BiobaseXNA-0.11.0.0: Efficient RNA/DNA/Protein Primary/Secondary Structure

Safe HaskellNone
LanguageHaskell2010

Biobase.Primary.AA

Contents

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

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.

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

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

MkPrimary (Vector Char) AA (n :: k) Source # 
Instance details

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

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

FromJSON (Letter AA n) Source # 
Instance details