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

Methods

(==) :: D1Secondary -> D1Secondary -> Bool

(/=) :: D1Secondary -> D1Secondary -> Bool

Read D1Secondary

Methods

readsPrec :: Int -> ReadS D1Secondary

readList :: ReadS [D1Secondary]

readPrec :: ReadPrec D1Secondary

readListPrec :: ReadPrec [D1Secondary]

Show D1Secondary

Methods

showsPrec :: Int -> D1Secondary -> ShowS

show :: D1Secondary -> String

showList :: [D1Secondary] -> ShowS

Generic D1Secondary

Associated Types

type Rep D1Secondary :: * -> *

Methods

from :: D1Secondary -> Rep D1Secondary x

to :: Rep D1Secondary x -> D1Secondary

FromJSON D1Secondary

Methods

parseJSON :: Value -> Parser D1Secondary

parseJSONList :: Value -> Parser [D1Secondary]

ToJSON D1Secondary

Methods

toJSON :: D1Secondary -> Value

toEncoding :: D1Secondary -> Encoding

toJSONList :: [D1Secondary] -> Value

toEncodingList :: [D1Secondary] -> Encoding

Binary D1Secondary

Methods

put :: D1Secondary -> Put

get :: Get D1Secondary

Serialize D1Secondary

Methods

put :: Putter D1Secondary

get :: Get D1Secondary

MkD2Secondary D1Secondary

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

TODO fromD2S makes me wanna rewrite everything...

Methods

mkD2S :: D1Secondary -> D2Secondary

fromD2S :: D2Secondary -> D1Secondary

type Rep D1Secondary

type Rep D1Secondary = D1 (MetaData "D1Secondary" "Biobase.Secondary.Diagrams" "BiobaseXNA-0.9.3.0-8oUGCIbMbYx8TN6nAPRU1W" True) (C1 (MetaCons "D1S" PrefixI True) (S1 (MetaSel (Just Symbol "unD1S") NoSourceUnpackedness NoSourceStrictness DecidedLazy) (Rec0 (Vector Int))))

newtype D2Secondary

Constructors

D2S

Fields

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

Instances

Eq D2Secondary

Methods

(==) :: D2Secondary -> D2Secondary -> Bool

(/=) :: D2Secondary -> D2Secondary -> Bool

Read D2Secondary

Methods

readsPrec :: Int -> ReadS D2Secondary

readList :: ReadS [D2Secondary]

readPrec :: ReadPrec D2Secondary

readListPrec :: ReadPrec [D2Secondary]

Show D2Secondary

Methods

showsPrec :: Int -> D2Secondary -> ShowS

show :: D2Secondary -> String

showList :: [D2Secondary] -> ShowS

Generic D2Secondary

Associated Types

type Rep D2Secondary :: * -> *

Methods

from :: D2Secondary -> Rep D2Secondary x

to :: Rep D2Secondary x -> D2Secondary

FromJSON D2Secondary

Methods

parseJSON :: Value -> Parser D2Secondary

parseJSONList :: Value -> Parser [D2Secondary]

ToJSON D2Secondary

Methods

toJSON :: D2Secondary -> Value

toEncoding :: D2Secondary -> Encoding

toJSONList :: [D2Secondary] -> Value

toEncodingList :: [D2Secondary] -> Encoding

Binary D2Secondary

Methods

put :: D2Secondary -> Put

get :: Get D2Secondary

Serialize D2Secondary

Methods

put :: Putter D2Secondary

get :: Get D2Secondary

MkD1Secondary D2Secondary

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

Methods

mkD1S :: D2Secondary -> D1Secondary

fromD1S :: D1Secondary -> D2Secondary

type Rep D2Secondary

type Rep D2Secondary = D1 (MetaData "D2Secondary" "Biobase.Secondary.Diagrams" "BiobaseXNA-0.9.3.0-8oUGCIbMbYx8TN6nAPRU1W" True) (C1 (MetaCons "D2S" PrefixI True) (S1 (MetaSel (Just Symbol "unD2S") NoSourceUnpackedness NoSourceStrictness DecidedLazy) (Rec0 (Vector ((Int, Edge, CTisomerism), (Int, Edge, CTisomerism))))))

class MkD1Secondary a where

Conversion to and from 1-diagrams.

Minimal complete definition

mkD1S, fromD1S

Methods

mkD1S :: a -> D1Secondary

fromD1S :: D1Secondary -> a

Instances

MkD1Secondary String

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

Methods

mkD1S :: String -> D1Secondary

fromD1S :: D1Secondary -> String

MkD1Secondary D2Secondary

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

Methods

mkD1S :: D2Secondary -> D1Secondary

fromD1S :: D1Secondary -> D2Secondary

MkD1Secondary (Vector Char)

Methods

mkD1S :: Vector Char -> D1Secondary

fromD1S :: D1Secondary -> Vector Char

MkD1Secondary (Int, [PairIdx])

(Length,List of Pairs)

Methods

mkD1S :: (Int, [PairIdx]) -> D1Secondary

fromD1S :: D1Secondary -> (Int, [PairIdx])

MkD1Secondary ([String], Vector Char)

Generate Secondary given that we have an unboxed vector of characters

Methods

mkD1S :: ([String], Vector Char) -> D1Secondary

fromD1S :: D1Secondary -> ([String], Vector Char)

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.

Methods

mkD1S :: ([String], String) -> D1Secondary

fromD1S :: D1Secondary -> ([String], String)

class MkD2Secondary a where

Conversion to and from 2-diagrams.

Minimal complete definition

mkD2S, fromD2S

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...

Methods

mkD2S :: D1Secondary -> D2Secondary

fromD2S :: D2Secondary -> D1Secondary

MkD2Secondary (Int, [ExtPairIdx])

Methods

mkD2S :: (Int, [ExtPairIdx]) -> D2Secondary

fromD2S :: D2Secondary -> (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)

Methods

(==) :: SSTree idx a -> SSTree idx a -> Bool

(/=) :: SSTree idx a -> SSTree idx a -> Bool

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

Methods

readsPrec :: Int -> ReadS (SSTree idx a)

readList :: ReadS [SSTree idx a]

readPrec :: ReadPrec (SSTree idx a)

readListPrec :: ReadPrec [SSTree idx a]

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

Methods

showsPrec :: Int -> SSTree idx a -> ShowS

show :: SSTree idx a -> String

showList :: [SSTree idx a] -> ShowS

Generic (SSTree idx a)

Associated Types

type Rep (SSTree idx a) :: * -> *

Methods

from :: SSTree idx a -> Rep (SSTree idx a) x

to :: Rep (SSTree idx a) x -> SSTree idx a

type Rep (SSTree idx a)

type Rep (SSTree idx a) = D1 (MetaData "SSTree" "Biobase.Secondary.Diagrams" "BiobaseXNA-0.9.3.0-8oUGCIbMbYx8TN6nAPRU1W" False) ((:+:) (C1 (MetaCons "SSTree" PrefixI False) ((:*:) (S1 (MetaSel (Nothing Symbol) NoSourceUnpackedness NoSourceStrictness DecidedLazy) (Rec0 idx)) ((:*:) (S1 (MetaSel (Nothing Symbol) NoSourceUnpackedness NoSourceStrictness DecidedLazy) (Rec0 a)) (S1 (MetaSel (Nothing Symbol) NoSourceUnpackedness NoSourceStrictness DecidedLazy) (Rec0 [SSTree idx a]))))) (C1 (MetaCons "SSExtern" PrefixI False) ((:*:) (S1 (MetaSel (Nothing Symbol) NoSourceUnpackedness NoSourceStrictness DecidedLazy) (Rec0 Int)) ((:*:) (S1 (MetaSel (Nothing Symbol) NoSourceUnpackedness NoSourceStrictness DecidedLazy) (Rec0 a)) (S1 (MetaSel (Nothing Symbol) NoSourceUnpackedness NoSourceStrictness DecidedLazy) (Rec0 [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 t3, Ord t2) => ((t2, t3), t) -> ((t2, t3), t1) -> Ordering

d2Grouping :: (Ord a1, Ord a) => ((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.