## 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.
org.biojavax.bio.db.biosql: Interface between biojava and biosql databases
org.biojavax.bio.seq: Rich implementations of Sequences, Locations and Features.

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

Methods in org.biojava.bio.gui.sequence with parameters of type Feature
`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` `RoundRectangularBeadRenderer.renderBead(Graphics2D g2, Feature f, SequenceRenderContext context)` `renderBead` renders features as a rectangle with rounded corners.
`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` `EllipticalBeadRenderer.renderBead(Graphics2D g2, Feature f, SequenceRenderContext context)` `renderBead` renders features as simple ellipse.
`void` `BeadFeatureRenderer.renderBead(Graphics2D g2, Feature f, SequenceRenderContext context)` `renderBead` should implement rendering for this bead type only.
`abstract void` `AbstractBeadRenderer.renderBead(Graphics2D g2, Feature f, SequenceRenderContext context)` `renderBead` should be overridden by the concrete `BeadRenderer`.
`void` `CircularFeatureRenderer.renderFeature(Graphics2D g, Feature f, CircularRendererContext context)`
`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` `RectangularImapRenderer.renderFeature(Graphics2D g2, Feature f, SequenceRenderContext context)`
`void` `GlyphFeatureRenderer.renderFeature(Graphics2D g2, Feature f, SequenceRenderContext src)`
`void` `FeatureRenderer.renderFeature(Graphics2D g2, Feature feat, SequenceRenderContext context)`
`void` `FeatureLabelRenderer.renderFeature(Graphics2D g, Feature feat, SequenceRenderContext src)`
`void` `BasicImapRenderer.renderFeature(Graphics2D g2, Feature f, SequenceRenderContext context)`
`void` `BasicFeatureRenderer.renderFeature(Graphics2D g, Feature f, SequenceRenderContext src)`
`void` `ArrowedFeatureRenderer.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.
`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` `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` `ImageMapRenderer.renderImageMap(Graphics2D g2, Feature f, SequenceRenderContext context)` `renderImageMap` renders the `Feature` as set of image map hotspots.
`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.

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 SimpleGFFRecord` `SequencesAsGFF.createGFFRecord(Feature feature, String id)` Internal method to create a GFFRecord from an individual Feature.
`protected void` `SequencesAsGFF.doProcessFeature(Feature feature, GFFDocumentHandler handler, String id)` Internal method to process 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)`
`String` `BasicXFFHelper.getFeatureID(Feature f)`
`void` `XFFHelper.writeDetails(XMLWriter xw, Feature f)`
`void` `PropertyWriter.writeDetails(XMLWriter xw, 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` `SimpleAssembly.createFeature(Feature.Template temp)`
`Feature` `NewSimpleAssembly.createFeature(Feature.Template temp)`
`Feature` `LazyFeatureHolder.createFeature(Feature.Template template)`
`Feature` `FeatureHolder.createFeature(Feature.Template ft)` Create a new Feature, and add it to this FeatureHolder.
`Feature` `FeatureHolder.EmptyFeatureHolder.createFeature(Feature.Template f)`
`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)`
`Feature` `FeatureFilter.ByFeature.getFeature()`
`Feature` `RemoteFeature.getRemoteFeature()` Retrieve the Feature on some assembly Sequence that can represent this RemoteFeature properly.
`Feature` `SimpleAssembly.realizeFeature(FeatureHolder fh, Feature.Template temp)`
`Feature` `RealizingFeatureHolder.realizeFeature(FeatureHolder parent, Feature.Template template)` Realize a feature template.
`Feature` `NewSimpleAssembly.realizeFeature(FeatureHolder fh, Feature.Template temp)`
`Feature` `SimpleFeatureRealizer.realizeFeature(Sequence seq, FeatureHolder parent, Feature.Template temp)`
`Feature` `FeatureRealizer.realizeFeature(Sequence seq, FeatureHolder parent, Feature.Template template)` Install a feature on the specified sequence.
`Feature` `RemoteFeature.Resolver.resolve(RemoteFeature rFeat)` Resolve rFeat.

Methods in org.biojava.bio.seq that return types with arguments of type Feature
`Iterator<Feature>` `FeatureHolder.features()` Iterate over the features in no well defined order.
`Iterator<Feature>` `FeatureHolder.EmptyFeatureHolder.features()`

Methods in org.biojava.bio.seq with parameters of type Feature
`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` `SimpleFeatureHolder.addFeature(Feature f)` Add a feature to the featureholder
`boolean` `SimpleFeatureHolder.containsFeature(Feature f)`
`boolean` `SimpleAssembly.containsFeature(Feature f)`
`boolean` `NewSimpleAssembly.containsFeature(Feature f)`
`boolean` `MergeFeatureHolder.containsFeature(Feature f)`
`boolean` `LazyFeatureHolder.containsFeature(Feature f)`
`boolean` `FeatureHolder.containsFeature(Feature f)` Check if the feature is present in this holder.
`boolean` `FeatureHolder.EmptyFeatureHolder.containsFeature(Feature f)`
`void` `SimpleFeatureHolder.removeFeature(Feature f)`
`void` `SimpleAssembly.removeFeature(Feature f)`
`void` `NewSimpleAssembly.removeFeature(Feature f)`
`void` `LazyFeatureHolder.removeFeature(Feature f)`
`void` `FeatureHolder.removeFeature(Feature f)` Remove a feature from this FeatureHolder.
`void` `FeatureHolder.EmptyFeatureHolder.removeFeature(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.createFeature(Feature.Template template)`
`Feature` `SubSequence.createFeature(Feature.Template templ)`
`Feature` `SimpleSequence.createFeature(Feature.Template template)`
`Feature` `SimpleGappedSequence.createFeature(Feature.Template templ)`
`Feature` `SimpleFeature.createFeature(Feature.Template temp)`
`Feature` `RevCompSequence.createFeature(Feature.Template ft)` createFeature() will call createFeature() on the underlying Sequence.
`Feature` `LazyFilterFeatureHolder.createFeature(Feature.Template temp)`
`Feature` `DummySequence.createFeature(Feature.Template template)`
`Feature` `SimpleSequence.createFeature(FeatureHolder fh, Feature.Template template)` Deprecated. Please use new 1-arg createFeature instead.
`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` `SimpleRemoteFeature.getRemoteFeature()`
`Feature` `SubSequence.SubProjectedFeatureContext.projectFeature(Feature origFeat)`
`Feature` `ViewSequence.realizeFeature(FeatureHolder parent, Feature.Template template)`
`Feature` `SimpleSequence.realizeFeature(FeatureHolder parent, Feature.Template template)`
`Feature` `SimpleFeature.realizeFeature(FeatureHolder fh, Feature.Template templ)`
`Feature` `SimpleRemoteFeature.DBResolver.resolve(RemoteFeature rFeat)`
`Feature` `SubSequence.SubProjectedFeatureContext.revertFeature(Feature projFeat)`

Methods in org.biojava.bio.seq.impl with parameters of type Feature
`boolean` `ViewSequence.containsFeature(Feature f)`
`boolean` `SubSequence.containsFeature(Feature f)`
`boolean` `SimpleSequence.containsFeature(Feature f)`
`boolean` `SimpleGappedSequence.containsFeature(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;
`boolean` `LazyFilterFeatureHolder.containsFeature(Feature f)`
`boolean` `DummySequence.containsFeature(Feature feature)`
`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.
`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 Feature.Template` `TemplateUtils.makeTemplate(Feature feat)`
`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.
`FeatureHolder` `SubSequence.SubProjectedFeatureContext.projectChildFeatures(Feature f, FeatureHolder parent)`
`Feature` `SubSequence.SubProjectedFeatureContext.projectFeature(Feature origFeat)`
`void` `ViewSequence.removeFeature(Feature f)` Remove a feature from this sequence.
`void` `SubSequence.removeFeature(Feature f)`
`void` `SimpleSequence.removeFeature(Feature f)` Remove a feature attached to this sequence.
`void` `SimpleGappedSequence.removeFeature(Feature f)`
`void` `SimpleFeature.removeFeature(Feature f)`
`void` `RevCompSequence.removeFeature(Feature f)`
`void` `LazyFilterFeatureHolder.removeFeature(Feature f)`
`void` `DummySequence.removeFeature(Feature feature)`
`Feature` `SubSequence.SubProjectedFeatureContext.revertFeature(Feature projFeat)`

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

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

Constructors in org.biojava.bio.seq.projection with parameters of type Feature
`ProjectedFeature(Feature f, ProjectionContext ctx)`

Uses of Feature in org.biojavax.bio.db.biosql

Methods in org.biojavax.bio.db.biosql with parameters of type Feature
`boolean` `BioSQLFeatureFilter.Not.accept(Feature f)`
`boolean` `BioSQLFeatureFilter.And.accept(Feature f)`
`boolean` `BioSQLFeatureFilter.Or.accept(Feature f)`
`boolean` `BioSQLFeatureFilter.ByName.accept(Feature f)` Returns true if the feature has a matching type property.
`boolean` `BioSQLFeatureFilter.ByRank.accept(Feature f)` Returns true if the feature has a matching type property.
`boolean` `BioSQLFeatureFilter.ByTypeTerm.accept(Feature f)` Returns true if the feature has a matching type property.
`boolean` `BioSQLFeatureFilter.BySourceTerm.accept(Feature f)` Returns true if the feature has a matching source property.
`boolean` `BioSQLFeatureFilter.ByTypeTermName.accept(Feature f)` Returns true if the feature has a matching type property.
`boolean` `BioSQLFeatureFilter.BySourceTermName.accept(Feature f)` Returns true if the feature has a matching source property.
`boolean` `BioSQLFeatureFilter.BySequenceName.accept(Feature f)`
`boolean` `BioSQLFeatureFilter.ContainedByRichLocation.accept(Feature f)` Returns true if the feature is within this filter's location.
`boolean` `BioSQLFeatureFilter.ByStrand.accept(Feature f)` Returns true if the feature overlaps this filter's location.
`boolean` `BioSQLFeatureFilter.OverlapsRichLocation.accept(Feature f)` Returns true if the feature overlaps this filter's location.
`boolean` `BioSQLFeatureFilter.ByNote.accept(Feature f)`
`boolean` `BioSQLFeatureFilter.ByNoteTermOnly.accept(Feature f)`
`boolean` `BioSQLAcceptNoneFilter.accept(Feature f)`
`boolean` `BioSQLAcceptAllFilter.accept(Feature f)`

Uses of Feature in org.biojavax.bio.seq

Subinterfaces of Feature in org.biojavax.bio.seq
`interface` `RichFeature` Represents a feature that can be given name and rank and be moved from one sequence to another.

Classes in org.biojavax.bio.seq that implement Feature
`class` `SimpleRichFeature` A simple implementation of RichFeature.

Methods in org.biojavax.bio.seq that return Feature
`Feature` `ThinRichSequence.createFeature(Feature.Template ft)` Create a new Feature, and add it to this FeatureHolder.
`Feature` `SimpleRichFeature.createFeature(Feature.Template ft)` Create a new Feature, and add it to this FeatureHolder.

Methods in org.biojavax.bio.seq that return types with arguments of type Feature
`Iterator<Feature>` `ThinRichSequence.features()` Iterate over the features in no well defined order. Warning this method gives access to the original Collection not a copy.
`Set<Feature>` `ThinRichSequence.getFeatureSet()` The features for this sequence. Warning this method gives access to the original Collection not a copy.
`Set<Feature>` `RichSequence.getFeatureSet()` The features for this sequence.

Methods in org.biojavax.bio.seq with parameters of type Feature
`boolean` `ThinRichSequence.containsFeature(Feature f)` Check if the feature is present in this holder.
`boolean` `SimpleRichFeature.containsFeature(Feature f)` Check if the feature is present in this holder.
`static RichFeature` `RichFeature.Tools.enrich(Feature f)` Takes a normal Feature and attempts to convert it into a RichFeature.
`void` `ThinRichSequence.removeFeature(Feature f)` Remove a feature from this FeatureHolder.
`void` `SimpleRichFeature.removeFeature(Feature f)` Remove a feature from this FeatureHolder.

Method parameters in org.biojavax.bio.seq with type arguments of type Feature
`void` `ThinRichSequence.setFeatureSet(Set<Feature> features)` Sets the features of this sequence. Warning this method gives access to the original Collection not a copy.
`void` `RichSequence.setFeatureSet(Set<Feature> features)` Sets the features of this sequence.