Uses of Interface
org.biojava.bio.symbol.Location

Packages that use Location

Package	Description
org.biojava.bio	The core classes that will be used throughout the bio packages.
org.biojava.bio.alignment	Classes to generate and describe sequence alignments.
org.biojava.bio.dp	HMM and Dynamic Programming Algorithms.
org.biojava.bio.gui.sequence	Graphical displays of biological sequences and associated annotations.
org.biojava.bio.program.xff	Event-driven parsing system for the Extensible Feature Format (XFF).
org.biojava.bio.seq	Classes and interfaces for defining biological sequences and informatics objects.
org.biojava.bio.seq.homol	The classes and interfaces for defining sequence similarity and honology.
org.biojava.bio.seq.impl	Standard in-memory implementations of Sequence and Feature.
org.biojava.bio.seq.io	Classes and interfaces for processing and producing flat-file representations of sequences.
org.biojava.bio.seq.io.agave	Classes for converting between AGAVE XML and BioJava objects.
org.biojava.bio.seq.io.game	Event-driven parsing system for the Gene Annotation Markup Elements (GAME).
org.biojava.bio.seq.projection	Code for projecting Feature objects and systematically altering their properties.
org.biojava.bio.symbol	Representation of the Symbols that make up a sequence, and locations within them.
org.biojavax.bio.seq	Rich implementations of Sequences, Locations and Features.

Uses of Location in org.biojava.bio

Fields in org.biojava.bio declared as Location

Modifier and Type	Field	Description
static Location	CardinalityConstraint.ANY	The property can have any number of values, including none.
static Location	CardinalityConstraint.NONE	This cardinality contains no intengers, not even zero.
static Location	CardinalityConstraint.ONE	The property should have exactly one value.
static Location	CardinalityConstraint.ONE_OR_MORE	The property should have one or more values.
static Location	CardinalityConstraint.ZERO	The property should have zero values.
static Location	CardinalityConstraint.ZERO_OR_ONE	The property should have zero or one values.

Methods in org.biojava.bio that return Location

Modifier and Type	Method	Description
Location	CollectionConstraint.AllValuesIn.getCardinalityConstraint()	Get the cardinality constraint used to validate the number of property values.
Location	CollectionConstraint.Contains.getCardinalityConstraint()	Get the cardinality constraint used to validate the number of property values.

Methods in org.biojava.bio with parameters of type Location

Modifier and Type	Method	Description
void	AnnotationType.Abstract.setConstraints(Object key, PropertyConstraint pc, Location cc)
void	AnnotationType.setConstraints(Object key, PropertyConstraint con, Location card)	Set the constraints associated with a property.
void	AnnotationType.Abstract.setDefaultConstraints(PropertyConstraint pc, Location cc)
void	AnnotationType.setDefaultConstraints(PropertyConstraint pc, Location cc)	Set the constraints that will apply to all properties without an explicitly defined set of constraints.

Constructors in org.biojava.bio with parameters of type Location

Constructor	Description
AllValuesIn(PropertyConstraint pc, Location card)	Create an AllValuesIn based upon a PropertyConstraint and a cardinality.
Contains(PropertyConstraint pc, Location card)	Create a Contains based upon a PropertyConstraint and a cardinality.
Impl(PropertyConstraint defaultPC, Location defaultCC)	Create a new Impl with a default property and cardinality constraint.

Uses of Location in org.biojava.bio.alignment

Fields in org.biojava.bio.alignment declared as Location

Modifier and Type	Field	Description
protected Location	FlexibleAlignment.alignmentRange
protected Location	SimpleAlignmentElement.loc

Methods in org.biojava.bio.alignment that return Location

Modifier and Type	Method	Description
Location	AlignmentElement.getLoc()
Location	SimpleAlignmentElement.getLoc()
Location	AbstractULAlignment.SubULAlignment.locInAlignment(Object label)	The location of an individual SymbolList relative to overall Alignment
Location	FlexibleAlignment.locInAlignment(Object label)	The location of an individual SymbolList relative to overall Alignment
Location	UnequalLengthAlignment.locInAlignment(Object label)	The location of an individual SymbolList relative to overall Alignment
protected Location	FlexibleAlignment.locInSeq(Object label, Location viewLoc)

Methods in org.biojava.bio.alignment with parameters of type Location

Modifier and Type	Method	Description
List<String>	AbstractULAlignment.labelsInRange(Location loc)
List<String>	AbstractULAlignment.SubULAlignment.labelsInRange(Location loc)
List<String>	UnequalLengthAlignment.labelsInRange(Location loc)	Returns list of all the labels that intersect that range
protected Location	FlexibleAlignment.locInSeq(Object label, Location viewLoc)
void	AlignmentElement.setLoc(Location nLoc)
void	SimpleAlignmentElement.setLoc(Location nLoc)
void	EditableAlignment.shiftAtAlignmentLoc(Object label, Location loc, int offset)	loc in this case is the Alignment Location
void	FlexibleAlignment.shiftAtAlignmentLoc(Object label, Location loc, int offset)	loc in this case is the Alignment Location
void	EditableAlignment.shiftAtSequenceLoc(Object label, Location loc, int offset)	loc in this case is the SymbolList Location
void	FlexibleAlignment.shiftAtSequenceLoc(Object label, Location loc, int offset)	loc in this case is the SymbolList Location
Alignment	AbstractULAlignment.subAlignment(Set<String> labels, Location loc)	Retrieves a subalignment specified by the location.
Alignment	AbstractULAlignment.SubULAlignment.subAlignment(Set<String> labels, Location loc)
Alignment	Alignment.subAlignment(Set<String> labels, Location loc)	Make a view onto this alignment.
Alignment	SimpleAlignment.subAlignment(Set<String> labels, Location loc)

Constructors in org.biojava.bio.alignment with parameters of type Location

Constructor	Description
SimpleAlignmentElement(String label, SymbolList seq, Location loc)
SubULAlignment(Set<String> labels, Location loc)

Uses of Location in org.biojava.bio.dp

Methods in org.biojava.bio.dp with parameters of type Location

Modifier and Type	Method	Description
Alignment	SimpleStatePath.subAlignment(Set labels, Location loc)

Uses of Location in org.biojava.bio.gui.sequence

Methods in org.biojava.bio.gui.sequence that return Location

Modifier and Type	Method	Description
static Location	GUITools.getVisibleRange(SequenceRenderContext src, Graphics2D g2)

Methods in org.biojava.bio.gui.sequence with parameters of type Location

Modifier and Type	Method	Description
void	SixFrameRenderer.renderLocation(Graphics2D g, SequenceRenderContext src, Location loc)	Render another "exon" in the correct translation frame.

Uses of Location in org.biojava.bio.program.xff

Methods in org.biojava.bio.program.xff with parameters of type Location

Modifier and Type	Method	Description
protected abstract void	LocationHandlerBase.setLocationValue(Location l)	Override this method to do something useful with the location we collect.

Uses of Location in org.biojava.bio.seq

Fields in org.biojava.bio.seq declared as Location

Modifier and Type	Field	Description
Location	ComponentFeature.Template.componentLocation
Location	Feature.Template.location

Methods in org.biojava.bio.seq that return Location

Modifier and Type	Method	Description
static Location	FilterUtils.extractOverlappingLocation(FeatureFilter ff)	Try to determine the minimal location which all features matching a given filter must overlap.
Location	ComponentFeature.getComponentLocation()	Return a location which identifies a portion of the component sequence which is to be included in the assembly.
Location	Feature.getLocation()	The location of this feature.
Location	FeatureFilter.ContainedByLocation.getLocation()
Location	FeatureFilter.OverlapsLocation.getLocation()
Location	FeatureFilter.ShadowContainedByLocation.getLocation()
Location	FeatureFilter.ShadowOverlapsLocation.getLocation()
Location	RemoteFeature.Region.getLocation()	Retrieve the Location of the Region.

Methods in org.biojava.bio.seq with parameters of type Location

Modifier and Type	Method	Description
static FeatureFilter	FilterUtils.containedByLocation(Location loc)	Construct a filter which matches features with locations wholly contained by the specified Location.
static FeatureFilter	FilterUtils.overlapsLocation(Location loc)	Construct a filter which matches features with locations contained by or overlapping the specified Location.
void	Feature.setLocation(Location loc)	The new location for this feature.
static FeatureFilter	FilterUtils.shadowContainedByLocation(Location loc)	Construct a filter which matches features with locations where the interval between the min and max positions are contained by the specified Location.
static FeatureFilter	FilterUtils.shadowOverlapsLocation(Location loc)	Construct a filter which matches features with locations where the interval between the min and max positions are contained by or overlap the specified Location.

Constructors in org.biojava.bio.seq with parameters of type Location

Constructor	Description
ContainedByLocation(Location loc)	Creates a filter that returns everything contained within loc.
OverlapsLocation(Location loc)	Creates a filter that returns everything overlapping loc.
Region(Location location, String seqID, boolean isRemote)	Create a new Region.
ShadowContainedByLocation(Location loc)	Creates a filter that returns everything contained within loc.
ShadowOverlapsLocation(Location loc)	Creates a filter that returns everything overlapping loc.

Uses of Location in org.biojava.bio.seq.homol

Methods in org.biojava.bio.seq.homol with parameters of type Location

Modifier and Type	Method	Description
Alignment	SimilarityPairFeature.EmptyPairwiseAlignment.subAlignment(Set<String> labels, Location loc)

Uses of Location in org.biojava.bio.seq.impl

Methods in org.biojava.bio.seq.impl that return Location

Modifier and Type	Method	Description
Location	SimpleFeature.getLocation()
Location	SimpleGappedSequence.GappedContext.mapLocation(Location loc)
Location	SimpleGappedSequence.GappedContext.projectLocation(Location loc)
Location	SubSequence.SubProjectedFeatureContext.projectLocation(Location toTransform)
Location	SimpleGappedSequence.GappedContext.revertLocation(Location oldLoc)

Methods in org.biojava.bio.seq.impl with parameters of type Location

Modifier and Type	Method	Description
Location	SimpleGappedSequence.GappedContext.mapLocation(Location loc)
Location	SimpleGappedSequence.GappedContext.projectLocation(Location loc)
Location	SubSequence.SubProjectedFeatureContext.projectLocation(Location toTransform)
void	AssembledSymbolList.putComponent(Location l, SymbolList sl)
void	AssembledSymbolList.removeComponent(Location loc)
Location	SimpleGappedSequence.GappedContext.revertLocation(Location oldLoc)
void	SimpleFeature.setLocation(Location loc)

Uses of Location in org.biojava.bio.seq.io

Methods in org.biojava.bio.seq.io with parameters of type Location

Modifier and Type	Method	Description
StringBuffer	SeqFileFormer.formatLocation(StringBuffer sb, Location loc, StrandedFeature.Strand strand)	Deprecated. formatLocation creates a String representation of a Location.
StringBuffer	SwissprotFileFormer.formatLocation(StringBuffer theBuffer, Location theLocation)	Deprecated. formatLocation creates a String representation of a Location.
StringBuffer	SwissprotFileFormer.formatLocation(StringBuffer theBuffer, Location theLocation, StrandedFeature.Strand theStrand)	Deprecated. formatLocation creates a String representation of a Location.

Uses of Location in org.biojava.bio.seq.io.agave

Methods in org.biojava.bio.seq.io.agave with parameters of type Location

Modifier and Type	Method	Description
void	AGAVEBioSeqCallbackItf.reportFeature(Location loc)	Allows nesting class that manages a gene template to gain information about its extent from nested elements.
void	AGAVEBioSeqHandler.reportFeature(Location loc)
void	AGAVEBioSequenceHandler.reportFeature(Location loc)
void	AGAVECompResultHandler.reportFeature(Location loc)
void	AGAVEFeatureCallbackItf.reportFeature(Location loc)
void	AGAVEFragmentOrderHandler.reportFeature(Location loc)
void	AGAVEFragmentOrientationHandler.reportFeature(Location loc)
void	AGAVEGeneHandler.reportFeature(Location loc)
void	AGAVESeqFeatureHandler.reportFeature(Location loc)

Uses of Location in org.biojava.bio.seq.io.game

Methods in org.biojava.bio.seq.io.game with parameters of type Location

Modifier and Type	Method	Description
void	GAMEAnnotationHandler.reportFeature(Location loc)
void	GAMEFeatureCallbackItf.reportFeature(Location loc)	Allows nesting class that manages a gene template to gain information about its extent from nested elements.

Uses of Location in org.biojava.bio.seq.projection

Methods in org.biojava.bio.seq.projection that return Location

Modifier and Type	Method	Description
static Location	ProjectionUtils.flipLocation(Location oldLoc, int translation)	Flip a location.
Location	TranslateFlipContext.projectLocation(Location oldLoc)
static Location	ProjectionUtils.revertLocation(Location oldLoc, int translation, boolean oppositeStrand)	Revert a location, translating and flipping as required.
Location	TranslateFlipContext.revertLocation(Location oldLoc)
static Location	ProjectionUtils.transformLocation(Location oldLoc, int translation, boolean oppositeStrand)	Transform a location, translating and flipping as required.

Methods in org.biojava.bio.seq.projection with parameters of type Location

Modifier and Type	Method	Description
static Location	ProjectionUtils.flipLocation(Location oldLoc, int translation)	Flip a location.
Location	TranslateFlipContext.projectLocation(Location oldLoc)
static Location	ProjectionUtils.revertLocation(Location oldLoc, int translation, boolean oppositeStrand)	Revert a location, translating and flipping as required.
Location	TranslateFlipContext.revertLocation(Location oldLoc)
static Location	ProjectionUtils.transformLocation(Location oldLoc, int translation, boolean oppositeStrand)	Transform a location, translating and flipping as required.

Uses of Location in org.biojava.bio.symbol

Classes in org.biojava.bio.symbol that implement Location

Modifier and Type	Class	Description
class	AbstractLocation	An abstract implementation of Location.
class	AbstractLocationDecorator	Abstract Location decorator (wrapper).
class	AbstractRangeLocation	Base class for simple contiguous Location implementations.
class	BetweenLocation	Between view onto an underlying Location instance.
class	CircularLocation	Circular view onto an underlying Location instance.
class	FuzzyLocation	A 'fuzzy' location a-la Embl fuzzy locations.
class	FuzzyPointLocation	FuzzyPointLocation represents two types of EMBL-style partially-defined locations.
class	MergeLocation	Produced by LocationTools as a result of union operations.
class	PointLocation	A location representing a single point.
class	RangeLocation	A simple implementation of Location that contains all points between getMin and getMax inclusive.

Fields in org.biojava.bio.symbol declared as Location

Modifier and Type	Field	Description
static Location	Location.empty	The Location which contains no points.
static Location	Location.full	The Location which contains all points.

Methods in org.biojava.bio.symbol that return Location

Modifier and Type	Method	Description
protected abstract Location	AbstractLocationDecorator.decorate(Location loc)
protected Location	BetweenLocation.decorate(Location loc)
protected Location	CircularLocation.decorate(Location loc)
static Location	LocationTools.flip(Location loc, int len)	Flips a location relative to a length.
Location	SimpleGappedSymbolList.gappedToLocation(Location l)	Translates a Location from the gapped view into the underlying sequence.
Location	AbstractLocation.getDecorator(Class decoratorClass)
Location	AbstractLocationDecorator.getDecorator(Class decoratorClass)
Location	Location.getDecorator(Class decoratorClass)	Checks the decorator chain for an instance of decoratorClass and return it if found.
Location	GappedSymbolList.getUngappedLocation()	Get a Location that contains exactly those positions that are not gaps.
Location	SimpleGappedSymbolList.getUngappedLocation()
protected Location	AbstractLocationDecorator.getWrapped()
Location	AbstractLocation.intersection(Location loc)
Location	AbstractLocationDecorator.intersection(Location l)
Location	CircularLocation.intersection(Location l)
Location	FuzzyPointLocation.intersection(Location loc)
Location	Location.intersection(Location l)	Returns a Location that contains all points common to both ranges.
static Location	LocationTools.intersection(Location locA, Location locB)	Return the intersection of two locations.
Location	SimpleGappedSymbolList.locationToGapped(Location l)	Translate a Location onto the gapped view, splitting blocks if necessary
static Location	LocationTools.makeLocation(int min, int max)	Return a contiguous Location from min to max.
Location	AbstractLocation.newInstance(Location loc)
Location	AbstractLocationDecorator.newInstance(Location loc)
Location	Location.newInstance(Location loc)	Create a new instance of Location with all of the same decorators as this instance but with the data stored in loc.
static Location	LocationTools.shadow(Location loc)	Return a contiguous location running from the minimum to the maximum points of the specified location.
static Location	LocationTools.subtract(Location keep, Location remove)	Subtract one location from another.
Location	AbstractLocationDecorator.translate(int dist)
Location	FuzzyLocation.translate(int dist)
Location	FuzzyPointLocation.translate(int dist)
Location	Location.translate(int dist)	Create a location that is a translation of this location.
Location	PointLocation.translate(int dist)
Location	RangeLocation.translate(int dist)
Location	AbstractLocation.union(Location loc)
Location	AbstractLocationDecorator.union(Location l)
Location	CircularLocation.union(Location l)
Location	Location.union(Location l)	Return a Location containing all points in either ranges.
static Location	LocationTools.union(Collection locs)	The n-way union of a Collection of locations.
static Location	LocationTools.union(Location locA, Location locB)	Return the union of two locations.

Methods in org.biojava.bio.symbol that return types with arguments of type Location

Modifier and Type	Method	Description
Iterator<Location>	Location.blockIterator()	Return an Iterator over the set of maximal contiguous sub-locations.

Methods in org.biojava.bio.symbol with parameters of type Location

Modifier and Type	Method	Description
static boolean	LocationTools.areEqual(Location locA, Location locB)	Return whether two locations are equal.
static int	LocationTools.blockCount(Location loc)	Return the number of contiguous blocks in a location.
static boolean	LocationTools.canMerge(Location locA, Location locB)	Determines whether the locations are touching or not (if they could be merged in a single Location.
boolean	AbstractLocation.contains(Location l)
boolean	AbstractLocationDecorator.contains(Location l)
boolean	CircularLocation.contains(Location l)
boolean	FuzzyPointLocation.contains(Location loc)
boolean	Location.contains(Location l)	Checks if this location contains the other.
static boolean	LocationTools.contains(Location locA, Location locB)	Return true iff all indices in locB are also contained by locA.
static int	LocationTools.coverage(Location loc)	Return the number of positions which are covered by a Location
protected abstract Location	AbstractLocationDecorator.decorate(Location loc)
protected Location	BetweenLocation.decorate(Location loc)
protected Location	CircularLocation.decorate(Location loc)
boolean	FuzzyPointLocation.equals(Location loc)
static Location	LocationTools.flip(Location loc, int len)	Flips a location relative to a length.
Location	SimpleGappedSymbolList.gappedToLocation(Location l)	Translates a Location from the gapped view into the underlying sequence.
Location	AbstractLocation.intersection(Location loc)
Location	AbstractLocationDecorator.intersection(Location l)
Location	CircularLocation.intersection(Location l)
Location	FuzzyPointLocation.intersection(Location loc)
Location	Location.intersection(Location l)	Returns a Location that contains all points common to both ranges.
static Location	LocationTools.intersection(Location locA, Location locB)	Return the intersection of two locations.
Location	SimpleGappedSymbolList.locationToGapped(Location l)	Translate a Location onto the gapped view, splitting blocks if necessary
static MergeLocation	MergeLocation.mergeLocations(Location locA, Location locB)
Location	AbstractLocation.newInstance(Location loc)
Location	AbstractLocationDecorator.newInstance(Location loc)
Location	Location.newInstance(Location loc)	Create a new instance of Location with all of the same decorators as this instance but with the data stored in loc.
boolean	AbstractLocation.overlaps(Location l)
boolean	AbstractLocationDecorator.overlaps(Location l)
boolean	CircularLocation.overlaps(Location l)
boolean	FuzzyPointLocation.overlaps(Location loc)
boolean	Location.overlaps(Location l)	Checks if these two locations overlap, using this location's concept of overlapping.
static boolean	LocationTools.overlaps(Location locA, Location locB)	Determines whether the locations overlap or not.
static Location	LocationTools.shadow(Location loc)	Return a contiguous location running from the minimum to the maximum points of the specified location.
Alignment	RelabeledAlignment.subAlignment(Set<String> labels, Location loc)
static Location	LocationTools.subtract(Location keep, Location remove)	Subtract one location from another.
Location	AbstractLocation.union(Location loc)
Location	AbstractLocationDecorator.union(Location l)
Location	CircularLocation.union(Location l)
Location	Location.union(Location l)	Return a Location containing all points in either ranges.
static Location	LocationTools.union(Location locA, Location locB)	Return the union of two locations.

Constructors in org.biojava.bio.symbol with parameters of type Location

Constructor	Description
AbstractLocationDecorator(Location wrapped)	Construct a new decorator wrapping the specified Location.
BetweenLocation(Location wrapped)
CircularLocation(Location wrapped, int length)	Constructs a CircularLocation by wrapping another Location It is preferable to use LocationTools to make CircularLocations
CircularLocation(Location wrapped, int length, int fivePrimeEnd)	Makes a CircularLocation where the 5' end of the Location is specified.

Uses of Location in org.biojavax.bio.seq

Subinterfaces of Location in org.biojavax.bio.seq

Modifier and Type	Interface	Description
interface	RichLocation	Describes locations, and adds the concepts of circularity, fuzziness, annotations, and cross-references to other databases.

Classes in org.biojavax.bio.seq that implement Location

Modifier and Type	Class	Description
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.

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

Modifier and Type	Method	Description
Location	CompoundRichLocation.getDecorator(Class decoratorClass)	Checks the decorator chain for an instance of decoratorClass and return it if found.
Location	EmptyRichLocation.getDecorator(Class decoratorClass)	Checks the decorator chain for an instance of decoratorClass and return it if found.
Location	SimpleRichLocation.getDecorator(Class decoratorClass)	Checks the decorator chain for an instance of decoratorClass and return it if found.
Location	SimpleRichFeature.getLocation()	The location of this feature.
Location	CompoundRichLocation.intersection(Location l)	Returns a Location that contains all points common to both ranges.
Location	EmptyRichLocation.intersection(Location l)	Returns a Location that contains all points common to both ranges.
Location	SimpleRichLocation.intersection(Location l)	Returns a Location that contains all points common to both ranges.
Location	CompoundRichLocation.newInstance(Location loc)	Create a new instance of Location with all of the same decorators as this instance but with the data stored in loc.
Location	EmptyRichLocation.newInstance(Location loc)	Create a new instance of Location with all of the same decorators as this instance but with the data stored in loc.
Location	SimpleRichLocation.newInstance(Location loc)	Create a new instance of Location with all of the same decorators as this instance but with the data stored in loc.
Location	CompoundRichLocation.translate(int dist)	Create a location that is a translation of this location.
Location	EmptyRichLocation.translate(int dist)	Create a location that is a translation of this location.
Location	MultiSourceCompoundRichLocation.translate(int dist)	Create a location that is a translation of this location.
Location	SimpleRichLocation.translate(int dist)	Create a location that is a translation of this location.
Location	CompoundRichLocation.union(Location l)	Return a Location containing all points in either ranges.
Location	EmptyRichLocation.union(Location l)	Return a Location containing all points in either ranges.
Location	SimpleRichLocation.union(Location l)	Return a Location containing all points in either ranges.

Methods in org.biojavax.bio.seq that return types with arguments of type Location

Modifier and Type	Method	Description
static Collection<Location>	RichLocation.Tools.flatten(Collection<Location> members)	Takes a set of locations and returns the set of all members.
static Collection<Location>	RichLocation.Tools.flatten(RichLocation location)	Takes a location and returns the set of all members.
static Collection<Location>	RichLocation.Tools.merge(Collection<Location> members)	Takes a set of locations and tries to merge all pairs where the union operation results in a simple rich location, not a compound one.

Methods in org.biojavax.bio.seq with parameters of type Location

Modifier and Type	Method	Description
boolean	CompoundRichLocation.contains(Location l)	Checks if this location contains the other.
boolean	EmptyRichLocation.contains(Location l)	Checks if this location contains the other.
boolean	SimpleRichLocation.contains(Location l)	Checks if this location contains the other.
static RichLocation	RichLocation.Tools.enrich(Location l)	Attempts to convert a plain Location into a RichLocation.
Location	CompoundRichLocation.intersection(Location l)	Returns a Location that contains all points common to both ranges.
Location	EmptyRichLocation.intersection(Location l)	Returns a Location that contains all points common to both ranges.
Location	SimpleRichLocation.intersection(Location l)	Returns a Location that contains all points common to both ranges.
static int[]	RichLocation.Tools.modulateCircularLocationPair(Location a, Location b, int seqLength)	Takes two circular locations of given length, and shifts them left along the sequence until they sit at the earliest possible point where they still would represent the same sequence.
Location	CompoundRichLocation.newInstance(Location loc)	Create a new instance of Location with all of the same decorators as this instance but with the data stored in loc.
Location	EmptyRichLocation.newInstance(Location loc)	Create a new instance of Location with all of the same decorators as this instance but with the data stored in loc.
Location	SimpleRichLocation.newInstance(Location loc)	Create a new instance of Location with all of the same decorators as this instance but with the data stored in loc.
boolean	CompoundRichLocation.overlaps(Location l)	Checks if these two locations overlap, using this location's concept of overlapping.
boolean	EmptyRichLocation.overlaps(Location l)	Checks if these two locations overlap, using this location's concept of overlapping.
boolean	SimpleRichLocation.overlaps(Location l)	Checks if these two locations overlap, using this location's concept of overlapping.
void	SimpleRichFeature.setLocation(Location loc)	The new location for this feature.
Location	CompoundRichLocation.union(Location l)	Return a Location containing all points in either ranges.
Location	EmptyRichLocation.union(Location l)	Return a Location containing all points in either ranges.
Location	SimpleRichLocation.union(Location l)	Return a Location containing all points in either ranges.

Method parameters in org.biojavax.bio.seq with type arguments of type Location

Modifier and Type	Method	Description
static RichLocation	RichLocation.Tools.construct(Collection<Location> members)	Constructs a RichLocation object based on the given collection of members.
static Collection<Location>	RichLocation.Tools.flatten(Collection<Location> members)	Takes a set of locations and returns the set of all members.
static boolean	RichLocation.Tools.isMultiSource(Collection<Location> members)	Returns false if all the locations in the set are from the same strand of the same sequence.
static Collection<Location>	RichLocation.Tools.merge(Collection<Location> members)	Takes a set of locations and tries to merge all pairs where the union operation results in a simple rich location, not a compound one.