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


-- | Collection of alignment algorithms
--   
--   A selection of (sequence) alignment algorithms. Both terminal, and
--   syntactic variables, as well as the index type is not fixed here. This
--   makes it possible to select the correct structure of the grammar here,
--   but bind the required data type for alignment in user code.
--   
--   
--   <a>https://github.com/choener/AlignmentAlgorithms/blob/master/README.md</a>
--   
--   That being said, these algorithms are mostly aimed towards sequence
--   alignment problems.
--   
--   <ul>
--   <li>global alignment (Needleman-Wunsch style)</li>
--   </ul>
--   
--   <pre>
--   Christian Hoener zu Siederdissen
--   Sneaking Around ConcatMap: Efficient Combinators for Dynamic Programming
--   2012. Proceedings of the 17th ACM SIGPLAN international conference on Functional programming
--   <a>http://doi.acm.org/10.1145/2364527.2364559</a> preprint: <a>http://www.tbi.univie.ac.at/newpapers/pdfs/TBI-p-2012-2.pdf</a>
--   </pre>
--   
--   <pre>
--   Andrew Farmer, Christian Höner zu Siederdissen, and Andy Gill.
--   The HERMIT in the stream: fusing stream fusion’s concatMap.
--   2014. Proceedings of the ACM SIGPLAN 2014 workshop on Partial evaluation and program manipulation.
--   <a>http://dl.acm.org/citation.cfm?doid=2543728.2543736</a>
--   </pre>
--   
--   <pre>
--   Christian Höner zu Siederdissen, Ivo L. Hofacker, and Peter F. Stadler.
--   Product Grammars for Alignment and Folding.
--   2014. IEEE/ACM Transactions on Computational Biology and Bioinformatics. 99.
--   <a>http://ieeexplore.ieee.org/xpl/articleDetails.jsp?arnumber=6819790</a>
--   </pre>
--   
--   <pre>
--   Christian Höner zu Siederdissen, Sonja J. Prohaska, and Peter F. Stadler.
--   Algebraic Dynamic Programming over General Data Structures.
--   2015. submitted.
--   </pre>
@package AlignmentAlgorithms
@version 0.0.1.0


-- | Very simple pairwise global alignment. The terminal tapes may contain
--   the atomic types <tt>u</tt> and <tt>l</tt> which means that one may
--   align sequences of different types.
--   
--   In case you want to align nucleotides to amino acids, this version
--   should only be used if the nucleotides are already in triplet form and
--   have no frameshift within the sequence. Alternatively, specify a
--   derived grammar of higher complexity.
module DP.Alignment.Global.Tapes2

-- | Define signature and grammar
data SigGlobal m_acjb s_acjc r_acjd t_l_acje t_u_acjf
SigGlobal :: (s_acjc -> (:.) ((:.) Z t_l_acje) t_u_acjf -> s_acjc) -> (s_acjc -> (:.) ((:.) Z t_l_acje) () -> s_acjc) -> ((:.) ((:.) Z ()) () -> s_acjc) -> (s_acjc -> (:.) ((:.) Z ()) t_u_acjf -> s_acjc) -> (Stream m_acjb s_acjc -> m_acjb r_acjd) -> SigGlobal m_acjb s_acjc r_acjd t_l_acje t_u_acjf
[align] :: SigGlobal m_acjb s_acjc r_acjd t_l_acje t_u_acjf -> s_acjc -> (:.) ((:.) Z t_l_acje) t_u_acjf -> s_acjc
[delin] :: SigGlobal m_acjb s_acjc r_acjd t_l_acje t_u_acjf -> s_acjc -> (:.) ((:.) Z t_l_acje) () -> s_acjc
[done] :: SigGlobal m_acjb s_acjc r_acjd t_l_acje t_u_acjf -> (:.) ((:.) Z ()) () -> s_acjc
[indel] :: SigGlobal m_acjb s_acjc r_acjd t_l_acje t_u_acjf -> s_acjc -> (:.) ((:.) Z ()) t_u_acjf -> s_acjc
[h] :: SigGlobal m_acjb s_acjc r_acjd t_l_acje t_u_acjf -> Stream m_acjb s_acjc -> m_acjb r_acjd
gGlobal :: (Apply ((:.) (Arg (Stack b2)) (TermArg (TermSymbol (TermSymbol M b) b1)) -> t1), Apply ((:.) (Arg (Stack b2)) (TermArg (TermSymbol (TermSymbol M Deletion) b1)) -> t1), Apply ((:.) (Arg (Stack b2)) ((:.) (TermArg (TermSymbol M b)) ()) -> t1), TerminalStream t (TermSymbol (TermSymbol M b) b1) r, TerminalStream t (TermSymbol (TermSymbol M b) Deletion) r, TerminalStream t (TermSymbol (TermSymbol M Deletion) b1) r, TerminalStream t (TermSymbol (TermSymbol M Epsilon) Epsilon) r, TermStaticVar (TermSymbol (TermSymbol M b) b1) r, TermStaticVar (TermSymbol (TermSymbol M b) Deletion) r, TermStaticVar (TermSymbol (TermSymbol M Deletion) b1) r, TermStaticVar (TermSymbol (TermSymbol M Epsilon) Epsilon) r, RuleContext r, Element (Stack b2) r, MkStream t (Stack b2) r, MkStream t S r, Build b2, (~) * (Fun ((:.) (Arg (Stack b2)) (TermArg (TermSymbol (TermSymbol M b) b1)) -> t1)) (t1 -> (:.) ((:.) Z t3) t4 -> t1), (~) * (Fun ((:.) (Arg (Stack b2)) ((:.) (TermArg (TermSymbol M b)) ()) -> t1)) (t1 -> (:.) ((:.) Z t3) () -> t1), (~) * (Fun ((:.) (Arg (Stack b2)) (TermArg (TermSymbol (TermSymbol M Deletion) b1)) -> t1)) (t1 -> (:.) ((:.) Z ()) t4 -> t1)) => SigGlobal t t1 t2 t3 t4 -> ((r -> r -> t t2) -> b2) -> b -> b1 -> (:.) Z b2

-- | Generic backtracking scheme via <tt>FMList</tt>s.
backtrack :: Monad m => u -> l -> SigGlobal m (FMList (l, u)) [FMList (l, u)] l u

-- | Turn a single <tt>FMList</tt> backtracking result into the
--   corresponding list.
runBacktrack :: FMList (u, l) -> [(u, l)]
instance (GHC.Base.Monad mL0, GHC.Base.Monad mR0, GHC.Classes.Eq xL0, mL0 ~ mR0) => ADP.Fusion.TH.Backtrack.BacktrackingProduct (DP.Alignment.Global.Tapes2.SigGlobal mL0 xL0 xL0 t_l0 t_u0) (DP.Alignment.Global.Tapes2.SigGlobal mR0 xR0 rR0 t_l0 t_u0)