Uses of Interface
org.biojavax.bio.seq.RichLocation

Packages that use RichLocation

Package	Description
org.biojavax	The Biojava extensions packages, classes that extend the core biojava functionality
org.biojavax.bio.db.biosql	Interface between biojava and biosql databases
org.biojavax.bio.seq	Rich implementations of Sequences, Locations and Features.
org.biojavax.bio.seq.io	Classes to support the I/O of RichSequence and Bioentry objects.

Uses of RichLocation in org.biojavax

Methods in org.biojavax that return RichLocation

Modifier and Type	Method	Description
RichLocation	RankedDocRef.getLocation()	If this object was constructed using a location instead of two integers, then this method will return that location.
RichLocation	SimpleRankedDocRef.getLocation()

Methods in org.biojavax with parameters of type RichLocation

Modifier and Type	Method	Description
void	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 RichLocation

Constructor	Description
SimpleRankedDocRef(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 RichLocation

Modifier and Type	Method	Description
RichLocation	BioSQLFeatureFilter.ContainedByRichLocation.getRichLocation()
RichLocation	BioSQLFeatureFilter.OverlapsRichLocation.getRichLocation()

Constructors in org.biojavax.bio.db.biosql with parameters of type RichLocation

Constructor	Description
ContainedByRichLocation(RichLocation loc)	Creates a filter that returns everything contained within loc.
OverlapsRichLocation(RichLocation 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 RichLocation

Modifier and Type	Class	Description
class	CompoundRichLocation	An implementation of RichLocation which covers multiple locations, but on the same strand of the same (optionally circular) sequence.
class	EmptyRichLocation	An Empty implementation of RichLocation.
class	MultiSourceCompoundRichLocation	An implementation of RichLocation which possibly covers multiple locations, on different strands, different circular lengths, or different sequences.
class	SimpleRichLocation	A simple implementation of RichLocation.

Fields in org.biojavax.bio.seq declared as RichLocation

Modifier and Type	Field	Description
static RichLocation	RichLocation.EMPTY_LOCATION	The empty location matches nothing.

Methods in org.biojavax.bio.seq that return RichLocation

Modifier and Type	Method	Description
static RichLocation	RichLocation.Tools.construct(Collection<Location> members)	Constructs a RichLocation object based on the given collection of members.
static RichLocation	RichLocation.Tools.enrich(Location l)	Attempts to convert a plain Location into a RichLocation.

Methods in org.biojavax.bio.seq with parameters of type RichLocation

Modifier and Type	Method	Description
static 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 RichLocation

Modifier and Type	Method	Description
static 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 RichLocation

Modifier and Type	Method	Description
static String	GenbankLocationParser.writeLocation(RichLocation l)	Writes a location in Genbank format.
static String	UniProtLocationParser.writeLocation(RichLocation l)	Writes a location in UniProt format.