Safe Haskell	None
Language	Haskell2010

Biobase.Primary.AA

Contents

Creating functions and aa data.
lookup tables
instances
Orphan instances

Description

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!

Synopsis

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
aa :: Int -> Letter AA n
aaRange :: Vector (Letter AA n)
charAA :: Char -> Letter AA n
aaChar :: Letter AA n -> Char
charBaa :: Bimap (HashMap Char (Letter AA n)) (HashMap (Letter AA n) Char)
twentyAA :: Vector (Letter AA n)

Documentation

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Creating functions and aa data.

aa :: Int -> Letter AA n Source #

aaRange :: Vector (Letter AA n) Source #

charAA :: Char -> Letter AA n Source #

Translate Char amino acid representation into efficient AA newtype.

aaChar :: Letter AA n -> Char Source #

Char representation of an AA.

lookup tables

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

twentyAA :: Vector (Letter AA n) Source #

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

instances

Orphan instances

LetterChar AA (n :: k) Source #
Instance details Methods letterChar :: Letter AA n -> Char Source # charLetter :: Char -> Letter AA n Source #
MkPrimary (Vector Char) AA (n :: k) Source #
Instance details Methods primary :: Vector Char -> Primary AA n Source #
Bounded (Letter AA n) Source #
Instance details Methods minBound :: Letter AA n # maxBound :: Letter AA n #
Enum (Letter AA n) Source #
Instance details 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) Source #
Instance details 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) Source #
Instance details Methods showsPrec :: Int -> Letter AA n -> ShowS # show :: Letter AA n -> String # showList :: [Letter AA n] -> ShowS #
ToJSON (Letter AA n) Source #
Instance details 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) Source #
Instance details Methods parseJSON :: Value -> Parser (Letter AA n) # parseJSONList :: Value -> Parser [Letter AA n] #