Bio.Chain

Documentation

class (Ixed m, Enum (Index m)) => ChainLike m where

Chain-like sequence, by default it is an array or a list

Minimal complete definition

bounds, assocs, modify, modifyBefore, modifyAfter

Methods

bounds :: m -> (Index m, Index m)

assocs :: m -> [(Index m, IxValue m)]

modify :: Index m -> (IxValue m -> IxValue m) -> m -> m

modifyBefore :: Index m -> (IxValue m -> IxValue m) -> m -> m

modifyAfter :: Index m -> (IxValue m -> IxValue m) -> m -> m

unsafeRead :: m -> Index m -> IxValue m

Instances

ChainLike [a]

Defined in Bio.Chain

Methods

bounds :: [a] -> (Index [a], Index [a])

assocs :: [a] -> [(Index [a], IxValue [a])]

modify :: Index [a] -> (IxValue [a] -> IxValue [a]) -> [a] -> [a]

modifyBefore :: Index [a] -> (IxValue [a] -> IxValue [a]) -> [a] -> [a]

modifyAfter :: Index [a] -> (IxValue [a] -> IxValue [a]) -> [a] -> [a]

unsafeRead :: [a] -> Index [a] -> IxValue [a]

ChainLike (Vector a)

Defined in Bio.Chain

Methods

bounds :: Vector a -> (Index (Vector a), Index (Vector a))

assocs :: Vector a -> [(Index (Vector a), IxValue (Vector a))]

modify :: Index (Vector a) -> (IxValue (Vector a) -> IxValue (Vector a)) -> Vector a -> Vector a

modifyBefore :: Index (Vector a) -> (IxValue (Vector a) -> IxValue (Vector a)) -> Vector a -> Vector a

modifyAfter :: Index (Vector a) -> (IxValue (Vector a) -> IxValue (Vector a)) -> Vector a -> Vector a

unsafeRead :: Vector a -> Index (Vector a) -> IxValue (Vector a)

(Ix i, Enum i) => ChainLike (Array i a)

Defined in Bio.Chain

Methods

bounds :: Array i a -> (Index (Array i a), Index (Array i a))

assocs :: Array i a -> [(Index (Array i a), IxValue (Array i a))]

modify :: Index (Array i a) -> (IxValue (Array i a) -> IxValue (Array i a)) -> Array i a -> Array i a

modifyBefore :: Index (Array i a) -> (IxValue (Array i a) -> IxValue (Array i a)) -> Array i a -> Array i a

modifyAfter :: Index (Array i a) -> (IxValue (Array i a) -> IxValue (Array i a)) -> Array i a -> Array i a

unsafeRead :: Array i a -> Index (Array i a) -> IxValue (Array i a)

(Ix i, Enum i) => ChainLike (ProteinChain i a)

Defined in Bio.Protein.Chain

Methods

bounds :: ProteinChain i a -> (Index (ProteinChain i a), Index (ProteinChain i a))

assocs :: ProteinChain i a -> [(Index (ProteinChain i a), IxValue (ProteinChain i a))]

modify :: Index (ProteinChain i a) -> (IxValue (ProteinChain i a) -> IxValue (ProteinChain i a)) -> ProteinChain i a -> ProteinChain i a

modifyBefore :: Index (ProteinChain i a) -> (IxValue (ProteinChain i a) -> IxValue (ProteinChain i a)) -> ProteinChain i a -> ProteinChain i a

modifyAfter :: Index (ProteinChain i a) -> (IxValue (ProteinChain i a) -> IxValue (ProteinChain i a)) -> ProteinChain i a -> ProteinChain i a

unsafeRead :: ProteinChain i a -> Index (ProteinChain i a) -> IxValue (ProteinChain i a)

(Ix i, Enum i) => ChainLike (NucleicAcidChain i a)

Defined in Bio.NucleicAcid.Chain

Methods

bounds :: NucleicAcidChain i a -> (Index (NucleicAcidChain i a), Index (NucleicAcidChain i a))

assocs :: NucleicAcidChain i a -> [(Index (NucleicAcidChain i a), IxValue (NucleicAcidChain i a))]

modify :: Index (NucleicAcidChain i a) -> (IxValue (NucleicAcidChain i a) -> IxValue (NucleicAcidChain i a)) -> NucleicAcidChain i a -> NucleicAcidChain i a

modifyBefore :: Index (NucleicAcidChain i a) -> (IxValue (NucleicAcidChain i a) -> IxValue (NucleicAcidChain i a)) -> NucleicAcidChain i a -> NucleicAcidChain i a

modifyAfter :: Index (NucleicAcidChain i a) -> (IxValue (NucleicAcidChain i a) -> IxValue (NucleicAcidChain i a)) -> NucleicAcidChain i a -> NucleicAcidChain i a

unsafeRead :: NucleicAcidChain i a -> Index (NucleicAcidChain i a) -> IxValue (NucleicAcidChain i a)

type Chain i a = Array i a

chain :: Ix i => (i, i) -> [(i, a)] -> Chain i a

Construct new chain from list

fromList :: [a] -> Chain Int a

Construct new int-labeled chain from list

(!) :: Ix i => Array i e -> i -> e infixl 9

The value at the given index in an array.

(//) :: Ix i => Array i e -> [(i, e)] -> Array i e infixl 9

Constructs an array identical to the first argument except that it has been updated by the associations in the right argument. For example, if m is a 1-origin, n by n matrix, then

m//[((i,i), 0) | i <- [1..n]]

is the same matrix, except with the diagonal zeroed.

Repeated indices in the association list are handled as for array: Haskell 2010 specifies that the resulting array is undefined (i.e. bottom), but GHC's implementation uses the last association for each index.