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

IsString [Letter * DEG]

Methods

fromString :: String -> [Letter * DEG]

MkPrimary * (Vector Char) DEG

Methods

primary :: DEG -> Primary (Vector Char) t

Bounded (Letter * DEG)

Methods

minBound :: Letter * DEG

maxBound :: Letter * DEG

Enum (Letter * DEG)

Methods

succ :: Letter * DEG -> Letter * DEG

pred :: Letter * DEG -> Letter * DEG

toEnum :: Int -> Letter * DEG

fromEnum :: Letter * DEG -> Int

enumFrom :: Letter * DEG -> [Letter * DEG]

enumFromThen :: Letter * DEG -> Letter * DEG -> [Letter * DEG]

enumFromTo :: Letter * DEG -> Letter * DEG -> [Letter * DEG]

enumFromThenTo :: Letter * DEG -> Letter * DEG -> Letter * DEG -> [Letter * DEG]

Show (Letter * DEG)

Methods

showsPrec :: Int -> Letter * DEG -> ShowS

show :: Letter * DEG -> String

showList :: [Letter * DEG] -> ShowS

pattern A :: Letter * DEG

pattern C :: Letter * DEG

pattern G :: Letter * DEG

pattern T :: Letter * DEG

pattern U :: Letter * DEG

pattern W :: Letter * DEG

pattern S :: Letter * DEG

pattern M :: Letter * DEG

pattern K :: Letter * DEG

pattern R :: Letter * DEG

pattern Y :: Letter * DEG

pattern B :: Letter * DEG

pattern D :: Letter * DEG

pattern H :: Letter * DEG

pattern V :: Letter * DEG

pattern N :: Letter * DEG

charDEG :: Char -> Letter * DEG

degChar :: Letter * DEG -> Char

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

Conversions

class Degenerate x where

Minimal complete definition

fromDegenerate, toDegenerate

Methods

fromDegenerate :: Char -> [x]

toDegenerate :: [x] -> Maybe Char

Instances

Degenerate Char

Methods

fromDegenerate :: Char -> [Char]

toDegenerate :: [Char] -> Maybe Char

Degenerate (Letter * DNA)

Methods

fromDegenerate :: Char -> [Letter * DNA]

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

Degenerate (Letter * RNA)

Methods

fromDegenerate :: Char -> [Letter * RNA]

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

Degenerate (Letter * XNA)

Methods

fromDegenerate :: Char -> [Letter * XNA]

toDegenerate :: [Letter * XNA] -> 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.