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


-- | Sequence alignment algorithms.
--   
@package align
@version 0.1.1.2


-- | Collection of functions for global, local and multi-sequence
--   alignment.
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, Ord s) => AlignConfig a s -> v a -> v a -> Trace a s
data AlignConfig a s

-- | Configures the scores used when aligning. The gap scores should be
--   negative in order to be penalties.
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]

-- | Align multiple sequences using the Center Star heuristic method by
--   Chin, Ho, Lam, Wong and Chan (2003).
--   <a>http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.90.7448&amp;rep=rep1&amp;type=pdf</a>.
--   Assumes the list of sequences to have length &gt; 1, and the indices
--   to be unique.
centerStar :: (Vector v a, Num s, Ord s, Ord i) => AlignConfig a s -> [(i, v a)] -> MultiTrace i a s

-- | A step in a multi-sequence alignment.
data MultiStep a

-- | <a>Nothing</a> means gap insertion.
center :: MultiStep a -> Maybe a

-- | Parallel to <a>otherIndices</a>.
others :: MultiStep a -> [Maybe a]

-- | The center step followed by other steps.
stepOfAll :: MultiStep a -> [Maybe a]

-- | The result of a multi-sequence alignment.
data MultiTrace i a s
centerIndex :: MultiTrace i a s -> i
otherIndices :: MultiTrace i a s -> [i]

-- | The center index followed by other indices.
allIndices :: MultiTrace i a s -> [i]
multiTrace :: MultiTrace i a s -> [MultiStep a]

-- | Utility for displaying a Char-based alignment.
debugAlign :: [Step Char] -> String

-- | Renders a char-based multi-alignment result to a string.
debugMultiAlign :: [MultiStep Char] -> String
instance (Show a, Show s) => Show (Trace a s)


-- | Browse the source of this module to see usage examples.
module Data.Align.Demo
sampleGlobalConfig :: Eq a => AlignConfig a Double
testIn1 :: [Char]
testIn2 :: [Char]
alignedGlobal :: Trace Char Double
debug :: Trace Char s -> IO ()
printAlignedGlobal :: IO ()

-- | Example from
--   <a>https://www.biostat.wisc.edu/bmi576/lectures/multiple-alignment.pdf</a>
nucs :: [[Char]]
alignNuc :: Eq a => [a] -> [a] -> Trace a Double
alignedNucPairs :: [Trace Char Double]
printAlignedNucPairs :: IO ()
alignedNucStar :: MultiTrace Integer Char Double
printAlignedNucStar :: IO ()