Data.Forest.Static.Align.Linear

A simple linear alignment module for forest-like structures. Currently all comparisons are on Newick-like forests.

Documentation

data SigGlobal m s r t_n_0_ t_n_1_

Constructors

SigGlobal

Fields

• gAlign :: ((:.) ((:.) Z t_n_0_) t_n_1_ -> s -> s)
• gDelin :: ((:.) ((:.) Z t_n_0_) () -> s -> s)
• gDone :: ((:.) ((:.) Z ()) () -> s)
• gIndel :: ((:.) ((:.) Z ()) t_n_1_ -> s -> s)
• gIter :: (s -> s -> s)
• gH :: (Stream m s -> m r)

Instances

(Monad mL0, Monad mR0, Eq xL0, (~) (* -> *) mL0 mR0, (~) * xL0 rL0) => ProductBacktracking (SigGlobal mL0 xL0 rL0 t_n_0_0 t_n_1_0) (SigGlobal mR0 xR0 rR0 t_n_0_0 t_n_1_0)

Associated Types

type SigBacktracking (SigGlobal mL0 xL0 rL0 t_n_0_0 t_n_1_0) (SigGlobal mR0 xR0 rR0 t_n_0_0 t_n_1_0) :: *

Methods

(<||) :: SigGlobal mL0 xL0 rL0 t_n_0_0 t_n_1_0 -> SigGlobal mR0 xR0 rR0 t_n_0_0 t_n_1_0 -> SigBacktracking (SigGlobal mL0 xL0 rL0 t_n_0_0 t_n_1_0) (SigGlobal mR0 xR0 rR0 t_n_0_0 t_n_1_0)

(Monad mL0, Monad mR0, Eq xL0, Ord xL0, Ord xR0, (~) (* -> *) mL0 mR0) => ProductCombining (SigGlobal mL0 xL0 rL0 t_n_0_0 t_n_1_0) (SigGlobal mR0 xR0 rR0 t_n_0_0 t_n_1_0)

Associated Types

type SigCombining (SigGlobal mL0 xL0 rL0 t_n_0_0 t_n_1_0) (SigGlobal mR0 xR0 rR0 t_n_0_0 t_n_1_0) :: *

Methods

(**>) :: SigGlobal mL0 xL0 rL0 t_n_0_0 t_n_1_0 -> SigGlobal mR0 xR0 rR0 t_n_0_0 t_n_1_0 -> SigCombining (SigGlobal mL0 xL0 rL0 t_n_0_0 t_n_1_0) (SigGlobal mR0 xR0 rR0 t_n_0_0 t_n_1_0)

type SigBacktracking (SigGlobal mL0 xL0 rL0 t_n_0_0 t_n_1_0) (SigGlobal mR0 xR0 rR0 t_n_0_0 t_n_1_0)

type SigBacktracking (SigGlobal mL0 xL0 rL0 t_n_0_0 t_n_1_0) (SigGlobal mR0 xR0 rR0 t_n_0_0 t_n_1_0) = SigGlobal mR0 (xL0, [xR0]) rR0 t_n_0_0 t_n_1_0

type SigCombining (SigGlobal mL0 xL0 rL0 t_n_0_0 t_n_1_0) (SigGlobal mR0 xR0 rR0 t_n_0_0 t_n_1_0)

type SigCombining (SigGlobal mL0 xL0 rL0 t_n_0_0 t_n_1_0) (SigGlobal mR0 xR0 rR0 t_n_0_0 t_n_1_0) = SigGlobal mR0 (xL0, [xR0]) (Vector (rL0, rR0)) t_n_0_0 t_n_1_0

data SigLabolg m s r t_n_0_ t_n_1_

Constructors

SigLabolg

Fields

• lAlign :: ((:.) ((:.) Z t_n_0_) t_n_1_ -> s -> s)
• lDelin :: ((:.) ((:.) Z t_n_0_) () -> s -> s)
• lDone :: ((:.) ((:.) Z ()) () -> s)
• lIndel :: ((:.) ((:.) Z ()) t_n_1_ -> s -> s)
• lIter :: (s -> s -> s)
• lH :: (Stream m s -> m r)

gLabolg :: ((~#) * * (Fun (Arg ((:!:) (Stack (TW t2 (i1 -> i1 -> t7 t5))) b2) -> t6)) (t6 -> t6 -> t6), (~#) * * (Fun (Arg ((:!:) (Stack a) (TW t2 (i1 -> i1 -> t7 t5))) -> t6)) (t6 -> t6 -> t6), (~#) * * (Fun (Arg ((:!:) (Stack a1) (TW t2 (i1 -> i1 -> t7 t5))) -> t6)) (t6 -> t6 -> t6), (~#) * * (Fun (Arg ((:!:) ((:!:) S (TermSymbol (TermSymbol M Deletion) b)) (TW t (i2 -> i2 -> t7 t5))) -> t6)) ((:.) ((:.) Z ()) t3 -> t6 -> t6), (~#) * * (Fun (Arg ((:!:) ((:!:) S (TermSymbol (TermSymbol M b1) Deletion)) (TW t (i2 -> i2 -> t7 t5))) -> t6)) ((:.) ((:.) Z t4) () -> t6 -> t6), (~#) * * (Fun (Arg ((:!:) ((:!:) S (TermSymbol (TermSymbol M b1) b)) (TW t1 (i -> i -> t7 t5))) -> t6)) ((:.) ((:.) Z t4) t3 -> t6 -> t6), Element ((:!:) ((:!:) S (TermSymbol (TermSymbol M Deletion) b)) (TW t (i2 -> i2 -> t7 t5))) i1, Element ((:!:) ((:!:) S (TermSymbol (TermSymbol M b1) Deletion)) (TW t (i2 -> i2 -> t7 t5))) i1, Element ((:!:) ((:!:) S (TermSymbol (TermSymbol M b1) b)) (TW t1 (i -> i -> t7 t5))) i1, Element ((:!:) (Stack (TW t2 (i1 -> i1 -> t7 t5))) b2) i2, Element ((:!:) (Stack (TW t2 (i1 -> i1 -> t7 t5))) b2) i, Element ((:!:) (Stack a) (TW t2 (i1 -> i1 -> t7 t5))) i1, Element ((:!:) (Stack a1) (TW t2 (i1 -> i1 -> t7 t5))) i1, MkStream t7 S i1, MkStream t7 ((:!:) ((:!:) S (TermSymbol (TermSymbol M Deletion) b)) (TW t (i2 -> i2 -> t7 t5))) i1, MkStream t7 ((:!:) ((:!:) S (TermSymbol (TermSymbol M b1) Deletion)) (TW t (i2 -> i2 -> t7 t5))) i1, MkStream t7 ((:!:) ((:!:) S (TermSymbol (TermSymbol M b1) b)) (TW t1 (i -> i -> t7 t5))) i1, MkStream t7 ((:!:) (Stack (TW t2 (i1 -> i1 -> t7 t5))) b2) i2, MkStream t7 ((:!:) (Stack (TW t2 (i1 -> i1 -> t7 t5))) b2) i, MkStream t7 ((:!:) (Stack a) (TW t2 (i1 -> i1 -> t7 t5))) i1, MkStream t7 ((:!:) (Stack a1) (TW t2 (i1 -> i1 -> t7 t5))) i1, RuleContext i2, RuleContext i, RuleContext i1, Apply (Arg ((:!:) (Stack (TW t2 (i1 -> i1 -> t7 t5))) b2) -> t6), Apply (Arg ((:!:) (Stack a) (TW t2 (i1 -> i1 -> t7 t5))) -> t6), Apply (Arg ((:!:) (Stack a1) (TW t2 (i1 -> i1 -> t7 t5))) -> t6), Apply (Arg ((:!:) ((:!:) S (TermSymbol (TermSymbol M Deletion) b)) (TW t (i2 -> i2 -> t7 t5))) -> t6), Apply (Arg ((:!:) ((:!:) S (TermSymbol (TermSymbol M b1) Deletion)) (TW t (i2 -> i2 -> t7 t5))) -> t6), Apply (Arg ((:!:) ((:!:) S (TermSymbol (TermSymbol M b1) b)) (TW t1 (i -> i -> t7 t5))) -> t6), Build (TW t2 (i1 -> i1 -> t7 t5)), Build a, Build a1, TermStream t7 (TermSymbol (TermSymbol M Epsilon) Epsilon) (Elm S i1) i1, TermStaticVar (TermSymbol (TermSymbol M Epsilon) Epsilon) i1) => SigLabolg t7 t6 t5 t4 t3 -> t2 -> t1 -> t -> b2 -> a1 -> a -> b1 -> b -> (:.) ((:.) ((:.) Z (TW t2 (i1 -> i1 -> t7 t5))) (TW t1 (i -> i -> t7 t5))) (TW t (i2 -> i2 -> t7 t5))

gGlobal :: ((~#) * * (Fun (Arg ((:!:) ((:!:) S (TermSymbol (TermSymbol M Deletion) b)) (TW t2 (i1 -> i1 -> t7 t5))) -> t6)) ((:.) ((:.) Z ()) t3 -> t6 -> t6), (~#) * * (Fun (Arg ((:!:) ((:!:) S (TermSymbol (TermSymbol M b1) Deletion)) (TW t2 (i1 -> i1 -> t7 t5))) -> t6)) ((:.) ((:.) Z t4) () -> t6 -> t6), (~#) * * (Fun (Arg ((:!:) ((:!:) S (TermSymbol (TermSymbol M b1) b)) (TW t2 (i1 -> i1 -> t7 t5))) -> t6)) ((:.) ((:.) Z t4) t3 -> t6 -> t6), (~#) * * (Fun (Arg ((:!:) (Stack (TW t (i2 -> i2 -> t7 t5))) (TW t2 (i1 -> i1 -> t7 t5))) -> t6)) (t6 -> t6 -> t6), (~#) * * (Fun (Arg ((:!:) (Stack (TW t1 (i -> i -> t7 t5))) (TW t2 (i1 -> i1 -> t7 t5))) -> t6)) (t6 -> t6 -> t6), Apply (Arg ((:!:) ((:!:) S (TermSymbol (TermSymbol M Deletion) b)) (TW t2 (i1 -> i1 -> t7 t5))) -> t6), Apply (Arg ((:!:) ((:!:) S (TermSymbol (TermSymbol M b1) Deletion)) (TW t2 (i1 -> i1 -> t7 t5))) -> t6), Apply (Arg ((:!:) ((:!:) S (TermSymbol (TermSymbol M b1) b)) (TW t2 (i1 -> i1 -> t7 t5))) -> t6), Apply (Arg ((:!:) (Stack (TW t (i2 -> i2 -> t7 t5))) (TW t2 (i1 -> i1 -> t7 t5))) -> t6), Apply (Arg ((:!:) (Stack (TW t1 (i -> i -> t7 t5))) (TW t2 (i1 -> i1 -> t7 t5))) -> t6), Element ((:!:) ((:!:) S (TermSymbol (TermSymbol M Deletion) b)) (TW t2 (i1 -> i1 -> t7 t5))) i2, Element ((:!:) ((:!:) S (TermSymbol (TermSymbol M b1) Deletion)) (TW t2 (i1 -> i1 -> t7 t5))) i2, Element ((:!:) ((:!:) S (TermSymbol (TermSymbol M b1) b)) (TW t2 (i1 -> i1 -> t7 t5))) i, Element ((:!:) (Stack (TW t (i2 -> i2 -> t7 t5))) (TW t2 (i1 -> i1 -> t7 t5))) i1, Element ((:!:) (Stack (TW t1 (i -> i -> t7 t5))) (TW t2 (i1 -> i1 -> t7 t5))) i1, MkStream t7 S i1, MkStream t7 ((:!:) ((:!:) S (TermSymbol (TermSymbol M Deletion) b)) (TW t2 (i1 -> i1 -> t7 t5))) i2, MkStream t7 ((:!:) ((:!:) S (TermSymbol (TermSymbol M b1) Deletion)) (TW t2 (i1 -> i1 -> t7 t5))) i2, MkStream t7 ((:!:) ((:!:) S (TermSymbol (TermSymbol M b1) b)) (TW t2 (i1 -> i1 -> t7 t5))) i, MkStream t7 ((:!:) (Stack (TW t (i2 -> i2 -> t7 t5))) (TW t2 (i1 -> i1 -> t7 t5))) i1, MkStream t7 ((:!:) (Stack (TW t1 (i -> i -> t7 t5))) (TW t2 (i1 -> i1 -> t7 t5))) i1, RuleContext i2, RuleContext i, RuleContext i1, Build (TW t (i2 -> i2 -> t7 t5)), Build (TW t1 (i -> i -> t7 t5)), TermStream t7 (TermSymbol (TermSymbol M Epsilon) Epsilon) (Elm S i1) i1, TermStaticVar (TermSymbol (TermSymbol M Epsilon) Epsilon) i1) => SigGlobal t7 t6 t5 t4 t3 -> t2 -> t1 -> t -> b1 -> b -> (:.) ((:.) ((:.) Z (TW t2 (i1 -> i1 -> t7 t5))) (TW t1 (i -> i -> t7 t5))) (TW t (i2 -> i2 -> t7 t5))

resig :: Monad m => SigGlobal m a b c d -> SigLabolg m a b c d

score :: Monad m => Int -> Int -> Int -> SigGlobal m Int Int Info Info

part :: Monad m => Log Double -> Log Double -> Log Double -> Log Double -> SigGlobal m (Log Double) (Log Double) Info Info

type Pretty = [[Tree (Info, Info)]]

pretty :: Monad m => SigGlobal m [Tree (Info, Info)] [[Tree (Info, Info)]] Info Info

type Trix = TreeIxR Pre Vector Info I

type Tbl x = TwITbl Id Unboxed ((Z :. EmptyOk) :. EmptyOk) ((Z :. Trix) :. Trix) x

type Frst = Forest Pre Vector Info

type TblBt x = TwITblBt Unboxed ((Z :. EmptyOk) :. EmptyOk) ((Z :. Trix) :. Trix) Int Id Id [x]

type B = Tree (Info, Info)

runForward :: Frst -> Frst -> Int -> Int -> Int -> ((Z :. Tbl Int) :. Tbl Int) :. Tbl Int

runInside :: Frst -> Frst -> Log Double -> Log Double -> Log Double -> Log Double -> ((Z :. Tbl (Log Double)) :. Tbl (Log Double)) :. Tbl (Log Double)

type Trox = TreeIxR Pre Vector Info O

type OTbl x = TwITbl Id Unboxed ((Z :. EmptyOk) :. EmptyOk) ((Z :. Trox) :. Trox) x

runOutside :: Frst -> Frst -> Log Double -> Log Double -> Log Double -> Log Double -> (((Z :. Tbl (Log Double)) :. Tbl (Log Double)) :. Tbl (Log Double)) -> ((Z :. OTbl (Log Double)) :. OTbl (Log Double)) :. OTbl (Log Double)

runS :: Frst -> Frst -> Int -> Int -> Int -> (((Z :. Tbl Int) :. Tbl Int) :. Tbl Int, Int, [[Tree (Info, Info)]])

runIO :: Frst -> Frst -> Log Double -> Log Double -> Log Double -> Log Double -> ((:.) ((:.) ((:.) Z (Tbl (Log Double))) (Tbl (Log Double))) (Tbl (Log Double)), (:.) ((:.) ((:.) Z (OTbl (Log Double))) (OTbl (Log Double))) (OTbl (Log Double)), Log Double)

t11 :: [Char]

t12 :: [Char]

t21 :: [Char]

t22 :: [Char]

t31 :: [Char]

t32 :: [Char]

t41 :: [Char]

t42 :: [Char]

t51 :: [Char]

t52 :: [Char]

t61 :: [Char]

t62 :: [Char]

t71 :: [Char]

t72 :: [Char]

test :: FilePath -> FilePath -> IO ()

runAlignScoreTrees

Arguments

:: Frst

Forest A to compare

-> Frst

Forest B to compare

-> Int

score for matching nodes between A and B.

-> Int

if nodes between A/B are matched up but have unequal labels, this score is chosen.

-> Int

Score for an in/del operation.

-> IO ()

This is the main entry for "main-like" calls that already provide trees. A match is defined as equality on the labels.

TODO this should be turned into the more ususual streaming-compatible behaviour.

runAlignScoreTreesIO :: FillWeight -> RenderChoice -> FilePath -> Frst -> Frst -> Log Double -> Log Double -> Log Double -> IO ()

runAlignS :: String -> String -> Int -> Int -> Int -> IO ()

runAlignIO :: FillWeight -> RenderChoice -> FilePath -> String -> String -> Log Double -> Log Double -> Log Double -> Log Double -> IO ()