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Bio.Location.SeqLocMap
Contents
Location lookup maps for named sequences Modifying location lookup maps Searching for target locations
Description
Efficient lookup of query positions in a collection of target sequence locations where positions and locations are associated with specific sequence names. This is an extension of LocMap to use locations and positions on named sequences as in SeqLocation.
Synopsis
type SeqLocMap a = OnSeqs (LocMap a)
empty :: SeqLocMap a
fromList :: [(SeqLoc, a)] -> SeqLocMap a
insert :: SeqLoc -> a -> SeqLocMap a -> SeqLocMap a
lookupWithin :: SeqPos -> SeqLocMap a -> [(SeqLoc, a)]
lookupOverlaps :: SeqLoc -> SeqLocMap a -> [(SeqLoc, a)]
Location lookup maps for named sequences
type SeqLocMap a = OnSeqs (LocMap a) | Source
A data structure for efficiently finding target sequence locations (SeqLoc.Loc) that overlap query positions or locations. Each target location can be associated with an arbitrary additional value in the lookup map.
empty :: SeqLocMap a | Source
Empty lookup map.
fromList :: [(SeqLoc, a)] -> SeqLocMap a | Source
Creates a `SeqLocMap` from a list of target locations and their associated objects
Modifying location lookup maps
insert :: SeqLoc -> a -> SeqLocMap a -> SeqLocMap a | Source
Inserts a new target location and associated object into the location lookup map.
Searching for target locations
lookupWithin :: SeqPos -> SeqLocMap a -> [(SeqLoc, a)] | Source
Find the (possibly empty) list of target locations and associated objects that contain a sequence position, in the sense of Loc.isWithin.
lookupOverlaps :: SeqLoc -> SeqLocMap a -> [(SeqLoc, a)] | Source
Find the (possibly empty) list of target locations and associated objects that overlap a sequence location, in the sense of Loc.overlaps.
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