Uses of Interface
org.biojavax.bio.seq.RichLocation
Packages that use RichLocation
Package
Description
The Biojava extensions packages, classes that extend the core biojava
functionality
Interface between biojava and biosql databases
Rich implementations of Sequences, Locations and Features.
Classes to support the I/O of RichSequence and
Bioentry objects.
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Uses of RichLocation in org.biojavax
Methods in org.biojavax that return RichLocationModifier and TypeMethodDescriptionRankedDocRef.getLocation()
If this object was constructed using a location instead of two integers, then this method will return that location.SimpleRankedDocRef.getLocation()
Methods in org.biojavax with parameters of type RichLocationModifier and TypeMethodDescriptionvoid
RankedDocRef.setLocation
(RichLocation location) Set the location of this reference.void
SimpleRankedDocRef.setLocation
(RichLocation location) Set the location of this reference.Constructors in org.biojavax with parameters of type RichLocationModifierConstructorDescriptionSimpleRankedDocRef
(DocRef docref, RichLocation location, int rank) Constructs a new docref for a given location. -
Uses of RichLocation in org.biojavax.bio.db.biosql
Methods in org.biojavax.bio.db.biosql that return RichLocationModifier and TypeMethodDescriptionBioSQLFeatureFilter.ContainedByRichLocation.getRichLocation()
BioSQLFeatureFilter.OverlapsRichLocation.getRichLocation()
Constructors in org.biojavax.bio.db.biosql with parameters of type RichLocationModifierConstructorDescriptionCreates a filter that returns everything contained within loc.Creates a filter that returns everything overlapping loc. -
Uses of RichLocation in org.biojavax.bio.seq
Classes in org.biojavax.bio.seq that implement RichLocationModifier and TypeClassDescriptionclass
An implementation of RichLocation which covers multiple locations, but on the same strand of the same (optionally circular) sequence.class
An Empty implementation of RichLocation.class
An implementation of RichLocation which possibly covers multiple locations, on different strands, different circular lengths, or different sequences.class
A simple implementation of RichLocation.Fields in org.biojavax.bio.seq declared as RichLocationModifier and TypeFieldDescriptionstatic final RichLocation
RichLocation.EMPTY_LOCATION
The empty location matches nothing.Methods in org.biojavax.bio.seq that return RichLocationModifier and TypeMethodDescriptionstatic RichLocation
RichLocation.Tools.construct
(Collection<Location> members) Constructs a RichLocation object based on the given collection of members.static RichLocation
Attempts to convert a plain Location into a RichLocation.Methods in org.biojavax.bio.seq with parameters of type RichLocationModifier and TypeMethodDescriptionstatic Collection
<Location> RichLocation.Tools.flatten
(RichLocation location) Takes a location and returns the set of all members. -
Uses of RichLocation in org.biojavax.bio.seq.io
Methods in org.biojavax.bio.seq.io that return RichLocationModifier and TypeMethodDescriptionstatic RichLocation
GenbankLocationParser.parseLocation
(Namespace featureNS, String featureAccession, String locationString) Parses a location.static RichLocation
UniProtLocationParser.parseLocation
(String loc) Parses a location.Methods in org.biojavax.bio.seq.io with parameters of type RichLocationModifier and TypeMethodDescriptionstatic String
GenbankLocationParser.writeLocation
(RichLocation l) Writes a location in Genbank format.static String
UniProtLocationParser.writeLocation
(RichLocation l) Writes a location in UniProt format.