Uses of Interface
org.biojava.bio.symbol.Location
Packages that use Location
Package
Description
The core classes that will be used throughout the bio packages.
Classes to generate and describe sequence alignments.
HMM and Dynamic Programming Algorithms.
Graphical displays of biological sequences and associated annotations.
Event-driven parsing system for the Extensible Feature Format (XFF).
Classes and interfaces for defining biological sequences and informatics
objects.
The classes and interfaces for defining sequence similarity and
honology.
Standard in-memory implementations of
Sequence
and
Feature
.Classes and interfaces for processing and producing flat-file representations
of sequences.
Classes for converting between AGAVE XML and BioJava objects.
Event-driven parsing system for the Gene Annotation Markup Elements (GAME).
Code for projecting Feature objects and systematically altering their
properties.
Representation of the Symbols that make up a sequence, and locations within
them.
Rich implementations of Sequences, Locations and Features.
-
Uses of Location in org.biojava.bio
Fields in org.biojava.bio declared as LocationModifier and TypeFieldDescriptionstatic final Location
CardinalityConstraint.ANY
The property can have any number of values, including none.static final Location
CardinalityConstraint.NONE
This cardinality contains no intengers, not even zero.static final Location
CardinalityConstraint.ONE
The property should have exactly one value.static final Location
CardinalityConstraint.ONE_OR_MORE
The property should have one or more values.static final Location
CardinalityConstraint.ZERO
The property should have zero values.static final Location
CardinalityConstraint.ZERO_OR_ONE
The property should have zero or one values.Methods in org.biojava.bio that return LocationModifier and TypeMethodDescriptionCollectionConstraint.AllValuesIn.getCardinalityConstraint()
Get the cardinality constraint used to validate the number of property values.CollectionConstraint.Contains.getCardinalityConstraint()
Get the cardinality constraint used to validate the number of property values.Methods in org.biojava.bio with parameters of type LocationModifier and TypeMethodDescriptionvoid
AnnotationType.Abstract.setConstraints
(Object key, PropertyConstraint pc, Location cc) void
AnnotationType.setConstraints
(Object key, PropertyConstraint con, Location card) Set the constraints associated with a property.void
AnnotationType.Abstract.setDefaultConstraints
(PropertyConstraint pc, Location cc) void
AnnotationType.setDefaultConstraints
(PropertyConstraint pc, Location cc) Set the constraints that will apply to all properties without an explicitly defined set of constraints.Constructors in org.biojava.bio with parameters of type LocationModifierConstructorDescriptionAllValuesIn
(PropertyConstraint pc, Location card) Create an AllValuesIn based upon a PropertyConstraint and a cardinality.Contains
(PropertyConstraint pc, Location card) Create a Contains based upon a PropertyConstraint and a cardinality.Impl
(PropertyConstraint defaultPC, Location defaultCC) Create a new Impl with a default property and cardinality constraint. -
Uses of Location in org.biojava.bio.alignment
Fields in org.biojava.bio.alignment declared as LocationModifier and TypeFieldDescriptionprotected Location
FlexibleAlignment.alignmentRange
protected Location
SimpleAlignmentElement.loc
Methods in org.biojava.bio.alignment that return LocationModifier and TypeMethodDescriptionAlignmentElement.getLoc()
SimpleAlignmentElement.getLoc()
AbstractULAlignment.SubULAlignment.locInAlignment
(Object label) The location of an individual SymbolList relative to overall AlignmentFlexibleAlignment.locInAlignment
(Object label) The location of an individual SymbolList relative to overall AlignmentUnequalLengthAlignment.locInAlignment
(Object label) The location of an individual SymbolList relative to overall Alignmentprotected Location
Methods in org.biojava.bio.alignment with parameters of type LocationModifier and TypeMethodDescriptionAbstractULAlignment.labelsInRange
(Location loc) AbstractULAlignment.SubULAlignment.labelsInRange
(Location loc) UnequalLengthAlignment.labelsInRange
(Location loc) Returns list of all the labels that intersect that rangeprotected Location
void
void
void
EditableAlignment.shiftAtAlignmentLoc
(Object label, Location loc, int offset) loc in this case is the Alignment Locationvoid
FlexibleAlignment.shiftAtAlignmentLoc
(Object label, Location loc, int offset) loc in this case is the Alignment Locationvoid
EditableAlignment.shiftAtSequenceLoc
(Object label, Location loc, int offset) loc in this case is the SymbolList Locationvoid
FlexibleAlignment.shiftAtSequenceLoc
(Object label, Location loc, int offset) loc in this case is the SymbolList LocationAbstractULAlignment.subAlignment
(Set<String> labels, Location loc) Retrieves a subalignment specified by the location.AbstractULAlignment.SubULAlignment.subAlignment
(Set<String> labels, Location loc) Alignment.subAlignment
(Set<String> labels, Location loc) Make a view onto this alignment.SimpleAlignment.subAlignment
(Set<String> labels, Location loc) Constructors in org.biojava.bio.alignment with parameters of type LocationModifierConstructorDescriptionSimpleAlignmentElement
(String label, SymbolList seq, Location loc) protected
SubULAlignment
(Set<String> labels, Location loc) -
Uses of Location in org.biojava.bio.dp
Methods in org.biojava.bio.dp with parameters of type Location -
Uses of Location in org.biojava.bio.gui.sequence
Methods in org.biojava.bio.gui.sequence that return LocationModifier and TypeMethodDescriptionstatic Location
GUITools.getVisibleRange
(SequenceRenderContext src, Graphics2D g2) Methods in org.biojava.bio.gui.sequence with parameters of type LocationModifier and TypeMethodDescriptionvoid
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 LocationModifier and TypeMethodDescriptionprotected 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 LocationModifier and TypeFieldDescriptionComponentFeature.Template.componentLocation
Feature.Template.location
Methods in org.biojava.bio.seq that return LocationModifier and TypeMethodDescriptionstatic Location
FilterUtils.extractOverlappingLocation
(FeatureFilter ff) Try to determine the minimal location which all features matching a given filter must overlap.ComponentFeature.getComponentLocation()
Return a location which identifies a portion of the component sequence which is to be included in the assembly.Feature.getLocation()
The location of this feature.FeatureFilter.ContainedByLocation.getLocation()
FeatureFilter.OverlapsLocation.getLocation()
FeatureFilter.ShadowContainedByLocation.getLocation()
FeatureFilter.ShadowOverlapsLocation.getLocation()
RemoteFeature.Region.getLocation()
Retrieve the Location of the Region.Methods in org.biojava.bio.seq with parameters of type LocationModifier and TypeMethodDescriptionstatic final FeatureFilter
FilterUtils.containedByLocation
(Location loc) Construct a filter which matches features with locations wholly contained by the specifiedLocation
.static final FeatureFilter
FilterUtils.overlapsLocation
(Location loc) Construct a filter which matches features with locations contained by or overlapping the specifiedLocation
.void
Feature.setLocation
(Location loc) The new location for this feature.static final FeatureFilter
FilterUtils.shadowContainedByLocation
(Location loc) Construct a filter which matches features with locations where the interval between themin
andmax
positions are contained by the specifiedLocation
.static final FeatureFilter
FilterUtils.shadowOverlapsLocation
(Location loc) Construct a filter which matches features with locations where the interval between themin
andmax
positions are contained by or overlap the specifiedLocation
.Constructors in org.biojava.bio.seq with parameters of type LocationModifierConstructorDescriptionCreates a filter that returns everything contained within loc.OverlapsLocation
(Location loc) Creates a filter that returns everything overlapping loc.Create a new Region.Creates a filter that returns everything contained within loc.Creates a filter that returns everything overlapping loc. -
Uses of Location in org.biojava.bio.seq.homol
Methods in org.biojava.bio.seq.homol with parameters of type LocationModifier and TypeMethodDescriptionSimilarityPairFeature.EmptyPairwiseAlignment.subAlignment
(Set<String> labels, Location loc) -
Uses of Location in org.biojava.bio.seq.impl
Methods in org.biojava.bio.seq.impl that return LocationModifier and TypeMethodDescriptionSimpleFeature.getLocation()
SimpleGappedSequence.GappedContext.mapLocation
(Location loc) SimpleGappedSequence.GappedContext.projectLocation
(Location loc) SubSequence.SubProjectedFeatureContext.projectLocation
(Location toTransform) SimpleGappedSequence.GappedContext.revertLocation
(Location oldLoc) Methods in org.biojava.bio.seq.impl with parameters of type LocationModifier and TypeMethodDescriptionSimpleGappedSequence.GappedContext.mapLocation
(Location loc) SimpleGappedSequence.GappedContext.projectLocation
(Location loc) SubSequence.SubProjectedFeatureContext.projectLocation
(Location toTransform) void
AssembledSymbolList.putComponent
(Location l, SymbolList sl) void
AssembledSymbolList.removeComponent
(Location loc) 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 LocationModifier and TypeMethodDescriptionSeqFileFormer.formatLocation
(StringBuffer sb, Location loc, StrandedFeature.Strand strand) Deprecated.formatLocation
creates a String representation of aLocation
.SwissprotFileFormer.formatLocation
(StringBuffer theBuffer, Location theLocation) Deprecated.formatLocation
creates a String representation of aLocation
.SwissprotFileFormer.formatLocation
(StringBuffer theBuffer, Location theLocation, StrandedFeature.Strand theStrand) Deprecated.formatLocation
creates a String representation of aLocation
. -
Uses of Location in org.biojava.bio.seq.io.agave
Methods in org.biojava.bio.seq.io.agave with parameters of type LocationModifier and TypeMethodDescriptionvoid
AGAVEBioSeqCallbackItf.reportFeature
(Location loc) Allows nesting class that manages a gene template to gain information about its extent from nested elements.void
AGAVEBioSeqHandler.reportFeature
(Location loc) void
AGAVEBioSequenceHandler.reportFeature
(Location loc) void
AGAVECompResultHandler.reportFeature
(Location loc) void
AGAVEFeatureCallbackItf.reportFeature
(Location loc) void
AGAVEFragmentOrderHandler.reportFeature
(Location loc) void
AGAVEFragmentOrientationHandler.reportFeature
(Location loc) void
AGAVEGeneHandler.reportFeature
(Location loc) void
AGAVESeqFeatureHandler.reportFeature
(Location loc) -
Uses of Location in org.biojava.bio.seq.io.game
Methods in org.biojava.bio.seq.io.game with parameters of type LocationModifier and TypeMethodDescriptionvoid
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 LocationModifier and TypeMethodDescriptionstatic Location
ProjectionUtils.flipLocation
(Location oldLoc, int translation) Flip a location.TranslateFlipContext.projectLocation
(Location oldLoc) static Location
ProjectionUtils.revertLocation
(Location oldLoc, int translation, boolean oppositeStrand) Revert a location, translating and flipping as required.final Location
TranslateFlipContext.revertLocation
(Location oldLoc) static Location
ProjectionUtils.transformLocation
(Location oldLoc, int translation, boolean oppositeStrand) Transform a location, translating and flipping as required.Methods in org.biojava.bio.seq.projection with parameters of type LocationModifier and TypeMethodDescriptionstatic Location
ProjectionUtils.flipLocation
(Location oldLoc, int translation) Flip a location.TranslateFlipContext.projectLocation
(Location oldLoc) static Location
ProjectionUtils.revertLocation
(Location oldLoc, int translation, boolean oppositeStrand) Revert a location, translating and flipping as required.final Location
TranslateFlipContext.revertLocation
(Location oldLoc) static Location
ProjectionUtils.transformLocation
(Location oldLoc, int translation, boolean oppositeStrand) Transform a location, translating and flipping as required. -
Uses of Location in org.biojava.bio.symbol
Classes in org.biojava.bio.symbol that implement LocationModifier and TypeClassDescriptionclass
An abstract implementation ofLocation
.class
AbstractLocation
decorator (wrapper).class
Base class for simple contiguous Location implementations.class
Between view onto an underlying Location instance.class
Circular view onto an underlying Location instance.class
A 'fuzzy' location a-la Embl fuzzy locations.class
FuzzyPointLocation
represents two types of EMBL-style partially-defined locations.class
Produced by LocationTools as a result of union operations.class
A location representing a single point.class
A simple implementation of Location that contains all points between getMin and getMax inclusive.Fields in org.biojava.bio.symbol declared as LocationModifier and TypeFieldDescriptionstatic final Location
Location.empty
TheLocation
which contains no points.static final Location
Location.full
TheLocation
which contains all points.Methods in org.biojava.bio.symbol that return LocationModifier and TypeMethodDescriptionprotected abstract Location
protected Location
protected Location
static Location
Flips a location relative to a length.SimpleGappedSymbolList.gappedToLocation
(Location l) Translates a Location from the gapped view into the underlying sequence.AbstractLocation.getDecorator
(Class decoratorClass) AbstractLocationDecorator.getDecorator
(Class decoratorClass) Location.getDecorator
(Class decoratorClass) Checks the decorator chain for an instance ofdecoratorClass and return it if found.GappedSymbolList.getUngappedLocation()
Get a Location that contains exactly those positions that are not gaps.SimpleGappedSymbolList.getUngappedLocation()
protected final Location
AbstractLocationDecorator.getWrapped()
AbstractLocation.intersection
(Location loc) AbstractLocationDecorator.intersection
(Location l) CircularLocation.intersection
(Location l) FuzzyPointLocation.intersection
(Location loc) Location.intersection
(Location l) Returns a Location that contains all points common to both ranges.static Location
LocationTools.intersection
(Location locA, Location locB) Return the intersection of two locations.SimpleGappedSymbolList.locationToGapped
(Location l) Translate a Location onto the gapped view, splitting blocks if necessarystatic Location
LocationTools.makeLocation
(int min, int max) Return a contiguous Location from min to max.AbstractLocation.newInstance
(Location loc) AbstractLocationDecorator.newInstance
(Location loc) Location.newInstance
(Location loc) Create a new instance of Location with all of the same decorators as this instance but with the data stored inloc
.static Location
Return a contiguous location running from the minimum to the maximum points of the specified location.static Location
Subtract one location from another.AbstractLocationDecorator.translate
(int dist) FuzzyLocation.translate
(int dist) FuzzyPointLocation.translate
(int dist) Location.translate
(int dist) Create a location that is a translation of this location.PointLocation.translate
(int dist) RangeLocation.translate
(int dist) Return a Location containing all points in either ranges.static Location
LocationTools.union
(Collection locs) The n-way union of a Collection of locations.static Location
Return the union of two locations.Methods in org.biojava.bio.symbol that return types with arguments of type LocationModifier and TypeMethodDescriptionLocation.blockIterator()
Return an Iterator over the set of maximal contiguous sub-locations.Methods in org.biojava.bio.symbol with parameters of type LocationModifier and TypeMethodDescriptionstatic boolean
Return whether two locations are equal.static int
LocationTools.blockCount
(Location loc) Return the number of contiguous blocks in a location.static boolean
Determines whether the locations are touching or not (if they could be merged in a single Location.boolean
boolean
boolean
boolean
boolean
Checks if this location contains the other.static boolean
Returntrue
iff all indices inlocB
are also contained bylocA
.static int
Return the number of positions which are covered by aLocation
protected abstract Location
protected Location
protected Location
boolean
static Location
Flips a location relative to a length.SimpleGappedSymbolList.gappedToLocation
(Location l) Translates a Location from the gapped view into the underlying sequence.AbstractLocation.intersection
(Location loc) AbstractLocationDecorator.intersection
(Location l) CircularLocation.intersection
(Location l) FuzzyPointLocation.intersection
(Location loc) Location.intersection
(Location l) Returns a Location that contains all points common to both ranges.static Location
LocationTools.intersection
(Location locA, Location locB) Return the intersection of two locations.SimpleGappedSymbolList.locationToGapped
(Location l) Translate a Location onto the gapped view, splitting blocks if necessarystatic MergeLocation
MergeLocation.mergeLocations
(Location locA, Location locB) AbstractLocation.newInstance
(Location loc) AbstractLocationDecorator.newInstance
(Location loc) Location.newInstance
(Location loc) Create a new instance of Location with all of the same decorators as this instance but with the data stored inloc
.boolean
boolean
boolean
boolean
boolean
Checks if these two locations overlap, using this location's concept of overlapping.static boolean
Determines whether the locations overlap or not.static Location
Return a contiguous location running from the minimum to the maximum points of the specified location.RelabeledAlignment.subAlignment
(Set<String> labels, Location loc) static Location
Subtract one location from another.Return a Location containing all points in either ranges.static Location
Return the union of two locations.Constructors in org.biojava.bio.symbol with parameters of type LocationModifierConstructorDescriptionprotected
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 CircularLocationsCircularLocation
(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.seqModifier and TypeInterfaceDescriptioninterface
Describes locations, and adds the concepts of circularity, fuzziness, annotations, and cross-references to other databases.Classes in org.biojavax.bio.seq that implement LocationModifier and TypeClassDescriptionclass
An implementation of RichLocation which covers multiple locations, but on the same strand of the same (optionally circular) sequence.class
An Empty implementation of RichLocation.class
An implementation of RichLocation which possibly covers multiple locations, on different strands, different circular lengths, or different sequences.class
A simple implementation of RichLocation.Methods in org.biojavax.bio.seq that return LocationModifier and TypeMethodDescriptionCompoundRichLocation.getDecorator
(Class decoratorClass) Checks the decorator chain for an instance ofdecoratorClass and return it if found.EmptyRichLocation.getDecorator
(Class decoratorClass) Checks the decorator chain for an instance ofdecoratorClass and return it if found.SimpleRichLocation.getDecorator
(Class decoratorClass) Checks the decorator chain for an instance ofdecoratorClass and return it if found.SimpleRichFeature.getLocation()
The location of this feature.CompoundRichLocation.intersection
(Location l) Returns a Location that contains all points common to both ranges.EmptyRichLocation.intersection
(Location l) Returns a Location that contains all points common to both ranges.SimpleRichLocation.intersection
(Location l) Returns a Location that contains all points common to both ranges.CompoundRichLocation.newInstance
(Location loc) Create a new instance of Location with all of the same decorators as this instance but with the data stored inloc
.EmptyRichLocation.newInstance
(Location loc) Create a new instance of Location with all of the same decorators as this instance but with the data stored inloc
.SimpleRichLocation.newInstance
(Location loc) Create a new instance of Location with all of the same decorators as this instance but with the data stored inloc
.CompoundRichLocation.translate
(int dist) Create a location that is a translation of this location.EmptyRichLocation.translate
(int dist) Create a location that is a translation of this location.MultiSourceCompoundRichLocation.translate
(int dist) Create a location that is a translation of this location.SimpleRichLocation.translate
(int dist) Create a location that is a translation of this location.Return a Location containing all points in either ranges.Return a Location containing all points in either ranges.Return a Location containing all points in either ranges.Methods in org.biojavax.bio.seq that return types with arguments of type LocationModifier and TypeMethodDescriptionstatic 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 LocationModifier and TypeMethodDescriptionboolean
Checks if this location contains the other.boolean
Checks if this location contains the other.boolean
Checks if this location contains the other.static RichLocation
Attempts to convert a plain Location into a RichLocation.CompoundRichLocation.intersection
(Location l) Returns a Location that contains all points common to both ranges.EmptyRichLocation.intersection
(Location l) Returns a Location that contains all points common to both ranges.SimpleRichLocation.intersection
(Location l) Returns a Location that contains all points common to both ranges.static int[]
RichLocation.Tools.modulateCircularLocationPair
(Location a, Location b, int seqLength) Takes two circular locations of given length, and shifts them left along the sequence until they sit at the earliest possible point where they still would represent the same sequence.CompoundRichLocation.newInstance
(Location loc) Create a new instance of Location with all of the same decorators as this instance but with the data stored inloc
.EmptyRichLocation.newInstance
(Location loc) Create a new instance of Location with all of the same decorators as this instance but with the data stored inloc
.SimpleRichLocation.newInstance
(Location loc) Create a new instance of Location with all of the same decorators as this instance but with the data stored inloc
.boolean
Checks if these two locations overlap, using this location's concept of overlapping.boolean
Checks if these two locations overlap, using this location's concept of overlapping.boolean
Checks if these two locations overlap, using this location's concept of overlapping.void
SimpleRichFeature.setLocation
(Location loc) The new location for this feature.Return a Location containing all points in either ranges.Return a Location containing all points in either ranges.Return a Location containing all points in either ranges.Method parameters in org.biojavax.bio.seq with type arguments of type LocationModifier and TypeMethodDescriptionstatic 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.