Safe Haskell	None
Language	Haskell2010

Biobase.Primary.IUPAC

Contents

Conversions
Raw embeddings

Description

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?

Synopsis

data DEG
pattern A :: forall k (n :: k). Letter DEG n
pattern C :: forall k (n :: k). Letter DEG n
pattern G :: forall k (n :: k). Letter DEG n
pattern T :: forall k (n :: k). Letter DEG n
pattern U :: forall k (n :: k). Letter DEG n
pattern W :: forall k (n :: k). Letter DEG n
pattern S :: forall k (n :: k). Letter DEG n
pattern M :: forall k (n :: k). Letter DEG n
pattern K :: forall k (n :: k). Letter DEG n
pattern R :: forall k (n :: k). Letter DEG n
pattern Y :: forall k (n :: k). Letter DEG n
pattern B :: forall k (n :: k). Letter DEG n
pattern D :: forall k (n :: k). Letter DEG n
pattern H :: forall k (n :: k). Letter DEG n
pattern V :: forall k (n :: k). Letter DEG n
pattern N :: forall k (n :: k). Letter DEG n
charDEG :: Char -> Letter DEG n
degChar :: Letter DEG n -> Char
degSeq :: MkPrimary p DEG n => p -> Primary DEG n
class Degenerate x where
- fromDegenerate :: Char -> [x]
- toDegenerate :: [x] -> Maybe Char
iupacXDNAchars :: [(Char, String)]
iupacNucleotides :: ByteString

Documentation

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 #

pattern A :: forall k (n :: k). Letter DEG n Source #

pattern C :: forall k (n :: k). Letter DEG n Source #

pattern G :: forall k (n :: k). Letter DEG n Source #

pattern T :: forall k (n :: k). Letter DEG n Source #

pattern U :: forall k (n :: k). Letter DEG n Source #

pattern W :: forall k (n :: k). Letter DEG n Source #

pattern S :: forall k (n :: k). Letter DEG n Source #

pattern M :: forall k (n :: k). Letter DEG n Source #

pattern K :: forall k (n :: k). Letter DEG n Source #

pattern R :: forall k (n :: k). Letter DEG n Source #

pattern Y :: forall k (n :: k). Letter DEG n Source #

pattern B :: forall k (n :: k). Letter DEG n Source #

pattern D :: forall k (n :: k). Letter DEG n Source #

pattern H :: forall k (n :: k). Letter DEG n Source #

pattern V :: forall k (n :: k). Letter DEG n Source #

pattern N :: forall k (n :: k). Letter DEG n Source #

charDEG :: Char -> Letter DEG n Source #

degChar :: Letter DEG n -> Char Source #

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

Conversions

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 #

Raw embeddings

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.