Biobase.Secondary.New

New parsers and structures for secondary structures. The structures here a strict.

TODO Parser should check if a #Vienna Secondary Structure or #Extended Secondary Structure precedes the entries.

Documentation

data SubStructure t a

A completely closed sub-structure. An unpaired region . is closed. A paired region (r) is closed, where r contains arbitrarily many unpaired and paired elements.

TODO Should be extended with Extended, but this requires knowing which of the ends overlap with paired: left, right, or both.

Constructors

Unpaired

Fields

• _label :: !a

Paired

Fields

• _label :: !a
• _subStructures :: !(Vector (SubStructure t a))

Instances

Functor (SubStructure k t)

Methods

fmap :: (a -> b) -> SubStructure k t a -> SubStructure k t b

(<$) :: a -> SubStructure k t b -> SubStructure k t a

Foldable (SubStructure k t)

Methods

fold :: Monoid m => SubStructure k t m -> m

foldMap :: Monoid m => (a -> m) -> SubStructure k t a -> m

foldr :: (a -> b -> b) -> b -> SubStructure k t a -> b

foldr' :: (a -> b -> b) -> b -> SubStructure k t a -> b

foldl :: (b -> a -> b) -> b -> SubStructure k t a -> b

foldl' :: (b -> a -> b) -> b -> SubStructure k t a -> b

foldr1 :: (a -> a -> a) -> SubStructure k t a -> a

foldl1 :: (a -> a -> a) -> SubStructure k t a -> a

toList :: SubStructure k t a -> [a]

null :: SubStructure k t a -> Bool

length :: SubStructure k t a -> Int

elem :: Eq a => a -> SubStructure k t a -> Bool

maximum :: Ord a => SubStructure k t a -> a

minimum :: Ord a => SubStructure k t a -> a

sum :: Num a => SubStructure k t a -> a

product :: Num a => SubStructure k t a -> a

Traversable (SubStructure k t)

Methods

traverse :: Applicative f => (a -> f b) -> SubStructure k t a -> f (SubStructure k t b)

sequenceA :: Applicative f => SubStructure k t (f a) -> f (SubStructure k t a)

mapM :: Monad m => (a -> m b) -> SubStructure k t a -> m (SubStructure k t b)

sequence :: Monad m => SubStructure k t (m a) -> m (SubStructure k t a)

Eq a => Eq (SubStructure k t a)

Methods

(==) :: SubStructure k t a -> SubStructure k t a -> Bool

(/=) :: SubStructure k t a -> SubStructure k t a -> Bool

Ord a => Ord (SubStructure k t a)

Methods

compare :: SubStructure k t a -> SubStructure k t a -> Ordering

(<) :: SubStructure k t a -> SubStructure k t a -> Bool

(<=) :: SubStructure k t a -> SubStructure k t a -> Bool

(>) :: SubStructure k t a -> SubStructure k t a -> Bool

(>=) :: SubStructure k t a -> SubStructure k t a -> Bool

max :: SubStructure k t a -> SubStructure k t a -> SubStructure k t a

min :: SubStructure k t a -> SubStructure k t a -> SubStructure k t a

Read a => Read (SubStructure k t a)

Methods

readsPrec :: Int -> ReadS (SubStructure k t a)

readList :: ReadS [SubStructure k t a]

readPrec :: ReadPrec (SubStructure k t a)

readListPrec :: ReadPrec [SubStructure k t a]

Show a => Show (SubStructure k t a)

Methods

showsPrec :: Int -> SubStructure k t a -> ShowS

show :: SubStructure k t a -> String

showList :: [SubStructure k t a] -> ShowS

Generic (SubStructure k t a)

Associated Types

type Rep (SubStructure k t a) :: * -> *

Methods

from :: SubStructure k t a -> Rep (SubStructure k t a) x

to :: Rep (SubStructure k t a) x -> SubStructure k t a

type Rep (SubStructure k t a)

type Rep (SubStructure k t a) = D1 (MetaData "SubStructure" "Biobase.Secondary.New" "BiobaseXNA-0.10.0.0-KYWIxTC5DTnJ4ZvJWky3ys" False) ((:+:) (C1 (MetaCons "Unpaired" PrefixI True) (S1 (MetaSel (Just Symbol "_label") NoSourceUnpackedness SourceStrict DecidedStrict) (Rec0 a))) (C1 (MetaCons "Paired" PrefixI True) ((:*:) (S1 (MetaSel (Just Symbol "_label") NoSourceUnpackedness SourceStrict DecidedStrict) (Rec0 a)) (S1 (MetaSel (Just Symbol "_subStructures") NoSourceUnpackedness SourceStrict DecidedUnpack) (Rec0 (Vector (SubStructure k t a)))))))

subStructures :: forall t a t. Traversal (SubStructure t a) (SubStructure t a) (Vector (SubStructure t a)) (Vector (SubStructure t a))

label :: forall t a. Lens' (SubStructure t a) a

_Paired :: forall t a t. Prism (SubStructure t a) (SubStructure t a) (a, Vector (SubStructure t a)) (a, Vector (SubStructure t a))

_Unpaired :: forall t a. Prism' (SubStructure t a) a

newtype FullStructure t a

A full structure is composed of a number of sub-structures. The empty structure is a full structure.

Constructors

FullStructure

Fields

• _fullStructure :: Vector (SubStructure t a)

Instances

Functor (FullStructure k t)

Methods

fmap :: (a -> b) -> FullStructure k t a -> FullStructure k t b

(<$) :: a -> FullStructure k t b -> FullStructure k t a

Foldable (FullStructure k t)

Methods

fold :: Monoid m => FullStructure k t m -> m

foldMap :: Monoid m => (a -> m) -> FullStructure k t a -> m

foldr :: (a -> b -> b) -> b -> FullStructure k t a -> b

foldr' :: (a -> b -> b) -> b -> FullStructure k t a -> b

foldl :: (b -> a -> b) -> b -> FullStructure k t a -> b

foldl' :: (b -> a -> b) -> b -> FullStructure k t a -> b

foldr1 :: (a -> a -> a) -> FullStructure k t a -> a

foldl1 :: (a -> a -> a) -> FullStructure k t a -> a

toList :: FullStructure k t a -> [a]

null :: FullStructure k t a -> Bool

length :: FullStructure k t a -> Int

elem :: Eq a => a -> FullStructure k t a -> Bool

maximum :: Ord a => FullStructure k t a -> a

minimum :: Ord a => FullStructure k t a -> a

sum :: Num a => FullStructure k t a -> a

product :: Num a => FullStructure k t a -> a

Traversable (FullStructure k t)

Methods

traverse :: Applicative f => (a -> f b) -> FullStructure k t a -> f (FullStructure k t b)

sequenceA :: Applicative f => FullStructure k t (f a) -> f (FullStructure k t a)

mapM :: Monad m => (a -> m b) -> FullStructure k t a -> m (FullStructure k t b)

sequence :: Monad m => FullStructure k t (m a) -> m (FullStructure k t a)

Eq a => Eq (FullStructure k t a)

Methods

(==) :: FullStructure k t a -> FullStructure k t a -> Bool

(/=) :: FullStructure k t a -> FullStructure k t a -> Bool

Ord a => Ord (FullStructure k t a)

Methods

compare :: FullStructure k t a -> FullStructure k t a -> Ordering

(<) :: FullStructure k t a -> FullStructure k t a -> Bool

(<=) :: FullStructure k t a -> FullStructure k t a -> Bool

(>) :: FullStructure k t a -> FullStructure k t a -> Bool

(>=) :: FullStructure k t a -> FullStructure k t a -> Bool

max :: FullStructure k t a -> FullStructure k t a -> FullStructure k t a

min :: FullStructure k t a -> FullStructure k t a -> FullStructure k t a

Read a => Read (FullStructure k t a)

Methods

readsPrec :: Int -> ReadS (FullStructure k t a)

readList :: ReadS [FullStructure k t a]

readPrec :: ReadPrec (FullStructure k t a)

readListPrec :: ReadPrec [FullStructure k t a]

Show a => Show (FullStructure k t a)

Methods

showsPrec :: Int -> FullStructure k t a -> ShowS

show :: FullStructure k t a -> String

showList :: [FullStructure k t a] -> ShowS

Generic (FullStructure k t a)

Associated Types

type Rep (FullStructure k t a) :: * -> *

Methods

from :: FullStructure k t a -> Rep (FullStructure k t a) x

to :: Rep (FullStructure k t a) x -> FullStructure k t a

type Rep (FullStructure k t a)

type Rep (FullStructure k t a) = D1 (MetaData "FullStructure" "Biobase.Secondary.New" "BiobaseXNA-0.10.0.0-KYWIxTC5DTnJ4ZvJWky3ys" True) (C1 (MetaCons "FullStructure" PrefixI True) (S1 (MetaSel (Just Symbol "_fullStructure") NoSourceUnpackedness NoSourceStrictness DecidedLazy) (Rec0 (Vector (SubStructure k t a)))))

fullStructure :: forall t a t a. Iso (FullStructure t a) (FullStructure t a) (Vector (SubStructure t a)) (Vector (SubStructure t a))

Parses a ViennaRNA secondary structure string.

pUnpaired :: Parser (SubStructure () ())

pPaired :: Parser (SubStructure () ())

pSubStructure :: Parser (SubStructure () ())

pFullStructure :: Parser (FullStructure () ())

newtype StructureParseError

Constructors

StructureParseError String

Instances

Show StructureParseError

Methods

showsPrec :: Int -> StructureParseError -> ShowS

show :: StructureParseError -> String

showList :: [StructureParseError] -> ShowS

parseVienna :: MonadError StructureParseError m => ByteString -> m (FullStructure () ())

Transform into a Tree.

toTree

Arguments

:: (SubStructure t a -> Maybe b)

how to handle substructure elements? Nothing means discard this substructure and all children.

-> b

The root label

-> FullStructure (t :: k) a

The FullStructure to transform into a Tree.

-> Tree b

Transform a FullStructure into a Tree.

Given a full structure generated like this: s = either (error . show) id $ parseVienna $ pack ".()(())."

a tree of just the base paired can be created with toTree (preview (_Paired._1)) () s