Safe Haskell	None
Language	Haskell2010

DP.Seq.Align.Global.Linear2

Description

Very simple pairwise global alignment. The terminal tapes may contain the atomic types u and l 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.

Synopsis

Documentation

data SigGlobal m s r t_l_0_ t_u_1_ Source #

Define signature and grammar

Constructors

SigGlobal
Fields align :: (s -> (:.) ((:.) Z t_l_0_) t_u_1_ -> s) delin :: (s -> (:.) ((:.) Z t_l_0_) () -> s) done :: ((:.) ((:.) Z ()) () -> s) indel :: (s -> (:.) ((:.) Z ()) t_u_1_ -> s) h :: (Stream m s -> m r)

Instances

(Monad mL0, Monad mR0, Eq xL0, (~) (* -> ) mL0 mR0, (~) xL0 rL0) => ProductBacktracking (SigGlobal mL0 xL0 rL0 t_l_0_0 t_u_1_0) (SigGlobal mR0 xR0 rR0 t_l_0_0 t_u_1_0) Source #
Associated Types type SigBacktracking (SigGlobal mL0 xL0 rL0 t_l_0_0 t_u_1_0) (SigGlobal mR0 xR0 rR0 t_l_0_0 t_u_1_0) :: * # Methods (<\|\|) :: SigGlobal mL0 xL0 rL0 t_l_0_0 t_u_1_0 -> SigGlobal mR0 xR0 rR0 t_l_0_0 t_u_1_0 -> SigBacktracking (SigGlobal mL0 xL0 rL0 t_l_0_0 t_u_1_0) (SigGlobal mR0 xR0 rR0 t_l_0_0 t_u_1_0) #
(Monad mL0, Monad mR0, Eq xL0, Ord xL0, Ord xR0, (~) (* -> *) mL0 mR0) => ProductCombining (SigGlobal mL0 xL0 rL0 t_l_0_0 t_u_1_0) (SigGlobal mR0 xR0 rR0 t_l_0_0 t_u_1_0) Source #
Associated Types type SigCombining (SigGlobal mL0 xL0 rL0 t_l_0_0 t_u_1_0) (SigGlobal mR0 xR0 rR0 t_l_0_0 t_u_1_0) :: * # Methods (**>) :: SigGlobal mL0 xL0 rL0 t_l_0_0 t_u_1_0 -> SigGlobal mR0 xR0 rR0 t_l_0_0 t_u_1_0 -> SigCombining (SigGlobal mL0 xL0 rL0 t_l_0_0 t_u_1_0) (SigGlobal mR0 xR0 rR0 t_l_0_0 t_u_1_0) #
type SigBacktracking (SigGlobal mL0 xL0 rL0 t_l_0_0 t_u_1_0) (SigGlobal mR0 xR0 rR0 t_l_0_0 t_u_1_0) Source #
type SigBacktracking (SigGlobal mL0 xL0 rL0 t_l_0_0 t_u_1_0) (SigGlobal mR0 xR0 rR0 t_l_0_0 t_u_1_0) = SigGlobal mR0 (xL0, [xR0]) rR0 t_l_0_0 t_u_1_0
type SigCombining (SigGlobal mL0 xL0 rL0 t_l_0_0 t_u_1_0) (SigGlobal mR0 xR0 rR0 t_l_0_0 t_u_1_0) Source #
type SigCombining (SigGlobal mL0 xL0 rL0 t_l_0_0 t_u_1_0) (SigGlobal mR0 xR0 rR0 t_l_0_0 t_u_1_0) = SigGlobal mR0 (xL0, [xR0]) (Vector (rL0, rR0)) t_l_0_0 t_u_1_0

gGlobal :: ((~#) * * (Fun ((:.) (Arg (Stack (TW t (i -> i -> t5 t3)))) ((:.) ((:.) Z ()) (TermArg b)) -> t4)) (t4 -> (:.) ((:.) Z ()) t1 -> t4), (~#) * * (Fun ((:.) (Arg (Stack (TW t (i -> i -> t5 t3)))) ((:.) ((:.) Z (TermArg b1)) ()) -> t4)) (t4 -> (:.) ((:.) Z t2) () -> t4), (~#) * * (Fun ((:.) (Arg (Stack (TW t (i -> i -> t5 t3)))) ((:.) ((:.) Z (TermArg b1)) (TermArg b)) -> t4)) (t4 -> (:.) ((:.) Z t2) t1 -> t4), Apply ((:.) (Arg (Stack (TW t (i -> i -> t5 t3)))) ((:.) ((:.) Z ()) (TermArg b)) -> t4), Apply ((:.) (Arg (Stack (TW t (i -> i -> t5 t3)))) ((:.) ((:.) Z (TermArg b1)) ()) -> t4), Apply ((:.) (Arg (Stack (TW t (i -> i -> t5 t3)))) ((:.) ((:.) Z (TermArg b1)) (TermArg b)) -> t4), TermStream t5 (TermSymbol (TermSymbol M Deletion) b) (Elm (Stack (TW t (i -> i -> t5 t3))) i) i, TermStream t5 (TermSymbol (TermSymbol M Epsilon) Epsilon) (Elm S i) i, TermStream t5 (TermSymbol (TermSymbol M b1) Deletion) (Elm (Stack (TW t (i -> i -> t5 t3))) i) i, TermStream t5 (TermSymbol (TermSymbol M b1) b) (Elm (Stack (TW t (i -> i -> t5 t3))) i) i, TermStaticVar (TermSymbol (TermSymbol M Deletion) b) i, TermStaticVar (TermSymbol (TermSymbol M Epsilon) Epsilon) i, TermStaticVar (TermSymbol (TermSymbol M b1) Deletion) i, TermStaticVar (TermSymbol (TermSymbol M b1) b) i, MkStream t5 S i, MkStream t5 (Stack (TW t (i -> i -> t5 t3))) i, Element (Stack (TW t (i -> i -> t5 t3))) i, Build (TW t (i -> i -> t5 t3)), RuleContext i) => SigGlobal t5 t4 t3 t2 t1 -> t -> b1 -> b -> (:.) Z (TW t (i -> i -> t5 t3)) Source #

backtrack :: Monad m => u -> l -> SigGlobal m (FMList (l, u)) [FMList (l, u)] l u Source #

Generic backtracking scheme via FMLists.

backtrackFun :: Monad m => (l -> u -> r) -> (l -> u -> r) -> u -> l -> SigGlobal m (FMList r) [FMList r] l u Source #

Backtracking with more options

runBacktrack :: FMList r -> [r] Source #

Turn a single FMList backtracking result into the corresponding list.