Biobase.Secondary.Vienna

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

Documentation

newtype ViennaPair

Use machine Ints internally

Constructors

ViennaPair

Fields

• unViennaPair :: Int

Instances

Bounded ViennaPair

Defined in Biobase.Secondary.Vienna

Methods

minBound :: ViennaPair

maxBound :: ViennaPair

Enum ViennaPair

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

Defined in Biobase.Secondary.Vienna

Methods

(==) :: ViennaPair -> ViennaPair -> Bool

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

Ord ViennaPair

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

Defined in Biobase.Secondary.Vienna

Methods

readsPrec :: Int -> ReadS ViennaPair

readList :: ReadS [ViennaPair]

readPrec :: ReadPrec ViennaPair

readListPrec :: ReadPrec [ViennaPair]

Show ViennaPair

Defined in Biobase.Secondary.Vienna

Methods

showsPrec :: Int -> ViennaPair -> ShowS

show :: ViennaPair -> String

showList :: [ViennaPair] -> ShowS

Ix ViennaPair

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

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

Defined in Biobase.Secondary.Vienna

Associated Types

data LimitType ViennaPair

Methods

linearIndex :: LimitType ViennaPair -> ViennaPair -> Int

fromLinearIndex :: LimitType ViennaPair -> Int -> ViennaPair

size :: LimitType ViennaPair -> Int

inBounds :: LimitType ViennaPair -> ViennaPair -> Bool

zeroBound :: ViennaPair

zeroBound' :: LimitType ViennaPair

totalSize :: LimitType ViennaPair -> [Integer]

showBound :: LimitType ViennaPair -> [String]

showIndex :: ViennaPair -> [String]

IndexStream ViennaPair

Defined in Biobase.Secondary.Vienna

Methods

streamUp :: forall (m :: Type -> Type). Monad m => LimitType ViennaPair -> LimitType ViennaPair -> Stream m ViennaPair

streamDown :: forall (m :: Type -> Type). Monad m => LimitType ViennaPair -> LimitType ViennaPair -> Stream m ViennaPair

ToJSON ViennaPair

Defined in Biobase.Secondary.Vienna

Methods

toJSON :: ViennaPair -> Value

toEncoding :: ViennaPair -> Encoding

toJSONList :: [ViennaPair] -> Value

toEncodingList :: [ViennaPair] -> Encoding

FromJSON ViennaPair

Defined in Biobase.Secondary.Vienna

Methods

parseJSON :: Value -> Parser ViennaPair

parseJSONList :: Value -> Parser [ViennaPair]

Binary ViennaPair

Defined in Biobase.Secondary.Vienna

Methods

put :: ViennaPair -> Put

get :: Get ViennaPair

putList :: [ViennaPair] -> Put

Serialize ViennaPair

Defined in Biobase.Secondary.Vienna

Methods

put :: Putter ViennaPair

get :: Get ViennaPair

Unbox ViennaPair

Defined in Biobase.Secondary.Vienna

Vector Vector ViennaPair

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

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

Defined in Biobase.Secondary.Convert

Methods

basepairConvert :: Basepair -> ViennaPair

BasepairConvert ViennaPair Basepair

Defined in Biobase.Secondary.Convert

Methods

basepairConvert :: ViennaPair -> Basepair

BasepairConvert ViennaPair (Letter RNA n, Letter RNA n)

Defined in Biobase.Secondary.Convert

Methods

basepairConvert :: ViennaPair -> (Letter RNA n, Letter RNA n)

IndexStream z => IndexStream (z :. ViennaPair)

Defined in Biobase.Secondary.Vienna

Methods

streamUp :: forall (m :: Type -> Type). Monad m => LimitType (z :. ViennaPair) -> LimitType (z :. ViennaPair) -> Stream m (z :. ViennaPair)

streamDown :: forall (m :: Type -> Type). Monad m => LimitType (z :. ViennaPair) -> LimitType (z :. ViennaPair) -> Stream m (z :. ViennaPair)

BasepairConvert (Letter RNA n, Letter RNA n) ViennaPair

Defined in Biobase.Secondary.Convert

Methods

basepairConvert :: (Letter RNA n, Letter RNA n) -> ViennaPair

type Rep ViennaPair

Defined in Biobase.Secondary.Vienna

type Rep ViennaPair = D1 ('MetaData "ViennaPair" "Biobase.Secondary.Vienna" "BiobaseXNA-0.11.1.1-HHobpxD2PHgJEMZxJBnKQo" 'True) (C1 ('MetaCons "ViennaPair" 'PrefixI 'True) (S1 ('MetaSel ('Just "unViennaPair") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 Int)))

data LimitType ViennaPair

Defined in Biobase.Secondary.Vienna

data LimitType ViennaPair

• = Canonical
• | Extended

newtype Vector ViennaPair

Defined in Biobase.Secondary.Vienna

newtype Vector ViennaPair = V_ViennaPair (Vector Int)

newtype MVector s ViennaPair

Defined in Biobase.Secondary.Vienna

newtype MVector s ViennaPair = MV_ViennaPair (MVector s 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

Non-standard base pair

pattern Undef :: ViennaPair

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

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

revPair :: ViennaPair -> ViennaPair

reverse a vienna pair

Convenience structures

cguaP :: [ViennaPair]

cgnsP :: [ViennaPair]

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