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 n

The hash of a primary sequence.

Constructors

HashedPrimary

Fields

• unHashedPrimary :: Int

Instances

Vector Vector (HashedPrimary t n)

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)

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)

Defined in Biobase.Primary.Hashed

Methods

minBound :: HashedPrimary t n

maxBound :: HashedPrimary t n

Enum (HashedPrimary t n)

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)

Defined in Biobase.Primary.Hashed

Methods

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

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

Ord (HashedPrimary t n)

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)

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)

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)

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)

Defined in Biobase.Primary.Hashed

newtype MVector s (HashedPrimary t n)

Defined in Biobase.Primary.Hashed

newtype MVector s (HashedPrimary t n) = MV_HashedPrimary (MVector s Int)

newtype Vector (HashedPrimary t n)

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

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

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