-- Hoogle documentation, generated by Haddock
-- See Hoogle, http://www.haskell.org/hoogle/


-- | Sequence alignment algorithms.
--   
--   Global or local sequence alignment, not exclusively for text.
@package align
@version 0.1.0.0

module Data.Align

-- | Aligns two sequences.
--   
--   <pre>
--   &gt;&gt;&gt; :{
--   let tr = align
--              (alignConfig (\a b -&gt; if a == b then 1 else (-0.25 :: Double)) 
--                           (-0.5) (-1))
--              (Data.Vector.fromList "dopple")
--              (Data.Vector.fromList "applied")
--   in do
--      print $ traceScore tr
--      putStrLn . debugAlign . trace $ tr
--   :}
--   1.25
--   doppl-e-
--   -applied
--   </pre>
align :: (Vector v a, Num s, Eq s, Ord s) => AlignConfig a s -> v a -> v a -> Trace a s
data AlignConfig a s
alignConfig :: (a -> a -> s) -> s -> s -> AlignConfig a s

-- | Either an unmatched item or a match.
type Step a = Either (Either a a) (a, a)

-- | The result of the alignment.
data Trace a s
traceScore :: Trace a s -> s
trace :: Trace a s -> [Step a]

-- | Aligns long streams by performing alignment on windowed sections.
windowedAlign :: (Num s, Eq s, Ord s) => AlignConfig a s -> Int -> [a] -> [a] -> [Step a]

-- | Utility for displaying a Char-based alignment.
debugAlign :: [Step Char] -> String
instance (Show a, Show s) => Show (Trace a s)