Biobase.Types.Shape

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.

Documentation

data ShapeLevel

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

Defined in Biobase.Types.Shape

Methods

(==) :: ShapeLevel -> ShapeLevel -> Bool

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

Data ShapeLevel

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

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

Defined in Biobase.Types.Shape

Methods

readsPrec :: Int -> ReadS ShapeLevel

readList :: ReadS [ShapeLevel]

readPrec :: ReadPrec ShapeLevel

readListPrec :: ReadPrec [ShapeLevel]

Show ShapeLevel

Defined in Biobase.Types.Shape

Methods

showsPrec :: Int -> ShapeLevel -> ShowS

show :: ShapeLevel -> String

showList :: [ShapeLevel] -> ShowS

Generic ShapeLevel

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

Defined in Biobase.Types.Shape

Methods

rnf :: ShapeLevel -> ()

type Rep ShapeLevel

Defined in Biobase.Types.Shape

type Rep ShapeLevel = D1 (MetaData "ShapeLevel" "Biobase.Types.Shape" "BiobaseTypes-0.1.4.0-2SJmLmHyrafG90Dl3d2I5j" 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

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

Defined in Biobase.Types.Shape

Methods

(==) :: RNAshape -> RNAshape -> Bool

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

Data RNAshape

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

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

Defined in Biobase.Types.Shape

Methods

readsPrec :: Int -> ReadS RNAshape

readList :: ReadS [RNAshape]

readPrec :: ReadPrec RNAshape

readListPrec :: ReadPrec [RNAshape]

Show RNAshape

Defined in Biobase.Types.Shape

Methods

showsPrec :: Int -> RNAshape -> ShowS

show :: RNAshape -> String

showList :: [RNAshape] -> ShowS

Generic RNAshape

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

Defined in Biobase.Types.Shape

Methods

rnf :: RNAshape -> ()

type Rep RNAshape

Defined in Biobase.Types.Shape

type Rep RNAshape = D1 (MetaData "RNAshape" "Biobase.Types.Shape" "BiobaseTypes-0.1.4.0-2SJmLmHyrafG90Dl3d2I5j" 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

rnashape :: Lens' RNAshape ByteString

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

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

TODO needs newtyping

rnass2shape :: ShapeLevel -> RNAss -> RNAshape

test :: ShapeLevel -> RNAshape

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

generateShape :: ShapeLevel -> RNAss -> RNAshape

Distance measures on the shape string itself.

data RNAshapepset

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

Constructors

RNAshapepset

Fields

• _rnashapepsetlevel :: ShapeLevel
• _rnashapepset :: Set (Int, Int)

Instances

Eq RNAshapepset

Defined in Biobase.Types.Shape

Methods

(==) :: RNAshapepset -> RNAshapepset -> Bool

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

Ord RNAshapepset

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

Defined in Biobase.Types.Shape

Methods

readsPrec :: Int -> ReadS RNAshapepset

readList :: ReadS [RNAshapepset]

readPrec :: ReadPrec RNAshapepset

readListPrec :: ReadPrec [RNAshapepset]

Show RNAshapepset

Defined in Biobase.Types.Shape

Methods

showsPrec :: Int -> RNAshapepset -> ShowS

show :: RNAshapepset -> String

showList :: [RNAshapepset] -> ShowS

Generic RNAshapepset

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

Defined in Biobase.Types.Shape

Methods

rnf :: RNAshapepset -> ()

type Rep RNAshapepset

Defined in Biobase.Types.Shape

type Rep RNAshapepset = D1 (MetaData "RNAshapepset" "Biobase.Types.Shape" "BiobaseTypes-0.1.4.0-2SJmLmHyrafG90Dl3d2I5j" 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

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

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

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

rnassPairSet' :: RNAshape -> RNAshapepset

RNA pair set, but a transformation error calls error.

shapePairDist :: RNAshapepset -> RNAshapepset -> Int

Calculates the number of different base pairs betwwen two structures.

TODO error out on different shape levels