Biobase.RNA

Encodings for nucleotides and pairs. Currently very ViennaRNA-centric. This might change over time.

TODO do not export Nucleotide ctor?

TODO consider adding nucAmpersand as a chain seperator. This could make some things easier.

single nucleotide encoding

newtype Nucleotide

Constructors

Nucleotide Int

Instances

Bounded Nucleotide

Enum Nucleotide

Eq Nucleotide

Ord Nucleotide

Read Nucleotide

Show Nucleotide

Ix Nucleotide

Prim Nucleotide

Unbox Nucleotide

Vector Vector Nucleotide

MVector MVector Nucleotide

nucCharList :: [(Int, Char)]

charNucList :: [(Char, Int)]

charToNucleotide :: Char -> Nucleotide

nucleotideToChar :: Nucleotide -> Char

Since this function is used rather often.

Represent nucleotide sequences using a PrimArray.

type Primary = PrimArray Int Nucleotide

class MkPrimary a where

Methods

mkPrimary :: a -> Primary

unPrimary :: Primary -> a

Instances

MkPrimary String

MkPrimary (Vector Char)

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

newtype ViennaPair

Constructors

ViennaPair Int

Instances

Bounded ViennaPair

Enum ViennaPair

Eq ViennaPair

Ord ViennaPair

Read ViennaPair

Show ViennaPair

Ix ViennaPair

Prim ViennaPair

Unbox ViennaPair

Vector Vector ViennaPair

MVector MVector ViennaPair

vpStrList :: [(Int, String)]

strVpList :: [(String, Int)]

convenience lists

Transformations between Nucleotide and ViennaPair

toPair :: Nucleotide -> Nucleotide -> ViennaPair

pairs :: Nucleotide -> Nucleotide -> Bool