Biobase.Types.Accession

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

Accession with phantom types.

newtype Accession t

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)

Methods

(==) :: Accession t -> Accession t -> Bool

(/=) :: Accession t -> Accession t -> Bool

Ord (Accession t)

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)

Methods

readsPrec :: Int -> ReadS (Accession t)

readList :: ReadS [Accession t]

readPrec :: ReadPrec (Accession t)

readListPrec :: ReadPrec [Accession t]

Show (Accession t)

Methods

showsPrec :: Int -> Accession t -> ShowS

show :: Accession t -> String

showList :: [Accession t] -> ShowS

IsString (Accession t)

Methods

fromString :: String -> Accession t

Generic (Accession t)

Associated Types

type Rep (Accession t) :: * -> *

Methods

from :: Accession t -> Rep (Accession t) x

to :: Rep (Accession t) x -> Accession t

Hashable (Accession t)

Methods

hashWithSalt :: Int -> Accession t -> Int

hash :: Accession t -> Int

ToJSON (Accession t)

Methods

toJSON :: Accession t -> Value

toEncoding :: Accession t -> Encoding

toJSONList :: [Accession t] -> Value

toEncodingList :: [Accession t] -> Encoding

FromJSON (Accession t)

Methods

parseJSON :: Value -> Parser (Accession t)

parseJSONList :: Value -> Parser [Accession t]

Binary (Accession t)

Methods

put :: Accession t -> Put

get :: Get (Accession t)

putList :: [Accession t] -> Put

Serialize (Accession t)

Methods

put :: Putter (Accession t)

get :: Get (Accession t)

NFData (Accession t)

Methods

rnf :: Accession t -> ()

type Rep (Accession t)

type Rep (Accession t) = D1 (MetaData "Accession" "Biobase.Types.Accession" "BiobaseTypes-0.1.2.1-1LTYzU1e5OWItpBBqXiV1g" True) (C1 (MetaCons "Accession" PrefixI True) (S1 (MetaSel (Just Symbol "_getAccession") NoSourceUnpackedness NoSourceStrictness DecidedLazy) (Rec0 Text)))

accession' :: ConvertibleStrings s Text => t -> s -> Accession t

Generate an accession with an explicit phantom type: accession' Nucleotide Bla has type :: Accession Nucleotide.

accession :: ConvertibleStrings s Text => s -> Accession t

Generate an accession when the type Accession t is clear from the context.

retagAccession :: Accession f -> Accession t

Retag an accession

Phantom types. All with an excliti data constructor to guide

NCBI phantom types

data Nucleotide

nucleotide sequence

Constructors

Nucleotide

data Protein

protein sequence

Constructors

Protein

Rfam phantom types

data Clan

Tag as being a clan.

Constructors

Clan

data Pfam

Tag as being a Pfam model.

Constructors

Pfam

data Rfam

Tag as being an Rfam model. Used for Stockholm and CM files.

Constructors

Rfam

data Species

Species have an accession number, too.

Constructors

Species

Helper functions

guessAccessionType :: Accession t -> Maybe Text

Guess the type of accession number. Returns Nothing if unknown structure.