Safe Haskell	None
Language	Haskell2010

Biobase.Types.Shape

Contents

Distance measures on the shape string itself.

Description

Shape abstractions of structures.

Shapes do not preserve sizes of structures (say unpaired regions or stem length). As such, distance measures provided here are to be used carefully!

TODO consider how to handle the different shape levels. One option would be to phantom-type everything.

Synopsis

data ShapeLevel
- = SL1
- | SL2
- | SL3
- | SL4
- | SL5
data RNAshape = RNAshape {
- _rnashapelevel :: !ShapeLevel
- _rnashape :: !ByteString
}
rnashapelevel :: Lens' RNAshape ShapeLevel
rnashape :: Lens' RNAshape ByteString
shapeForest :: ShapeLevel -> SPForest ByteString ByteString -> SPForest Char Char
rnass2shape :: ShapeLevel -> RNAss -> RNAshape
test :: ShapeLevel -> RNAshape
shapeForestshape :: ShapeLevel -> SPForest Char Char -> RNAshape
generateShape :: ShapeLevel -> RNAss -> RNAshape
data RNAshapepset = RNAshapepset {
- _rnashapepsetlevel :: ShapeLevel
- _rnashapepset :: Set (Int, Int)
}
rnashapepsetlevel :: Lens' RNAshapepset ShapeLevel
rnashapepset :: Lens' RNAshapepset (Set (Int, Int))
rnashapePairSet :: MonadError String m => RNAshape -> m RNAshapepset
rnassPairSet' :: RNAshape -> RNAshapepset
shapePairDist :: RNAshapepset -> RNAshapepset -> Int

Documentation

data ShapeLevel Source #

Shape levels are hardcoded according to their specification.

TODO Allow compile-time check on accepted shape levels?

Constructors

SL1
SL2
SL3
SL4
SL5

Instances

Eq ShapeLevel Source #
Instance details Defined in Biobase.Types.Shape Methods (==) :: ShapeLevel -> ShapeLevel -> Bool # (/=) :: ShapeLevel -> ShapeLevel -> Bool #
Data ShapeLevel Source #
Instance details Defined in Biobase.Types.Shape Methods gfoldl :: (forall d b. Data d => c (d -> b) -> d -> c b) -> (forall g. g -> c g) -> ShapeLevel -> c ShapeLevel # gunfold :: (forall b r. Data b => c (b -> r) -> c r) -> (forall r. r -> c r) -> Constr -> c ShapeLevel # toConstr :: ShapeLevel -> Constr # dataTypeOf :: ShapeLevel -> DataType # dataCast1 :: Typeable t => (forall d. Data d => c (t d)) -> Maybe (c ShapeLevel) # dataCast2 :: Typeable t => (forall d e. (Data d, Data e) => c (t d e)) -> Maybe (c ShapeLevel) # gmapT :: (forall b. Data b => b -> b) -> ShapeLevel -> ShapeLevel # gmapQl :: (r -> r' -> r) -> r -> (forall d. Data d => d -> r') -> ShapeLevel -> r # gmapQr :: (r' -> r -> r) -> r -> (forall d. Data d => d -> r') -> ShapeLevel -> r # gmapQ :: (forall d. Data d => d -> u) -> ShapeLevel -> [u] # gmapQi :: Int -> (forall d. Data d => d -> u) -> ShapeLevel -> u # gmapM :: Monad m => (forall d. Data d => d -> m d) -> ShapeLevel -> m ShapeLevel # gmapMp :: MonadPlus m => (forall d. Data d => d -> m d) -> ShapeLevel -> m ShapeLevel # gmapMo :: MonadPlus m => (forall d. Data d => d -> m d) -> ShapeLevel -> m ShapeLevel #
Ord ShapeLevel Source #
Instance details Defined in Biobase.Types.Shape Methods compare :: ShapeLevel -> ShapeLevel -> Ordering # (<) :: ShapeLevel -> ShapeLevel -> Bool # (<=) :: ShapeLevel -> ShapeLevel -> Bool # (>) :: ShapeLevel -> ShapeLevel -> Bool # (>=) :: ShapeLevel -> ShapeLevel -> Bool # max :: ShapeLevel -> ShapeLevel -> ShapeLevel # min :: ShapeLevel -> ShapeLevel -> ShapeLevel #
Read ShapeLevel Source #
Instance details Defined in Biobase.Types.Shape Methods readsPrec :: Int -> ReadS ShapeLevel # readList :: ReadS [ShapeLevel] # readPrec :: ReadPrec ShapeLevel # readListPrec :: ReadPrec [ShapeLevel] #
Show ShapeLevel Source #
Instance details Defined in Biobase.Types.Shape Methods showsPrec :: Int -> ShapeLevel -> ShowS # show :: ShapeLevel -> String # showList :: [ShapeLevel] -> ShowS #
Generic ShapeLevel Source #
Instance details Defined in Biobase.Types.Shape Associated Types type Rep ShapeLevel :: Type -> Type # Methods from :: ShapeLevel -> Rep ShapeLevel x # to :: Rep ShapeLevel x -> ShapeLevel #
NFData ShapeLevel Source #
Instance details Defined in Biobase.Types.Shape Methods rnf :: ShapeLevel -> () #
type Rep ShapeLevel Source #
Instance details Defined in Biobase.Types.Shape type Rep ShapeLevel = D1 (MetaData "ShapeLevel" "Biobase.Types.Shape" "BiobaseTypes-0.2.0.1-B9coIbijR6NEFcCxvqIOZp" False) ((C1 (MetaCons "SL1" PrefixI False) (U1 :: Type -> Type) :+: C1 (MetaCons "SL2" PrefixI False) (U1 :: Type -> Type)) :+: (C1 (MetaCons "SL3" PrefixI False) (U1 :: Type -> Type) :+: (C1 (MetaCons "SL4" PrefixI False) (U1 :: Type -> Type) :+: C1 (MetaCons "SL5" PrefixI False) (U1 :: Type -> Type))))

data RNAshape Source #

The type of RNA shapes. Keeps the type

Constructors

RNAshape
Fields _rnashapelevel :: !ShapeLevel The type of shape encoded here. _rnashape :: !ByteString The actual shape as a string.

Instances

Eq RNAshape Source #
Instance details Defined in Biobase.Types.Shape Methods (==) :: RNAshape -> RNAshape -> Bool # (/=) :: RNAshape -> RNAshape -> Bool #
Data RNAshape Source #
Instance details Defined in Biobase.Types.Shape Methods gfoldl :: (forall d b. Data d => c (d -> b) -> d -> c b) -> (forall g. g -> c g) -> RNAshape -> c RNAshape # gunfold :: (forall b r. Data b => c (b -> r) -> c r) -> (forall r. r -> c r) -> Constr -> c RNAshape # toConstr :: RNAshape -> Constr # dataTypeOf :: RNAshape -> DataType # dataCast1 :: Typeable t => (forall d. Data d => c (t d)) -> Maybe (c RNAshape) # dataCast2 :: Typeable t => (forall d e. (Data d, Data e) => c (t d e)) -> Maybe (c RNAshape) # gmapT :: (forall b. Data b => b -> b) -> RNAshape -> RNAshape # gmapQl :: (r -> r' -> r) -> r -> (forall d. Data d => d -> r') -> RNAshape -> r # gmapQr :: (r' -> r -> r) -> r -> (forall d. Data d => d -> r') -> RNAshape -> r # gmapQ :: (forall d. Data d => d -> u) -> RNAshape -> [u] # gmapQi :: Int -> (forall d. Data d => d -> u) -> RNAshape -> u # gmapM :: Monad m => (forall d. Data d => d -> m d) -> RNAshape -> m RNAshape # gmapMp :: MonadPlus m => (forall d. Data d => d -> m d) -> RNAshape -> m RNAshape # gmapMo :: MonadPlus m => (forall d. Data d => d -> m d) -> RNAshape -> m RNAshape #
Ord RNAshape Source #
Instance details Defined in Biobase.Types.Shape Methods compare :: RNAshape -> RNAshape -> Ordering # (<) :: RNAshape -> RNAshape -> Bool # (<=) :: RNAshape -> RNAshape -> Bool # (>) :: RNAshape -> RNAshape -> Bool # (>=) :: RNAshape -> RNAshape -> Bool # max :: RNAshape -> RNAshape -> RNAshape # min :: RNAshape -> RNAshape -> RNAshape #
Read RNAshape Source #
Instance details Defined in Biobase.Types.Shape Methods readsPrec :: Int -> ReadS RNAshape # readList :: ReadS [RNAshape] # readPrec :: ReadPrec RNAshape # readListPrec :: ReadPrec [RNAshape] #
Show RNAshape Source #
Instance details Defined in Biobase.Types.Shape Methods showsPrec :: Int -> RNAshape -> ShowS # show :: RNAshape -> String # showList :: [RNAshape] -> ShowS #
Generic RNAshape Source #
Instance details Defined in Biobase.Types.Shape Associated Types type Rep RNAshape :: Type -> Type # Methods from :: RNAshape -> Rep RNAshape x # to :: Rep RNAshape x -> RNAshape #
NFData RNAshape Source #
Instance details Defined in Biobase.Types.Shape Methods rnf :: RNAshape -> () #
type Rep RNAshape Source #
Instance details Defined in Biobase.Types.Shape type Rep RNAshape = D1 (MetaData "RNAshape" "Biobase.Types.Shape" "BiobaseTypes-0.2.0.1-B9coIbijR6NEFcCxvqIOZp" False) (C1 (MetaCons "RNAshape" PrefixI True) (S1 (MetaSel (Just "_rnashapelevel") NoSourceUnpackedness SourceStrict DecidedStrict) (Rec0 ShapeLevel) :*: S1 (MetaSel (Just "_rnashape") NoSourceUnpackedness SourceStrict DecidedStrict) (Rec0 ByteString)))

rnashapelevel :: Lens' RNAshape ShapeLevel Source #

rnashape :: Lens' RNAshape ByteString Source #

shapeForest :: ShapeLevel -> SPForest ByteString ByteString -> SPForest Char Char Source #

Given a compactified SPForest, creates a shape forest of the given level.

TODO needs newtyping

rnass2shape :: ShapeLevel -> RNAss -> RNAshape Source #

test :: ShapeLevel -> RNAshape Source #

turn into unit test. also reverse of the input should give reverse shape! this then gives a quickcheck test, reversing the input should reverse the shape

TODO requires generating secondary structures via Arbitrary.

shapeForestshape :: ShapeLevel -> SPForest Char Char -> RNAshape Source #

generateShape :: ShapeLevel -> RNAss -> RNAshape Source #

Distance measures on the shape string itself.

data RNAshapepset Source #

Wrapper for string-positional shapes. Intentionally chosen long name.

Constructors

RNAshapepset
Fields _rnashapepsetlevel :: ShapeLevel _rnashapepset :: Set (Int, Int)

Instances

Eq RNAshapepset Source #
Instance details Defined in Biobase.Types.Shape Methods (==) :: RNAshapepset -> RNAshapepset -> Bool # (/=) :: RNAshapepset -> RNAshapepset -> Bool #
Ord RNAshapepset Source #
Instance details Defined in Biobase.Types.Shape Methods compare :: RNAshapepset -> RNAshapepset -> Ordering # (<) :: RNAshapepset -> RNAshapepset -> Bool # (<=) :: RNAshapepset -> RNAshapepset -> Bool # (>) :: RNAshapepset -> RNAshapepset -> Bool # (>=) :: RNAshapepset -> RNAshapepset -> Bool # max :: RNAshapepset -> RNAshapepset -> RNAshapepset # min :: RNAshapepset -> RNAshapepset -> RNAshapepset #
Read RNAshapepset Source #
Instance details Defined in Biobase.Types.Shape Methods readsPrec :: Int -> ReadS RNAshapepset # readList :: ReadS [RNAshapepset] # readPrec :: ReadPrec RNAshapepset # readListPrec :: ReadPrec [RNAshapepset] #
Show RNAshapepset Source #
Instance details Defined in Biobase.Types.Shape Methods showsPrec :: Int -> RNAshapepset -> ShowS # show :: RNAshapepset -> String # showList :: [RNAshapepset] -> ShowS #
Generic RNAshapepset Source #
Instance details Defined in Biobase.Types.Shape Associated Types type Rep RNAshapepset :: Type -> Type # Methods from :: RNAshapepset -> Rep RNAshapepset x # to :: Rep RNAshapepset x -> RNAshapepset #
NFData RNAshapepset Source #
Instance details Defined in Biobase.Types.Shape Methods rnf :: RNAshapepset -> () #
type Rep RNAshapepset Source #
Instance details Defined in Biobase.Types.Shape type Rep RNAshapepset = D1 (MetaData "RNAshapepset" "Biobase.Types.Shape" "BiobaseTypes-0.2.0.1-B9coIbijR6NEFcCxvqIOZp" False) (C1 (MetaCons "RNAshapepset" PrefixI True) (S1 (MetaSel (Just "_rnashapepsetlevel") NoSourceUnpackedness NoSourceStrictness DecidedLazy) (Rec0 ShapeLevel) :*: S1 (MetaSel (Just "_rnashapepset") NoSourceUnpackedness NoSourceStrictness DecidedLazy) (Rec0 (Set (Int, Int)))))

rnashapepsetlevel :: Lens' RNAshapepset ShapeLevel Source #

rnashapepset :: Lens' RNAshapepset (Set (Int, Int)) Source #

rnashapePairSet :: MonadError String m => RNAshape -> m RNAshapepset Source #

Transform an RNAss into a set of base pairs (i,j). The pairs are 0-based.

rnassPairSet' :: RNAshape -> RNAshapepset Source #

RNA pair set, but a transformation error calls error.

shapePairDist :: RNAshapepset -> RNAshapepset -> Int Source #

Calculates the number of different base pairs betwwen two structures.

TODO error out on different shape levels