{-# LANGUAGE RecordWildCards #-}

-- | Holds the 'FR3DBasepairs' structure extracted from a FR3D basepairs file.
-- The other files are still on the TODO list
--
-- TODO write data structures and parsers for the other files.
--
-- TODO rewrite by reducing all those data-structures to something more
-- intelligent. Use 'Nucleotide's for encoding. Have a converter to 'Complex',
-- too.

module Biobase.DataSource.FR3D where

import Data.Map (Map)
import qualified Data.Map as M
import Data.Char (isDigit)
import Control.Monad.Error -- TODO GHC < 7.0.0 only ???
import Data.List (nubBy)

import qualified Biobase.RNA.Complex as C
import Biobase.RNA.Pairs (ExtPair)



-- * FR3D data structures

-- | Wrap everything up, giving us our data source.

data FR3D = FR3D
  { complex :: C.Complex ExtPair -- ^ parsed PDB/FR3D as normal 'Complex'
  , fr3dBasepairs :: FR3DBasepairs -- ^ the source information
  } deriving (Show)

-- | A complete 'FR3DBasepairs' structure. We have the 'pdbID' from which the FR3D
-- came from, the 'versions' of different programs, the 'chains' or different
-- nucleotide sequences used in the structure, the 'pairs' themselves and other
-- 'comments' which could not be identified correctly.

data FR3DBasepairs = FR3DBasepairs
  { pdbID :: String
  , versions :: String
  , chains :: Map String String
  , pairs :: [Pair]
  , comments :: [String] -- unknown comments, maybe really just comments
  } deriving (Read,Show)

-- | Each 'Pair' is a triple of the 'interaction' between the two 'Nucleotide's
-- 'nuc1' and nuc2'.

data Pair = Pair
  { interaction :: Interaction
  , nuc1 :: Nucleotide
  , nuc2 :: Nucleotide
  } deriving (Read,Show,Eq,Ord)

-- | Each 'Nucleotide' is described by the 'nuc' itself (A,C,G,U) (something
-- else?), the pdb 'num'ber (whatever that is), the 'chain' id and the
-- 'pos'ition in the chain.

data Nucleotide = Nucleotide
  { nuc :: Char
  , num :: String -- should be "20" but could be "20A" (grr)
  , chain :: String -- could be "chain 1" or "chain E" or so
  , pos :: Int
  } deriving (Read,Show,Eq,Ord)

type Interaction = String -- ?



-- | fix the 'pos' in all 'Nucleotide's. Not actually clear, if this /DOES/ fix
-- the problem!

fixLengths :: FR3DBasepairs -> FR3DBasepairs
fixLengths b = b {pairs = map f $ pairs b} where
  f p = p{nuc1 = g $ nuc1 p, nuc2 = g $ nuc2 p}
  g n
    | pos n > (length $ chains b M.! chain n) = n{pos = read $ filter isDigit $ num n}
    | otherwise = n

-- | Check if a given 'FR3DBasepairs' structure is correct, or if there are errors

checkFR3DBasepairs :: FR3DBasepairs -> Either String FR3DBasepairs
checkFR3DBasepairs b' = checkChains b' >>= checkLength >>= return where
  checkChains b
    | null cnucs = Right b
    | otherwise  = Left $ "CHAIN: " ++ show cnucs
    where cnucs = filter (\n -> not $ chain n `M.member` chains b) ps
  checkLength b
    | null cnucs = Right b
    | otherwise  = Left $ "LENGTH: " ++ show b ++ show cnucs
    where cnucs = filter (\n -> length (chains b M.! chain n) < pos n) ps -- positions start countaing at "1"
  checkNucs b
    | null cnucs = Right b
    | otherwise = Left $ "NUCS: " ++ show cnucs
    where cnucs = filter (\n -> (chains b M.! chain n !! (pos n -1)) == nuc n) ps
  ps = concatMap (\x -> [nuc1 x, nuc2 x]) $ pairs b'



-- * Transform 'FR3DBasepairs' into 'Complex'

-- | Aquire a 'Complex' from the data read.
--
-- TODO write me

makeComplex :: FR3DBasepairs -> C.Complex ExtPair
makeComplex b@FR3DBasepairs{..}
  | length sqnc /= length chns = error $ "makeComplex: " ++ show b
  | otherwise = C.mkComplex "TODO write me" {- sqnc strc chns -} where
  sqnc = concatMap snd $ M.toAscList chains
  strc = nubBy eqT12 $ map (\(Pair z n1 n2) -> (pos n1-1,pos n2-1,z)) pairs
  chns = concatMap (\(k,v) -> concat $ replicate (length v) k) $ M.toAscList chains

eqT12 (a,b,_) (x,y,_) = (a,b)==(x,y) || (a,b)==(y,x)

-- | Simple wrapper fixing up an 'FR3D'

mkFR3D :: FR3DBasepairs -> FR3D
mkFR3D b = FR3D {complex=makeComplex b, fr3dBasepairs=b}