Safe Haskell	None
Language	Haskell2010

Biobase.Secondary.Vienna

Contents

Convenience structures

Description

Encoding of Watson-Crick and Wobble Pairs in the Vienna RNA package style.

Synopsis

newtype ViennaPair = ViennaPair {
- unViennaPair :: Int
}
pattern NP :: ViennaPair
pattern CG :: ViennaPair
pattern GC :: ViennaPair
pattern GU :: ViennaPair
pattern UG :: ViennaPair
pattern AU :: ViennaPair
pattern UA :: ViennaPair
pattern NS :: ViennaPair
pattern Undef :: ViennaPair
isViennaPair :: Letter RNA m -> Letter RNA n -> Bool
viennaPairTable :: Unboxed ((Z :. Letter RNA n) :. Letter RNA n) ViennaPair
revPair :: ViennaPair -> ViennaPair
cguaP :: [ViennaPair]
cgnsP :: [ViennaPair]
pairToString :: [(ViennaPair, [Char])]

Documentation

newtype ViennaPair Source #

Use machine Ints internally

Constructors

ViennaPair
Fields unViennaPair :: Int

Instances

Bounded ViennaPair Source #
Instance details Defined in Biobase.Secondary.Vienna Methods minBound :: ViennaPair # maxBound :: ViennaPair #
Enum ViennaPair Source #
Instance details Defined in Biobase.Secondary.Vienna Methods succ :: ViennaPair -> ViennaPair # pred :: ViennaPair -> ViennaPair # toEnum :: Int -> ViennaPair # fromEnum :: ViennaPair -> Int # enumFrom :: ViennaPair -> [ViennaPair] # enumFromThen :: ViennaPair -> ViennaPair -> [ViennaPair] # enumFromTo :: ViennaPair -> ViennaPair -> [ViennaPair] # enumFromThenTo :: ViennaPair -> ViennaPair -> ViennaPair -> [ViennaPair] #
Eq ViennaPair Source #
Instance details Defined in Biobase.Secondary.Vienna Methods (==) :: ViennaPair -> ViennaPair -> Bool # (/=) :: ViennaPair -> ViennaPair -> Bool #
Ord ViennaPair Source #
Instance details Defined in Biobase.Secondary.Vienna Methods compare :: ViennaPair -> ViennaPair -> Ordering # (<) :: ViennaPair -> ViennaPair -> Bool # (<=) :: ViennaPair -> ViennaPair -> Bool # (>) :: ViennaPair -> ViennaPair -> Bool # (>=) :: ViennaPair -> ViennaPair -> Bool # max :: ViennaPair -> ViennaPair -> ViennaPair # min :: ViennaPair -> ViennaPair -> ViennaPair #
Read ViennaPair Source #
Instance details Defined in Biobase.Secondary.Vienna Methods readsPrec :: Int -> ReadS ViennaPair # readList :: ReadS [ViennaPair] # readPrec :: ReadPrec ViennaPair # readListPrec :: ReadPrec [ViennaPair] #
Show ViennaPair Source #
Instance details Defined in Biobase.Secondary.Vienna Methods showsPrec :: Int -> ViennaPair -> ShowS # show :: ViennaPair -> String # showList :: [ViennaPair] -> ShowS #
Ix ViennaPair Source #
Instance details Defined in Biobase.Secondary.Vienna Methods range :: (ViennaPair, ViennaPair) -> [ViennaPair] # index :: (ViennaPair, ViennaPair) -> ViennaPair -> Int # unsafeIndex :: (ViennaPair, ViennaPair) -> ViennaPair -> Int inRange :: (ViennaPair, ViennaPair) -> ViennaPair -> Bool # rangeSize :: (ViennaPair, ViennaPair) -> Int # unsafeRangeSize :: (ViennaPair, ViennaPair) -> Int
Generic ViennaPair Source #
Instance details Defined in Biobase.Secondary.Vienna Associated Types type Rep ViennaPair :: Type -> Type # Methods from :: ViennaPair -> Rep ViennaPair x # to :: Rep ViennaPair x -> ViennaPair #
Index ViennaPair Source #
Instance details Defined in Biobase.Secondary.Vienna Associated Types data LimitType ViennaPair :: Type # Methods linearIndex :: LimitType ViennaPair -> ViennaPair -> Int # size :: LimitType ViennaPair -> Int # inBounds :: LimitType ViennaPair -> ViennaPair -> Bool # zeroBound :: ViennaPair # zeroBound' :: LimitType ViennaPair # totalSize :: LimitType ViennaPair -> [Integer] #
IndexStream ViennaPair Source #
Instance details Defined in Biobase.Secondary.Vienna Methods streamUp :: Monad m => LimitType ViennaPair -> LimitType ViennaPair -> Stream m ViennaPair # streamDown :: Monad m => LimitType ViennaPair -> LimitType ViennaPair -> Stream m ViennaPair #
ToJSON ViennaPair Source #
Instance details Defined in Biobase.Secondary.Vienna Methods toJSON :: ViennaPair -> Value # toEncoding :: ViennaPair -> Encoding # toJSONList :: [ViennaPair] -> Value # toEncodingList :: [ViennaPair] -> Encoding #
FromJSON ViennaPair Source #
Instance details Defined in Biobase.Secondary.Vienna Methods parseJSON :: Value -> Parser ViennaPair # parseJSONList :: Value -> Parser [ViennaPair] #
Binary ViennaPair Source #
Instance details Defined in Biobase.Secondary.Vienna Methods put :: ViennaPair -> Put # get :: Get ViennaPair # putList :: [ViennaPair] -> Put #
Serialize ViennaPair Source #
Instance details Defined in Biobase.Secondary.Vienna Methods put :: Putter ViennaPair # get :: Get ViennaPair #
Unbox ViennaPair Source #
Instance details Defined in Biobase.Secondary.Vienna
Vector Vector ViennaPair Source #
Instance details Defined in Biobase.Secondary.Vienna Methods basicUnsafeFreeze :: PrimMonad m => Mutable Vector (PrimState m) ViennaPair -> m (Vector ViennaPair) # basicUnsafeThaw :: PrimMonad m => Vector ViennaPair -> m (Mutable Vector (PrimState m) ViennaPair) # basicLength :: Vector ViennaPair -> Int # basicUnsafeSlice :: Int -> Int -> Vector ViennaPair -> Vector ViennaPair # basicUnsafeIndexM :: Monad m => Vector ViennaPair -> Int -> m ViennaPair # basicUnsafeCopy :: PrimMonad m => Mutable Vector (PrimState m) ViennaPair -> Vector ViennaPair -> m () # elemseq :: Vector ViennaPair -> ViennaPair -> b -> b #
MVector MVector ViennaPair Source #
Instance details Defined in Biobase.Secondary.Vienna Methods basicLength :: MVector s ViennaPair -> Int # basicUnsafeSlice :: Int -> Int -> MVector s ViennaPair -> MVector s ViennaPair # basicOverlaps :: MVector s ViennaPair -> MVector s ViennaPair -> Bool # basicUnsafeNew :: PrimMonad m => Int -> m (MVector (PrimState m) ViennaPair) # basicInitialize :: PrimMonad m => MVector (PrimState m) ViennaPair -> m () # basicUnsafeReplicate :: PrimMonad m => Int -> ViennaPair -> m (MVector (PrimState m) ViennaPair) # basicUnsafeRead :: PrimMonad m => MVector (PrimState m) ViennaPair -> Int -> m ViennaPair # basicUnsafeWrite :: PrimMonad m => MVector (PrimState m) ViennaPair -> Int -> ViennaPair -> m () # basicClear :: PrimMonad m => MVector (PrimState m) ViennaPair -> m () # basicSet :: PrimMonad m => MVector (PrimState m) ViennaPair -> ViennaPair -> m () # basicUnsafeCopy :: PrimMonad m => MVector (PrimState m) ViennaPair -> MVector (PrimState m) ViennaPair -> m () # basicUnsafeMove :: PrimMonad m => MVector (PrimState m) ViennaPair -> MVector (PrimState m) ViennaPair -> m () # basicUnsafeGrow :: PrimMonad m => MVector (PrimState m) ViennaPair -> Int -> m (MVector (PrimState m) ViennaPair) #
BasepairConvert Basepair ViennaPair Source #
Instance details Defined in Biobase.Secondary.Convert Methods basepairConvert :: Basepair -> ViennaPair Source #
BasepairConvert ViennaPair Basepair Source #
Instance details Defined in Biobase.Secondary.Convert Methods basepairConvert :: ViennaPair -> Basepair Source #
BasepairConvert ViennaPair (Letter RNA n, Letter RNA n) Source #
Instance details Defined in Biobase.Secondary.Convert Methods basepairConvert :: ViennaPair -> (Letter RNA n, Letter RNA n) Source #
IndexStream z => IndexStream (z :. ViennaPair) Source #
Instance details Defined in Biobase.Secondary.Vienna Methods streamUp :: Monad m => LimitType (z :. ViennaPair) -> LimitType (z :. ViennaPair) -> Stream m (z :. ViennaPair) # streamDown :: Monad m => LimitType (z :. ViennaPair) -> LimitType (z :. ViennaPair) -> Stream m (z :. ViennaPair) #
BasepairConvert (Letter RNA n, Letter RNA n) ViennaPair Source #
Instance details Defined in Biobase.Secondary.Convert Methods basepairConvert :: (Letter RNA n, Letter RNA n) -> ViennaPair Source #
type Rep ViennaPair Source #
Instance details Defined in Biobase.Secondary.Vienna type Rep ViennaPair = D1 (MetaData "ViennaPair" "Biobase.Secondary.Vienna" "BiobaseXNA-0.11.0.0-6sSV7wA2ZNJ62zYFxZDZpd" True) (C1 (MetaCons "ViennaPair" PrefixI True) (S1 (MetaSel (Just "unViennaPair") NoSourceUnpackedness NoSourceStrictness DecidedLazy) (Rec0 Int)))
data LimitType ViennaPair Source #
Instance details Defined in Biobase.Secondary.Vienna data LimitType ViennaPair = Canonical \| Extended
newtype Vector ViennaPair Source #
Instance details Defined in Biobase.Secondary.Vienna newtype Vector ViennaPair = V_ViennaPair (Vector Int)
newtype MVector s ViennaPair Source #
Instance details Defined in Biobase.Secondary.Vienna newtype MVector s ViennaPair = MV_ViennaPair (MVector s Int)

pattern NP :: ViennaPair Source #

pattern CG :: ViennaPair Source #

pattern GC :: ViennaPair Source #

pattern GU :: ViennaPair Source #

pattern UG :: ViennaPair Source #

pattern AU :: ViennaPair Source #

pattern UA :: ViennaPair Source #

pattern NS :: ViennaPair Source #

Non-standard base pair

pattern Undef :: ViennaPair Source #

isViennaPair :: Letter RNA m -> Letter RNA n -> Bool Source #

viennaPairTable :: Unboxed ((Z :. Letter RNA n) :. Letter RNA n) ViennaPair Source #

revPair :: ViennaPair -> ViennaPair Source #

reverse a vienna pair

Convenience structures

cguaP :: [ViennaPair] Source #

cgnsP :: [ViennaPair] Source #

pairToString :: [(ViennaPair, [Char])] Source #