Safe Haskell	None
Language	Haskell2010

Biobase.Types.Accession

Contents

Accession with phantom types.
Phantom types. All with an excliti data constructor to guide
- NCBI phantom types
- Rfam phantom types
Helper functions

Description

Accession numbers. These numbers are not really numbers because they they are made up of alphanumeric characters.

Synopsis

newtype Accession t = Accession {
- _getAccession :: Text
}
accession' :: ConvertibleStrings s Text => t -> s -> Accession t
accession :: ConvertibleStrings s Text => s -> Accession t
retagAccession :: Accession f -> Accession t
data Nucleotide = Nucleotide
data Protein = Protein
data Clan = Clan
data Pfam = Pfam
data Rfam = Rfam
data Species = Species
guessAccessionType :: Accession t -> Maybe Text

`Accession` with phantom types.

newtype Accession t Source #

The accession number is a unique identifier in bioinformatics.

Depending on the source, accession numbers follow different alphanumeric formats! While letters-than-numbers is quite common, swissprot uses a mix. Hence, we just use a text string as accession.

A phantom type is provided to enable type safety annotations. Helper functions provide smart construction from the Accession tagged generic type.

Constructors

Accession
Fields _getAccession :: Text

Instances

Eq (Accession t) Source #
Instance details Defined in Biobase.Types.Accession Methods (==) :: Accession t -> Accession t -> Bool # (/=) :: Accession t -> Accession t -> Bool #
Ord (Accession t) Source #
Instance details Defined in Biobase.Types.Accession Methods compare :: Accession t -> Accession t -> Ordering # (<) :: Accession t -> Accession t -> Bool # (<=) :: Accession t -> Accession t -> Bool # (>) :: Accession t -> Accession t -> Bool # (>=) :: Accession t -> Accession t -> Bool # max :: Accession t -> Accession t -> Accession t # min :: Accession t -> Accession t -> Accession t #
Read (Accession t) Source #
Instance details Defined in Biobase.Types.Accession Methods readsPrec :: Int -> ReadS (Accession t) # readList :: ReadS [Accession t] # readPrec :: ReadPrec (Accession t) # readListPrec :: ReadPrec [Accession t] #
Show (Accession t) Source #
Instance details Defined in Biobase.Types.Accession Methods showsPrec :: Int -> Accession t -> ShowS # show :: Accession t -> String # showList :: [Accession t] -> ShowS #
IsString (Accession t) Source #
Instance details Defined in Biobase.Types.Accession Methods fromString :: String -> Accession t #
Generic (Accession t) Source #
Instance details Defined in Biobase.Types.Accession Associated Types type Rep (Accession t) :: Type -> Type # Methods from :: Accession t -> Rep (Accession t) x # to :: Rep (Accession t) x -> Accession t #
NFData (Accession t) Source #
Instance details Defined in Biobase.Types.Accession Methods rnf :: Accession t -> () #
Hashable (Accession t) Source #
Instance details Defined in Biobase.Types.Accession Methods hashWithSalt :: Int -> Accession t -> Int # hash :: Accession t -> Int #
ToJSON (Accession t) Source #
Instance details Defined in Biobase.Types.Accession Methods toJSON :: Accession t -> Value # toEncoding :: Accession t -> Encoding # toJSONList :: [Accession t] -> Value # toEncodingList :: [Accession t] -> Encoding #
FromJSON (Accession t) Source #
Instance details Defined in Biobase.Types.Accession Methods parseJSON :: Value -> Parser (Accession t) # parseJSONList :: Value -> Parser [Accession t] #
Binary (Accession t) Source #
Instance details Defined in Biobase.Types.Accession Methods put :: Accession t -> Put # get :: Get (Accession t) # putList :: [Accession t] -> Put #
Serialize (Accession t) Source #
Instance details Defined in Biobase.Types.Accession Methods put :: Putter (Accession t) # get :: Get (Accession t) #
type Rep (Accession t) Source #
Instance details Defined in Biobase.Types.Accession type Rep (Accession t) = D1 (MetaData "Accession" "Biobase.Types.Accession" "BiobaseTypes-0.2.0.1-B9coIbijR6NEFcCxvqIOZp" True) (C1 (MetaCons "Accession" PrefixI True) (S1 (MetaSel (Just "_getAccession") NoSourceUnpackedness NoSourceStrictness DecidedLazy) (Rec0 Text)))