Biobase.Primary.Nuc.RNA

Documentation

data RNA

RNA nucleotides.

Instances

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]

BasepairConvert ViennaPair (Letter * RNA, Letter * RNA)

Methods

basepairConvert :: ViennaPair -> (Letter * RNA, Letter * RNA)

BasepairConvert Basepair (Letter * RNA, Letter * RNA)

Methods

basepairConvert :: Basepair -> (Letter * RNA, Letter * RNA)

IsString [Letter * RNA]

Methods

fromString :: String -> [Letter * RNA]

LetterChar * RNA

Methods

letterChar :: Letter RNA t -> Char

charLetter :: Char -> Letter RNA t

MkPrimary * (Vector Char) RNA

Methods

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

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

FromJSON (Letter * RNA)

Methods

parseJSON :: Value -> Parser (Letter * RNA)

parseJSONList :: Value -> Parser [Letter * RNA]

ToJSON (Letter * RNA)

Methods

toJSON :: Letter * RNA -> Value

toEncoding :: Letter * RNA -> Encoding

toJSONList :: [Letter * RNA] -> Value

toEncodingList :: [Letter * RNA] -> Encoding

Degenerate (Letter * RNA)

Methods

fromDegenerate :: Char -> [Letter * RNA]

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

BasepairConvert (Letter * RNA, Letter * RNA) ViennaPair

Methods

basepairConvert :: (Letter * RNA, Letter * RNA) -> ViennaPair

BasepairConvert (Letter * RNA, Letter * RNA) Basepair

Methods

basepairConvert :: (Letter * RNA, Letter * RNA) -> Basepair

type TranscribeTo (Primary * RNA)

type TranscribeTo (Primary * RNA) = Primary * DNA

type TranscribeTo (Letter * RNA)

type TranscribeTo (Letter * RNA) = Letter * DNA

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

crna :: Iso' Char (Letter RNA)

An isomorphism from Char to 'Letter RNA'. This assumes that the underlying Chars actually represent an RNA sequence. This allows typesafe modification of RNA sequences since only [A,C,G,U,N] are allowed.

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