Biobase.Types.Index

Biological sequence data is oftentimes indexed either 0- or 1-based. The Index type developed provides static guarantees that there is no confusion what index is in use.

This module does not export the ctor Index. If you want to (unsafely) use it, import Biobase.Types.Index.Type directly. Use fromInt0 to make clear that you count from 0 and transform to an Index t. I.e. fromInt0 0 :: Index 1 yields the lowest 1-base index.

Documentation

checkIndex :: forall t. KnownNat t => Index t -> Index t

Uses index to guarantee that the Index is ok.

reIndex :: forall n m. (KnownNat n, KnownNat m) => Index n -> Index m

Re-Index an index of type Index n as Index m. This is always safe, as 0 :: Index 0 gives 1 :: Index 1 for example. I.e. valid indices become valid indices.

(+.) :: forall t. KnownNat t => Index t -> Int -> Index t

Helper function that allows addition of an Index and an Int, with the Int on the right.

unsafePlus :: forall t. KnownNat t => Index t -> Int -> Index t

Unsafe plus.

(-.) :: forall t. KnownNat t => Index t -> Int -> Index t

Helper function that allows subtraction of an Index and an Int, with the Int on the right.

unsafeMinus :: forall t. KnownNat t => Index t -> Int -> Index t

Unsafe minus.

toInt0 :: forall t. KnownNat t => Index t -> Int

Return the index as an Int-style index that is zero-based.

fromInt0 :: forall t. KnownNat t => Int -> Index t

As an index from an Int-style zero-based one.

TODO We might want to check that the argument is [0..].

type I0 = Index 0

Zero-based indices.

type I1 = Index 1

One-based indices.

getIndex :: Index t -> Int

index :: forall t. KnownNat t => Int -> Index t

Turn an Int into an Index safely.

maybeIndex :: forall t. KnownNat t => Int -> Maybe (Index t)

Produce Just and Index or Nothing.

data Index t

A linear Int-based index type.

Instances

Vector Vector (Index t)

MVector MVector (Index t)

Eq (Index t)

KnownNat t => Num (Index t)

Ord (Index t)

Read (Index t)

Show (Index t)

Ix (Index t)

Generic (Index t)

KnownNat t => Index (Index t)

IndexStream (Index t)

Arbitrary (Index t)

ToJSON (Index t)

FromJSON (Index t)

Binary (Index t)

Serialize (Index t)

NFData (Index t)

Hashable (Index t)

Unbox (Index t)

IndexStream z => IndexStream ((:.) z (Index t))

data MVector s0 (Index t0) = MV_Index (MVector s Int)

type Rep (Index t)

data Vector (Index t0) = V_Index (Vector Int)