Uses of Interface
org.biojava3.core.sequence.location.template.Location

Packages that use Location

org.biojava3.core.sequence.location
org.biojava3.core.sequence.location.template

Uses of Location in org.biojava3.core.sequence.location

Classes in org.biojava3.core.sequence.location that implement Location

static class	InsdcLocations.BondLocation Used to represent bond locations equivalent to bond(7,8) or bond(7).
static class	InsdcLocations.GroupLocation Deprecated in INSDC yet still appears; equivalent to the order() directive except no 5' to 3' ordering is defined.
static class	InsdcLocations.OneOfLocation Deprecated in INSDC; refers to a set of locations of which one location could be valid e.g. one-of(location, location, location).
static class	InsdcLocations.OrderLocation Used to describe a 5' to 3' ordering but no firm assurance it is correct
class	SequenceLocation<S extends AbstractSequence<C>,C extends Compound> A location in a sequence that keeps a reference to its parent sequence
class	SimpleLocation Very basic implementation of the Location interface which defines a series of simple constructors.

Methods in org.biojava3.core.sequence.location that return Location

static Location	LocationHelper.circularLocation(int start, int end, Strand strand, int length) Converts a location which defines the outer bounds of a circular location and splits it into the required portions.
static Location	LocationHelper.getMax(List<Location> locations) Scans through a list of locations to find the Location with the highest end
static Location	LocationHelper.getMin(List<Location> locations) Scans through a list of locations to find the Location with the lowest start
static Location	LocationHelper.location(int start, int end, Strand strand, int length) Returns a location object which unlike the location constructors allows you to input reverse coordinates and will convert these into the right location on the positive strand.
static Location	LocationHelper.location(List<Location> subLocations) Used as a thin wrapper to the LocationHelper.location(java.util.List, java.lang.String) method to bring the given location list together as a join (the default type)
static Location	LocationHelper.location(List<Location> subLocations, String type) Builds a location from a List of locations; this can be circular or linear joins.
Location	InsdcParser.parse(Reader reader) Reader based version of the parse methods.
Location	InsdcParser.parse(String locationString) Main method for parsing a location from a String instance
protected Location	InsdcParser.parseLocation(String location, Strand strand)
protected Location	InsdcParser.parseRange(Matcher matcher, Strand strand)
protected Location	InsdcParser.parseSingle(Matcher matcher, Strand strand)

Methods in org.biojava3.core.sequence.location that return types with arguments of type Location

protected List<Location>

InsdcParser.parse(Reader reader, Strand strand)

Method parameters in org.biojava3.core.sequence.location with type arguments of type Location

static boolean	LocationHelper.consistentAccessions(List<Location> subLocations) Scans a list of locations and returns true if all the given locations are linked to the same sequence.
static boolean	LocationHelper.detectCicular(List<Location> subLocations) Loops through the given list of locations and returns true if it looks like they represent a circular location.
static Point	LocationHelper.detectEnd(List<Location> subLocations, boolean isCircular) This will attempt to find what the last point is and returns that position.
static Point	LocationHelper.detectStart(List<Location> subLocations) Assumes that the first element is the start & clones it
static Strand	LocationHelper.detectStrand(List<Location> subLocations) Loops through the given list of locations and returns the consensus Strand class.
static Location	LocationHelper.getMax(List<Location> locations) Scans through a list of locations to find the Location with the highest end
static Location	LocationHelper.getMin(List<Location> locations) Scans through a list of locations to find the Location with the lowest start
static Location	LocationHelper.location(List<Location> subLocations) Used as a thin wrapper to the LocationHelper.location(java.util.List, java.lang.String) method to bring the given location list together as a join (the default type)
static Location	LocationHelper.location(List<Location> subLocations, String type) Builds a location from a List of locations; this can be circular or linear joins.

Constructors in org.biojava3.core.sequence.location with parameters of type Location

InsdcLocations.BondLocation(Location... subLocations)

InsdcLocations.GroupLocation(int start, int end, Strand strand, Location... subLocations)

InsdcLocations.GroupLocation(Point start, Point end, Strand strand, boolean circular, Location... subLocations)

InsdcLocations.GroupLocation(Point start, Point end, Strand strand, Location... subLocations)

InsdcLocations.OneOfLocation(Location... locations)

InsdcLocations.OrderLocation(int start, int end, Strand strand, Location... subLocations)

InsdcLocations.OrderLocation(Point start, Point end, Strand strand, boolean circular, Location... subLocations)

InsdcLocations.OrderLocation(Point start, Point end, Strand strand, Location... subLocations)

SimpleLocation(int start, int end, Strand strand, Location... subLocations)

SimpleLocation(Point start, Point end, Strand strand, boolean circular, Location... subLocations)

SimpleLocation(Point start, Point end, Strand strand, Location... subLocations)

Constructor parameters in org.biojava3.core.sequence.location with type arguments of type Location

InsdcLocations.BondLocation(List<Location> subLocations)

InsdcLocations.GroupLocation(int start, int end, Strand strand, List<Location> subLocations)

InsdcLocations.GroupLocation(Point start, Point end, Strand strand, boolean circular, List<Location> subLocations)

InsdcLocations.GroupLocation(Point start, Point end, Strand strand, List<Location> subLocations)

InsdcLocations.OneOfLocation(List<Location> locations)

InsdcLocations.OrderLocation(int start, int end, Strand strand, List<Location> subLocations)

InsdcLocations.OrderLocation(Point start, Point end, Strand strand, boolean circular, List<Location> subLocations)

InsdcLocations.OrderLocation(Point start, Point end, Strand strand, List<Location> subLocations)

SimpleLocation(Point start, Point end, Strand strand, boolean circular, boolean betweenBases, List<Location> subLocations)

SimpleLocation(Point start, Point end, Strand strand, boolean circular, List<Location> subLocations)

Uses of Location in org.biojava3.core.sequence.location.template

Subinterfaces of Location in org.biojava3.core.sequence.location.template

interface

AccesionedLocation A location which is bound to an AccessionID.

Classes in org.biojava3.core.sequence.location.template that implement Location

class

AbstractLocation Base abstraction of a location which encodes for the majority of important features about a location such as the start, end and strand

Fields in org.biojava3.core.sequence.location.template declared as Location

static Location

Location.EMPTY Basic location which is set to the minimum and maximum bounds of Integer.

Methods in org.biojava3.core.sequence.location.template that return Location

static Location	Location.Tools.circularLocation(int start, int end, Strand strand, int length) Converts a location which defines the outer bounds of a circular location and splits it into the required portions.
static Location	Location.Tools.getMax(List<Location> locations) Scans through a list of locations to find the Location with the highest end
static Location	Location.Tools.getMin(List<Location> locations) Scans through a list of locations to find the Location with the lowest start
static Location	Location.Tools.location(int start, int end, Strand strand, int length) Returns a location object which unlike the location constructors allows you to input reverse coordinates and will convert these into the right location on the positive strand.
static Location	Location.Tools.location(List<Location> locations, Integer sequenceLength, String type) Used for building a location from a series of sub-locations

Methods in org.biojava3.core.sequence.location.template that return types with arguments of type Location

List<Location>	Location.getRelevantSubLocations() An extension to getSubLocations() which returns sub-locations of sub-locations; this will continue until it runs out of those locations.
List<Location>	AbstractLocation.getRelevantSubLocations() Returns the normalised list of sub locations i.e. only those locations which do not have a sub location.
List<Location>	Location.getSubLocations() Gives access to the sub locations for this location.
List<Location>	AbstractLocation.getSubLocations()
Iterator<Location>	AbstractLocation.iterator() Iterates through all known sub-locations for this location but does not descend

Method parameters in org.biojava3.core.sequence.location.template with type arguments of type Location

static Location	Location.Tools.getMax(List<Location> locations) Scans through a list of locations to find the Location with the highest end
static Location	Location.Tools.getMin(List<Location> locations) Scans through a list of locations to find the Location with the lowest start
static Location	Location.Tools.location(List<Location> locations, Integer sequenceLength, String type) Used for building a location from a series of sub-locations
protected void	AbstractLocation.setSubLocations(List<Location> subLocations)

Constructor parameters in org.biojava3.core.sequence.location.template with type arguments of type Location

AbstractLocation(Point start, Point end, Strand strand, boolean circular, boolean betweenCompounds, AccessionID accession, List<Location> subLocations)
Default constructor

AbstractLocation(Point start, Point end, Strand strand, boolean circular, boolean betweenCompounds, List<Location> subLocations)
Default constructor