Safe Haskell	None
Language	Haskell2010

Biobase.Secondary.New

Contents

Parses a ViennaRNA secondary structure string.
Transform into a Tree.

Description

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.

Synopsis

data SubStructure (t :: k) a
- = Unpaired {
  - _label :: !a
  }
- | Paired {
  - _label :: !a
  - _subStructures :: !(Vector (SubStructure 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 :: k) a = FullStructure {
- _fullStructure :: Vector (SubStructure t a)
}
fullStructure :: forall t a t a. Iso (FullStructure t a) (FullStructure t a) (Vector (SubStructure t a)) (Vector (SubStructure t a))
pUnpaired :: Parser (SubStructure () ())
pPaired :: Parser (SubStructure () ())
pSubStructure :: Parser (SubStructure () ())
pFullStructure :: Parser (FullStructure () ())
newtype StructureParseError = StructureParseError String
parseVienna :: MonadError StructureParseError m => ByteString -> m (FullStructure () ())
toTree :: (SubStructure t a -> Maybe b) -> b -> FullStructure (t :: k) a -> Tree b

Documentation

data SubStructure (t :: k) a Source #

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 t) Source #
Instance details Defined in Biobase.Secondary.New Methods fmap :: (a -> b) -> SubStructure t a -> SubStructure t b # (<$) :: a -> SubStructure t b -> SubStructure t a #
Foldable (SubStructure t) Source #
Instance details Defined in Biobase.Secondary.New Methods fold :: Monoid m => SubStructure t m -> m # foldMap :: Monoid m => (a -> m) -> SubStructure t a -> m # foldr :: (a -> b -> b) -> b -> SubStructure t a -> b # foldr' :: (a -> b -> b) -> b -> SubStructure t a -> b # foldl :: (b -> a -> b) -> b -> SubStructure t a -> b # foldl' :: (b -> a -> b) -> b -> SubStructure t a -> b # foldr1 :: (a -> a -> a) -> SubStructure t a -> a # foldl1 :: (a -> a -> a) -> SubStructure t a -> a # toList :: SubStructure t a -> [a] # null :: SubStructure t a -> Bool # length :: SubStructure t a -> Int # elem :: Eq a => a -> SubStructure t a -> Bool # maximum :: Ord a => SubStructure t a -> a # minimum :: Ord a => SubStructure t a -> a # sum :: Num a => SubStructure t a -> a # product :: Num a => SubStructure t a -> a #
Traversable (SubStructure t) Source #
Instance details Defined in Biobase.Secondary.New Methods traverse :: Applicative f => (a -> f b) -> SubStructure t a -> f (SubStructure t b) # sequenceA :: Applicative f => SubStructure t (f a) -> f (SubStructure t a) # mapM :: Monad m => (a -> m b) -> SubStructure t a -> m (SubStructure t b) # sequence :: Monad m => SubStructure t (m a) -> m (SubStructure t a) #
Eq a => Eq (SubStructure t a) Source #
Instance details Defined in Biobase.Secondary.New Methods (==) :: SubStructure t a -> SubStructure t a -> Bool # (/=) :: SubStructure t a -> SubStructure t a -> Bool #
Ord a => Ord (SubStructure t a) Source #
Instance details Defined in Biobase.Secondary.New Methods compare :: SubStructure t a -> SubStructure t a -> Ordering # (<) :: SubStructure t a -> SubStructure t a -> Bool # (<=) :: SubStructure t a -> SubStructure t a -> Bool # (>) :: SubStructure t a -> SubStructure t a -> Bool # (>=) :: SubStructure t a -> SubStructure t a -> Bool # max :: SubStructure t a -> SubStructure t a -> SubStructure t a # min :: SubStructure t a -> SubStructure t a -> SubStructure t a #
Read a => Read (SubStructure t a) Source #
Instance details Defined in Biobase.Secondary.New Methods readsPrec :: Int -> ReadS (SubStructure t a) # readList :: ReadS [SubStructure t a] # readPrec :: ReadPrec (SubStructure t a) # readListPrec :: ReadPrec [SubStructure t a] #
Show a => Show (SubStructure t a) Source #
Instance details Defined in Biobase.Secondary.New Methods showsPrec :: Int -> SubStructure t a -> ShowS # show :: SubStructure t a -> String # showList :: [SubStructure t a] -> ShowS #
Generic (SubStructure t a) Source #
Instance details Defined in Biobase.Secondary.New Associated Types type Rep (SubStructure t a) :: Type -> Type # Methods from :: SubStructure t a -> Rep (SubStructure t a) x # to :: Rep (SubStructure t a) x -> SubStructure t a #
type Rep (SubStructure t a) Source #
Instance details Defined in Biobase.Secondary.New type Rep (SubStructure t a) = D1 (MetaData "SubStructure" "Biobase.Secondary.New" "BiobaseXNA-0.11.0.0-6sSV7wA2ZNJ62zYFxZDZpd" False) (C1 (MetaCons "Unpaired" PrefixI True) (S1 (MetaSel (Just "_label") NoSourceUnpackedness SourceStrict DecidedStrict) (Rec0 a)) :+: C1 (MetaCons "Paired" PrefixI True) (S1 (MetaSel (Just "_label") NoSourceUnpackedness SourceStrict DecidedStrict) (Rec0 a) :*: S1 (MetaSel (Just "_subStructures") NoSourceUnpackedness SourceStrict DecidedStrict) (Rec0 (Vector (SubStructure t a)))))

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

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

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

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

newtype FullStructure (t :: k) a Source #

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 t) Source #
Instance details Defined in Biobase.Secondary.New Methods fmap :: (a -> b) -> FullStructure t a -> FullStructure t b # (<$) :: a -> FullStructure t b -> FullStructure t a #
Foldable (FullStructure t) Source #
Instance details Defined in Biobase.Secondary.New Methods fold :: Monoid m => FullStructure t m -> m # foldMap :: Monoid m => (a -> m) -> FullStructure t a -> m # foldr :: (a -> b -> b) -> b -> FullStructure t a -> b # foldr' :: (a -> b -> b) -> b -> FullStructure t a -> b # foldl :: (b -> a -> b) -> b -> FullStructure t a -> b # foldl' :: (b -> a -> b) -> b -> FullStructure t a -> b # foldr1 :: (a -> a -> a) -> FullStructure t a -> a # foldl1 :: (a -> a -> a) -> FullStructure t a -> a # toList :: FullStructure t a -> [a] # null :: FullStructure t a -> Bool # length :: FullStructure t a -> Int # elem :: Eq a => a -> FullStructure t a -> Bool # maximum :: Ord a => FullStructure t a -> a # minimum :: Ord a => FullStructure t a -> a # sum :: Num a => FullStructure t a -> a # product :: Num a => FullStructure t a -> a #
Traversable (FullStructure t) Source #
Instance details Defined in Biobase.Secondary.New Methods traverse :: Applicative f => (a -> f b) -> FullStructure t a -> f (FullStructure t b) # sequenceA :: Applicative f => FullStructure t (f a) -> f (FullStructure t a) # mapM :: Monad m => (a -> m b) -> FullStructure t a -> m (FullStructure t b) # sequence :: Monad m => FullStructure t (m a) -> m (FullStructure t a) #
Eq a => Eq (FullStructure t a) Source #
Instance details Defined in Biobase.Secondary.New Methods (==) :: FullStructure t a -> FullStructure t a -> Bool # (/=) :: FullStructure t a -> FullStructure t a -> Bool #
Ord a => Ord (FullStructure t a) Source #
Instance details Defined in Biobase.Secondary.New Methods compare :: FullStructure t a -> FullStructure t a -> Ordering # (<) :: FullStructure t a -> FullStructure t a -> Bool # (<=) :: FullStructure t a -> FullStructure t a -> Bool # (>) :: FullStructure t a -> FullStructure t a -> Bool # (>=) :: FullStructure t a -> FullStructure t a -> Bool # max :: FullStructure t a -> FullStructure t a -> FullStructure t a # min :: FullStructure t a -> FullStructure t a -> FullStructure t a #
Read a => Read (FullStructure t a) Source #
Instance details Defined in Biobase.Secondary.New Methods readsPrec :: Int -> ReadS (FullStructure t a) # readList :: ReadS [FullStructure t a] # readPrec :: ReadPrec (FullStructure t a) # readListPrec :: ReadPrec [FullStructure t a] #
Show a => Show (FullStructure t a) Source #
Instance details Defined in Biobase.Secondary.New Methods showsPrec :: Int -> FullStructure t a -> ShowS # show :: FullStructure t a -> String # showList :: [FullStructure t a] -> ShowS #
Generic (FullStructure t a) Source #
Instance details Defined in Biobase.Secondary.New Associated Types type Rep (FullStructure t a) :: Type -> Type # Methods from :: FullStructure t a -> Rep (FullStructure t a) x # to :: Rep (FullStructure t a) x -> FullStructure t a #
type Rep (FullStructure t a) Source #
Instance details Defined in Biobase.Secondary.New type Rep (FullStructure t a) = D1 (MetaData "FullStructure" "Biobase.Secondary.New" "BiobaseXNA-0.11.0.0-6sSV7wA2ZNJ62zYFxZDZpd" True) (C1 (MetaCons "FullStructure" PrefixI True) (S1 (MetaSel (Just "_fullStructure") NoSourceUnpackedness NoSourceStrictness DecidedLazy) (Rec0 (Vector (SubStructure t a)))))

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

Parses a ViennaRNA secondary structure string.

pUnpaired :: Parser (SubStructure () ()) Source #

pPaired :: Parser (SubStructure () ()) Source #

pSubStructure :: Parser (SubStructure () ()) Source #

pFullStructure :: Parser (FullStructure () ()) Source #

newtype StructureParseError Source #

Constructors

StructureParseError String

Instances

Show StructureParseError Source #
Instance details Defined in Biobase.Secondary.New Methods showsPrec :: Int -> StructureParseError -> ShowS # show :: StructureParseError -> String # showList :: [StructureParseError] -> ShowS #

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

Transform into a `Tree`.

toTree Source #

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

Documentation

Parses a ViennaRNA secondary structure string.

Transform into a Tree.

Transform into a `Tree`.