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

Packages that use Location
org.biojava.bio: The core classes that will be used throughout the bio packages.
org.biojava.bio.alignment: Implementation of the `Alignment` interface.
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 into alternate coordinate systems.
org.biojava.bio.symbol: Representation of the Symbols that make up a sequence, and locations within them.

Uses of Location in org.biojava.bio

Fields in org.biojava.bio declared as Location
`static Location` `CardinalityConstraint.NONE` This cardinality contains no intengers, not even zero.
`static Location` `CardinalityConstraint.ZERO` The property should have zero values.
`static Location` `CardinalityConstraint.ZERO_OR_ONE` The property should have zero or one values.
`static Location` `CardinalityConstraint.ANY` The property can have any number of values, including none.
`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.

Methods in org.biojava.bio that return Location
`Location` `CollectionConstraint.AllValuesIn.getCardinalityConstraint()`
`Location` `CollectionConstraint.Contains.getCardinalityConstraint()`

Methods in org.biojava.bio with parameters of type Location
`void` `AnnotationType.setConstraints(java.lang.Object key, PropertyConstraint con, Location card)` Set the constraints associated with a property.
`void` `AnnotationType.setDefaultConstraints(PropertyConstraint pc, Location cc)` Set the constraints that will apply to all properties without an explicitly defined set of constraints.
`void` `AnnotationType.Abstract.setConstraints(java.lang.Object key, PropertyConstraint pc, Location cc)`
`void` `AnnotationType.Abstract.setDefaultConstraints(PropertyConstraint pc, Location cc)`

Constructors in org.biojava.bio with parameters of type Location
`AnnotationType.Impl(PropertyConstraint defaultPC, Location defaultCC)` Create a new Impl with a default property and cardinality constraint.
`CollectionConstraint.AllValuesIn(PropertyConstraint pc, Location card)`
`CollectionConstraint.Contains(PropertyConstraint pc, Location card)`

Uses of Location in org.biojava.bio.alignment

Fields in org.biojava.bio.alignment declared as Location
`protected Location` `SimpleAlignmentElement.loc`
`protected Location` `FlexibleAlignment.alignmentRange`

Methods in org.biojava.bio.alignment that return Location
`Location` `SimpleAlignmentElement.getLoc()`
`Location` `AbstractULAlignment.SubULAlignment.locInAlignment(java.lang.Object label)` The location of an individual SymbolList relative to overall Alignment
`Location` `AlignmentElement.getLoc()`
`Location` `UnequalLengthAlignment.locInAlignment(java.lang.Object label)` The location of an individual SymbolList relative to overall Alignment
`Location` `FlexibleAlignment.locInAlignment(java.lang.Object label)` The location of an individual SymbolList relative to overall Alignment
`protected Location` `FlexibleAlignment.locInSeq(java.lang.Object label, Location viewLoc)`

Methods in org.biojava.bio.alignment with parameters of type Location
`void` `SimpleAlignmentElement.setLoc(Location nLoc)`
`java.util.List` `AbstractULAlignment.labelsInRange(Location loc)`
`Alignment` `AbstractULAlignment.subAlignment(java.util.Set labels, Location loc)` Retrieves a subalignment specified by the location.
`Alignment` `AbstractULAlignment.SubULAlignment.subAlignment(java.util.Set labels, Location loc)`
`java.util.List` `AbstractULAlignment.SubULAlignment.labelsInRange(Location loc)`
`void` `AlignmentElement.setLoc(Location nLoc)`
`java.util.List` `UnequalLengthAlignment.labelsInRange(Location loc)` Returns list of all the labels that intersect that range
`void` `EditableAlignment.shiftAtAlignmentLoc(java.lang.Object label, Location loc, int offset)` loc in this case is the Alignment Location
`void` `EditableAlignment.shiftAtSequenceLoc(java.lang.Object label, Location loc, int offset)` loc in this case is the SymbolList Location
`void` `FlexibleAlignment.shiftAtAlignmentLoc(java.lang.Object label, Location loc, int offset)` loc in this case is the Alignment Location
`void` `FlexibleAlignment.shiftAtSequenceLoc(java.lang.Object label, Location loc, int offset)` loc in this case is the SymbolList Location
`protected Location` `FlexibleAlignment.locInSeq(java.lang.Object label, Location viewLoc)`

Constructors in org.biojava.bio.alignment with parameters of type Location
`SimpleAlignmentElement(java.lang.Object label, SymbolList seq, Location loc)`
`AbstractULAlignment.SubULAlignment(java.util.Set labels, Location loc)`

Uses of Location in org.biojava.bio.dp

Methods in org.biojava.bio.dp with parameters of type Location
`Alignment` `SimpleStatePath.subAlignment(java.util.Set labels, Location loc)`

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

Methods in org.biojava.bio.gui.sequence with parameters of type Location
`void` `SixFrameRenderer.renderLocation(java.awt.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
`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
`Location` `Feature.Template.location`
`Location` `ComponentFeature.Template.componentLocation`

Methods in org.biojava.bio.seq that return Location
`Location` `FeatureFilter.ContainedByLocation.getLocation()`
`Location` `FeatureFilter.OverlapsLocation.getLocation()`
`Location` `FeatureFilter.ShadowOverlapsLocation.getLocation()`
`Location` `FeatureFilter.ShadowContainedByLocation.getLocation()`
`static Location` `FilterUtils.extractOverlappingLocation(FeatureFilter ff)` Try to determine the minimal location which all features matching a given filter must overlap.
`Location` `Feature.getLocation()` The location of this feature.
`Location` `ComponentFeature.getComponentLocation()` Return a location which identifies a portion of the component sequence which is to be included in the assembly.
`protected Location` `ProjectedFeatureHolder.transformLocation(Location oldLoc)` Called to transform a location from underlying to projection coordinates.
`protected Location` `ProjectedFeatureHolder.untransformLocation(Location oldLoc)` Called to transform a location from projection to underlying coordinates.
`Location` `ProjectedFeatureHolder.getLocation(Feature f)`
`Location` `RemoteFeature.Region.getLocation()` Retrieve the Location of the Region.

Methods in org.biojava.bio.seq with parameters of type Location
`static FeatureFilter` `FilterUtils.containedByLocation(Location loc)`
`static FeatureFilter` `FilterUtils.overlapsLocation(Location loc)`
`void` `Feature.setLocation(Location loc)` The new location for this feature.
`protected Location` `ProjectedFeatureHolder.transformLocation(Location oldLoc)` Called to transform a location from underlying to projection coordinates.
`protected Location` `ProjectedFeatureHolder.untransformLocation(Location oldLoc)` Called to transform a location from projection to underlying coordinates.

Constructors in org.biojava.bio.seq with parameters of type Location
`FeatureFilter.ContainedByLocation(Location loc)` Creates a filter that returns everything contained within loc.
`FeatureFilter.OverlapsLocation(Location loc)` Creates a filter that returns everything overlapping loc.
`FeatureFilter.ShadowOverlapsLocation(Location loc)` Creates a filter that returns everything overlapping loc.
`FeatureFilter.ShadowContainedByLocation(Location loc)` Creates a filter that returns everything contained within loc.
`RemoteFeature.Region(Location location, java.lang.String seqID, boolean isRemote)` Create a new Region.

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

Methods in org.biojava.bio.seq.homol with parameters of type Location
`Alignment` `SimilarityPairFeature.EmptyPairwiseAlignment.subAlignment(java.util.Set labels, Location loc)`

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

Methods in org.biojava.bio.seq.impl that return Location
`Location` `SimpleFeature.getLocation()`

Methods in org.biojava.bio.seq.impl with parameters of type Location
`void` `AssembledSymbolList.putComponent(Location l, SymbolList sl)`
`void` `AssembledSymbolList.removeComponent(Location loc)`
`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
`java.lang.StringBuffer` `SwissprotFileFormer.formatLocation(java.lang.StringBuffer theBuffer, Location theLocation, StrandedFeature.Strand theStrand)` `formatLocation` creates a String representation of a `Location`.
`java.lang.StringBuffer` `SwissprotFileFormer.formatLocation(java.lang.StringBuffer theBuffer, Location theLocation)` `formatLocation` creates a String representation of a `Location`.
`java.lang.StringBuffer` `SeqFileFormer.formatLocation(java.lang.StringBuffer sb, Location loc, StrandedFeature.Strand strand)` `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
`void` `AGAVEBioSeqCallbackItf.reportFeature(Location loc)` Allows nesting class that manages a gene template to gain information about its extent from nested elements.
`void` `AGAVEFragmentOrientationHandler.reportFeature(Location loc)`
`void` `AGAVEGeneHandler.reportFeature(Location loc)`
`void` `AGAVEBioSequenceHandler.reportFeature(Location loc)`
`void` `AGAVEBioSeqHandler.reportFeature(Location loc)`
`void` `AGAVESeqFeatureHandler.reportFeature(Location loc)`
`void` `AGAVECompResultHandler.reportFeature(Location loc)`
`void` `AGAVEFeatureCallbackItf.reportFeature(Location loc)`
`void` `AGAVEFragmentOrderHandler.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
`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
`Location` `ProjectedFeature.getLocation()`
`static Location` `ProjectionUtils.transformLocation(Location oldLoc, int translate, boolean oppositeStrand)`
`Location` `ProjectionContext.getLocation(Feature f)` Get the location of the projected feature

Methods in org.biojava.bio.seq.projection with parameters of type Location
`void` `ProjectedFeature.setLocation(Location loc)`
`static Location` `ProjectionUtils.transformLocation(Location oldLoc, int translate, boolean oppositeStrand)`

Uses of Location in org.biojava.bio.symbol

Classes in org.biojava.bio.symbol that implement Location
`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
`static Location` `Location.empty` The `Location` which contains no points.

Methods in org.biojava.bio.symbol that return Location
`static Location` `LocationTools.union(Location locA, Location locB)` Return the union of two locations.
`static Location` `LocationTools.intersection(Location locA, Location locB)` Return the intersection of two locations.
`static Location` `LocationTools.union(java.util.Collection locs)` The n-way union of a Collection of locations.
`static Location` `LocationTools.makeLocation(int min, int max)` Return a contiguous Location from min to max.
`static Location` `LocationTools.flip(Location loc, int len)` Flips a location relative to a length.
`static Location` `LocationTools.subtract(Location x, Location y)` Subtract one location from another.
`protected Location` `CircularLocation.decorate(Location loc)`
`Location` `CircularLocation.intersection(Location l)`
`Location` `CircularLocation.union(Location l)`
`Location` `AbstractLocation.getDecorator(java.lang.Class decoratorClass)`
`Location` `AbstractLocation.newInstance(Location loc)`
`Location` `AbstractLocation.union(Location loc)`
`Location` `AbstractLocation.intersection(Location loc)`
`Location` `PointLocation.translate(int dist)`
`protected Location` `BetweenLocation.decorate(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`.
`Location` `Location.getDecorator(java.lang.Class decoratorClass)` Checks the decorator chain for an instance of <class>decoratorClass</class> and return it if found.
`Location` `Location.intersection(Location l)` Returns a Location that contains all points common to both ranges.
`Location` `Location.union(Location l)` Return a Location containing all points in either ranges.
`Location` `Location.translate(int dist)` Create a location that is a translation of this location.
`protected Location` `AbstractLocationDecorator.getWrapped()`
`protected abstract Location` `AbstractLocationDecorator.decorate(Location loc)`
`Location` `AbstractLocationDecorator.newInstance(Location loc)`
`Location` `AbstractLocationDecorator.getDecorator(java.lang.Class decoratorClass)`
`Location` `AbstractLocationDecorator.intersection(Location l)`
`Location` `AbstractLocationDecorator.union(Location l)`
`Location` `AbstractLocationDecorator.translate(int dist)`
`Location` `FuzzyPointLocation.intersection(Location loc)`
`Location` `FuzzyPointLocation.translate(int dist)`
`Location` `SimpleGappedSymbolList.locationToGapped(Location l)` Translate a Location onto the gapped view, splitting blocks if necessary
`Location` `SimpleGappedSymbolList.gappedToLocation(Location l)` Translates a Location from the gapped view into the underlying sequence.
`Location` `RangeLocation.translate(int dist)`
`Location` `FuzzyLocation.translate(int dist)`

Methods in org.biojava.bio.symbol with parameters of type Location
`static Location` `LocationTools.union(Location locA, Location locB)` Return the union of two locations.
`static Location` `LocationTools.intersection(Location locA, Location locB)` Return the intersection of two locations.
`static boolean` `LocationTools.overlaps(Location locA, Location locB)` Determines whether the locations overlap or not.
`static boolean` `LocationTools.contains(Location locA, Location locB)` Return `true` iff all indices in `locB` are also contained by `locA`.
`static boolean` `LocationTools.areEqual(Location locA, Location locB)` Return whether two locations are equal.
`static Location` `LocationTools.flip(Location loc, int len)` Flips a location relative to a length.
`static Location` `LocationTools.subtract(Location x, Location y)` Subtract one location from another.
`protected Location` `CircularLocation.decorate(Location loc)`
`Location` `CircularLocation.intersection(Location l)`
`boolean` `CircularLocation.overlaps(Location l)`
`Location` `CircularLocation.union(Location l)`
`boolean` `CircularLocation.contains(Location l)`
`Alignment` `SimpleAlignment.subAlignment(java.util.Set labels, Location loc)`
`Location` `AbstractLocation.newInstance(Location loc)`
`boolean` `AbstractLocation.contains(Location l)`
`boolean` `AbstractLocation.overlaps(Location l)`
`Location` `AbstractLocation.union(Location loc)`
`Location` `AbstractLocation.intersection(Location loc)`
`protected Location` `BetweenLocation.decorate(Location loc)`
`Alignment` `RelabeledAlignment.subAlignment(java.util.Set labels, 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` `Location.overlaps(Location l)` Checks if these two locations overlap, using this location's concept of overlapping.
`boolean` `Location.contains(Location l)` Checks if this location contains the other.
`Location` `Location.intersection(Location l)` Returns a Location that contains all points common to both ranges.
`Location` `Location.union(Location l)` Return a Location containing all points in either ranges.
`protected abstract Location` `AbstractLocationDecorator.decorate(Location loc)`
`Location` `AbstractLocationDecorator.newInstance(Location loc)`
`boolean` `AbstractLocationDecorator.overlaps(Location l)`
`boolean` `AbstractLocationDecorator.contains(Location l)`
`Location` `AbstractLocationDecorator.intersection(Location l)`
`Location` `AbstractLocationDecorator.union(Location l)`
`static MergeLocation` `MergeLocation.mergeLocations(Location locA, Location locB)`
`boolean` `FuzzyPointLocation.overlaps(Location loc)`
`boolean` `FuzzyPointLocation.contains(Location loc)`
`boolean` `FuzzyPointLocation.equals(Location loc)`
`Location` `FuzzyPointLocation.intersection(Location loc)`
`Location` `SimpleGappedSymbolList.locationToGapped(Location l)` Translate a Location onto the gapped view, splitting blocks if necessary
`Location` `SimpleGappedSymbolList.gappedToLocation(Location l)` Translates a Location from the gapped view into the underlying sequence.
`Alignment` `Alignment.subAlignment(java.util.Set labels, Location loc)` Make a view onto this alignment.

Constructors in org.biojava.bio.symbol with parameters of type Location
`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.
`BetweenLocation(Location wrapped)`
`AbstractLocationDecorator(Location wrapped)` Construct a new decorator wrapping the specified Location.