Biobase.Primary.Hashed

Fast hash functions for Primary sequences. A hash is just an Int, so use these only for short sequences.

Documentation

newtype HashedPrimary

Constructors

HashedPrimary Int

Instances

Bounded HashedPrimary

Enum HashedPrimary

Eq HashedPrimary

Ord HashedPrimary

Read HashedPrimary

Show HashedPrimary

Ix HashedPrimary

Prim HashedPrimary

Unbox HashedPrimary

Vector Vector HashedPrimary

MVector MVector HashedPrimary

mkHashedPrimary :: (Nuc, Nuc) -> Primary -> HashedPrimary

Given a piece of primary sequence information, reduce it to an index.

Will throw an assertion in debug code if ps are not within bounds. Note that mkPrimary [minBound] and mkPrimary [minBound,minBound] map to the same index. Meaning that indices are only unique within the same length group. Furthermore, indices with different (l,u)-bounds are not compatible with each other. All indices start at 0.

The empty input produces an index of 0.

TODO currently goes the very inefficient way of creating a temporary vector for ps. We could in O(1) create a vector from a Primary ...