RNAFoldProgs-0.0.0.1: RNAFold.hs

-- | Simple wrapper around the fold function.
--
-- TODO same TODOs as for RNAEval

module Main where

import Control.Monad
import Control.Monad.ST
import Text.Printf

import Biobase.RNA
import Biobase.Structure.DotBracket
import Biobase.Vienna.Default
import Biobase.Vienna.Modification.NonStandard
import BioInf.RNAFold.EnergyInt
import Data.PrimitiveArray


{- This is needed for debugging
import Data.List.Split



printArr a = g a where
    (_,n) = snd $ bounds a
    f x
      | x > 999 = "   x"
      | x < -999 = "-999"
      | otherwise = printf "%4d" x
    g t = mapM_ (\xs -> mapM_ putStr xs >> putStrLn"") $ splitEvery (n+1) $ map f $ toList t
-}

-- | given a sequence, fold it and print all results.

doFold trnr cnt = do
  let inp = mkPrimary cnt
  let tbls@(weak,strong,m,m1,external) = fold trnr inp
  let bts = backtrack trnr inp tbls 0
  -- print $ external ! (0,length cnt -1)
  {-
  print "strong"
  printArr strong
  print "external"
  printArr external
  -}
  putStrLn cnt
  if null bts
    then
      putStrLn $ replicate (length cnt) '.' ++ " (  0.00)"
    else
      mapM_ (\(s,e) -> printf "%s (%6.2f)\n" (dotbracket s) (fromIntegral e / 100 :: Double)) bts
  return ()

main = do
  let trnr = nonStandardMax . fst $ turner2004GH -- default energy tables
  cnts <- liftM lines $ getContents
  mapM_ (doFold trnr) cnts