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 a)

MVector MVector (HashedPrimary a)

Bounded (HashedPrimary t)

Enum (HashedPrimary t)

Eq (HashedPrimary t)

Ord (HashedPrimary t)

Read (HashedPrimary t)

Show (HashedPrimary t)

Ix (HashedPrimary t)

Unbox (HashedPrimary a)

data MVector s0 (HashedPrimary a0) = MV_HashedPrimary (MVector s Int)

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.