Biobase.Secondary.Diagrams

Types for RNA secondary structure. Types vary from the simplest array (D1Secondary) to rather complex ones.

Documentation

newtype D1Secondary

RNA secondary structure with 1-diagrams. Each nucleotide is paired with at most one other nucleotide. A nucleotide with index k in [0..len-1] is paired if unD1S VU.! k >=0 0 Unpaired status is -1.

Constructors

D1S

Fields

unD1S :: Vector Int

Instances

Eq D1Secondary

Read D1Secondary

Show D1Secondary

Generic D1Secondary

ToJSON D1Secondary

FromJSON D1Secondary

Binary D1Secondary

Serialize D1Secondary

MkD2Secondary D1Secondary

Conversion between D1S and D2S is lossy in D2S -> D1S

TODO fromD2S makes me wanna rewrite everything...

type Rep D1Secondary

newtype D2Secondary

Constructors

D2S

Fields

unD2S :: Vector ((Int, Edge, CTisomerism), (Int, Edge, CTisomerism))

Instances

Eq D2Secondary

Read D2Secondary

Show D2Secondary

Generic D2Secondary

ToJSON D2Secondary

FromJSON D2Secondary

Binary D2Secondary

Serialize D2Secondary

MkD1Secondary D2Secondary

Conversion between D1S and D2S is lossy in D2S -> D1S

type Rep D2Secondary

class MkD1Secondary a where

Conversion to and from 1-diagrams.

Methods

mkD1S :: a -> D1Secondary

fromD1S :: D1Secondary -> a

Instances

MkD1Secondary String

A "fast" instance for getting the pair list of vienna-structures.

MkD1Secondary D2Secondary

Conversion between D1S and D2S is lossy in D2S -> D1S

MkD1Secondary (Vector Char)

MkD1Secondary (Int, [PairIdx])

(Length,List of Pairs)

MkD1Secondary ([String], String)

A second primitive generator, requiring dictionary and String. This one generates pairs that are then used by the above instance. The dict is a list of possible brackets: ["()"] being the minimal set.

MkD1Secondary ([String], Vector Char)

Generate Secondary given that we have an unboxed vector of characters

class MkD2Secondary a where

Conversion to and from 2-diagrams.

Methods

mkD2S :: a -> D2Secondary

fromD2S :: D2Secondary -> a

Instances

MkD2Secondary D1Secondary

Conversion between D1S and D2S is lossy in D2S -> D1S

TODO fromD2S makes me wanna rewrite everything...

MkD2Secondary (Int, [ExtPairIdx])

Tree-based representation

data SSTree idx a

A secondary-structure tree. Has no notion of pseudoknots.

Constructors

SSTree idx a [SSTree idx a]

SSExtern Int a [SSTree idx a]

Instances

(Eq idx, Eq a) => Eq (SSTree idx a)

(Read idx, Read a) => Read (SSTree idx a)

(Show idx, Show a) => Show (SSTree idx a)

Generic (SSTree idx a)

type Rep (SSTree idx a)

d1sTree :: D1Secondary -> SSTree PairIdx ()

Create a tree from (pseudoknot-free [not checked]) 1-diagrams.

d2sTree :: D2Secondary -> SSTree ExtPairIdx ()

Create a tree from (pseudoknot-free [not checked]) 2-diagrams.

d2Compare :: (Ord t2, Ord t3) => ((t2, t3), t) -> ((t2, t3), t1) -> Ordering

d2Grouping :: (Ord a, Ord a1) => ((a, a1), t) -> ((a, a1), t1) -> Bool

Instances for D1S

Instances for D2S

Older instances (should still work)

High-level parsing functionality for secondary structures

isCanonicalStructure :: String -> Bool

Completely canonical structure.

TODO Check size of hairpins and interior loops?

isConstraintStructure :: String -> Bool

Is constraint type structure, i.e. there can also be symbols present that denote up- or downstream pairing.

structures :: Iso' String [String]

Take a structural string and split it into its constituents.

If we decide to NOT depend on lens explicitly, another way to write this is:

structures :: forall p f . (Profunctor p, Functor f) => p [String] (f [String]) -> p String (f String)
structures = dimap (splitOn "&") (fmap (concat . intersperse "&"))

foldStructure :: Prism' String String

A fold structure is a single structure

cofoldStructure :: Prism' String (String, String)

A cofold structure has exactly two structures split by & (which the prism removes).

Helper functions

unsafeDotBracket2pairlist :: [String] -> String -> [(Int, Int)]

Secondary structure parser which allows pseudoknots, if they use different kinds of brackets.

dotBracket2pairlist :: [String] -> String -> Either String [(Int, Int)]

Secondary structure parser with a notion of errors. We either return a Right structure, including flags, or a Left error.

viennaStringDistance :: Bool -> Bool -> String -> String -> (String, Int)

Calculates the distance between two vienna strings.