Biobase.Primary.AA

This module has the translation tables for the genetic code. We do have a symbol Undef for undefined amino acids (say because of Ns in the nucleotide code).

Documentation

data AA

Amino acid phantom type.

Instances

LetterChar * AA

Methods

letterChar :: Letter AA t -> Char

charLetter :: Char -> Letter AA t

MkPrimary * (Vector Char) AA

Methods

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

Enum (Letter * AA)

Methods

succ :: Letter * AA -> Letter * AA

pred :: Letter * AA -> Letter * AA

toEnum :: Int -> Letter * AA

fromEnum :: Letter * AA -> Int

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

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

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

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

Read (Letter * AA)

Methods

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

readList :: ReadS [Letter * AA]

readPrec :: ReadPrec (Letter * AA)

readListPrec :: ReadPrec [Letter * AA]

Show (Letter * AA)

Methods

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

show :: Letter * AA -> String

showList :: [Letter * AA] -> ShowS

FromJSON (Letter * AA)

Methods

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

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

ToJSON (Letter * AA)

Methods

toJSON :: Letter * AA -> Value

toEncoding :: Letter * AA -> Encoding

toJSONList :: [Letter * AA] -> Value

toEncodingList :: [Letter * AA] -> Encoding

pattern Stop :: Letter * AA

pattern A :: Letter * AA

pattern B :: Letter * AA

pattern C :: Letter * AA

pattern D :: Letter * AA

pattern E :: Letter * AA

pattern F :: Letter * AA

pattern G :: Letter * AA

pattern H :: Letter * AA

pattern I :: Letter * AA

pattern K :: Letter * AA

pattern L :: Letter * AA

pattern M :: Letter * AA

pattern N :: Letter * AA

pattern P :: Letter * AA

pattern Q :: Letter * AA

pattern R :: Letter * AA

pattern S :: Letter * AA

pattern T :: Letter * AA

pattern V :: Letter * AA

pattern W :: Letter * AA

pattern X :: Letter * AA

pattern Y :: Letter * AA

pattern Z :: Letter * AA

pattern Undef :: Letter * AA

Creating functions and aa data.

aa :: Int -> Letter AA

aaRange :: [Letter * AA]

charAA :: Char -> Letter AA

Translate Char amino acid representation into efficient AA newtype.

aaChar :: Letter AA -> Char

Char representation of an AA.

lookup tables

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

instances