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

Safe HaskellNone
LanguageHaskell2010

Biobase.Primary

Description

TODO make sequence types stringable?

Synopsis

Documentation

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

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

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.

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.

module Biobase.Primary.Hashed

class Degenerate x where Source #

Methods

fromDegenerate :: Char -> [x] Source #

toDegenerate :: [x] -> Maybe Char Source #

Instances
Degenerate Char Source # 
Instance details

Defined in Biobase.Primary.IUPAC

Methods

fromDegenerate :: Char -> [Char] Source #

toDegenerate :: [Char] -> Maybe Char Source #

Degenerate (Letter XNA n) Source # 
Instance details

Defined in Biobase.Primary.IUPAC

Methods

fromDegenerate :: Char -> [Letter XNA n] Source #

toDegenerate :: [Letter XNA n] -> Maybe Char Source #

Degenerate (Letter DNA n) Source # 
Instance details

Defined in Biobase.Primary.IUPAC

Methods

fromDegenerate :: Char -> [Letter DNA n] Source #

toDegenerate :: [Letter DNA n] -> Maybe Char Source #

Degenerate (Letter RNA n) Source # 
Instance details

Defined in Biobase.Primary.IUPAC

Methods

fromDegenerate :: Char -> [Letter RNA n] Source #

toDegenerate :: [Letter RNA n] -> Maybe Char Source #

data DEG Source #

Allow the full, including degenerates, alphabet.

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

Defined in Biobase.Primary.IUPAC

Methods

primary :: Vector Char -> Primary DEG n Source #

IsString [Letter DEG n] Source # 
Instance details

Defined in Biobase.Primary.IUPAC

Methods

fromString :: String -> [Letter DEG n] #

Bounded (Letter DEG n) Source # 
Instance details

Defined in Biobase.Primary.IUPAC

Methods

minBound :: Letter DEG n #

maxBound :: Letter DEG n #

Enum (Letter DEG n) Source # 
Instance details

Defined in Biobase.Primary.IUPAC

Methods

succ :: Letter DEG n -> Letter DEG n #

pred :: Letter DEG n -> Letter DEG n #

toEnum :: Int -> Letter DEG n #

fromEnum :: Letter DEG n -> Int #

enumFrom :: Letter DEG n -> [Letter DEG n] #

enumFromThen :: Letter DEG n -> Letter DEG n -> [Letter DEG n] #

enumFromTo :: Letter DEG n -> Letter DEG n -> [Letter DEG n] #

enumFromThenTo :: Letter DEG n -> Letter DEG n -> Letter DEG n -> [Letter DEG n] #

Show (Letter DEG n) Source # 
Instance details

Defined in Biobase.Primary.IUPAC

Methods

showsPrec :: Int -> Letter DEG n -> ShowS #

show :: Letter DEG n -> String #

showList :: [Letter DEG n] -> ShowS #

charDEG :: Char -> Letter DEG n Source #

degChar :: Letter DEG n -> Char Source #

degSeq :: MkPrimary p DEG n => p -> Primary DEG n Source #

iupacXDNAchars :: [(Char, String)] Source #

list of characters, using the XNA alphabet, but degenerate chars assume DNA characters.

iupacNucleotides :: ByteString Source #

Raw iupac data, embedded into the library.

module Biobase.Primary.Letter

module Biobase.Primary.Nuc

module Biobase.Primary.Trans

module Biobase.Primary.Unknown