Safe Haskell	None
Language	Haskell2010

Biobase.Secondary.Structure

Description

A secondary structure, with sequence, Vienna compatible canonical secondary structure, extended structure, and additional information.

This is the structure that will be returned by prediction algorithms in the future.

TODO we will need ex- and import functions to a number of standard formats. There is an open feature request to export to something that resembles FASTA with additional information.

Synopsis

data SecondaryStructure = SS {
- _ssSeq :: !Text
- _ssVienna :: !D1Secondary
- _ssExt :: !D2Secondary
- _ssViennaE :: Maybe ()
- _ssAux :: Map Text Text
}

Documentation

data SecondaryStructure Source #

A sequence, complete with secondary structure. While this structure is rather RNA-centric, there is nothing that prohibits us from using this for DNA.

TODO Generics, Cereal, Binary, Aeson instances

Constructors

SS
Fields _ssSeq :: !Text sequence; we use `Text` whenever possible _ssVienna :: !D1Secondary canonical Vienna secondary structure _ssExt :: !D2Secondary extended secondary structure _ssViennaE :: Maybe () TODO will be the energy, measured or predicted _ssAux :: Map Text Text any auxiliary info in key/value format

Instances

Eq SecondaryStructure Source #
Instance details Defined in Biobase.Secondary.Structure Methods (==) :: SecondaryStructure -> SecondaryStructure -> Bool # (/=) :: SecondaryStructure -> SecondaryStructure -> Bool #
Read SecondaryStructure Source #
Instance details Defined in Biobase.Secondary.Structure Methods readsPrec :: Int -> ReadS SecondaryStructure # readList :: ReadS [SecondaryStructure] # readPrec :: ReadPrec SecondaryStructure # readListPrec :: ReadPrec [SecondaryStructure] #
Show SecondaryStructure Source #
Instance details Defined in Biobase.Secondary.Structure Methods showsPrec :: Int -> SecondaryStructure -> ShowS # show :: SecondaryStructure -> String # showList :: [SecondaryStructure] -> ShowS #