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 TypeMethodDescriptionvoidRankedDocRef.setLocation(RichLocation location) Set the location of this reference.voidSimpleRankedDocRef.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 TypeClassDescriptionclassAn implementation of RichLocation which covers multiple locations, but on the same strand of the same (optionally circular) sequence.classAn Empty implementation of RichLocation.classAn implementation of RichLocation which possibly covers multiple locations, on different strands, different circular lengths, or different sequences.classA simple implementation of RichLocation.Fields in org.biojavax.bio.seq declared as RichLocationModifier and TypeFieldDescriptionstatic final RichLocationRichLocation.EMPTY_LOCATIONThe empty location matches nothing.Methods in org.biojavax.bio.seq that return RichLocationModifier and TypeMethodDescriptionstatic RichLocationRichLocation.Tools.construct(Collection<Location> members) Constructs a RichLocation object based on the given collection of members.static RichLocationAttempts 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 RichLocationGenbankLocationParser.parseLocation(Namespace featureNS, String featureAccession, String locationString) Parses a location.static RichLocationUniProtLocationParser.parseLocation(String loc) Parses a location.Methods in org.biojavax.bio.seq.io with parameters of type RichLocationModifier and TypeMethodDescriptionstatic StringGenbankLocationParser.writeLocation(RichLocation l) Writes a location in Genbank format.static StringUniProtLocationParser.writeLocation(RichLocation l) Writes a location in UniProt format.