Biobase.Primary.Nuc.RNA

Documentation

data RNA

RNA nucleotides.

Instances

LetterChar RNA

Methods

letterChar :: Letter RNA -> Char

charLetter :: Char -> Letter RNA

IsostericityLookup ExtPair

For extended basepairs, we take the default mapping and go from there.

TODO inClass missing

Methods

getClasses :: ExtPair -> [String]

inClass :: String -> [ExtPair]

IsostericityLookup Pair

Normal basepairs are assumed to have cWW basepairing.

TODO inClass missing

Methods

getClasses :: Pair -> [String]

inClass :: String -> [Pair]

Bounded (Letter RNA)

Methods

minBound :: Letter RNA

maxBound :: Letter RNA

Enum (Letter RNA)

Methods

succ :: Letter RNA -> Letter RNA

pred :: Letter RNA -> Letter RNA

toEnum :: Int -> Letter RNA

fromEnum :: Letter RNA -> Int

enumFrom :: Letter RNA -> [Letter RNA]

enumFromThen :: Letter RNA -> Letter RNA -> [Letter RNA]

enumFromTo :: Letter RNA -> Letter RNA -> [Letter RNA]

enumFromThenTo :: Letter RNA -> Letter RNA -> Letter RNA -> [Letter RNA]

Read (Letter RNA)

Methods

readsPrec :: Int -> ReadS (Letter RNA)

readList :: ReadS [Letter RNA]

readPrec :: ReadPrec (Letter RNA)

readListPrec :: ReadPrec [Letter RNA]

Show (Letter RNA)

Methods

showsPrec :: Int -> Letter RNA -> ShowS

show :: Letter RNA -> String

showList :: [Letter RNA] -> ShowS

IsString [Letter RNA]

Methods

fromString :: String -> [Letter RNA]

ToJSON (Letter RNA)

Methods

toJSON :: Letter RNA -> Value

toEncoding :: Letter RNA -> Encoding

toJSONList :: [Letter RNA] -> Value

toEncodingList :: [Letter RNA] -> Encoding

FromJSON (Letter RNA)

Methods

parseJSON :: Value -> Parser (Letter RNA)

parseJSONList :: Value -> Parser [Letter RNA]

Degenerate (Letter RNA)

Methods

fromDegenerate :: Char -> [Letter RNA]

toDegenerate :: [Letter RNA] -> Maybe Char

MkPrimary (Vector Char) RNA

Methods

primary :: Vector Char -> Primary RNA

Complement (Letter DNA) (Letter RNA)

Methods

complement :: Letter DNA -> Letter RNA

Complement (Letter RNA) (Letter DNA)

Methods

complement :: Letter RNA -> Letter DNA

Complement (Letter RNA) (Letter RNA)

Methods

complement :: Letter RNA -> Letter RNA

MkViennaPair (Letter RNA, Letter RNA)

Methods

mkViennaPair :: (Letter RNA, Letter RNA) -> ViennaPair

fromViennaPair :: ViennaPair -> (Letter RNA, Letter RNA)

pattern A :: Letter RNA

pattern C :: Letter RNA

pattern G :: Letter RNA

pattern U :: Letter RNA

pattern N :: Letter RNA

acgu :: [Letter RNA]

charRNA :: Char -> Letter RNA

rnaChar :: Letter RNA -> Char

rnaSeq :: MkPrimary n RNA => n -> Primary RNA