Safe Haskell	None
Language	Haskell2010

Biobase.Primary.Hashed

Description

Fast hash functions for Primary sequences. This function maps primary sequences to a continuous set of Ints [0 ..] where the maximum is dependent on the input length. This allows us to map short sequences into contiguous memory locations. Useful for, say, energy lookup tables.

Synopsis

newtype HashedPrimary t n = HashedPrimary {
- unHashedPrimary :: Int
}
mkHashedPrimary :: forall t n. (Unbox (Letter t n), Bounded (Letter t n), Enum (Letter t n)) => Primary t n -> HashedPrimary t n
hash2primary :: forall t n. (Unbox (Letter t n), Bounded (Letter t n), Enum (Letter t n)) => HashedPrimary t n -> Primary t n

Documentation

newtype HashedPrimary t n Source #

The hash of a primary sequence.

Constructors

HashedPrimary
Fields unHashedPrimary :: Int

Instances

Vector Vector (HashedPrimary t n) Source #
Instance details Defined in Biobase.Primary.Hashed Methods basicUnsafeFreeze :: PrimMonad m => Mutable Vector (PrimState m) (HashedPrimary t n) -> m (Vector (HashedPrimary t n)) # basicUnsafeThaw :: PrimMonad m => Vector (HashedPrimary t n) -> m (Mutable Vector (PrimState m) (HashedPrimary t n)) # basicLength :: Vector (HashedPrimary t n) -> Int # basicUnsafeSlice :: Int -> Int -> Vector (HashedPrimary t n) -> Vector (HashedPrimary t n) # basicUnsafeIndexM :: Monad m => Vector (HashedPrimary t n) -> Int -> m (HashedPrimary t n) # basicUnsafeCopy :: PrimMonad m => Mutable Vector (PrimState m) (HashedPrimary t n) -> Vector (HashedPrimary t n) -> m () # elemseq :: Vector (HashedPrimary t n) -> HashedPrimary t n -> b -> b #
MVector MVector (HashedPrimary t n) Source #
Instance details Defined in Biobase.Primary.Hashed Methods basicLength :: MVector s (HashedPrimary t n) -> Int # basicUnsafeSlice :: Int -> Int -> MVector s (HashedPrimary t n) -> MVector s (HashedPrimary t n) # basicOverlaps :: MVector s (HashedPrimary t n) -> MVector s (HashedPrimary t n) -> Bool # basicUnsafeNew :: PrimMonad m => Int -> m (MVector (PrimState m) (HashedPrimary t n)) # basicInitialize :: PrimMonad m => MVector (PrimState m) (HashedPrimary t n) -> m () # basicUnsafeReplicate :: PrimMonad m => Int -> HashedPrimary t n -> m (MVector (PrimState m) (HashedPrimary t n)) # basicUnsafeRead :: PrimMonad m => MVector (PrimState m) (HashedPrimary t n) -> Int -> m (HashedPrimary t n) # basicUnsafeWrite :: PrimMonad m => MVector (PrimState m) (HashedPrimary t n) -> Int -> HashedPrimary t n -> m () # basicClear :: PrimMonad m => MVector (PrimState m) (HashedPrimary t n) -> m () # basicSet :: PrimMonad m => MVector (PrimState m) (HashedPrimary t n) -> HashedPrimary t n -> m () # basicUnsafeCopy :: PrimMonad m => MVector (PrimState m) (HashedPrimary t n) -> MVector (PrimState m) (HashedPrimary t n) -> m () # basicUnsafeMove :: PrimMonad m => MVector (PrimState m) (HashedPrimary t n) -> MVector (PrimState m) (HashedPrimary t n) -> m () # basicUnsafeGrow :: PrimMonad m => MVector (PrimState m) (HashedPrimary t n) -> Int -> m (MVector (PrimState m) (HashedPrimary t n)) #
Bounded (HashedPrimary t n) Source #
Instance details Defined in Biobase.Primary.Hashed Methods minBound :: HashedPrimary t n # maxBound :: HashedPrimary t n #
Enum (HashedPrimary t n) Source #
Instance details Defined in Biobase.Primary.Hashed Methods succ :: HashedPrimary t n -> HashedPrimary t n # pred :: HashedPrimary t n -> HashedPrimary t n # toEnum :: Int -> HashedPrimary t n # fromEnum :: HashedPrimary t n -> Int # enumFrom :: HashedPrimary t n -> [HashedPrimary t n] # enumFromThen :: HashedPrimary t n -> HashedPrimary t n -> [HashedPrimary t n] # enumFromTo :: HashedPrimary t n -> HashedPrimary t n -> [HashedPrimary t n] # enumFromThenTo :: HashedPrimary t n -> HashedPrimary t n -> HashedPrimary t n -> [HashedPrimary t n] #
Eq (HashedPrimary t n) Source #
Instance details Defined in Biobase.Primary.Hashed Methods (==) :: HashedPrimary t n -> HashedPrimary t n -> Bool # (/=) :: HashedPrimary t n -> HashedPrimary t n -> Bool #
Ord (HashedPrimary t n) Source #
Instance details Defined in Biobase.Primary.Hashed Methods compare :: HashedPrimary t n -> HashedPrimary t n -> Ordering # (<) :: HashedPrimary t n -> HashedPrimary t n -> Bool # (<=) :: HashedPrimary t n -> HashedPrimary t n -> Bool # (>) :: HashedPrimary t n -> HashedPrimary t n -> Bool # (>=) :: HashedPrimary t n -> HashedPrimary t n -> Bool # max :: HashedPrimary t n -> HashedPrimary t n -> HashedPrimary t n # min :: HashedPrimary t n -> HashedPrimary t n -> HashedPrimary t n #
Read (HashedPrimary t n) Source #
Instance details Defined in Biobase.Primary.Hashed Methods readsPrec :: Int -> ReadS (HashedPrimary t n) # readList :: ReadS [HashedPrimary t n] # readPrec :: ReadPrec (HashedPrimary t n) # readListPrec :: ReadPrec [HashedPrimary t n] #
Show (HashedPrimary t n) Source #
Instance details Defined in Biobase.Primary.Hashed Methods showsPrec :: Int -> HashedPrimary t n -> ShowS # show :: HashedPrimary t n -> String # showList :: [HashedPrimary t n] -> ShowS #
Ix (HashedPrimary t n) Source #
Instance details Defined in Biobase.Primary.Hashed Methods range :: (HashedPrimary t n, HashedPrimary t n) -> [HashedPrimary t n] # index :: (HashedPrimary t n, HashedPrimary t n) -> HashedPrimary t n -> Int # unsafeIndex :: (HashedPrimary t n, HashedPrimary t n) -> HashedPrimary t n -> Int inRange :: (HashedPrimary t n, HashedPrimary t n) -> HashedPrimary t n -> Bool # rangeSize :: (HashedPrimary t n, HashedPrimary t n) -> Int # unsafeRangeSize :: (HashedPrimary t n, HashedPrimary t n) -> Int
Unbox (HashedPrimary t n) Source #
Instance details Defined in Biobase.Primary.Hashed
newtype MVector s (HashedPrimary t n) Source #
Instance details Defined in Biobase.Primary.Hashed newtype MVector s (HashedPrimary t n) = MV_HashedPrimary (MVector s Int)
newtype Vector (HashedPrimary t n) Source #
Instance details Defined in Biobase.Primary.Hashed newtype Vector (HashedPrimary t n) = V_HashedPrimary (Vector Int)

mkHashedPrimary :: forall t n. (Unbox (Letter t n), Bounded (Letter t n), Enum (Letter t n)) => Primary t n -> HashedPrimary t n Source #

Given a piece of primary sequence information, reduce it to an index. The empty input produces an index of 0.

hash2primary :: forall t n. (Unbox (Letter t n), Bounded (Letter t n), Enum (Letter t n)) => HashedPrimary t n -> Primary t n Source #

Turn a hash back into a sequence. Will fail if the resulting sequence has more than 100 elements.