org.biojava.nbio.core.sequence.location.template

Interface Location

All Superinterfaces:

Accessioned, Iterable<Location>

All Known Subinterfaces:

AccesionedLocation

All Known Implementing Classes:

AbstractLocation, InsdcLocations.BondLocation, InsdcLocations.GroupLocation, InsdcLocations.OneOfLocation, InsdcLocations.OrderLocation, SequenceLocation, SimpleLocation

public interface Location
extends Iterable<Location>, Accessioned

Sets of integers used to represent the location of features on sequence. A location can be a single set of bounds or composed of multiple sub-locations. Each sub-location is a Location and therefore subject to the same rules.

Author:

ayates

Nested Class Summary

Nested Classes

Modifier and Type	Interface and Description
static class	Location.Tools Helper methods for use with the Location classes.

Field Summary

Fields

Modifier and Type	Field and Description
static Location	EMPTY Basic location which is set to the minimum and maximum bounds of Integer.

Method Summary

Methods

Modifier and Type	Method and Description
Point	getEnd() End of the location
int	getLength() Returns the length of the outer bounds of this location
List<Location>	getRelevantSubLocations() An extension to getSubLocations() which returns sub-locations of sub-locations; this will continue until it runs out of those locations.
<C extends Compound> Sequence<C>	getRelevantSubSequence(Sequence<C> sequence) Will return a SequenceReader object which offers a view of all resolved locations i.e.
Point	getStart() Start of the location
Strand	getStrand() Strand which the location is located on
List<Location>	getSubLocations() Gives access to the sub locations for this location.
<C extends Compound> Sequence<C>	getSubSequence(Sequence<C> sequence) Will return a SequenceReader object which represents the outer bounds of this Location
boolean	isBetweenCompounds() Returns true if the position is meant to represent a point between two points such as 78^79.
boolean	isCircular() Indicates if this location is circular.
boolean	isComplex() Returns true if the location is considered to be complex meaning the location is actually composed of sub-locations.

Methods inherited from interface java.lang.Iterable

iterator

Methods inherited from interface org.biojava.nbio.core.sequence.template.Accessioned

getAccession

Field Detail

EMPTY

static final Location EMPTY

Basic location which is set to the minimum and maximum bounds of Integer. Strand is set to Strand.UNDEFINED.

Method Detail

getStart

Point getStart()

Start of the location

getEnd

Point getEnd()

End of the location

getLength

int getLength()

Returns the length of the outer bounds of this location

getStrand

Strand getStrand()

Strand which the location is located on

getSubLocations

List<Location> getSubLocations()

Gives access to the sub locations for this location. However this does not return sub-locations of sub-locations. For that functionality use #getAllSubLocations().

Returns:

A list of a single level of sub-locations

getRelevantSubLocations

List<Location> getRelevantSubLocations()

An extension to getSubLocations() which returns sub-locations of sub-locations; this will continue until it runs out of those locations.

Returns:

List of all sub locations including sub-locations of sub locations

isComplex

boolean isComplex()

Returns true if the location is considered to be complex meaning the location is actually composed of sub-locations.

isCircular

boolean isCircular()

Indicates if this location is circular.

isBetweenCompounds

boolean isBetweenCompounds()

Returns true if the position is meant to represent a point between two points such as 78^79. Only valid if start and stop are next to each other.

getSubSequence

<C extends Compound> Sequence<C> getSubSequence(Sequence<C> sequence)

Will return a SequenceReader object which represents the outer bounds of this Location

Parameters:

<C> - The type of compound to use

sequence - The sequence object to work with

Returns:

The sequence

getRelevantSubSequence

<C extends Compound> Sequence<C> getRelevantSubSequence(Sequence<C> sequence)

Will return a SequenceReader object which offers a view of all resolved locations i.e. those locations which are not complex and define the true Sequence represented

Parameters:

<C> - The type of compound to use

sequence - The sequence object to work with

Returns:

The full assembled sequence