Uses of Interface org.biojava.nbio.core.sequence.location.template.Location (biojava-core 6.0.0 API)

Packages that use Location
Package	Description
org.biojava.nbio.core.alignment
org.biojava.nbio.core.alignment.template
org.biojava.nbio.core.sequence.location
org.biojava.nbio.core.sequence.location.template

Uses of Location in org.biojava.nbio.core.alignment

Methods in org.biojava.nbio.core.alignment that return Location
Modifier and Type Method Description

Location SimpleAlignedSequence.getLocationInAlignment()

Methods in org.biojava.nbio.core.alignment with parameters of type Location
Modifier and Type Method Description

ProfileView<S,C> SimpleProfile.getSubProfile(Location location)

Uses of Location in org.biojava.nbio.core.alignment.template

Methods in org.biojava.nbio.core.alignment.template that return Location
Modifier and Type	Method	Description
`Location`	AlignedSequence.`getLocationInAlignment()`	Returns the `Location` of the original `Sequence` within an alignment.

Methods in org.biojava.nbio.core.alignment.template with parameters of type Location
Modifier and Type	Method	Description
`ProfileView<S,C>`	Profile.`getSubProfile(Location location)`	Returns a `ProfileView` windowed to contain only the given `Location`.
`void`	MutableAlignedSequence.`setLocationInAlignment(Location location)`	Sets the position of the `AlignedSequence` to the given `Location` (start, gaps, end).
`void`	MutableAlignedSequence.`shiftAtAlignmentLocation(Location location, int shift)`	Slides a part of the `AlignedSequence`.
`void`	MutableAlignedSequence.`shiftAtSequenceLocation(Location location, int shift)`	Slides a part of the `AlignedSequence`.

Uses of Location in org.biojava.nbio.core.sequence.location

Classes in org.biojava.nbio.core.sequence.location that implement Location
Modifier and Type	Class	Description
`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.
`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.biojava.nbio.core.sequence.location that return Location
Modifier and Type	Method	Description
`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(String locationString)`	Main method for parsing a location from a String instance

Method parameters in org.biojava.nbio.core.sequence.location with type arguments of type Location
Modifier and Type	Method	Description
`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.biojava.nbio.core.sequence.location with parameters of type Location
Constructor	Description
`BondLocation(Location... subLocations)`
`GroupLocation(boolean isCircular, Location... subLocations)`
`GroupLocation(int start, int end, Strand strand, Location... subLocations)`
`GroupLocation(Location... subLocations)`
`GroupLocation(Point start, Point end, Strand strand, boolean circular, Location... subLocations)`
`GroupLocation(Point start, Point end, Strand strand, Location... subLocations)`
`OneOfLocation(Location... locations)`
`OrderLocation(int start, int end, Strand strand, Location... subLocations)`
`OrderLocation(Location... subLocations)`
`OrderLocation(Point start, Point end, Strand strand, boolean circular, Location... subLocations)`
`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.biojava.nbio.core.sequence.location with type arguments of type Location
Constructor	Description
`BondLocation(List<Location> subLocations)`
`GroupLocation(int start, int end, Strand strand, List<Location> subLocations)`
`GroupLocation(List<Location> subLocations)`
`GroupLocation(Point start, Point end, Strand strand, boolean circular, List<Location> subLocations)`
`GroupLocation(Point start, Point end, Strand strand, List<Location> subLocations)`
`OneOfLocation(List<Location> locations)`
`OrderLocation(int start, int end, Strand strand, List<Location> subLocations)`
`OrderLocation(List<Location> subLocations)`
`OrderLocation(Point start, Point end, Strand strand, boolean circular, List<Location> subLocations)`
`OrderLocation(Point start, Point end, Strand strand, List<Location> subLocations)`
`SequenceLocation(int start, int end, S sequence, Strand strand, boolean circular, List<Location> subLocations)`
`SimpleLocation(int start, int 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)`
`SimpleLocation(Point start, Point end, Strand strand, List<Location> subLocations)`

Uses of Location in org.biojava.nbio.core.sequence.location.template

Subinterfaces of Location in org.biojava.nbio.core.sequence.location.template
Modifier and Type	Interface	Description
`interface`	`AccesionedLocation`	A location which is bound to an AccessionID.

Classes in org.biojava.nbio.core.sequence.location.template that implement Location
Modifier and Type	Class	Description
`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.biojava.nbio.core.sequence.location.template declared as Location
Modifier and Type	Field	Description
`static Location`	Location.`EMPTY`	Basic location which is set to the minimum and maximum bounds of `Integer`.

Methods in org.biojava.nbio.core.sequence.location.template that return Location
Modifier and Type	Method	Description
`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.biojava.nbio.core.sequence.location.template that return types with arguments of type Location
Modifier and Type	Method	Description
`List<Location>`	AbstractLocation.`getRelevantSubLocations()`	Returns the normalised list of sub locations i.e.
`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.`getSubLocations()`
`List<Location>`	Location.`getSubLocations()`	Gives access to the sub locations for this location.
`Iterator<Location>`	AbstractLocation.`iterator()`	Iterates through all known sub-locations for this location but does not descend

Method parameters in org.biojava.nbio.core.sequence.location.template with type arguments of type Location
Modifier and Type	Method	Description
`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
`void`	AbstractLocation.`setSubLocations(List<Location> subLocations)`

Constructor parameters in org.biojava.nbio.core.sequence.location.template with type arguments of type Location
Constructor	Description
`AbstractLocation(Point start, Point end, Strand strand, boolean circular, boolean betweenCompounds, List<Location> subLocations)`	Default constructor
`AbstractLocation(Point start, Point end, Strand strand, boolean circular, boolean betweenCompounds, AccessionID accession, List<Location> subLocations)`	Default constructor