Transcribe (Letter DNA n) where
  type TranscribeTo (Letter DNA n) = Letter RNA n
  transcribe = from transcribe
  {-# Inline transcribe #-}

instance Transcribe (Primary RNA n) where
  type TranscribeTo (Primary RNA n) = Primary DNA n
  transcribe = iso (VU.map rnaTdna) (VU.map dnaTrna)
  {-# Inline transcribe #-}

instance Transcribe (Primary DNA n) where
  type TranscribeTo (Primary DNA n) = Primary RNA n
  transcribe = iso (VU.map dnaTrna) (VU.map rnaTdna)
  {-# Inline transcribe #-}


-- TODO to be removed soon

---- * Reverse-complement of characters.
--
---- | Produce the complement of a RNA or DNA sequence. Does intentionally
---- not work for XNA sequences as it is not possible to uniquely translate
---- @A@ into either @U@ or @T@.
--
--class Complement s t where
--    complement :: s -> t
--
---- | To 'transcribe' a DNA sequence into RNA we reverse the complement of
---- the sequence.
--
--transcribe :: Primary D.DNA -> Primary R.RNA
--transcribe = VU.reverse . complement
--
--instance Complement (Letter R.RNA) (Letter R.RNA) where
--    complement = \case
--      R.A -> R.U
--      R.C -> R.G
--      R.G -> R.C
--      R.U -> R.A
--      R.N -> R.N
--
--instance Complement (Letter D.DNA) (Letter D.DNA) where
--    complement = \case
--      D.A -> D.T
--      D.C -> D.G
--      D.G -> D.C
--      D.T -> D.A
--      D.N -> D.N
--
--instance Complement (Letter D.DNA) (Letter R.RNA) where
--    complement = \case
--      D.A -> R.U
--      D.C -> R.G
--      D.G -> R.C
--      D.T -> R.A
--      D.N -> R.N
--
--instance Complement (Letter R.RNA) (Letter D.DNA) where
--    complement = \case
--      R.A -> D.T
--      R.C -> D.G
--      R.G -> D.C
--      R.U -> D.A
--      R.N -> D.N
--
-- #if __GLASGOW_HASKELL__ >= 710
-- instance {-# OVERLAPPING #-}
-- #else
-- instance
-- #endif
--   ( Complement s t, VU.Unbox s, VU.Unbox t)
--   => Complement (VU.Vector s) (VU.Vector t)
--   where complement = VU.map complement
-- 
-- #if __GLASGOW_HASKELL__ >= 710
-- instance {-# Overlappable #-}
-- #else
-- instance
-- #endif
--   ( Complement s t, Functor f) => Complement (f s) (f t)
--   where complement = fmap complement