-- | Performs operations on cyclearrays, most importantly calculating energies
-- for "E" cases.
--
-- TODO MotifDB -> MotifDB should be the type.
--
-- TODO two different cases (i) activate "E" with reasonable defaults (ii)
-- generic sparse data correction. If (ii) is used, it should come before (i)
-- in order to produce reasonable results for motifs with "E"

module Biobase.DataSource.MCFold.Conversions
  ( maxArray
  ) where

import qualified Data.Vector.Unboxed as VU

import Data.PrimitiveArray

import Biobase.Constants
import Biobase.DataSource.MCFold
import Biobase.RNA
import Biobase.RNA.Hashes
import Biobase.RNA.NucBounds



-- * activate

-- | Given a CycleArray, create entries for all keys containing at least one E.
-- Set said energy to maximum over all non-E containing neighbors.

maxArray :: CycleArray -> Int -> CycleArray
maxArray arr k = fromAssocs l u eInf xs where
  (l,u) = bounds arr
  xs = map (\k -> let p = mkPrimary k in (mkHashedPrimary (minExtended,maxExtended) p,maxOver arr p)) $ genKeys k

-- | Perform maximum calculation for one element

maxOver :: CycleArray -> Primary -> Double
maxOver arr p
  | VU.all (/=nucE) p = arr ! mkci p
  | otherwise = maximum $ map ((arr !) . mkci . mkPrimary) keys
  where
    mkci = mkHashedPrimary (minExtended,maxExtended)
    keys = mkKeys $ VU.toList p

-- | Create all neighboring keys for a given one

mkKeys :: [Nucleotide] -> [[Nucleotide]]
mkKeys [x] = if x==nucE then [[y] |y<-acgu] else [[x]]
mkKeys (x:xs) = [ head y:ys | y<-mkKeys [x], ys<-mkKeys xs ]

-- | Generate all keys of a given size

genKeys :: Int -> [[Nucleotide]]
genKeys k
  | k==1 = [[y] | y<-eacgu]
  | k> 1 = [ y:ys | y<-eacgu, ys<-genKeys (k-1) ]