BioInf.RNAFold.Energy

Documentation

class (Show a, Ring a, Unbox a, Prim a) => FoldFunctions a where

The folding functions. It could happen that we need different folding functions with the same type, hence the class-based approach. The default instance uses the usual ring methods.

Methods

stackOpt :: TurnerTables a -> Primary -> Table a -> Int -> Int -> a

stackIdx :: TurnerTables a -> Primary -> Table a -> Int -> Int -> [(Cell, a)]

hairpinOpt :: TurnerTables a -> Primary -> Int -> Int -> a

hairpinIdx :: TurnerTables a -> Primary -> Int -> Int -> [a]

largeInteriorLoopOpt :: TurnerTables a -> Primary -> Table a -> Int -> Int -> a

largeInteriorLoopIdx :: TurnerTables a -> Primary -> Table a -> Int -> Int -> [(Cell, a)]

tabbedInteriorLoopOpt :: TurnerTables a -> Primary -> Table a -> Int -> Int -> a

tabbedInteriorLoopIdx :: TurnerTables a -> Primary -> Table a -> Int -> Int -> [(Cell, a)]

bulgeLOpt :: TurnerTables a -> Primary -> Table a -> Int -> Int -> a

bulgeLIdx :: TurnerTables a -> Primary -> Table a -> Int -> Int -> [(Cell, a)]

bulgeROpt :: TurnerTables a -> Primary -> Table a -> Int -> Int -> a

bulgeRIdx :: TurnerTables a -> Primary -> Table a -> Int -> Int -> [(Cell, a)]

interior1xnLOpt :: TurnerTables a -> Primary -> Table a -> Int -> Int -> a

interior1xnLIdx :: TurnerTables a -> Primary -> Table a -> Int -> Int -> [(Cell, a)]

interior1xnROpt :: TurnerTables a -> Primary -> Table a -> Int -> Int -> a

interior1xnRIdx :: TurnerTables a -> Primary -> Table a -> Int -> Int -> [(Cell, a)]

multibranchIJLoopOpt :: TurnerTables a -> Primary -> Table a -> Int -> Int -> a

multibranchIJLoopIdx :: TurnerTables a -> Primary -> Table a -> Int -> Int -> [(Cell, a)]

multibranchUnpairedJOpt :: TurnerTables a -> Primary -> Table a -> Int -> Int -> a

multibranchUnpairedJIdx :: TurnerTables a -> Primary -> Table a -> Int -> Int -> [(Cell, a)]

multibranchKJHelixOpt :: TurnerTables a -> Primary -> Table a -> Int -> Int -> a

multibranchKJHelixIdx :: TurnerTables a -> Primary -> Table a -> Int -> Int -> [(Int, a)]

multibranchAddKJHelixOpt :: TurnerTables a -> Primary -> Table a -> Table a -> Int -> Int -> a

multibranchAddKJHelixIdx :: TurnerTables a -> Primary -> Table a -> Table a -> Int -> Int -> [(Int, a)]

multibranchCloseOpt :: TurnerTables a -> Primary -> Table a -> Table a -> Int -> Int -> a

multibranchCloseIdx :: TurnerTables a -> Primary -> Table a -> Table a -> Int -> Int -> [(Int, a)]

externalLoopOpt :: TurnerTables a -> Primary -> Table a -> Int -> Int -> a

externalLoopIdx :: TurnerTables a -> Primary -> Table a -> Int -> Int -> [(Cell, a)]

externalAddLoopOpt :: TurnerTables a -> Primary -> Table a -> Table a -> Int -> Int -> a

externalAddLoopIdx :: TurnerTables a -> Primary -> Table a -> Table a -> Int -> Int -> [(Int, a)]

calcNinio :: a -> a -> Int -> a

Calculate the ninio asymmetric malus. Can not be written using ring functions alone as a min or max functions is required.

calcTermAU

Arguments

:: a

-> ViennaPair

-> a

Apply terminal AU penalty

Applies a terminal AU/GU penalty, where required.

TODO shouldn't this be just: if CG||GC then one else termAU?

calcLargeLoop :: Int -> a

large hairpin loops >30 require special calculations that involve floor, rounding and other stuff that can not be handled by the Ring class alone

Instances

FoldFunctions Int

FoldFunctions Energy

class FoldFunctions a => Fold a where

Methods

fold :: TurnerTables a -> Primary -> ResultTables a

foldST :: TurnerTables a -> Primary -> ST s (ResultTables a)

backtrack :: TurnerTables a -> Primary -> ResultTables a -> a -> [(Secondary, a)]

Instances

Fold Int

Fold Energy