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

Safe HaskellNone
LanguageHaskell2010

Biobase.Primary.IUPAC

Contents

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

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

IsString [Letter DEG n] Source # 
Instance details

Defined in Biobase.Primary.IUPAC

Methods

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

Bounded (Letter DEG n) Source # 
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Defined in Biobase.Primary.IUPAC

Enum (Letter DEG n) Source # 
Instance details

Defined in Biobase.Primary.IUPAC

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 #

Conversions

class Degenerate x where Source #

Instances
Degenerate Char Source # 
Instance details

Defined in Biobase.Primary.IUPAC

Degenerate (Letter XNA n) Source # 
Instance details

Defined in Biobase.Primary.IUPAC

Degenerate (Letter DNA n) Source # 
Instance details

Defined in Biobase.Primary.IUPAC

Degenerate (Letter RNA n) Source # 
Instance details

Defined in Biobase.Primary.IUPAC

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.