Copyright	(C) 2017 Ricky Elrod
License	BSD2 (see LICENSE file)
Maintainer	Ricky Elrod <ricky@elrod.me>
Stability	experimental
Portability	lens
Safe Haskell	None
Language	Haskell2010

Bio.Algorithm.Types

Contents

Macromolecule types
Patterns
Prisms (DNA)
Prisms (RNA)
Transcription isomorphism
Trivial isomorphisms
Helper Functions

Description

We emphasize making illegal states unrepresentable. As such, creating something representing a particular kind of genetic string will be done by way of smart constructors. The default constructors will not be exported.

We represent three different kinds of genetic strings (as per Rosalind), DNA, RNA, and Protein.

A DNA is created with mkDNA, an RNA is created with mkRNA, and a Protein is created with mkProtein.

Because we don't export the constructors, pattern matching becomes impossible. To rectify this, we use PatternSynonyms and export patterns for each type. These are PDNA, PRNA, and PProtein, respectively. Internally, we represent sequences as lazy Texts, and this is what you deconstruct one using one of these pattern synonyms.

Synopsis

Macromolecule types

data DNA #

A DNA sequence. This is constructed using the mkDNA smart constructor below.

Instances

Eq DNA #
Methods (==) :: DNA -> DNA -> Bool # (/=) :: DNA -> DNA -> Bool #
Ord DNA #
Methods compare :: DNA -> DNA -> Ordering # (<) :: DNA -> DNA -> Bool # (<=) :: DNA -> DNA -> Bool # (>) :: DNA -> DNA -> Bool # (>=) :: DNA -> DNA -> Bool # max :: DNA -> DNA -> DNA # min :: DNA -> DNA -> DNA #
Show DNA #
Methods showsPrec :: Int -> DNA -> ShowS # show :: DNA -> String # showList :: [DNA] -> ShowS #
Semigroup DNA #
Methods (<>) :: DNA -> DNA -> DNA # sconcat :: NonEmpty DNA -> DNA # stimes :: Integral b => b -> DNA -> DNA #
Monoid DNA #
Methods mempty :: DNA # mappend :: DNA -> DNA -> DNA # mconcat :: [DNA] -> DNA #

data RNA #

An RNA sequence. This is constructed using the mkRNA smart constructor below.

Instances

Eq RNA #
Methods (==) :: RNA -> RNA -> Bool # (/=) :: RNA -> RNA -> Bool #
Ord RNA #
Methods compare :: RNA -> RNA -> Ordering # (<) :: RNA -> RNA -> Bool # (<=) :: RNA -> RNA -> Bool # (>) :: RNA -> RNA -> Bool # (>=) :: RNA -> RNA -> Bool # max :: RNA -> RNA -> RNA # min :: RNA -> RNA -> RNA #
Show RNA #
Methods showsPrec :: Int -> RNA -> ShowS # show :: RNA -> String # showList :: [RNA] -> ShowS #
Semigroup RNA #
Methods (<>) :: RNA -> RNA -> RNA # sconcat :: NonEmpty RNA -> RNA # stimes :: Integral b => b -> RNA -> RNA #
Monoid RNA #
Methods mempty :: RNA # mappend :: RNA -> RNA -> RNA # mconcat :: [RNA] -> RNA #

Patterns

pattern PDNA :: Text -> DNA #

Since raw constructors are not exported, we provide these a pattern for deconstructing DNA and RNA. This is one such pattern for DNA. Generally it should not be needed (use the lens combinators instead), but we provide it here anyway, and use it internally in some places.

pattern PRNA :: Text -> RNA #

And this is the same for RNA.