module Diversity.GenerateDiversity ( fragmentPos
, generatePositionMap ) where
import qualified Data.Map as M
import Data.List
import Data.Fasta.String
import Diversity.Types
fragmentPos :: Bool -> Int -> [(Position, String)] -> [(Position, String)]
fragmentPos whole win xs | whole && null xs = error "Empty line in file!!"
| whole = combine xs : []
| length xs < win = []
| otherwise = combine (take win xs)
: fragmentPos whole win (tail xs)
where
combine = foldl1' (\(x, ys) (_, y) -> (x, ys ++ y))
generatePositionMap :: Bool -> Window -> [FastaSequence] -> PositionMap
generatePositionMap whole win = M.fromListWith (++) . posSeqList
where
posSeqList = map toList . concatMap (\x -> fragmentPos whole win
. map (\(p, f) -> (p, [f]))
. filter (\(_, f) -> noGaps f)
. zip [1..]
. fastaSeq
$ x)
toList (x, y) = (x, [y])
noGaps y = y /= '-' && y /= '.'