{-# LANGUAGE GeneralizedNewtypeDeriving #-}

-- | The next iteration of MC-Fold-DP which is, hopefully, a bit faster. It can
-- be seen that the dsConnect and ddConnect data structures do not care about
-- the type of connection, only which kind of NCM is involved and the pair.
-- This follows the way MC-Fold integrates away the specific type of pair
-- family involved.

module Biobase.DataSource.MCFold where

import Control.DeepSeq
import Data.Ix
import Data.Ix.Tuple
import Data.PrimitiveArray
import Data.PrimitiveArray.Ix -- only needed for the ghci part?
import qualified Data.Vector.Unboxed as VU

import Biobase.RNA
import Biobase.RNA.Hashes



-- | This version of the motif database accepts ACGU+E as nucleotides.
-- Occurances of E lead to a maximization over all strings where the E are
-- replaced by ACGU -- if the corresponding function was used, otherwise all E
-- map to infinity (actually only a large number).
--
-- The dsConnect and ddConnect database stores the combined information for
-- connections between different cycles.

data MotifDB = MotifDB
  -- The most important data, NCMs and connections between two of those
  { sCycles :: [(Int,CycleArray)] -- ^ store length of cycles, cycle array for this length
  , dCycles :: [((Int,Int),CycleArray)] -- ^ store (left,right) lengths, cycle array
  , dsConnect :: [(((Int,Int),Int),ConnectArray)]
  , ddConnect :: [(((Int,Int),(Int,Int)),ConnectArray)]
  -- Following is other data, mostly from the importer
  , rawPairScores :: PairScoreArray
  , rawJunctionScores :: JunctionArray
  , rawSHingeCounts :: [(Int,[RawHinge])] -- ^ length of cycle, hinge data
  , rawDHingeCounts :: [((Int,Int),[RawHinge])] -- ^ length of cycle, length of cycle, hinge data
  } deriving (Show)



-- * Newtypes for different annotations

newtype TransCis = TransCis Int
  deriving (Eq,Ord,Ix,NFData,Read,Show,Enum)
(trans:cis:_) = map TransCis [0..]

instance Bounded TransCis where
  minBound = trans
  maxBound = cis

newtype AntiPara = AntiPara Int
  deriving (Eq,Ord,Ix,NFData,Read,Show,Enum)
(anti:para:_) = map AntiPara [0..]

instance Bounded AntiPara where
  minBound = anti
  maxBound = para

newtype Slash = Slash Int
  deriving (Eq,Ord,Ix,NFData,Read,Show,Enum)
(wsp:hsp:csp:ssp:bsp:_) = map Slash [0..]

instance Bounded Slash where
  minBound = wsp
  maxBound = bsp

newtype Prime = Prime Int
  deriving (Eq,Ord,Ix,NFData,Read,Show,Enum)
(p5:p3:_) = map Prime [0..]

instance Bounded Prime where
  minBound = p5
  maxBound = p3

-- | log-scores as derived from probabilities.
--
-- TODO apply (min eInf)?

logScore :: Double -> Double
logScore x = (-0.606) * log x

type CycleArray = PrimArray HashedPrimary Double
type ConnectArray = PrimArray (Nucleotide,Nucleotide) Double -- ,Slash,Slash,AntiPara,TransCis) Double
type RawHinge = (((Prime,Nucleotide,Nucleotide),(Slash,Slash,AntiPara,TransCis)),Double)
type PairScoreArray = PrimArray (Nucleotide,Nucleotide) Double
type JunctionArray = PrimArray (Int,Int) Double



-- * A lot of static information

-- | Known single-pair types. (Length of nucleotide string, 0-based index).

-- 4 -> (5,2)
-- 5 -> (5,3)
-- 6 -> (5,4)
--
-- found to be wrong
-- 5 -> (0,5)

knownSingleNCM :: VU.Vector (Int,Int)
knownSingleNCM = VU.fromList
  [ (4,2)
  , (5,3)
  , (6,4)
  ]

-- | Known double-pair types. ((Length of left...,Length of right nucleotide
-- string), 0-based index

-- found to be right through hacking!
-- all are (..) to next type
-- NCM type -> junctions IV.! (a,b)
-- (a+1,b+1) for the junction.db
-- (2,2) -> (5,5)
-- (2,3) -> (8,2)
-- (3,2) -> (9,2)

knownDoubleNCM :: VU.Vector ((Int,Int),Int)
knownDoubleNCM = VU.fromList
  [ ((2,2), 5)
  , ((3,3), 6)
  , ((2,3), 7)
  , ((3,2), 8)
  , ((2,4), 9)
  , ((4,2),10)
  ]

-- | This is a list of known hinge types. If it has to be regenerated at some
-- point, run the following command inside the MCfold DB:
--
-- cat *hinge | grep -v "^\[" | awk '{print $1 " " $2 " " $3}' | sort | uniq | awk '{printf "  , \"%s\"\n", $0}'

knownHinges =
  [ "B/B anti trans"
  , "B/H anti trans"
  , "B/H para cis"
  , "B/S anti cis"
  , "B/S anti trans"
  , "B/S para trans"
  , "B/W anti cis"
  , "B/W anti trans"
  , "B/W para cis"
  , "B/W para trans"
  , "C/H para trans"
  , "H/B anti trans"
  , "H/C para trans"
  , "H/H anti cis"
  , "H/H para trans"
  , "H/S anti trans"
  , "H/S para trans"
  , "H/W anti cis"
  , "H/W anti trans"
  , "H/W para cis"
  , "H/W para trans"
  , "S/B anti cis"
  , "S/B para trans"
  , "S/C para cis"
  , "S/H anti cis"
  , "S/H anti trans"
  , "S/H para cis"
  , "S/H para trans"
  , "S/S anti cis"
  , "S/S para trans"
  , "S/W anti cis"
  , "S/W anti trans"
  , "S/W para cis"
  , "S/W para trans"
  , "W/B anti cis"
  , "W/B anti trans"
  , "W/B para cis"
  , "W/C anti trans"
  , "W/H anti cis"
  , "W/H anti trans"
  , "W/H para cis"
  , "W/H para trans"
  , "W/S anti cis"
  , "W/S anti trans"
  , "W/S para cis"
  , "W/S para trans"
  , "W/W anti cis"
  , "W/W anti trans"
  , "W/W para cis"
  , "W/W para trans"
  ]