Uses of Interface
org.biojava.bio.seq.Feature
Packages that use Feature
Package
Description
Graphical displays of biological sequences and associated annotations.
The classes and interfaces in this package cover common molecular
biological techniques such as restriction digests and PCR.
GFF manipulation.
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.
Code for projecting Feature objects and systematically altering their
properties.
Interface between biojava and biosql databases
Rich implementations of Sequences, Locations and Features.
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Uses of Feature in org.biojava.bio.gui.sequence
Methods in org.biojava.bio.gui.sequence with parameters of type FeatureModifier and TypeMethodDescriptionabstract void
AbstractBeadRenderer.renderBead
(Graphics2D g2, Feature f, SequenceRenderContext context) renderBead
should be overridden by the concreteBeadRenderer
.void
BeadFeatureRenderer.renderBead
(Graphics2D g2, Feature f, SequenceRenderContext context) renderBead
should implement rendering for this bead type only.void
EllipticalBeadRenderer.renderBead
(Graphics2D g2, Feature f, SequenceRenderContext context) renderBead
renders features as simple ellipse.void
RectangularBeadRenderer.renderBead
(Graphics2D g2, Feature f, SequenceRenderContext context) renderBead
renders features as simple rectangle.void
RectangularImapRenderer.renderBead
(Graphics2D g2, Feature f, SequenceRenderContext context) void
RoundRectangularBeadRenderer.renderBead
(Graphics2D g2, Feature f, SequenceRenderContext context) renderBead
renders features as a rectangle with rounded corners.void
AbstractBeadRenderer.renderFeature
(Graphics2D g2, Feature f, SequenceRenderContext context) renderFeature
draws a feature using the supplied graphics context.void
ArrowedFeatureRenderer.renderFeature
(Graphics2D g, Feature f, SequenceRenderContext src) void
BasicFeatureRenderer.renderFeature
(Graphics2D g, Feature f, SequenceRenderContext src) void
BasicImapRenderer.renderFeature
(Graphics2D g2, Feature f, SequenceRenderContext context) void
CircularFeatureRenderer.renderFeature
(Graphics2D g, Feature f, CircularRendererContext context) void
FeatureLabelRenderer.renderFeature
(Graphics2D g, Feature feat, SequenceRenderContext src) void
FeatureRenderer.renderFeature
(Graphics2D g2, Feature feat, SequenceRenderContext context) void
GlyphFeatureRenderer.renderFeature
(Graphics2D g2, Feature f, SequenceRenderContext src) void
RectangularImapRenderer.renderFeature
(Graphics2D g2, Feature f, SequenceRenderContext context) void
SixFrameZiggyRenderer.renderFeature
(Graphics2D g, Feature f, SequenceRenderContext context) void
StackedFeatureRenderer.renderFeature
(Graphics2D g, Feature f, SequenceRenderContext src) void
TickFeatureRenderer.renderFeature
(Graphics2D g, Feature f, SequenceRenderContext src) void
ZiggyFeatureRenderer.renderFeature
(Graphics2D g, Feature f, SequenceRenderContext context) void
ZiggyImapRenderer.renderFeature
(Graphics2D g2, Feature f, SequenceRenderContext context) 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
ImageMapRenderer.renderImageMap
(Graphics2D g2, Feature f, SequenceRenderContext context) renderImageMap
renders theFeature
as set of image map hotspots.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
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. -
Uses of Feature in org.biojava.bio.molbio
Subinterfaces of Feature in org.biojava.bio.molbioModifier and TypeInterfaceDescriptioninterface
RestrictionSite
represents the recognition site of a restriction enzyme. -
Uses of Feature in org.biojava.bio.program.gff
Methods in org.biojava.bio.program.gff with parameters of type FeatureModifier and TypeMethodDescriptionprotected 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 FeatureModifier and TypeMethodDescriptionBasicXFFHelper.getFeatureID
(Feature f) XFFHelper.getFeatureID
(Feature f) void
BasicXFFHelper.writeDetails
(XMLWriter xw, Feature f) void
PropertyWriter.writeDetails
(XMLWriter xw, Feature f) void
XFFHelper.writeDetails
(XMLWriter xw, Feature f) -
Uses of Feature in org.biojava.bio.seq
Subinterfaces of Feature in org.biojava.bio.seqModifier and TypeInterfaceDescriptioninterface
Feature which represents a component in an assembly (contig).interface
Title: FramedFeature.interface
A feature that indicates that there is some remote feature that can't be represented entirely on a single Sequence.interface
Adds the concept of 'strand' to features.Methods in org.biojava.bio.seq that return FeatureModifier and TypeMethodDescriptionAbstractFeatureHolder.createFeature
(Feature.Template temp) 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).FeatureHolder.createFeature
(Feature.Template ft) Create a new Feature, and add it to this FeatureHolder.FeatureHolder.EmptyFeatureHolder.createFeature
(Feature.Template f) LazyFeatureHolder.createFeature
(Feature.Template template) NewSimpleAssembly.createFeature
(Feature.Template temp) SimpleAssembly.createFeature
(Feature.Template temp) FeatureFilter.ByFeature.getFeature()
RemoteFeature.getRemoteFeature()
Retrieve the Feature on some assembly Sequence that can represent this RemoteFeature properly.FeatureRealizer.realizeFeature
(Sequence seq, FeatureHolder parent, Feature.Template template) Install a feature on the specified sequence.NewSimpleAssembly.realizeFeature
(FeatureHolder fh, Feature.Template temp) RealizingFeatureHolder.realizeFeature
(FeatureHolder parent, Feature.Template template) Realize a feature template.SimpleAssembly.realizeFeature
(FeatureHolder fh, Feature.Template temp) SimpleFeatureRealizer.realizeFeature
(Sequence seq, FeatureHolder parent, Feature.Template temp) RemoteFeature.Resolver.resolve
(RemoteFeature rFeat) Resolve rFeat.Methods in org.biojava.bio.seq that return types with arguments of type FeatureModifier and TypeMethodDescriptionFeatureHolder.EmptyFeatureHolder.features()
FeatureHolder.features()
Iterate over the features in no well defined order.SimpleFeatureHolder.features()
Methods in org.biojava.bio.seq with parameters of type FeatureModifier and TypeMethodDescriptionboolean
This method determines whether a feature is to be accepted.boolean
boolean
boolean
boolean
boolean
boolean
boolean
boolean
boolean
Accept a Feature if it is an instance of SimilarityPairFeature and its score is invalid input: '<'= filter's minimum score and >= filter's maximum score.boolean
boolean
boolean
boolean
Returns true if the feature has a matching type property.boolean
Returns true if the feature is within this filter's location.boolean
Accept the Feature if it is an instance of FramedFeature and matches the value of getFrame().boolean
boolean
boolean
boolean
boolean
Returns true if the feature overlaps this filter's location.boolean
Returns true if the feature is within this filter's location.boolean
Returns true if the feature overlaps this filter's location.boolean
Accept the Feature if it is an instance of StrandedFeature and matches the value of getStrand().void
SimpleFeatureHolder.addFeature
(Feature f) Add a feature to the featureholderboolean
FeatureHolder.containsFeature
(Feature f) Check if the feature is present in this holder.boolean
FeatureHolder.EmptyFeatureHolder.containsFeature
(Feature f) boolean
LazyFeatureHolder.containsFeature
(Feature f) boolean
MergeFeatureHolder.containsFeature
(Feature f) boolean
NewSimpleAssembly.containsFeature
(Feature f) boolean
SimpleAssembly.containsFeature
(Feature f) boolean
SimpleFeatureHolder.containsFeature
(Feature f) void
AbstractFeatureHolder.removeFeature
(Feature f) void
FeatureHolder.EmptyFeatureHolder.removeFeature
(Feature f) void
FeatureHolder.removeFeature
(Feature f) Remove a feature from this FeatureHolder.void
LazyFeatureHolder.removeFeature
(Feature f) void
NewSimpleAssembly.removeFeature
(Feature f) void
SimpleAssembly.removeFeature
(Feature f) void
SimpleFeatureHolder.removeFeature
(Feature f) Constructors in org.biojava.bio.seq with parameters of type Feature -
Uses of Feature in org.biojava.bio.seq.homol
Subinterfaces of Feature in org.biojava.bio.seq.homolModifier and TypeInterfaceDescriptioninterface
interface
SimilarityPairFeature
describes a pairwise similarity between two nucleotide sequences (as it extendsStrandedFeature
). -
Uses of Feature in org.biojava.bio.seq.impl
Classes in org.biojava.bio.seq.impl that implement FeatureModifier and TypeClassDescriptionclass
A no-frills implementation of a feature.class
Title: SimpleFramedFeature.class
class
A no-frills implementation of a remote feature.class
SimpleRestrictionSite
represents the recognition site of a restriction enzyme.class
SimpleSimilarityPairFeature
represents a similarity between a query sequence and a subject sequence as produced by a search program.class
A no-frills implementation of StrandedFeature.Methods in org.biojava.bio.seq.impl that return FeatureModifier and TypeMethodDescriptionDummySequence.createFeature
(Feature.Template template) LazyFilterFeatureHolder.createFeature
(Feature.Template temp) RevCompSequence.createFeature
(Feature.Template ft) createFeature() will call createFeature() on the underlying Sequence.SimpleFeature.createFeature
(Feature.Template temp) SimpleGappedSequence.createFeature
(Feature.Template templ) SimpleSequence.createFeature
(Feature.Template template) SimpleSequence.createFeature
(FeatureHolder fh, Feature.Template template) Deprecated.Please use new 1-arg createFeature instead.SubSequence.createFeature
(Feature.Template templ) ViewSequence.createFeature
(Feature.Template template) 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.SimpleRemoteFeature.getRemoteFeature()
SubSequence.SubProjectedFeatureContext.projectFeature
(Feature origFeat) SimpleFeature.realizeFeature
(FeatureHolder fh, Feature.Template templ) SimpleSequence.realizeFeature
(FeatureHolder parent, Feature.Template template) ViewSequence.realizeFeature
(FeatureHolder parent, Feature.Template template) SimpleRemoteFeature.DBResolver.resolve
(RemoteFeature rFeat) SubSequence.SubProjectedFeatureContext.revertFeature
(Feature projFeat) Methods in org.biojava.bio.seq.impl that return types with arguments of type FeatureMethods in org.biojava.bio.seq.impl with parameters of type FeatureModifier and TypeMethodDescriptionboolean
DummySequence.containsFeature
(Feature feature) boolean
LazyFilterFeatureHolder.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
SimpleFeature.containsFeature
(Feature f) boolean
SimpleGappedSequence.containsFeature
(Feature f) boolean
SimpleSequence.containsFeature
(Feature f) boolean
SubSequence.containsFeature
(Feature f) boolean
ViewSequence.containsFeature
(Feature f) 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.SubSequence.SubProjectedFeatureContext.projectChildFeatures
(Feature f, FeatureHolder parent) SubSequence.SubProjectedFeatureContext.projectFeature
(Feature origFeat) void
DummySequence.removeFeature
(Feature feature) void
LazyFilterFeatureHolder.removeFeature
(Feature f) void
RevCompSequence.removeFeature
(Feature f) void
SimpleFeature.removeFeature
(Feature f) void
SimpleGappedSequence.removeFeature
(Feature f) void
SimpleSequence.removeFeature
(Feature f) Remove a feature attached to this sequence.void
SubSequence.removeFeature
(Feature f) void
ViewSequence.removeFeature
(Feature f) Remove a feature from this sequence.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 FeatureModifier and TypeMethodDescriptionSeqFileFormer.formatLocation
(Feature theFeature) Deprecated.Formats the location of a feature.SwissprotFileFormer.formatLocation
(Feature theFeature) Deprecated.Creates a string representation of 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 FeatureModifier and TypeMethodDescriptionprotected 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 FeatureModifier and TypeClassDescriptionclass
Internal class used by ProjectionEngine to wrap Feature objects.Methods in org.biojava.bio.seq.projection that return FeatureModifier and TypeMethodDescriptionProjectedFeature.createFeature
(Feature.Template temp) ProjectedFeatureHolder.createFeature
(Feature.Template templ) ProjectionContext.createFeature
(Feature.Template projTempl) Create a projected feature with properties matching the template.ProjectionContext.createFeature
(Feature projParent, Feature.Template projTempl) Create a new projected feature.final Feature
ReparentContext.createFeature
(Feature.Template projTempl) final Feature
ReparentContext.createFeature
(Feature f, Feature.Template projTempl) ProjectedFeature.getViewedFeature()
Projection.getViewedFeature()
ProjectionContext.projectFeature
(Feature feat) Project a single feature.ProjectionEngine.projectFeature
(Feature f, ProjectionContext ctx) Return a projection of Featuref
into the system defined by a given ProjectionContext.ReparentContext.projectFeature
(Feature feat) Create a single projected feature using the rules of thisProjectedFeatureHolder
.ProjectionContext.revertFeature
(Feature projFeat) Unproject a feature.ReparentContext.revertFeature
(Feature feat) Methods in org.biojava.bio.seq.projection with parameters of type FeatureModifier and TypeMethodDescriptionvoid
ProjectionContext.addChangeListener
(Feature projFeat, ChangeListener cl, ChangeType ct) Add a ChangeListener to a projected feature.final void
ReparentContext.addChangeListener
(Feature f, ChangeListener cl, ChangeType ct) boolean
ProjectedFeature.containsFeature
(Feature f) boolean
ProjectedFeatureHolder.containsFeature
(Feature f) ProjectionContext.createFeature
(Feature projParent, Feature.Template projTempl) Create a new projected feature.final Feature
ReparentContext.createFeature
(Feature f, Feature.Template projTempl) final FeatureHolder
final FeatureFilter
ProjectionContext.getSequence
(Feature projFeat) Get the sequence for a feature.final Sequence
ReparentContext.getSequence
(Feature f) ProjectionContext.projectChildFeatures
(Feature feature, FeatureHolder parent) Project all features that are children of feature so that they become children of parent.ReparentContext.projectChildFeatures
(Feature f, FeatureHolder parent) ProjectionContext.projectFeature
(Feature feat) Project a single feature.ProjectionEngine.projectFeature
(Feature f, ProjectionContext ctx) Return a projection of Featuref
into the system defined by a given ProjectionContext.ReparentContext.projectFeature
(Feature feat) Create a single projected feature using the rules of thisProjectedFeatureHolder
.void
ProjectionContext.removeChangeListener
(Feature projFeat, ChangeListener cl, ChangeType ct) Remove a ChangeListener from a projected feature.final void
ReparentContext.removeChangeListener
(Feature f, ChangeListener cl, ChangeType ct) void
ProjectedFeature.removeFeature
(Feature f) void
ProjectedFeatureHolder.removeFeature
(Feature dyingChild) void
ProjectionContext.removeFeature
(Feature dyingChild) Remove the dying child.void
ProjectionContext.removeFeature
(Feature projParent, Feature dyingChild) Remove the dying child.final void
ReparentContext.removeFeature
(Feature dyingChild) final void
ReparentContext.removeFeature
(Feature f, Feature f2) ProjectionContext.revertFeature
(Feature projFeat) Unproject a feature.ReparentContext.revertFeature
(Feature feat) Constructors in org.biojava.bio.seq.projection with parameters of type Feature -
Uses of Feature in org.biojavax.bio.db.biosql
Methods in org.biojavax.bio.db.biosql with parameters of type FeatureModifier and TypeMethodDescriptionboolean
boolean
boolean
boolean
Returns true if the feature has a matching type property.boolean
boolean
boolean
Returns true if the feature has a matching type property.boolean
boolean
Returns true if the feature has a matching source property.boolean
Returns true if the feature has a matching source property.boolean
Returns true if the feature overlaps this filter's location.boolean
Returns true if the feature has a matching type property.boolean
Returns true if the feature has a matching type property.boolean
Returns true if the feature is within this filter's location.boolean
boolean
boolean
Returns true if the feature overlaps this filter's location. -
Uses of Feature in org.biojavax.bio.seq
Subinterfaces of Feature in org.biojavax.bio.seqModifier and TypeInterfaceDescriptioninterface
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 FeatureMethods in org.biojavax.bio.seq that return FeatureModifier and TypeMethodDescriptionSimpleRichFeature.createFeature
(Feature.Template ft) Create a new Feature, and add it to this FeatureHolder.ThinRichSequence.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 FeatureModifier and TypeMethodDescriptionThinRichSequence.features()
Iterate over the features in no well defined order.RichSequence.getFeatureSet()
The features for this sequence.ThinRichSequence.getFeatureSet()
The features for this sequence.Methods in org.biojavax.bio.seq with parameters of type FeatureModifier and TypeMethodDescriptionboolean
SimpleRichFeature.containsFeature
(Feature f) Check if the feature is present in this holder.boolean
ThinRichSequence.containsFeature
(Feature f) Check if the feature is present in this holder.static RichFeature
Takes a normal Feature and attempts to convert it into a RichFeature.void
SimpleRichFeature.removeFeature
(Feature f) Remove a feature from this FeatureHolder.void
ThinRichSequence.removeFeature
(Feature f) Remove a feature from this FeatureHolder.Method parameters in org.biojavax.bio.seq with type arguments of type FeatureModifier and TypeMethodDescriptionvoid
RichSequence.setFeatureSet
(Set<Feature> features) Sets the features of this sequence.void
ThinRichSequence.setFeatureSet
(Set<Feature> features) Sets the features of this sequence.