Biobase.Primary.AA

This module has the translation tables for the genetic code.

In addition, Any is included to denote that any amino acid is ok, and Unknown to denote unknown data. We do have a symbol Undef for undefined amino acids, which denotes error condition.

TODO this nomenclature might change!

Documentation

pattern Stop :: forall k (n :: k). Letter AA n

pattern A :: forall k (n :: k). Letter AA n

pattern B :: forall k (n :: k). Letter AA n

pattern C :: forall k (n :: k). Letter AA n

pattern D :: forall k (n :: k). Letter AA n

pattern E :: forall k (n :: k). Letter AA n

pattern F :: forall k (n :: k). Letter AA n

pattern G :: forall k (n :: k). Letter AA n

pattern H :: forall k (n :: k). Letter AA n

pattern I :: forall k (n :: k). Letter AA n

pattern K :: forall k (n :: k). Letter AA n

pattern L :: forall k (n :: k). Letter AA n

pattern M :: forall k (n :: k). Letter AA n

pattern N :: forall k (n :: k). Letter AA n

pattern P :: forall k (n :: k). Letter AA n

pattern Q :: forall k (n :: k). Letter AA n

pattern R :: forall k (n :: k). Letter AA n

pattern S :: forall k (n :: k). Letter AA n

pattern T :: forall k (n :: k). Letter AA n

pattern V :: forall k (n :: k). Letter AA n

pattern W :: forall k (n :: k). Letter AA n

pattern X :: forall k (n :: k). Letter AA n

pattern Y :: forall k (n :: k). Letter AA n

pattern Z :: forall k (n :: k). Letter AA n

pattern Any :: forall k (n :: k). Letter AA n

pattern Unknown :: forall k (n :: k). Letter AA n

pattern Undef :: forall k (n :: k). Letter AA n

Creating functions and aa data.

aa :: Int -> Letter AA n

aaRange :: Vector (Letter AA n)

charAA :: Char -> Letter AA n

Translate Char amino acid representation into efficient AA newtype.

aaChar :: Letter AA n -> Char

Char representation of an AA.

lookup tables

charBaa :: Bimap (HashMap Char (Letter AA n)) (HashMap (Letter AA n) Char)

twentyAA :: Vector (Letter AA n)

List of the twenty "default" amino acids. Used, for example, by HMMer.

instances

Orphan instances

LetterChar AA (n :: k)

Methods

letterChar :: Letter AA n -> Char

charLetter :: Char -> Letter AA n

MkPrimary (Vector Char) AA (n :: k)

Methods

primary :: Vector Char -> Primary AA n

Bounded (Letter AA n)

Methods

minBound :: Letter AA n

maxBound :: Letter AA n

Enum (Letter AA n)

Methods

succ :: Letter AA n -> Letter AA n

pred :: Letter AA n -> Letter AA n

toEnum :: Int -> Letter AA n

fromEnum :: Letter AA n -> Int

enumFrom :: Letter AA n -> [Letter AA n]

enumFromThen :: Letter AA n -> Letter AA n -> [Letter AA n]

enumFromTo :: Letter AA n -> Letter AA n -> [Letter AA n]

enumFromThenTo :: Letter AA n -> Letter AA n -> Letter AA n -> [Letter AA n]

Read (Letter AA n)

Methods

readsPrec :: Int -> ReadS (Letter AA n)

readList :: ReadS [Letter AA n]

readPrec :: ReadPrec (Letter AA n)

readListPrec :: ReadPrec [Letter AA n]

Show (Letter AA n)

Methods

showsPrec :: Int -> Letter AA n -> ShowS

show :: Letter AA n -> String

showList :: [Letter AA n] -> ShowS

ToJSON (Letter AA n)

Methods

toJSON :: Letter AA n -> Value

toEncoding :: Letter AA n -> Encoding

toJSONList :: [Letter AA n] -> Value

toEncodingList :: [Letter AA n] -> Encoding

FromJSON (Letter AA n)

Methods

parseJSON :: Value -> Parser (Letter AA n)

parseJSONList :: Value -> Parser [Letter AA n]