Biobase.Primary.Hashed

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.

Documentation

newtype HashedPrimary t

The hash of a primary sequence.

Constructors

HashedPrimary

Fields

• unHashedPrimary :: Int

Instances

Vector Vector (HashedPrimary a0)

Methods

basicUnsafeFreeze :: PrimMonad m => Mutable Vector (PrimState m) (HashedPrimary a0) -> m (Vector (HashedPrimary a0))

basicUnsafeThaw :: PrimMonad m => Vector (HashedPrimary a0) -> m (Mutable Vector (PrimState m) (HashedPrimary a0))

basicLength :: Vector (HashedPrimary a0) -> Int

basicUnsafeSlice :: Int -> Int -> Vector (HashedPrimary a0) -> Vector (HashedPrimary a0)

basicUnsafeIndexM :: Monad m => Vector (HashedPrimary a0) -> Int -> m (HashedPrimary a0)

basicUnsafeCopy :: PrimMonad m => Mutable Vector (PrimState m) (HashedPrimary a0) -> Vector (HashedPrimary a0) -> m ()

elemseq :: Vector (HashedPrimary a0) -> HashedPrimary a0 -> b -> b

MVector MVector (HashedPrimary a0)

Methods

basicLength :: MVector s (HashedPrimary a0) -> Int

basicUnsafeSlice :: Int -> Int -> MVector s (HashedPrimary a0) -> MVector s (HashedPrimary a0)

basicOverlaps :: MVector s (HashedPrimary a0) -> MVector s (HashedPrimary a0) -> Bool

basicUnsafeNew :: PrimMonad m => Int -> m (MVector (PrimState m) (HashedPrimary a0))

basicInitialize :: PrimMonad m => MVector (PrimState m) (HashedPrimary a0) -> m ()

basicUnsafeReplicate :: PrimMonad m => Int -> HashedPrimary a0 -> m (MVector (PrimState m) (HashedPrimary a0))

basicUnsafeRead :: PrimMonad m => MVector (PrimState m) (HashedPrimary a0) -> Int -> m (HashedPrimary a0)

basicUnsafeWrite :: PrimMonad m => MVector (PrimState m) (HashedPrimary a0) -> Int -> HashedPrimary a0 -> m ()

basicClear :: PrimMonad m => MVector (PrimState m) (HashedPrimary a0) -> m ()

basicSet :: PrimMonad m => MVector (PrimState m) (HashedPrimary a0) -> HashedPrimary a0 -> m ()

basicUnsafeCopy :: PrimMonad m => MVector (PrimState m) (HashedPrimary a0) -> MVector (PrimState m) (HashedPrimary a0) -> m ()

basicUnsafeMove :: PrimMonad m => MVector (PrimState m) (HashedPrimary a0) -> MVector (PrimState m) (HashedPrimary a0) -> m ()

basicUnsafeGrow :: PrimMonad m => MVector (PrimState m) (HashedPrimary a0) -> Int -> m (MVector (PrimState m) (HashedPrimary a0))

Bounded (HashedPrimary t)

Methods

minBound :: HashedPrimary t

maxBound :: HashedPrimary t

Enum (HashedPrimary t)

Methods

succ :: HashedPrimary t -> HashedPrimary t

pred :: HashedPrimary t -> HashedPrimary t

toEnum :: Int -> HashedPrimary t

fromEnum :: HashedPrimary t -> Int

enumFrom :: HashedPrimary t -> [HashedPrimary t]

enumFromThen :: HashedPrimary t -> HashedPrimary t -> [HashedPrimary t]

enumFromTo :: HashedPrimary t -> HashedPrimary t -> [HashedPrimary t]

enumFromThenTo :: HashedPrimary t -> HashedPrimary t -> HashedPrimary t -> [HashedPrimary t]

Eq (HashedPrimary t)

Methods

(==) :: HashedPrimary t -> HashedPrimary t -> Bool

(/=) :: HashedPrimary t -> HashedPrimary t -> Bool

Ord (HashedPrimary t)

Methods

compare :: HashedPrimary t -> HashedPrimary t -> Ordering

(<) :: HashedPrimary t -> HashedPrimary t -> Bool

(<=) :: HashedPrimary t -> HashedPrimary t -> Bool

(>) :: HashedPrimary t -> HashedPrimary t -> Bool

(>=) :: HashedPrimary t -> HashedPrimary t -> Bool

max :: HashedPrimary t -> HashedPrimary t -> HashedPrimary t

min :: HashedPrimary t -> HashedPrimary t -> HashedPrimary t

Read (HashedPrimary t)

Methods

readsPrec :: Int -> ReadS (HashedPrimary t)

readList :: ReadS [HashedPrimary t]

readPrec :: ReadPrec (HashedPrimary t)

readListPrec :: ReadPrec [HashedPrimary t]

Show (HashedPrimary t)

Methods

showsPrec :: Int -> HashedPrimary t -> ShowS

show :: HashedPrimary t -> String

showList :: [HashedPrimary t] -> ShowS

Ix (HashedPrimary t)

Methods

range :: (HashedPrimary t, HashedPrimary t) -> [HashedPrimary t]

index :: (HashedPrimary t, HashedPrimary t) -> HashedPrimary t -> Int

unsafeIndex :: (HashedPrimary t, HashedPrimary t) -> HashedPrimary t -> Int

inRange :: (HashedPrimary t, HashedPrimary t) -> HashedPrimary t -> Bool

rangeSize :: (HashedPrimary t, HashedPrimary t) -> Int

unsafeRangeSize :: (HashedPrimary t, HashedPrimary t) -> Int

Unbox (HashedPrimary a0)

data MVector s (HashedPrimary a0)

data MVector s (HashedPrimary a0) = MV_HashedPrimary (MVector s Int)

data Vector (HashedPrimary a0)

data Vector (HashedPrimary a0) = V_HashedPrimary (Vector Int)

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

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

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

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