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 voidAbstractBeadRenderer.renderBead(Graphics2D g2, Feature f, SequenceRenderContext context) renderBeadshould be overridden by the concreteBeadRenderer.voidBeadFeatureRenderer.renderBead(Graphics2D g2, Feature f, SequenceRenderContext context) renderBeadshould implement rendering for this bead type only.voidEllipticalBeadRenderer.renderBead(Graphics2D g2, Feature f, SequenceRenderContext context) renderBeadrenders features as simple ellipse.voidRectangularBeadRenderer.renderBead(Graphics2D g2, Feature f, SequenceRenderContext context) renderBeadrenders features as simple rectangle.voidRectangularImapRenderer.renderBead(Graphics2D g2, Feature f, SequenceRenderContext context) voidRoundRectangularBeadRenderer.renderBead(Graphics2D g2, Feature f, SequenceRenderContext context) renderBeadrenders features as a rectangle with rounded corners.voidAbstractBeadRenderer.renderFeature(Graphics2D g2, Feature f, SequenceRenderContext context) renderFeaturedraws a feature using the supplied graphics context.voidArrowedFeatureRenderer.renderFeature(Graphics2D g, Feature f, SequenceRenderContext src) voidBasicFeatureRenderer.renderFeature(Graphics2D g, Feature f, SequenceRenderContext src) voidBasicImapRenderer.renderFeature(Graphics2D g2, Feature f, SequenceRenderContext context) voidCircularFeatureRenderer.renderFeature(Graphics2D g, Feature f, CircularRendererContext context) voidFeatureLabelRenderer.renderFeature(Graphics2D g, Feature feat, SequenceRenderContext src) voidFeatureRenderer.renderFeature(Graphics2D g2, Feature feat, SequenceRenderContext context) voidGlyphFeatureRenderer.renderFeature(Graphics2D g2, Feature f, SequenceRenderContext src) voidRectangularImapRenderer.renderFeature(Graphics2D g2, Feature f, SequenceRenderContext context) voidSixFrameZiggyRenderer.renderFeature(Graphics2D g, Feature f, SequenceRenderContext context) voidStackedFeatureRenderer.renderFeature(Graphics2D g, Feature f, SequenceRenderContext src) voidTickFeatureRenderer.renderFeature(Graphics2D g, Feature f, SequenceRenderContext src) voidZiggyFeatureRenderer.renderFeature(Graphics2D g, Feature f, SequenceRenderContext context) voidZiggyImapRenderer.renderFeature(Graphics2D g2, Feature f, SequenceRenderContext context) voidBasicImapRenderer.renderImageMap(Graphics2D g2, Feature f, SequenceRenderContext context) renderImageMapwrites a set of image map coordinates corresponding to the rectangle sections drawn by the renderer.voidImageMapRenderer.renderImageMap(Graphics2D g2, Feature f, SequenceRenderContext context) renderImageMaprenders theFeatureas set of image map hotspots.voidRectangularImapRenderer.renderImageMap(Graphics2D g2, Feature f, SequenceRenderContext context) renderImageMapwrites a set of image map coordinates corresponding to the rectangle drawn by the renderer.voidZiggyImapRenderer.renderImageMap(Graphics2D g2, Feature f, SequenceRenderContext context) renderImageMapwrites 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 TypeInterfaceDescriptioninterfaceRestrictionSiterepresents 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 SimpleGFFRecordSequencesAsGFF.createGFFRecord(Feature feature, String id) Internal method to create a GFFRecord from an individual Feature.protected voidSequencesAsGFF.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) voidBasicXFFHelper.writeDetails(XMLWriter xw, Feature f) voidPropertyWriter.writeDetails(XMLWriter xw, Feature f) voidXFFHelper.writeDetails(XMLWriter xw, Feature f) -
Uses of Feature in org.biojava.bio.seq
Subinterfaces of Feature in org.biojava.bio.seqModifier and TypeInterfaceDescriptioninterfaceFeature which represents a component in an assembly (contig).interfaceTitle: FramedFeature.interfaceA feature that indicates that there is some remote feature that can't be represented entirely on a single Sequence.interfaceAdds 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 TypeMethodDescriptionbooleanThis method determines whether a feature is to be accepted.booleanbooleanbooleanbooleanbooleanbooleanbooleanbooleanbooleanAccept a Feature if it is an instance of SimilarityPairFeature and its score is <= filter's minimum score and >= filter's maximum score.booleanbooleanbooleanbooleanReturns true if the feature has a matching type property.booleanReturns true if the feature is within this filter's location.booleanAccept the Feature if it is an instance of FramedFeature and matches the value of getFrame().booleanbooleanbooleanbooleanbooleanReturns true if the feature overlaps this filter's location.booleanReturns true if the feature is within this filter's location.booleanReturns true if the feature overlaps this filter's location.booleanAccept the Feature if it is an instance of StrandedFeature and matches the value of getStrand().voidSimpleFeatureHolder.addFeature(Feature f) Add a feature to the featureholderbooleanFeatureHolder.containsFeature(Feature f) Check if the feature is present in this holder.booleanFeatureHolder.EmptyFeatureHolder.containsFeature(Feature f) booleanLazyFeatureHolder.containsFeature(Feature f) booleanMergeFeatureHolder.containsFeature(Feature f) booleanNewSimpleAssembly.containsFeature(Feature f) booleanSimpleAssembly.containsFeature(Feature f) booleanSimpleFeatureHolder.containsFeature(Feature f) voidAbstractFeatureHolder.removeFeature(Feature f) voidFeatureHolder.EmptyFeatureHolder.removeFeature(Feature f) voidFeatureHolder.removeFeature(Feature f) Remove a feature from this FeatureHolder.voidLazyFeatureHolder.removeFeature(Feature f) voidNewSimpleAssembly.removeFeature(Feature f) voidSimpleAssembly.removeFeature(Feature f) voidSimpleFeatureHolder.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 TypeInterfaceDescriptioninterfaceinterfaceSimilarityPairFeaturedescribes 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 TypeClassDescriptionclassA no-frills implementation of a feature.classTitle: SimpleFramedFeature.classclassA no-frills implementation of a remote feature.classSimpleRestrictionSiterepresents the recognition site of a restriction enzyme.classSimpleSimilarityPairFeaturerepresents a similarity between a query sequence and a subject sequence as produced by a search program.classA 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 TypeMethodDescriptionbooleanDummySequence.containsFeature(Feature feature) booleanLazyFilterFeatureHolder.containsFeature(Feature f) booleanRevCompSequence.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;booleanSimpleFeature.containsFeature(Feature f) booleanSimpleGappedSequence.containsFeature(Feature f) booleanSimpleSequence.containsFeature(Feature f) booleanSubSequence.containsFeature(Feature f) booleanViewSequence.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.TemplateTemplateUtils.instantiateTemplate(Feature feat) This attempts to divine the 'best' template class for a feature and return a new instance readly for pupulating.static Feature.TemplateTemplateUtils.makeTemplate(Feature feat) static voidTemplateUtils.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) voidDummySequence.removeFeature(Feature feature) voidLazyFilterFeatureHolder.removeFeature(Feature f) voidRevCompSequence.removeFeature(Feature f) voidSimpleFeature.removeFeature(Feature f) voidSimpleGappedSequence.removeFeature(Feature f) voidSimpleSequence.removeFeature(Feature f) Remove a feature attached to this sequence.voidSubSequence.removeFeature(Feature f) voidViewSequence.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 voidStAXFeatureHandler.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 TypeClassDescriptionclassInternal 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 FeatureReparentContext.createFeature(Feature.Template projTempl) final FeatureReparentContext.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 Featurefinto 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 TypeMethodDescriptionvoidProjectionContext.addChangeListener(Feature projFeat, ChangeListener cl, ChangeType ct) Add a ChangeListener to a projected feature.final voidReparentContext.addChangeListener(Feature f, ChangeListener cl, ChangeType ct) booleanProjectedFeature.containsFeature(Feature f) booleanProjectedFeatureHolder.containsFeature(Feature f) ProjectionContext.createFeature(Feature projParent, Feature.Template projTempl) Create a new projected feature.final FeatureReparentContext.createFeature(Feature f, Feature.Template projTempl) final FeatureHolderfinal FeatureFilterProjectionContext.getSequence(Feature projFeat) Get the sequence for a feature.final SequenceReparentContext.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 Featurefinto the system defined by a given ProjectionContext.ReparentContext.projectFeature(Feature feat) Create a single projected feature using the rules of thisProjectedFeatureHolder.voidProjectionContext.removeChangeListener(Feature projFeat, ChangeListener cl, ChangeType ct) Remove a ChangeListener from a projected feature.final voidReparentContext.removeChangeListener(Feature f, ChangeListener cl, ChangeType ct) voidProjectedFeature.removeFeature(Feature f) voidProjectedFeatureHolder.removeFeature(Feature dyingChild) voidProjectionContext.removeFeature(Feature dyingChild) Remove the dying child.voidProjectionContext.removeFeature(Feature projParent, Feature dyingChild) Remove the dying child.final voidReparentContext.removeFeature(Feature dyingChild) final voidReparentContext.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 TypeMethodDescriptionbooleanbooleanbooleanbooleanReturns true if the feature has a matching type property.booleanbooleanbooleanReturns true if the feature has a matching type property.booleanbooleanReturns true if the feature has a matching source property.booleanReturns true if the feature has a matching source property.booleanReturns true if the feature overlaps this filter's location.booleanReturns true if the feature has a matching type property.booleanReturns true if the feature has a matching type property.booleanReturns true if the feature is within this filter's location.booleanbooleanbooleanReturns 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 TypeInterfaceDescriptioninterfaceRepresents 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 TypeMethodDescriptionbooleanSimpleRichFeature.containsFeature(Feature f) Check if the feature is present in this holder.booleanThinRichSequence.containsFeature(Feature f) Check if the feature is present in this holder.static RichFeatureTakes a normal Feature and attempts to convert it into a RichFeature.voidSimpleRichFeature.removeFeature(Feature f) Remove a feature from this FeatureHolder.voidThinRichSequence.removeFeature(Feature f) Remove a feature from this FeatureHolder.Method parameters in org.biojavax.bio.seq with type arguments of type FeatureModifier and TypeMethodDescriptionvoidRichSequence.setFeatureSet(Set<Feature> features) Sets the features of this sequence.voidThinRichSequence.setFeatureSet(Set<Feature> features) Sets the features of this sequence.