Uses of Class
org.biojava.nbio.genome.parsers.gff.Location

Packages that use Location

Package	Description
org.biojava.nbio.genome.parsers.gff

Uses of Location in org.biojava.nbio.genome.parsers.gff

Methods in org.biojava.nbio.genome.parsers.gff that return Location

Modifier and Type	Method and Description
Location	FeatureList.bounds() The union of all locations of all features in this list, mapped to the positive strand.
Location	Location.downstream(int length) Return the adjacent location of specified length directly downstream of this location.
static Location	Location.fromBio(int start, int end, char strand) Create location from "biocoordinates", as in GFF file.
static Location	Location.fromBioExt(int start, int length, char strand, int totalLength) Create a location from MAF file coordinates, which represent negative strand locations as the distance from the end of the sequence.
Location	Location.intersection(Location other) Return the intersection, or null if no overlap.
Location	FeatureI.location() Get the location of the feature.
Location	Feature.location() Get location of feature.
Location	Location.minus() Return location that is in same position on negative strand.
Location	LocIterator.next() Get next window of default size, then increment position by default amount.
Location	LocIterator.next(int windowSize, int increment) Get next window of specified size, then increment position by specified amount.
Location	Location.opposite() Return location that is in same position on opposite strand.
Location	Location.plus() Return location that is in same position on plus strand.
Location	Location.prefix(int position) The part of this location before the specified position.
Location	Location.prefix(Location other) The part of this location before the other location (not inclusive).
Location	LocIterator.remainder() Get portion of bounding location that has not yet been retrieved by next() method.
Location	Location.suffix(int position) The part of this location after the specified position.
Location	Location.suffix(Location other) The part of this location after the other location (not inclusive).
Location	Location.union(Location other) Return the union.
Location	Location.upstream(int length) Return the adjacent location of specified length directly upstream of this location.

Methods in org.biojava.nbio.genome.parsers.gff that return types with arguments of type Location

Modifier and Type	Method and Description
java.lang.Iterable<Location>	Location.window(int windowSize, int increment) Enable a "sliding window" iteration over a location to use with Java's "for" loop construct.

Methods in org.biojava.nbio.genome.parsers.gff with parameters of type Location

Modifier and Type	Method and Description
boolean	Location.contains(Location other) Check if this location contains the other.
int	Location.distance(Location other) Return distance between this location and the other location.
boolean	Location.endsAfter(Location other) Check if this location ends after other location ends.
boolean	Location.endsBefore(Location other) Check if this location ends before other location ends.
Location	Location.intersection(Location other) Return the intersection, or null if no overlap.
boolean	Location.isAfter(Location other) Check if this location is entirely after the other location (no overlap).
boolean	Location.isBefore(Location other) Check if this location is entirely before other location (no overlap).
boolean	Location.isSameStrand(Location other) Check if this location is on same strand as other location.
FeatureList	FeatureList.omitOverlapping(java.lang.String seqname, Location location, boolean useBothStrands) Create a list of all features that do not overlap the specified location on the specified sequence.
boolean	Location.overlaps(Location other) Check if this location and other location overlap.
double	Location.percentOverlap(Location other) Return percent overlap of two locations.
Location	Location.prefix(Location other) The part of this location before the other location (not inclusive).
FeatureList	FeatureList.selectOverlapping(java.lang.String seqname, Location location, boolean useBothStrands) Create a list of all features that overlap the specified location on the specified sequence.
boolean	Location.startsAfter(Location other) Check if this location starts after the other location starts.
boolean	Location.startsBefore(Location other) Check if this location starts before other location starts.
Location	Location.suffix(Location other) The part of this location after the other location (not inclusive).
Location	Location.union(Location other) Return the union.

Constructors in org.biojava.nbio.genome.parsers.gff with parameters of type Location

Constructor and Description
Feature(java.lang.String seqname, java.lang.String source, java.lang.String type, Location location, java.lang.Double score, int frame, java.lang.String attributes) Construct a new Feature from raw data (usually a GFF row).
Location(Location other) Clone other location.
LocIterator(Location bounds, int windowSize, int increment) Construct an iterator that slides a window over a Location.