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.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 into alternate coordinate systems. 
 

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

Methods in org.biojava.bio.gui.sequence with parameters of type Feature
 void RoundRectangularBeadRenderer.renderBead(java.awt.Graphics2D g2, Feature f, SequenceRenderContext context)
          renderBead renders features as a rectangle with rounded corners.
 void ZiggyImapRenderer.renderImageMap(java.awt.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(java.awt.Graphics2D g2, Feature f, SequenceRenderContext context)
           
 void BeadFeatureRenderer.renderBead(java.awt.Graphics2D g2, Feature f, SequenceRenderContext context)
          renderBead should implement rendering for this bead type only.
 void RectangularImapRenderer.renderImageMap(java.awt.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(java.awt.Graphics2D g2, Feature f, SequenceRenderContext context)
           
 void RectangularImapRenderer.renderBead(java.awt.Graphics2D g2, Feature f, SequenceRenderContext context)
           
 void EllipticalBeadRenderer.renderBead(java.awt.Graphics2D g2, Feature f, SequenceRenderContext context)
          renderBead renders features as simple ellipse.
 void TickFeatureRenderer.renderFeature(java.awt.Graphics2D g, Feature f, SequenceRenderContext src)
           
 void SixFrameZiggyRenderer.renderFeature(java.awt.Graphics2D g, Feature f, SequenceRenderContext context)
           
 void StackedFeatureRenderer.renderFeature(java.awt.Graphics2D g, Feature f, SequenceRenderContext src)
           
 void BasicFeatureRenderer.renderFeature(java.awt.Graphics2D g, Feature f, SequenceRenderContext src)
           
 void ImageMapRenderer.renderImageMap(java.awt.Graphics2D g2, Feature f, SequenceRenderContext context)
          renderImageMap renders the Feature as set of image map hotspots.
 void RectangularBeadRenderer.renderBead(java.awt.Graphics2D g2, Feature f, SequenceRenderContext context)
          renderBead renders features as simple rectangle.
 void FeatureRenderer.renderFeature(java.awt.Graphics2D g, Feature f, SequenceRenderContext context)
           
 void FeatureLabelRenderer.renderFeature(java.awt.Graphics2D g, Feature feat, SequenceRenderContext src)
           
 java.lang.String FeatureLabelRenderer.LabelMaker.makeLabel(Feature f)
           
 java.lang.String FeatureLabelRenderer.SourceLabelMaker.makeLabel(Feature f)
           
 java.lang.String FeatureLabelRenderer.TypeLabelMaker.makeLabel(Feature f)
           
 java.lang.String FeatureLabelRenderer.AnnotationLabelMaker.makeLabel(Feature feat)
           
 void AbstractBeadRenderer.renderFeature(java.awt.Graphics2D g2, Feature f, SequenceRenderContext context)
          renderFeature draws a feature using the supplied graphics context.
abstract  void AbstractBeadRenderer.renderBead(java.awt.Graphics2D g2, Feature f, SequenceRenderContext context)
          renderBead should be overridden by the concrete BeadRenderer.
 void ZiggyFeatureRenderer.renderFeature(java.awt.Graphics2D g, Feature f, SequenceRenderContext context)
           
 

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.xff
 

Methods in org.biojava.bio.program.xff with parameters of type Feature
 void PropertyWriter.writeDetails(XMLWriter xw, Feature f)
           
 java.lang.String XFFHelper.getFeatureID(Feature f)
           
 void XFFHelper.writeDetails(XMLWriter xw, Feature f)
           
 java.lang.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 FeatureRealizer.realizeFeature(Sequence seq, FeatureHolder parent, Feature.Template template)
          Install a feature on the specified sequence.
 Feature FeatureFilter.ByFeature.getFeature()
           
 Feature ViewSequence.realizeFeature(FeatureHolder parent, Feature.Template template)
           
 Feature ViewSequence.createFeature(Feature.Template template)
           
 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 SimpleAssembly.createFeature(Feature.Template temp)
           
 Feature SimpleAssembly.realizeFeature(FeatureHolder fh, Feature.Template temp)
           
 Feature FeatureHolder.createFeature(Feature.Template ft)
          Create a new Feature, and add it to this FeatureHolder.
 Feature FeatureHolder.EmptyFeatureHolder.createFeature(Feature.Template f)
           
 Feature SimpleGappedSequence.createFeature(Feature.Template templ)
           
 Feature SimpleFeatureRealizer.realizeFeature(Sequence seq, FeatureHolder parent, Feature.Template temp)
           
 Feature ProjectedFeatureHolder.createFeature(Feature.Template templ)
           
 Feature ProjectedFeatureHolder.projectFeature(Feature f)
          Create a single projected feature using the rules of this ProjectedFeatureHolder.
 Feature ProjectedFeatureHolder.createFeature(Feature f, Feature.Template templ)
           
 Feature RealizingFeatureHolder.realizeFeature(FeatureHolder parent, Feature.Template template)
          Realize a feature template.
 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 AbstractFeatureHolder.createFeature(Feature.Template temp)
           
 Feature SubSequence.createFeature(Feature.Template templ)
           
 Feature DummySequence.createFeature(Feature.Template template)
           
 Feature LazyFeatureHolder.createFeature(Feature.Template template)
           
 

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 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 Feature.Template.populate(Feature feat)
          This attempts to populate the fields of this template using the publically accessible information in a feature.
 void ViewSequence.removeFeature(Feature f)
          Remove a feature from this sequence.
 boolean ViewSequence.containsFeature(Feature f)
           
 boolean SimpleAssembly.containsFeature(Feature f)
           
 void SimpleAssembly.removeFeature(Feature f)
           
 boolean MergeFeatureHolder.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 SimpleGappedSequence.containsFeature(Feature f)
           
 void SimpleGappedSequence.removeFeature(Feature f)
           
 boolean ProjectedFeatureHolder.containsFeature(Feature f)
           
 void ProjectedFeatureHolder.removeFeature(Feature f)
           
 Feature ProjectedFeatureHolder.projectFeature(Feature f)
          Create a single projected feature using the rules of this ProjectedFeatureHolder.
 FeatureHolder ProjectedFeatureHolder.getParent(Feature f)
           
 Sequence ProjectedFeatureHolder.getSequence(Feature f)
           
 Location ProjectedFeatureHolder.getLocation(Feature f)
           
 Annotation ProjectedFeatureHolder.getAnnotation(Feature f)
           
 FeatureHolder ProjectedFeatureHolder.projectChildFeatures(Feature f, FeatureHolder parent)
           
 Feature ProjectedFeatureHolder.createFeature(Feature f, Feature.Template templ)
           
 void ProjectedFeatureHolder.removeFeature(Feature f, Feature f2)
           
 FeatureFilter ProjectedFeatureHolder.getSchema(Feature f)
           
 void ProjectedFeatureHolder.addChangeListener(Feature f, ChangeListener cl, ChangeType ct)
           
 void ProjectedFeatureHolder.removeChangeListener(Feature f, ChangeListener cl, ChangeType ct)
           
protected  ChangeEvent ProjectedFeatureHolder.forwardFeatureChangeEvent(Feature f, ChangeEvent cev)
          Called internally to generate a forwarded version of a ChangeEvent from a ProjectedFeature
 void AbstractFeatureHolder.removeFeature(Feature f)
           
 boolean SubSequence.containsFeature(Feature f)
           
 void SubSequence.removeFeature(Feature f)
           
 void DummySequence.removeFeature(Feature feature)
           
 boolean DummySequence.containsFeature(Feature feature)
           
 void LazyFeatureHolder.removeFeature(Feature f)
           
 boolean LazyFeatureHolder.containsFeature(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 SimpleRemoteFeature.getRemoteFeature()
           
 Feature SimpleRemoteFeature.DBResolver.resolve(RemoteFeature rFeat)
           
 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 LazyFilterFeatureHolder.createFeature(Feature.Template temp)
           
 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.
 

Methods in org.biojava.bio.seq.impl with parameters of type Feature
 boolean SimpleSequence.containsFeature(Feature f)
           
 void SimpleSequence.removeFeature(Feature f)
          Remove a feature attached to this sequence.
 boolean LazyFilterFeatureHolder.containsFeature(Feature f)
           
 void LazyFilterFeatureHolder.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.
 

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

Methods in org.biojava.bio.seq.io with parameters of type Feature
 java.lang.String SwissprotFileFormer.formatLocation(Feature theFeature)
          Creates a string representation of the location of a feature
 java.lang.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.
 class ProjectedStrandedFeature
          Internal class used by ProjectedFeatureHolder to wrap StrandedFeatures.
 

Methods in org.biojava.bio.seq.projection that return Feature
 Feature ProjectionEngine.projectFeature(Feature f, ProjectionContext ctx)
          Return a projection of Feature f into the system defined by a given ProjectionContext.
 Feature ProjectedFeature.getViewedFeature()
           
 Feature ProjectedFeature.createFeature(Feature.Template temp)
           
 Feature ProjectionContext.createFeature(Feature f, Feature.Template templ)
          Delegate for createFeature
 Feature Projection.getViewedFeature()
           
 

Methods in org.biojava.bio.seq.projection with parameters of type Feature
 Feature ProjectionEngine.projectFeature(Feature f, ProjectionContext ctx)
          Return a projection of Feature f into the system defined by a given ProjectionContext.
 boolean ProjectedFeature.containsFeature(Feature f)
           
 void ProjectedFeature.removeFeature(Feature f)
           
 FeatureHolder ProjectionContext.getParent(Feature f)
          Get the parent FeatureHolder into which a feature should be projected
 Sequence ProjectionContext.getSequence(Feature f)
          Get the Sequence which defines the coordinate system for the projected feature.
 Location ProjectionContext.getLocation(Feature f)
          Get the location of the projected feature
 Annotation ProjectionContext.getAnnotation(Feature f)
          Get the annotation bundle of the projected feature.
 FeatureHolder ProjectionContext.projectChildFeatures(Feature f, FeatureHolder parent)
          Get the child features of the projected feature.
 Feature ProjectionContext.createFeature(Feature f, Feature.Template templ)
          Delegate for createFeature
 void ProjectionContext.removeFeature(Feature f, Feature dyingChild)
          Delegate for removeFeature
 void ProjectionContext.addChangeListener(Feature f, ChangeListener cl, ChangeType ct)
          Delegate for addChangeListener
 void ProjectionContext.removeChangeListener(Feature f, ChangeListener cl, ChangeType ct)
          Delegate for removeChangeListener
 FeatureFilter ProjectionContext.getSchema(Feature f)
          Delegate for getSchema
 

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