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 FlexibleAlignment.alignmentRange
           
protected  Location SimpleAlignmentElement.loc
           
 

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

Methods in org.biojava.bio.alignment with parameters of type Location
 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 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)
           
 void SimpleAlignmentElement.setLoc(Location nLoc)
           
 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
 

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 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
 Location FeatureFilter.ContainedByLocation.getLocation()
           
 Location FeatureFilter.OverlapsLocation.getLocation()
           
 Location FeatureFilter.ShadowOverlapsLocation.getLocation()
           
 Location FeatureFilter.ShadowContainedByLocation.getLocation()
           
 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.
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.
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)
           
 

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 SimpleFeature.setLocation(Location loc)
           
 void AssembledSymbolList.putComponent(Location l, SymbolList sl)
           
 void AssembledSymbolList.removeComponent(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 AGAVEGeneHandler.reportFeature(Location loc)
           
 void AGAVEFeatureCallbackItf.reportFeature(Location loc)
           
 void AGAVESeqFeatureHandler.reportFeature(Location loc)
           
 void AGAVEBioSeqHandler.reportFeature(Location loc)
           
 void AGAVECompResultHandler.reportFeature(Location loc)
           
 void AGAVEFragmentOrientationHandler.reportFeature(Location loc)
           
 void AGAVEFragmentOrderHandler.reportFeature(Location loc)
           
 void AGAVEBioSequenceHandler.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
 Location ProjectionContext.getLocation(Feature f)
          Get the location of the projected feature
static Location ProjectionUtils.transformLocation(Location oldLoc, int translate, boolean oppositeStrand)
           
 Location ProjectedFeature.getLocation()
           
 

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

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
 Location PointLocation.translate(int dist)
           
 Location FuzzyPointLocation.intersection(Location loc)
           
 Location FuzzyPointLocation.translate(int dist)
           
 Location RangeLocation.translate(int dist)
           
 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 decoratorClass 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 BetweenLocation.decorate(Location loc)
           
 Location FuzzyLocation.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.
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)
           
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)
           
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.
 

Methods in org.biojava.bio.symbol with parameters of type Location
 Alignment RelabeledAlignment.subAlignment(java.util.Set labels, Location loc)
           
static MergeLocation MergeLocation.mergeLocations(Location locA, Location locB)
           
 Alignment SimpleAlignment.subAlignment(java.util.Set labels, Location loc)
           
 boolean FuzzyPointLocation.overlaps(Location loc)
           
 boolean FuzzyPointLocation.contains(Location loc)
           
 boolean FuzzyPointLocation.equals(Location loc)
           
 Location FuzzyPointLocation.intersection(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  Location BetweenLocation.decorate(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.
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)
           
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)
           
 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)
           
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.
 

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