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(java.lang.Object key, PropertyConstraint con, Location card)
          Set the constraints associated with a property.
 void AnnotationType.Abstract.setConstraints(java.lang.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 AbstractULAlignment.SubULAlignment.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
 Location UnequalLengthAlignment.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
 java.util.List AbstractULAlignment.labelsInRange(Location loc)
           
 java.util.List AbstractULAlignment.SubULAlignment.labelsInRange(Location loc)
           
 java.util.List UnequalLengthAlignment.labelsInRange(Location loc)
          Returns list of all the labels that intersect that range
protected  Location FlexibleAlignment.locInSeq(java.lang.Object label, Location viewLoc)
           
 void SimpleAlignmentElement.setLoc(Location nLoc)
           
 void AlignmentElement.setLoc(Location nLoc)
           
 void FlexibleAlignment.shiftAtAlignmentLoc(java.lang.Object label, Location loc, int offset)
          loc in this case is the Alignment Location
 void EditableAlignment.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
 void EditableAlignment.shiftAtSequenceLoc(java.lang.Object label, Location loc, int offset)
          loc in this case is the SymbolList Location
 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)
           
 

Constructors in org.biojava.bio.alignment with parameters of type Location
AbstractULAlignment.SubULAlignment(java.util.Set labels, Location loc)
           
SimpleAlignmentElement(java.lang.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(java.util.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, java.awt.Graphics2D g2)
           
 

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 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 FeatureFilter.ContainedByLocation.getLocation()
           
 Location FeatureFilter.OverlapsLocation.getLocation()
           
 Location FeatureFilter.ShadowOverlapsLocation.getLocation()
           
 Location FeatureFilter.ShadowContainedByLocation.getLocation()
           
 Location Feature.getLocation()
          The location of this feature.
 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)
          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, 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()
           
 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
 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
 java.lang.StringBuffer SwissprotFileFormer.formatLocation(java.lang.StringBuffer theBuffer, Location theLocation)
          Deprecated. formatLocation creates a String representation of a Location.
 java.lang.StringBuffer SwissprotFileFormer.formatLocation(java.lang.StringBuffer theBuffer, Location theLocation, StrandedFeature.Strand theStrand)
          Deprecated. formatLocation creates a String representation of a Location.
 java.lang.StringBuffer SeqFileFormer.formatLocation(java.lang.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 AGAVEGeneHandler.reportFeature(Location loc)
           
 void AGAVEFragmentOrientationHandler.reportFeature(Location loc)
           
 void AGAVEFeatureCallbackItf.reportFeature(Location loc)
           
 void AGAVECompResultHandler.reportFeature(Location loc)
           
 void AGAVEFragmentOrderHandler.reportFeature(Location loc)
           
 void AGAVEBioSequenceHandler.reportFeature(Location loc)
           
 void AGAVESeqFeatureHandler.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.
 void AGAVEBioSeqHandler.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 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 abstract  Location AbstractLocationDecorator.decorate(Location loc)
           
protected  Location BetweenLocation.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 AbstractLocationDecorator.getDecorator(java.lang.Class decoratorClass)
           
 Location Location.getDecorator(java.lang.Class decoratorClass)
          Checks the decorator chain for an instance of decoratorClass and return it if found.
 Location AbstractLocation.getDecorator(java.lang.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 CircularLocation.intersection(Location l)
           
 Location FuzzyPointLocation.intersection(Location loc)
           
 Location AbstractLocationDecorator.intersection(Location l)
           
 Location Location.intersection(Location l)
          Returns a Location that contains all points common to both ranges.
 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 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.
 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 FuzzyLocation.translate(int dist)
           
 Location FuzzyPointLocation.translate(int dist)
           
 Location AbstractLocationDecorator.translate(int dist)
           
 Location Location.translate(int dist)
          Create a location that is a translation of this location.
static Location LocationTools.union(java.util.Collection locs)
          The n-way union of a Collection of locations.
 Location CircularLocation.union(Location l)
           
 Location AbstractLocationDecorator.union(Location l)
           
 Location Location.union(Location l)
          Return a Location containing all points in either ranges.
 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 CircularLocation.contains(Location l)
           
 boolean FuzzyPointLocation.contains(Location loc)
           
 boolean AbstractLocationDecorator.contains(Location l)
           
 boolean Location.contains(Location l)
          Checks if this location contains the other.
 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 abstract  Location AbstractLocationDecorator.decorate(Location loc)
           
protected  Location BetweenLocation.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 CircularLocation.intersection(Location l)
           
 Location FuzzyPointLocation.intersection(Location loc)
           
 Location AbstractLocationDecorator.intersection(Location l)
           
 Location Location.intersection(Location l)
          Returns a Location that contains all points common to both ranges.
 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 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.
 Location AbstractLocation.newInstance(Location loc)
           
 boolean CircularLocation.overlaps(Location l)
           
 boolean FuzzyPointLocation.overlaps(Location loc)
           
 boolean AbstractLocationDecorator.overlaps(Location l)
           
 boolean Location.overlaps(Location l)
          Checks if these two locations overlap, using this location's concept of overlapping.
 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 RelabeledAlignment.subAlignment(java.util.Set labels, Location loc)
           
 Alignment Alignment.subAlignment(java.util.Set labels, Location loc)
           Make a view onto this alignment.
 Alignment SimpleAlignment.subAlignment(java.util.Set labels, Location loc)
           
static Location LocationTools.subtract(Location keep, Location remove)
          Subtract one location from another.
 Location CircularLocation.union(Location l)
           
 Location AbstractLocationDecorator.union(Location l)
           
 Location Location.union(Location l)
          Return a Location containing all points in either ranges.
 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(java.lang.Class decoratorClass)
          Checks the decorator chain for an instance of decoratorClass and return it if found.
 Location EmptyRichLocation.getDecorator(java.lang.Class decoratorClass)
          Checks the decorator chain for an instance of decoratorClass and return it if found. ALWAYS RETURNS NULL
 Location CompoundRichLocation.getDecorator(java.lang.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 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 SimpleRichLocation.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. 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 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().