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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 |
RectangularBeadRenderer.renderBead(java.awt.Graphics2D g2,
Feature f,
SequenceRenderContext context)
renderBead renders features as simple rectangle. |
void |
ZiggyFeatureRenderer.renderFeature(java.awt.Graphics2D g,
Feature f,
SequenceRenderContext context)
|
void |
EllipticalBeadRenderer.renderBead(java.awt.Graphics2D g2,
Feature f,
SequenceRenderContext context)
renderBead renders features as simple ellipse. |
void |
StackedFeatureRenderer.renderFeature(java.awt.Graphics2D g,
Feature f,
SequenceRenderContext src)
|
void |
BeadFeatureRenderer.renderBead(java.awt.Graphics2D g2,
Feature f,
SequenceRenderContext context)
renderBead should implement rendering for this
bead type only. |
void |
ImageMapRenderer.renderImageMap(java.awt.Graphics2D g2,
Feature f,
SequenceRenderContext context)
renderImageMap renders the Feature as
set of image map hotspots. |
void |
RoundRectangularBeadRenderer.renderBead(java.awt.Graphics2D g2,
Feature f,
SequenceRenderContext context)
renderBead renders features as a rectangle with
rounded corners. |
void |
BasicFeatureRenderer.renderFeature(java.awt.Graphics2D g,
Feature f,
SequenceRenderContext src)
|
void |
FeatureRenderer.renderFeature(java.awt.Graphics2D g,
Feature f,
SequenceRenderContext context)
|
void |
TickFeatureRenderer.renderFeature(java.awt.Graphics2D g,
Feature f,
SequenceRenderContext src)
|
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 |
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 |
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 |
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 |
SixFrameZiggyRenderer.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 | |
java.lang.String |
XFFHelper.getFeatureID(Feature f)
|
void |
XFFHelper.writeDetails(XMLWriter xw,
Feature f)
|
void |
PropertyWriter.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 |
FeatureFilter.ByFeature.getFeature()
|
Feature |
SubSequence.createFeature(Feature.Template templ)
|
Feature |
SimpleGappedSequence.createFeature(Feature.Template templ)
|
Feature |
FeatureRealizer.realizeFeature(Sequence seq,
FeatureHolder parent,
Feature.Template template)
Install a feature on the specified sequence. |
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 |
RemoteFeature.getRemoteFeature()
Retrieve the Feature on some assembly Sequence that can represent this RemoteFeature properly. |
Feature |
RemoteFeature.Resolver.resolve(RemoteFeature rFeat)
Resolve rFeat. |
Feature |
FeatureHolder.createFeature(Feature.Template ft)
Create a new Feature, and add it to this FeatureHolder. |
Feature |
FeatureHolder.EmptyFeatureHolder.createFeature(Feature.Template f)
|
Feature |
AbstractFeatureHolder.createFeature(Feature.Template temp)
|
Feature |
SimpleFeatureRealizer.realizeFeature(Sequence seq,
FeatureHolder parent,
Feature.Template temp)
|
Feature |
DummySequence.createFeature(Feature.Template template)
|
Feature |
LazyFeatureHolder.createFeature(Feature.Template template)
|
Feature |
SimpleAssembly.createFeature(Feature.Template temp)
|
Feature |
SimpleAssembly.realizeFeature(FeatureHolder fh,
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. |
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)
|
boolean |
SubSequence.containsFeature(Feature f)
|
void |
SubSequence.removeFeature(Feature f)
|
boolean |
SimpleGappedSequence.containsFeature(Feature f)
|
void |
SimpleGappedSequence.removeFeature(Feature f)
|
void |
ViewSequence.removeFeature(Feature f)
Remove a feature from this sequence. |
boolean |
ViewSequence.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)
|
void |
AbstractFeatureHolder.removeFeature(Feature f)
|
void |
DummySequence.removeFeature(Feature feature)
|
boolean |
DummySequence.containsFeature(Feature feature)
|
boolean |
MergeFeatureHolder.containsFeature(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 |
LazyFeatureHolder.removeFeature(Feature f)
|
boolean |
LazyFeatureHolder.containsFeature(Feature f)
|
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 |
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 |
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 |
SimpleFeature.realizeFeature(FeatureHolder fh,
Feature.Template templ)
|
Feature |
SimpleFeature.createFeature(Feature.Template temp)
|
Feature |
LazyFilterFeatureHolder.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 |
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. |
Methods in org.biojava.bio.seq.impl with parameters of type Feature | |
void |
SimpleFeature.removeFeature(Feature f)
|
boolean |
SimpleFeature.containsFeature(Feature f)
|
boolean |
LazyFilterFeatureHolder.containsFeature(Feature f)
|
void |
LazyFilterFeatureHolder.removeFeature(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 |
SimpleSequence.containsFeature(Feature f)
|
void |
SimpleSequence.removeFeature(Feature f)
Remove a feature attached to this 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 |
ProjectionContext.createFeature(Feature f,
Feature.Template templ)
Delegate for createFeature |
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 |
Projection.getViewedFeature()
|
Methods in org.biojava.bio.seq.projection with parameters of type Feature | |
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 |
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)
|
Constructors in org.biojava.bio.seq.projection with parameters of type Feature | |
ProjectedFeature(Feature f,
ProjectionContext ctx)
|
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