Biobase.Secondary.Vienna

Encoding of Watson-Crick and Wobble Pairs in the Vienna RNA package style.

Documentation

newtype ViennaPair

Use machine Ints internally

Constructors

ViennaPair

Fields

unViennaPair :: Int

Instances

Bounded ViennaPair

Enum ViennaPair

Eq ViennaPair

Ord ViennaPair

Read ViennaPair

Show ViennaPair

Ix ViennaPair

Generic ViennaPair

Index ViennaPair

IndexStream ViennaPair

ToJSON ViennaPair

FromJSON ViennaPair

Binary ViennaPair

Serialize ViennaPair

Unbox ViennaPair

Vector Vector ViennaPair

MVector MVector ViennaPair

IndexStream z => IndexStream ((:.) z ViennaPair)

type Rep ViennaPair

data Vector ViennaPair = V_ViennaPair (Vector Int)

data MVector s0 ViennaPair = MV_ViennaPair (MVector s Int)

pattern NP :: ViennaPair

pattern CG :: ViennaPair

pattern GC :: ViennaPair

pattern GU :: ViennaPair

pattern UG :: ViennaPair

pattern AU :: ViennaPair

pattern UA :: ViennaPair

pattern NS :: ViennaPair

pattern Undef :: ViennaPair

class MkViennaPair a where

Methods

mkViennaPair :: a -> ViennaPair

fromViennaPair :: ViennaPair -> a

Instances

MkViennaPair (Letter RNA, Letter RNA)

isViennaPair :: Letter RNA -> Letter RNA -> Bool

viennaPairTable :: Unboxed ((Z :. Letter RNA) :. Letter RNA) ViennaPair

revPair :: ViennaPair -> ViennaPair

reverse a vienna pair

Convenience structures

cguaP :: [ViennaPair]

cgnsP :: [ViennaPair]

pairToString :: [(ViennaPair, [Char])]