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

Packages that use RichLocation

org.biojavax	The Biojava extensions packages, classes that extend the core biojava functionality
org.biojavax.bio.db.biosql
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

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

protected void

SimpleRankedDocRef.setLocation(RichLocation location)

Constructors in org.biojavax with parameters of type RichLocation

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

RichLocation	BioSQLFeatureFilter.ContainedByRichLocation.getRichLocation()
RichLocation	BioSQLFeatureFilter.OverlapsRichLocation.getRichLocation()

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

BioSQLFeatureFilter.ContainedByRichLocation(RichLocation loc)
Creates a filter that returns everything contained within loc.

BioSQLFeatureFilter.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

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

static RichLocation

RichLocation.EMPTY_LOCATION The empty location matches nothing.

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

static RichLocation	RichLocation.Tools.construct(Collection 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

static Collection

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

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

static String	GenbankLocationParser.writeLocation(RichLocation l) Writes a location in Genbank format.
static String	UniProtLocationParser.writeLocation(RichLocation l) Writes a location in UniProt format.