Overview | Package | Class | Use | Tree | Deprecated | Index | Help
PREV NEXT | FRAMES NO FRAMES

## 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 | 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
`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
`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
`void` | `AnnotationType.setConstraints(Object key, PropertyConstraint con, Location card)` Set the constraints associated with a property.
`void` | `AnnotationType.Abstract.setConstraints(Object key, 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.
`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)` Create an AllValuesIn based upon a PropertyConstraint and a cardinality.
`CollectionConstraint.Contains(PropertyConstraint pc, Location card)` Create a Contains based upon a PropertyConstraint and a cardinality.

Uses of Location in org.biojava.bio.alignment

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

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

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

Uses of Location in org.biojava.bio.dp

Methods in org.biojava.bio.dp with parameters of type Location
`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
`static Location` | `GUITools.getVisibleRange(SequenceRenderContext src, Graphics2D g2)`

Methods in org.biojava.bio.gui.sequence with parameters of type Location
`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
`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` | `ComponentFeature.Template.componentLocation`
`Location` | `Feature.Template.location`

Methods in org.biojava.bio.seq that return Location
`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` | `RemoteFeature.Region.getLocation()` Retrieve the Location of the Region.
`Location` | `FeatureFilter.ContainedByLocation.getLocation()`
`Location` | `FeatureFilter.OverlapsLocation.getLocation()`
`Location` | `FeatureFilter.ShadowOverlapsLocation.getLocation()`
`Location` | `FeatureFilter.ShadowContainedByLocation.getLocation()`
`Location` | `Feature.getLocation()` The location of this feature.

Methods in org.biojava.bio.seq with parameters of type Location
`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
`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.ShadowContainedByLocation(Location loc)` Creates a filter that returns everything contained within loc.
`FeatureFilter.ShadowOverlapsLocation(Location loc)` Creates a filter that returns everything overlapping loc.
`RemoteFeature.Region(Location location, 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(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()`
`Location` | `SimpleGappedSequence.GappedContext.mapLocation(Location loc)`
`Location` | `SubSequence.SubProjectedFeatureContext.projectLocation(Location toTransform)`
`Location` | `SimpleGappedSequence.GappedContext.projectLocation(Location loc)`
`Location` | `SimpleGappedSequence.GappedContext.revertLocation(Location oldLoc)`

Methods in org.biojava.bio.seq.impl with parameters of type Location
`Location` | `SimpleGappedSequence.GappedContext.mapLocation(Location loc)`
`Location` | `SubSequence.SubProjectedFeatureContext.projectLocation(Location toTransform)`
`Location` | `SimpleGappedSequence.GappedContext.projectLocation(Location loc)`
`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
`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`.
`StringBuffer` | `SeqFileFormer.formatLocation(StringBuffer sb, Location loc, StrandedFeature.Strand strand)` 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
`void` | `AGAVESeqFeatureHandler.reportFeature(Location loc)`
`void` | `AGAVEGeneHandler.reportFeature(Location loc)`
`void` | `AGAVEFragmentOrientationHandler.reportFeature(Location loc)`
`void` | `AGAVEFragmentOrderHandler.reportFeature(Location loc)`
`void` | `AGAVEFeatureCallbackItf.reportFeature(Location loc)`
`void` | `AGAVECompResultHandler.reportFeature(Location loc)`
`void` | `AGAVEBioSequenceHandler.reportFeature(Location loc)`
`void` | `AGAVEBioSeqHandler.reportFeature(Location loc)`
`void` | `AGAVEBioSeqCallbackItf.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.io.game

Methods in org.biojava.bio.seq.io.game with parameters of type Location
`void` | `GAMEFeatureCallbackItf.reportFeature(Location loc)` Allows nesting class that manages a gene template to gain information about its extent from nested elements.
`void` | `GAMEAnnotationHandler.reportFeature(Location loc)`

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

Methods in org.biojava.bio.seq.projection that return Location
`static Location` | `ProjectionUtils.flipLocation(Location oldLoc, int translation)` Flip a location.
`Location` | `TranslateFlipContext.projectLocation(Location oldLoc)`
`Location` | `TranslateFlipContext.revertLocation(Location oldLoc)`
`static Location` | `ProjectionUtils.revertLocation(Location oldLoc, int translation, boolean oppositeStrand)` Revert a location, translating and flipping as required.
`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
`static Location` | `ProjectionUtils.flipLocation(Location oldLoc, int translation)` Flip a location.
`Location` | `TranslateFlipContext.projectLocation(Location oldLoc)`
`Location` | `TranslateFlipContext.revertLocation(Location oldLoc)`
`static Location` | `ProjectionUtils.revertLocation(Location oldLoc, int translation, boolean oppositeStrand)` Revert a location, translating and flipping as required.
`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
`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.
`static Location` | `Location.full` The `Location` which contains all points.

Methods in org.biojava.bio.symbol that return Location
`protected Location` | `CircularLocation.decorate(Location loc)`
`protected Location` | `BetweenLocation.decorate(Location loc)`
`protected abstract Location` | `AbstractLocationDecorator.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` | `Location.getDecorator(Class decoratorClass)` Checks the decorator chain for an instance of decoratorClass and return it if found.
`Location` | `AbstractLocationDecorator.getDecorator(Class decoratorClass)`
`Location` | `AbstractLocation.getDecorator(Class decoratorClass)`
`Location` | `SimpleGappedSymbolList.getUngappedLocation()`
`Location` | `GappedSymbolList.getUngappedLocation()` Get a Location that contains exactly those positions that are not gaps.
`protected Location` | `AbstractLocationDecorator.getWrapped()`
`Location` | `Location.intersection(Location l)` Returns a Location that contains all points common to both ranges.
`Location` | `FuzzyPointLocation.intersection(Location loc)`
`Location` | `CircularLocation.intersection(Location l)`
`Location` | `AbstractLocationDecorator.intersection(Location l)`
`Location` | `AbstractLocation.intersection(Location loc)`
`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` | `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` | `AbstractLocationDecorator.newInstance(Location loc)`
`Location` | `AbstractLocation.newInstance(Location 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` | `RangeLocation.translate(int dist)`
`Location` | `PointLocation.translate(int dist)`
`Location` | `Location.translate(int dist)` Create a location that is a translation of this location.
`Location` | `FuzzyPointLocation.translate(int dist)`
`Location` | `FuzzyLocation.translate(int dist)`
`Location` | `AbstractLocationDecorator.translate(int dist)`
`static Location` | `LocationTools.union(Collection locs)` The n-way union of a Collection of locations.
`Location` | `Location.union(Location l)` Return a Location containing all points in either ranges.
`Location` | `CircularLocation.union(Location l)`
`Location` | `AbstractLocationDecorator.union(Location l)`
`Location` | `AbstractLocation.union(Location loc)`
`static Location` | `LocationTools.union(Location locA, Location locB)` Return the union of two locations.

Methods in org.biojava.bio.symbol with parameters of type Location
`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` | `Location.contains(Location l)` Checks if this location contains the other.
`boolean` | `FuzzyPointLocation.contains(Location loc)`
`boolean` | `CircularLocation.contains(Location l)`
`boolean` | `AbstractLocationDecorator.contains(Location l)`
`boolean` | `AbstractLocation.contains(Location l)`
`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 Location` | `CircularLocation.decorate(Location loc)`
`protected Location` | `BetweenLocation.decorate(Location loc)`
`protected abstract Location` | `AbstractLocationDecorator.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` | `Location.intersection(Location l)` Returns a Location that contains all points common to both ranges.
`Location` | `FuzzyPointLocation.intersection(Location loc)`
`Location` | `CircularLocation.intersection(Location l)`
`Location` | `AbstractLocationDecorator.intersection(Location l)`
`Location` | `AbstractLocation.intersection(Location loc)`
`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` | `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` | `AbstractLocationDecorator.newInstance(Location loc)`
`Location` | `AbstractLocation.newInstance(Location loc)`
`boolean` | `Location.overlaps(Location l)` Checks if these two locations overlap, using this location's concept of overlapping.
`boolean` | `FuzzyPointLocation.overlaps(Location loc)`
`boolean` | `CircularLocation.overlaps(Location l)`
`boolean` | `AbstractLocationDecorator.overlaps(Location l)`
`boolean` | `AbstractLocation.overlaps(Location l)`
`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` | `SimpleAlignment.subAlignment(Set labels, Location loc)`
`Alignment` | `RelabeledAlignment.subAlignment(Set labels, Location loc)`
`Alignment` | `Alignment.subAlignment(Set labels, Location loc)` Make a view onto this alignment.
`static Location` | `LocationTools.subtract(Location keep, Location remove)` Subtract one location from another.
`Location` | `Location.union(Location l)` Return a Location containing all points in either ranges.
`Location` | `CircularLocation.union(Location l)`
`Location` | `AbstractLocationDecorator.union(Location l)`
`Location` | `AbstractLocation.union(Location loc)`
`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
`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
`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
`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
`Location` | `SimpleRichLocation.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. ALWAYS RETURNS NULL
`Location` | `CompoundRichLocation.getDecorator(Class decoratorClass)` Checks the decorator chain for an instance of decoratorClass and return it if found. The default behavior is to return null. If the current object is a decorator and is an instance of decoratorClass it should return itself. Otherwise, the decorator should chain this method onto the instance it wraps. ALWAYS RETURNS NULL
`Location` | `SimpleRichFeature.getLocation()` The location of this feature.
`Location` | `SimpleRichLocation.intersection(Location l)` Returns a Location that contains all points common to both ranges. If the locations overlap and are on the same strand, the intersection is returned.
`Location` | `EmptyRichLocation.intersection(Location l)` Returns a Location that contains all points common to both ranges. ALWAYS RETURNS SELF
`Location` | `CompoundRichLocation.intersection(Location l)` Returns a Location that contains all points common to both ranges. If the locations overlap and are on the same strand, the intersection is returned. If passed a Location which is not a RichLocation, it converts it first using RichLocation.Tools.enrich().
`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` | `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`. ALWAYS RETURNS PASSED LOCATION
`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`. The default behavior is to return loc unchanged. If the class is a location decorator then it should instantiate an instance of the same type that decorates `loc`. ALWAYS RETURNS SELF
`Location` | `SimpleRichLocation.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. Recursively translates all members of this location. Recursively translates all members of this location.
`Location` | `EmptyRichLocation.translate(int dist)` Create a location that is a translation of this location. ALWAYS RETURNS SELF
`Location` | `CompoundRichLocation.translate(int dist)` Create a location that is a translation of this location. Recursively translates all members of this location.
`Location` | `SimpleRichLocation.union(Location l)` Return a Location containing all points in either ranges. A merged SimpleRichLocation is returned if the two locations overlap and are on the same strand.
`Location` | `EmptyRichLocation.union(Location l)` Return a Location containing all points in either ranges. ALWAYS RETURNS PASSED LOCATION
`Location` | `CompoundRichLocation.union(Location l)` Return a Location containing all points in either ranges. A merged SimpleRichLocation is returned if the two locations overlap and are on the same strand. If passed a Location which is not a RichLocation, it converts it first using RichLocation.Tools.enrich().

Methods in org.biojavax.bio.seq that return types with arguments of type Location
`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
`boolean` | `SimpleRichLocation.contains(Location l)` Checks if this location contains the other. A location contains another location if it overlaps it, and the coordinates enclose those of the other location at both ends, and they fall on the same strand.
`boolean` | `EmptyRichLocation.contains(Location l)` Checks if this location contains the other. ALWAYS RETURNS FALSE
`boolean` | `CompoundRichLocation.contains(Location l)` Checks if this location contains the other. Abstractly, a location contains another if every point in the other location is contained within this one. A location contains another location if it overlaps it, and the coordinates enclose those of the other location at both ends, and they fall on the same strand. Recursively applies this call to all members.
`static RichLocation` | `RichLocation.Tools.enrich(Location l)` Attempts to convert a plain Location into a RichLocation.
`Location` | `SimpleRichLocation.intersection(Location l)` Returns a Location that contains all points common to both ranges. If the locations overlap and are on the same strand, the intersection is returned.
`Location` | `EmptyRichLocation.intersection(Location l)` Returns a Location that contains all points common to both ranges. ALWAYS RETURNS SELF
`Location` | `CompoundRichLocation.intersection(Location l)` Returns a Location that contains all points common to both ranges. If the locations overlap and are on the same strand, the intersection is returned. If passed a Location which is not a RichLocation, it converts it first using RichLocation.Tools.enrich().
`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` | `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` | `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`. ALWAYS RETURNS PASSED LOCATION
`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`. The default behavior is to return loc unchanged. If the class is a location decorator then it should instantiate an instance of the same type that decorates `loc`. ALWAYS RETURNS SELF
`boolean` | `SimpleRichLocation.overlaps(Location l)` Checks if these two locations overlap, using this location's concept of overlapping. A location overlaps another location if it is on the same sequence, and the coordinates overlap, and both are of the same circularity.
`boolean` | `EmptyRichLocation.overlaps(Location l)` Checks if these two locations overlap, using this location's concept of overlapping. ALWAYS RETURNS FALSE
`boolean` | `CompoundRichLocation.overlaps(Location l)` Checks if these two locations overlap, using this location's concept of overlapping. Abstractly, two locations overlap if they both contain any point. A location overlaps another location if it is on the same sequence, and the coordinates overlap, and both are of the same circularity. Recursively applies this call to all members.
`void` | `SimpleRichFeature.setLocation(Location loc)` The new location for this feature.
`Location` | `SimpleRichLocation.union(Location l)` Return a Location containing all points in either ranges. A merged SimpleRichLocation is returned if the two locations overlap and are on the same strand.
`Location` | `EmptyRichLocation.union(Location l)` Return a Location containing all points in either ranges. ALWAYS RETURNS PASSED LOCATION
`Location` | `CompoundRichLocation.union(Location l)` Return a Location containing all points in either ranges. A merged SimpleRichLocation is returned if the two locations overlap and are on the same strand. If passed a Location which is not a RichLocation, it converts it first using RichLocation.Tools.enrich().

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

Overview | Package | Class | Use | Tree | Deprecated | Index | Help
PREV NEXT | FRAMES NO FRAMES