Biobase.Primary.IUPAC

Degenerate base symbol representation. We use the same conventions as in which ignores Uracil, except if it stands alone for Char and XNA targets. If the Degenerate target is RNA, then we create Us instead of Ts.

TODO Shall we handle Complement for degenerates?

Documentation

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

pattern A :: Letter DEG n

pattern C :: Letter DEG n

pattern G :: Letter DEG n

pattern T :: Letter DEG n

pattern U :: Letter DEG n

pattern W :: Letter DEG n

pattern S :: Letter DEG n

pattern M :: Letter DEG n

pattern K :: Letter DEG n

pattern R :: Letter DEG n

pattern Y :: Letter DEG n

pattern B :: Letter DEG n

pattern D :: Letter DEG n

pattern H :: Letter DEG n

pattern V :: Letter DEG n

pattern N :: Letter DEG n

charDEG :: forall k (n :: k). Char -> Letter DEG n

degChar :: forall k (n :: k). Letter DEG n -> Char

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

Conversions

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

Raw embeddings

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.