Uses of Interface
org.biojava.bio.seq.Feature

Packages that use Feature

org.biojava.bio.gui.sequence	Graphical displays of biological sequences and associated annotations.
org.biojava.bio.molbio	The classes and interfaces in this package cover common molecular biological techniques such as restriction digests and PCR.
org.biojava.bio.program.das	Development client for the Distributed Annotation System.
org.biojava.bio.program.gff	GFF manipulation.
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.projection	Code for projecting Feature objects and systematically altering their properties.

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

Methods in org.biojava.bio.gui.sequence with parameters of type Feature

void	ZiggyImapRenderer.renderImageMap(Graphics2D g2, Feature f, SequenceRenderContext context) renderImageMap writes a set of image map coordinates corresponding to the rectangle sections drawn by the renderer.
void	ZiggyImapRenderer.renderFeature(Graphics2D g2, Feature f, SequenceRenderContext context)
void	ZiggyFeatureRenderer.renderFeature(Graphics2D g, Feature f, SequenceRenderContext context)
void	TickFeatureRenderer.renderFeature(Graphics2D g, Feature f, SequenceRenderContext src)
void	StackedFeatureRenderer.renderFeature(Graphics2D g, Feature f, SequenceRenderContext src)
void	SixFrameZiggyRenderer.renderFeature(Graphics2D g, Feature f, SequenceRenderContext context)
void	RoundRectangularBeadRenderer.renderBead(Graphics2D g2, Feature f, SequenceRenderContext context) renderBead renders features as a rectangle with rounded corners.
void	RectangularImapRenderer.renderImageMap(Graphics2D g2, Feature f, SequenceRenderContext context) renderImageMap writes a set of image map coordinates corresponding to the rectangle drawn by the renderer.
void	RectangularImapRenderer.renderFeature(Graphics2D g2, Feature f, SequenceRenderContext context)
void	RectangularImapRenderer.renderBead(Graphics2D g2, Feature f, SequenceRenderContext context)
void	RectangularBeadRenderer.renderBead(Graphics2D g2, Feature f, SequenceRenderContext context) renderBead renders features as simple rectangle.
void	ImageMapRenderer.renderImageMap(Graphics2D g2, Feature f, SequenceRenderContext context) renderImageMap renders the Feature as set of image map hotspots.
void	FeatureRenderer.renderFeature(Graphics2D g2, Feature feat, SequenceRenderContext context)
void	FeatureLabelRenderer.renderFeature(Graphics2D g, Feature feat, SequenceRenderContext src)
String	FeatureLabelRenderer.LabelMaker.makeLabel(Feature f)
String	FeatureLabelRenderer.SourceLabelMaker.makeLabel(Feature f)
String	FeatureLabelRenderer.TypeLabelMaker.makeLabel(Feature f)
String	FeatureLabelRenderer.AnnotationLabelMaker.makeLabel(Feature feat)
void	EllipticalBeadRenderer.renderBead(Graphics2D g2, Feature f, SequenceRenderContext context) renderBead renders features as simple ellipse.
void	CircularFeatureRenderer.renderFeature(Graphics2D g, Feature f, CircularRendererContext context)
void	BeadFeatureRenderer.renderBead(Graphics2D g2, Feature f, SequenceRenderContext context) renderBead should implement rendering for this bead type only.
void	BasicImapRenderer.renderImageMap(Graphics2D g2, Feature f, SequenceRenderContext context) renderImageMap writes a set of image map coordinates corresponding to the rectangle sections drawn by the renderer.
void	BasicImapRenderer.renderFeature(Graphics2D g2, Feature f, SequenceRenderContext context)
void	BasicFeatureRenderer.renderFeature(Graphics2D g, Feature f, SequenceRenderContext src)
void	AbstractBeadRenderer.renderFeature(Graphics2D g2, Feature f, SequenceRenderContext context) renderFeature draws a feature using the supplied graphics context.
abstract void	AbstractBeadRenderer.renderBead(Graphics2D g2, Feature f, SequenceRenderContext context) renderBead should be overridden by the concrete BeadRenderer.

Uses of Feature in org.biojava.bio.molbio

Subinterfaces of Feature in org.biojava.bio.molbio

interface

RestrictionSite RestrictionSite represents the recognition site of a restriction enzyme.

Uses of Feature in org.biojava.bio.program.das

Methods in org.biojava.bio.program.das that return Feature

Feature	DASSequence.createFeature(Feature.Template temp)
Feature	DASSequence.realizeFeature(FeatureHolder dest, Feature.Template temp)

Methods in org.biojava.bio.program.das with parameters of type Feature

boolean	DASSequence.containsFeature(Feature f)
void	DASSequence.removeFeature(Feature f)

Uses of Feature in org.biojava.bio.program.gff

Methods in org.biojava.bio.program.gff with parameters of type Feature

protected void	SequencesAsGFF.doProcessFeature(Feature feature, GFFDocumentHandler handler, String id) Internal method to process an individual Feature.
protected SimpleGFFRecord	SequencesAsGFF.createGFFRecord(Feature feature, String id) Internal method to create a GFFRecord from an individual Feature.

Uses of Feature in org.biojava.bio.program.xff

Methods in org.biojava.bio.program.xff with parameters of type Feature

String	XFFHelper.getFeatureID(Feature f)
void	XFFHelper.writeDetails(XMLWriter xw, Feature f)
void	PropertyWriter.writeDetails(XMLWriter xw, Feature f)
String	BasicXFFHelper.getFeatureID(Feature f)
void	BasicXFFHelper.writeDetails(XMLWriter xw, Feature f)

Uses of Feature in org.biojava.bio.seq

Subinterfaces of Feature in org.biojava.bio.seq

interface	ComponentFeature Feature which represents a component in an assembly (contig).
interface	FramedFeature Title: FramedFeature.
interface	RemoteFeature A feature that indicates that there is some remote feature that can't be represented entirely on a single Sequence.
interface	StrandedFeature Adds the concept of 'strand' to features.

Methods in org.biojava.bio.seq that return Feature

Feature	SimpleFeatureRealizer.realizeFeature(Sequence seq, FeatureHolder parent, Feature.Template temp)
Feature	SimpleAssembly.createFeature(Feature.Template temp)
Feature	SimpleAssembly.realizeFeature(FeatureHolder fh, Feature.Template temp)
Feature	RemoteFeature.getRemoteFeature() Retrieve the Feature on some assembly Sequence that can represent this RemoteFeature properly.
Feature	RemoteFeature.Resolver.resolve(RemoteFeature rFeat) Resolve rFeat.
Feature	RealizingFeatureHolder.realizeFeature(FeatureHolder parent, Feature.Template template) Realize a feature template.
Feature	NewSimpleAssembly.createFeature(Feature.Template temp)
Feature	NewSimpleAssembly.realizeFeature(FeatureHolder fh, Feature.Template temp)
Feature	LazyFeatureHolder.createFeature(Feature.Template template)
Feature	FeatureRealizer.realizeFeature(Sequence seq, FeatureHolder parent, Feature.Template template) Install a feature on the specified sequence.
Feature	FeatureHolder.createFeature(Feature.Template ft) Create a new Feature, and add it to this FeatureHolder.
Feature	FeatureHolder.EmptyFeatureHolder.createFeature(Feature.Template f)
Feature	FeatureFilter.ByFeature.getFeature()
Feature	CircularView.createFeature(Feature.Template template) Over rides ViewSequence to allow the use of locations that have coordinates outside of the sequence length (which are needed to describe locations that overlap the origin of a circular sequence).
Feature	AbstractFeatureHolder.createFeature(Feature.Template temp)

Methods in org.biojava.bio.seq with parameters of type Feature

void	SimpleFeatureHolder.addFeature(Feature f) Add a feature to the featureholder
void	SimpleFeatureHolder.removeFeature(Feature f)
boolean	SimpleFeatureHolder.containsFeature(Feature f)
boolean	SimpleAssembly.containsFeature(Feature f)
void	SimpleAssembly.removeFeature(Feature f)
boolean	NewSimpleAssembly.containsFeature(Feature f)
void	NewSimpleAssembly.removeFeature(Feature f)
boolean	MergeFeatureHolder.containsFeature(Feature f)
void	LazyFeatureHolder.removeFeature(Feature f)
boolean	LazyFeatureHolder.containsFeature(Feature f)
void	FeatureHolder.removeFeature(Feature f) Remove a feature from this FeatureHolder.
boolean	FeatureHolder.containsFeature(Feature f) Check if the feature is present in this holder.
void	FeatureHolder.EmptyFeatureHolder.removeFeature(Feature f)
boolean	FeatureHolder.EmptyFeatureHolder.containsFeature(Feature f)
boolean	FeatureFilter.accept(Feature f) This method determines whether a feature is to be accepted.
boolean	FeatureFilter.Not.accept(Feature f)
boolean	FeatureFilter.And.accept(Feature f)
boolean	FeatureFilter.Or.accept(Feature f)
boolean	FeatureFilter.ByType.accept(Feature f) Returns true if the feature has a matching type property.
boolean	FeatureFilter.BySource.accept(Feature f)
boolean	FeatureFilter.ByClass.accept(Feature f)
boolean	FeatureFilter.StrandFilter.accept(Feature f) Accept the Feature if it is an instance of StrandedFeature and matches the value of getStrand().
boolean	FeatureFilter.BySequenceName.accept(Feature f)
boolean	FeatureFilter.ContainedByLocation.accept(Feature f) Returns true if the feature is within this filter's location.
boolean	FeatureFilter.OverlapsLocation.accept(Feature f) Returns true if the feature overlaps this filter's location.
boolean	FeatureFilter.ShadowOverlapsLocation.accept(Feature f) Returns true if the feature overlaps this filter's location.
boolean	FeatureFilter.ShadowContainedByLocation.accept(Feature f) Returns true if the feature is within this filter's location.
boolean	FeatureFilter.ByAnnotationType.accept(Feature f)
boolean	FeatureFilter.ByParent.accept(Feature f)
boolean	FeatureFilter.ByAncestor.accept(Feature f)
boolean	FeatureFilter.OnlyChildren.accept(Feature f)
boolean	FeatureFilter.OnlyDescendants.accept(Feature f)
boolean	FeatureFilter.ByChild.accept(Feature f)
boolean	FeatureFilter.ByDescendant.accept(Feature f)
boolean	FeatureFilter.FrameFilter.accept(Feature f) Accept the Feature if it is an instance of FramedFeature and matches the value of getFrame().
boolean	FeatureFilter.ByPairwiseScore.accept(Feature f) Accept a Feature if it is an instance of SimilarityPairFeature and its score is <= filter's minimum score and >= filter's maximum score.
boolean	FeatureFilter.ByComponentName.accept(Feature f)
boolean	FeatureFilter.ByFeature.accept(Feature f)
void	AbstractFeatureHolder.removeFeature(Feature f)

Constructors in org.biojava.bio.seq with parameters of type Feature

FeatureFilter.ByFeature(Feature f)

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

Subinterfaces of Feature in org.biojava.bio.seq.homol

interface	HomologyFeature
interface	SimilarityPairFeature SimilarityPairFeature describes a pairwise similarity between two nucleotide sequences (as it extends StrandedFeature).

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

Classes in org.biojava.bio.seq.impl that implement Feature

class	SimpleFeature A no-frills implementation of a feature.
class	SimpleFramedFeature Title: SimpleFramedFeature.
class	SimpleHomologyFeature
class	SimpleRemoteFeature A no-frills implementation of a remote feature.
class	SimpleRestrictionSite SimpleRestrictionSite represents the recognition site of a restriction enzyme.
class	SimpleSimilarityPairFeature SimpleSimilarityPairFeature represents a similarity between a query sequence and a subject sequence as produced by a search program.
class	SimpleStrandedFeature A no-frills implementation of StrandedFeature.

Methods in org.biojava.bio.seq.impl that return Feature

Feature	ViewSequence.realizeFeature(FeatureHolder parent, Feature.Template template)
Feature	ViewSequence.createFeature(Feature.Template template)
Feature	SubSequence.createFeature(Feature.Template templ)
Feature	SubSequence.SubProjectedFeatureContext.projectFeature(Feature origFeat)
Feature	SubSequence.SubProjectedFeatureContext.revertFeature(Feature projFeat)
Feature	SimpleSequence.realizeFeature(FeatureHolder parent, Feature.Template template)
Feature	SimpleSequence.createFeature(Feature.Template template)
Feature	SimpleSequence.createFeature(FeatureHolder fh, Feature.Template template) Deprecated. Please use new 1-arg createFeature instead.
Feature	SimpleRemoteFeature.getRemoteFeature()
Feature	SimpleRemoteFeature.DBResolver.resolve(RemoteFeature rFeat)
Feature	SimpleGappedSequence.createFeature(Feature.Template templ)
Feature	SimpleFeature.realizeFeature(FeatureHolder fh, Feature.Template templ)
Feature	SimpleFeature.createFeature(Feature.Template temp)
Feature	RevCompSequence.createFeature(Feature.Template ft) createFeature() will call createFeature() on the underlying Sequence.
Feature	RevCompSequence.getFeatureFromOriginal(Feature f) getFeatureFromOriginal() Since you can not create a feature on a projectedFeature at this time, I am including this method so that you can get the corresponding feature from the original sequence.
Feature	LazyFilterFeatureHolder.createFeature(Feature.Template temp)
Feature	DummySequence.createFeature(Feature.Template template)

Methods in org.biojava.bio.seq.impl with parameters of type Feature

void	ViewSequence.removeFeature(Feature f) Remove a feature from this sequence.
boolean	ViewSequence.containsFeature(Feature f)
static Feature.Template	TemplateUtils.instantiateTemplate(Feature feat) This attempts to divine the 'best' template class for a feature and return a new instance readly for pupulating.
static void	TemplateUtils.populate(Feature.Template templ, Feature feat) This attempts to populate the fields of a template using the publically accessible information in a feature.
static Feature.Template	TemplateUtils.makeTemplate(Feature feat)
boolean	SubSequence.containsFeature(Feature f)
void	SubSequence.removeFeature(Feature f)
Feature	SubSequence.SubProjectedFeatureContext.projectFeature(Feature origFeat)
Feature	SubSequence.SubProjectedFeatureContext.revertFeature(Feature projFeat)
FeatureHolder	SubSequence.SubProjectedFeatureContext.projectChildFeatures(Feature f, FeatureHolder parent)
boolean	SimpleSequence.containsFeature(Feature f)
void	SimpleSequence.removeFeature(Feature f) Remove a feature attached to this sequence.
boolean	SimpleGappedSequence.containsFeature(Feature f)
void	SimpleGappedSequence.removeFeature(Feature f)
void	SimpleFeature.removeFeature(Feature f)
boolean	SimpleFeature.containsFeature(Feature f)
boolean	RevCompSequence.containsFeature(Feature f) containsFeature() will return true if this seq contains the feature in question, or if if the original (non reverse complement) sequence contains the feature;
void	RevCompSequence.removeFeature(Feature f)
Feature	RevCompSequence.getFeatureFromOriginal(Feature f) getFeatureFromOriginal() Since you can not create a feature on a projectedFeature at this time, I am including this method so that you can get the corresponding feature from the original sequence.
boolean	LazyFilterFeatureHolder.containsFeature(Feature f)
void	LazyFilterFeatureHolder.removeFeature(Feature f)
void	DummySequence.removeFeature(Feature feature)
boolean	DummySequence.containsFeature(Feature feature)

Uses of Feature in org.biojava.bio.seq.io

Methods in org.biojava.bio.seq.io with parameters of type Feature

String	SwissprotFileFormer.formatLocation(Feature theFeature) Creates a string representation of the location of a feature
String	SeqFileFormer.formatLocation(Feature theFeature) Formats the location of a feature.

Uses of Feature in org.biojava.bio.seq.io.agave

Methods in org.biojava.bio.seq.io.agave with parameters of type Feature

protected void

StAXFeatureHandler.realizeSubFeatures(Feature feature) recursively attach children features to parent

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

Classes in org.biojava.bio.seq.projection that implement Feature

class

ProjectedFeature Internal class used by ProjectionEngine to wrap Feature objects.

Methods in org.biojava.bio.seq.projection that return Feature

Feature	ReparentContext.projectFeature(Feature feat) Create a single projected feature using the rules of this ProjectedFeatureHolder.
Feature	ReparentContext.revertFeature(Feature feat)
Feature	ReparentContext.createFeature(Feature.Template projTempl)
Feature	ReparentContext.createFeature(Feature f, Feature.Template projTempl)
Feature	ProjectionEngine.projectFeature(Feature f, ProjectionContext ctx) Return a projection of Feature f into the system defined by a given ProjectionContext.
Feature	ProjectionContext.projectFeature(Feature feat) Project a single feature.
Feature	ProjectionContext.revertFeature(Feature projFeat) Unproject a feature.
Feature	ProjectionContext.createFeature(Feature.Template projTempl) Create a projected feature with properties matching the template.
Feature	ProjectionContext.createFeature(Feature projParent, Feature.Template projTempl) Create a new projected feature.
Feature	Projection.getViewedFeature()
Feature	ProjectedFeatureHolder.createFeature(Feature.Template templ)
Feature	ProjectedFeature.getViewedFeature()
Feature	ProjectedFeature.createFeature(Feature.Template temp)

Methods in org.biojava.bio.seq.projection with parameters of type Feature

Feature	ReparentContext.projectFeature(Feature feat) Create a single projected feature using the rules of this ProjectedFeatureHolder.
Feature	ReparentContext.revertFeature(Feature feat)
FeatureHolder	ReparentContext.getParent(Feature f)
Sequence	ReparentContext.getSequence(Feature f)
FeatureHolder	ReparentContext.projectChildFeatures(Feature f, FeatureHolder parent)
void	ReparentContext.removeFeature(Feature dyingChild)
Feature	ReparentContext.createFeature(Feature f, Feature.Template projTempl)
void	ReparentContext.removeFeature(Feature f, Feature f2)
FeatureFilter	ReparentContext.getSchema(Feature f)
void	ReparentContext.addChangeListener(Feature f, ChangeListener cl, ChangeType ct)
void	ReparentContext.removeChangeListener(Feature f, ChangeListener cl, ChangeType ct)
Feature	ProjectionEngine.projectFeature(Feature f, ProjectionContext ctx) Return a projection of Feature f into the system defined by a given ProjectionContext.
FeatureHolder	ProjectionContext.getParent(Feature projFeat)
Sequence	ProjectionContext.getSequence(Feature projFeat) Get the sequence for a feature.
Feature	ProjectionContext.projectFeature(Feature feat) Project a single feature.
Feature	ProjectionContext.revertFeature(Feature projFeat) Unproject a feature.
FeatureHolder	ProjectionContext.projectChildFeatures(Feature feature, FeatureHolder parent) Project all features that are children of feature so that they become children of parent.
void	ProjectionContext.removeFeature(Feature dyingChild) Remove the dying child.
Feature	ProjectionContext.createFeature(Feature projParent, Feature.Template projTempl) Create a new projected feature.
void	ProjectionContext.removeFeature(Feature projParent, Feature dyingChild) Remove the dying child.
void	ProjectionContext.addChangeListener(Feature projFeat, ChangeListener cl, ChangeType ct) Add a ChangeListener to a projected feature.
void	ProjectionContext.removeChangeListener(Feature projFeat, ChangeListener cl, ChangeType ct) Remove a ChangeListener from a projected feature.
boolean	ProjectedFeatureHolder.containsFeature(Feature f)
void	ProjectedFeatureHolder.removeFeature(Feature dyingChild)
boolean	ProjectedFeature.containsFeature(Feature f)
void	ProjectedFeature.removeFeature(Feature f)

Constructors in org.biojava.bio.seq.projection with parameters of type Feature

ProjectedFeature(Feature f, ProjectionContext ctx)