bio-0.4.6: A bioinformatics library Source code Contents Index

Bio.Location.OnSeq

Contents Data types Utility functions Sequence collections indexed by name

Description

Data types for functorially lifting sequence positions and locations onto named sequences. These are useful for taking functions that work with sequence positions and locations and associating them specific, named sequences.

Synopsis

type SeqName = SeqData data OnSeq a = OnSeq { onSeqName :: !SeqName onSeqObj :: !a } withSeqData :: Monad m => (SeqData -> a -> m b) -> (SeqName -> m SeqData) -> OnSeq a -> m b andSameSeq :: (a -> b -> Bool) -> OnSeq a -> OnSeq b -> Bool onSameSeq :: (Error e, MonadError e m) => (a -> b -> m c) -> OnSeq a -> OnSeq b -> m c type OnSeqs a = Map SeqName a perSeq :: Monoid b => (a -> b -> c) -> OnSeq a -> OnSeqs b -> c perSeqUpdate :: Monoid b => (a -> b -> b) -> OnSeq a -> OnSeqs b -> OnSeqs b withNameAndSeq :: Monad m => (SeqName -> a -> b -> m c) -> OnSeq a -> OnSeqs b -> m c

Data types

type SeqName = SeqData Source

Sequence name, as in a Sequence

data OnSeq a Source

Data type for an object associated with a specific, named sequence Constructors OnSeq onSeqName :: !SeqName onSeqObj :: !a Instances Functor OnSeq Eq a => Eq (OnSeq a) Ord a => Ord (OnSeq a) Show a => Show (OnSeq a)

Utility functions

withSeqData Source

:: Monad m => SeqData -> a -> m b Function using sequence data -> SeqName -> m SeqData Lookup sequence by name -> OnSeq a Object with named sequence -> m b Looks up a sequence by name and applies a function to it

andSameSeq :: (a -> b -> Bool) -> OnSeq a -> OnSeq b -> Bool Source

Tests a predicate when two objects are on the same sequence, returning False if they are on different sequences.

onSameSeq :: (Error e, MonadError e m) => (a -> b -> m c) -> OnSeq a -> OnSeq b -> m c Source

Performs an action when two objects are on the same sequence and produces an error otherwise.

Sequence collections indexed by name

type OnSeqs a = Map SeqName a Source

Data type for a collection of objects indexed by sequence name

perSeq :: Monoid b => (a -> b -> c) -> OnSeq a -> OnSeqs b -> c Source

Lifts a function on an underlying object to look up the sequence name in a name-indexed collection.

perSeqUpdate :: Monoid b => (a -> b -> b) -> OnSeq a -> OnSeqs b -> OnSeqs b Source

Lifts a function that updates an underlying object to look up the named sequence and update a named-index collection.

withNameAndSeq :: Monad m => (SeqName -> a -> b -> m c) -> OnSeq a -> OnSeqs b -> m c Source

Lifts a function on underlying objects to look up a sequence in a name-indexed collection

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