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


-- | Data structures and helper functions for calculating alignments
--   
--   Data structures and helper functions for calculating alignments
@package bioalign
@version 0.0.5


-- | Data structures and helper functions for calculating alignments
--   
--   There are two ways to view an alignment: either as a list of edits
--   (i.e., insertions, deletions, or substitutions), or as a set of
--   sequences with inserted gaps.
--   
--   The edit list approach is perhaps more restrictive model but doesn't
--   generalize to multiple alignments.
--   
--   The gap approach is more general, and probably more commonly used by
--   other software (see e.g. the ACE file format).
module Bio.Alignment.AlignData
data Sequence
Seq :: SeqLabel -> SeqData -> (Maybe QualData) -> Sequence
type Gaps = [Offset]
type Alignment = [(Offset, Strand, Sequence, Gaps)]

-- | Gaps are coded as <a>*</a>s, this function removes them, and returns
--   the sequence along with the list of gap positions. note that gaps are
--   positioned relative to the *gapped* sequence (contrast to
--   stmassembler/Cluster.hs)
extractGaps :: SeqData -> (SeqData, Gaps)
insertGaps :: Char -> (SeqData, Gaps) -> SeqData

-- | An Edit is either the insertion, the deletion, or the replacement of a
--   character.
data Edit
Ins :: Chr -> Edit
Del :: Chr -> Edit
Repl :: Chr -> Chr -> Edit

-- | An alignment is a sequence of edits.
type EditList = [Edit]

-- | A substitution matrix gives scores for replacing a character with
--   another. Typically, it will be symmetric. It is type-tagged with the
--   alphabet - Nuc or Amino.
type SubstMx t a = (Chr, Chr) -> a

-- | A Selector consists of a zero element, and a funcition that chooses a
--   possible Edit operation, and generates an updated result.
type Selector a = [(a, Edit)] -> a

-- | The sequence element type, used in alignments.
type Chr = Word8

-- | Calculate a set of columns containing scores This represents the
--   columns of the alignment matrix, but will only require linear space
--   for score calculation.
columns :: Selector a -> a -> Sequence -> Sequence -> [[a]]

-- | Evaluate an Edit based on SubstMx and gap penalty
eval :: SubstMx t a -> a -> Edit -> a

-- | True if the Edit is a Repl.
isRepl :: Edit -> Bool
on :: (t1 -> t1 -> t) -> (t2 -> t1) -> t2 -> t2 -> t
showalign :: EditList -> [Char]

-- | turn an alignment into sequences with <a>-</a> representing gaps (for
--   checking, filtering out the <a>-</a> characters should return the
--   original sequences, provided <a>-</a> isn't part of the sequence
--   alphabet)
toStrings :: EditList -> (String, String)
instance Eq Sequence
instance Show Edit
instance Eq Edit
instance BioSeq Sequence