Biobase.Primary.Nuc.DNA

Documentation

data DNA

DNA nucleotides.

Instances

IsString [Letter * DNA]

Methods

fromString :: String -> [Letter * DNA]

LetterChar * DNA

Methods

letterChar :: Letter DNA t -> Char

charLetter :: Char -> Letter DNA t

MkPrimary * (Vector Char) DNA

Methods

primary :: DNA -> Primary (Vector Char) t

Bounded (Letter * DNA)

Methods

minBound :: Letter * DNA

maxBound :: Letter * DNA

Enum (Letter * DNA)

Methods

succ :: Letter * DNA -> Letter * DNA

pred :: Letter * DNA -> Letter * DNA

toEnum :: Int -> Letter * DNA

fromEnum :: Letter * DNA -> Int

enumFrom :: Letter * DNA -> [Letter * DNA]

enumFromThen :: Letter * DNA -> Letter * DNA -> [Letter * DNA]

enumFromTo :: Letter * DNA -> Letter * DNA -> [Letter * DNA]

enumFromThenTo :: Letter * DNA -> Letter * DNA -> Letter * DNA -> [Letter * DNA]

Read (Letter * DNA)

Methods

readsPrec :: Int -> ReadS (Letter * DNA)

readList :: ReadS [Letter * DNA]

readPrec :: ReadPrec (Letter * DNA)

readListPrec :: ReadPrec [Letter * DNA]

Show (Letter * DNA)

Methods

showsPrec :: Int -> Letter * DNA -> ShowS

show :: Letter * DNA -> String

showList :: [Letter * DNA] -> ShowS

Degenerate (Letter * DNA)

Methods

fromDegenerate :: Char -> [Letter * DNA]

toDegenerate :: [Letter * DNA] -> Maybe Char

type TranscribeTo (Primary * DNA)

type TranscribeTo (Primary * DNA) = Primary * RNA

type TranscribeTo (Letter * DNA)

type TranscribeTo (Letter * DNA) = Letter * RNA

pattern A :: Letter * DNA

pattern C :: Letter * DNA

pattern G :: Letter * DNA

pattern T :: Letter * DNA

pattern N :: Letter * DNA

acgt :: [Letter DNA]

charDNA :: Char -> Letter * DNA

dnaChar :: Letter * DNA -> Char

cdna :: Iso' Char (Letter DNA)

An isomorphism from Char to 'Letter DNA'. This assumes that the underlying Chars actually represent a DNA sequence. This allows typesafe modification of DNA sequences since only [A,C,G,T,N] are allowed.

dnaSeq :: MkPrimary n DNA => n -> Primary DNA