Biobase.Primary

TODO make sequence types stringable?

Documentation

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

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

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.

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.

module Biobase.Primary.Hashed

class Degenerate x where

Methods

fromDegenerate :: Char -> [x]

toDegenerate :: [x] -> Maybe Char

Instances

Degenerate Char

Defined in Biobase.Primary.IUPAC

Methods

fromDegenerate :: Char -> [Char]

toDegenerate :: [Char] -> Maybe Char

Degenerate (Letter XNA n)

Defined in Biobase.Primary.IUPAC

Methods

fromDegenerate :: Char -> [Letter XNA n]

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

Degenerate (Letter DNA n)

Defined in Biobase.Primary.IUPAC

Methods

fromDegenerate :: Char -> [Letter DNA n]

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

Degenerate (Letter RNA n)

Defined in Biobase.Primary.IUPAC

Methods

fromDegenerate :: Char -> [Letter RNA n]

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

data DEG

Allow the full, including degenerates, alphabet.

Instances

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

Defined in Biobase.Primary.IUPAC

Methods

primary :: Vector Char -> Primary DEG n

IsString [Letter DEG n]

Defined in Biobase.Primary.IUPAC

Methods

fromString :: String -> [Letter DEG n]

Bounded (Letter DEG n)

Defined in Biobase.Primary.IUPAC

Methods

minBound :: Letter DEG n

maxBound :: Letter DEG n

Enum (Letter DEG n)

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)

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

degChar :: Letter DEG n -> Char

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

iupacXDNAchars :: [(Char, String)]

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

iupacNucleotides :: ByteString

Raw iupac data, embedded into the library.

module Biobase.Primary.Letter

module Biobase.Primary.Nuc

module Biobase.Primary.Trans

module Biobase.Primary.Unknown