Uses of Interface
org.biojava.bio.seq.FeatureHolder
Packages that use FeatureHolder
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.
Parser for Phred output
Event-driven parsing system for the Extensible Feature Format (XFF).
Classes and interfaces for defining biological sequences and informatics
objects.
Collections of biological sequence data.
General purpose Sequence storage in a relational database.
Sequences and SequenceDBs which are composed from data taken
from a number of data sources.
The classes and interfaces for defining sequence similarity and
honology.
Standard in-memory implementations of
Sequence
and
Feature
.Classes for converting between AGAVE XML and BioJava objects.
Code for projecting Feature objects and systematically altering their
properties.
Interactions between biojavax objects and a DB.
Interface between biojava and biosql databases
Rich implementations of Sequences, Locations and Features.
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Uses of FeatureHolder in org.biojava.bio.gui.sequence
Methods in org.biojava.bio.gui.sequence that return FeatureHolderModifier and TypeMethodDescriptionFeatureSource.getFeatureHolder()
CircularRendererContext.getFeatures()
The features to render.HeadlessRenderContext.getFeatures()
PairwiseSequencePanel.getFeatures()
getFeatures
returns all of theFeature
s belonging to the currently renderedSequence
.SequencePanel.getFeatures()
SequencePoster.getFeatures()
Deprecated.SequenceRenderContext.getFeatures()
The features to render.SubCircularRendererContext.getFeatures()
SubPairwiseRenderContext.getFeatures()
SubSequenceRenderContext.getFeatures()
TranslatedSequencePanel.getFeatures()
getFeatures
returns all of theFeature
s belonging to the currently renderedSequence
.PairwiseRenderContext.getSecondaryFeatures()
getSecondaryFeatures
returns the features on the secondary sequence.PairwiseSequencePanel.getSecondaryFeatures()
getSecondaryFeatures
returns all of theFeature
s belonging to the currently rendered secondarySequence
.SubPairwiseRenderContext.getSecondaryFeatures()
AbstractBeadRenderer.processMouseEvent
(FeatureHolder holder, SequenceRenderContext context, MouseEvent mEvent) processMouseEvent
defines the behaviour on revieving a mouse event.ArrowedFeatureRenderer.processMouseEvent
(FeatureHolder hits, SequenceRenderContext src, MouseEvent me) BasicFeatureRenderer.processMouseEvent
(FeatureHolder hits, SequenceRenderContext src, MouseEvent me) BasicImapRenderer.processMouseEvent
(FeatureHolder holder, SequenceRenderContext context, MouseEvent mEvent) FeatureLabelRenderer.processMouseEvent
(FeatureHolder hits, SequenceRenderContext src, MouseEvent me) FeatureRenderer.processMouseEvent
(FeatureHolder hits, SequenceRenderContext src, MouseEvent me) GlyphFeatureRenderer.processMouseEvent
(FeatureHolder fh, SequenceRenderContext src, MouseEvent me) RectangularImapRenderer.processMouseEvent
(FeatureHolder holder, SequenceRenderContext context, MouseEvent mEvent) SixFrameZiggyRenderer.processMouseEvent
(FeatureHolder hits, SequenceRenderContext src, MouseEvent me) StackedFeatureRenderer.processMouseEvent
(FeatureHolder hits, SequenceRenderContext src, MouseEvent me) TickFeatureRenderer.processMouseEvent
(FeatureHolder hits, SequenceRenderContext src, MouseEvent me) ZiggyFeatureRenderer.processMouseEvent
(FeatureHolder hits, SequenceRenderContext src, MouseEvent me) ZiggyImapRenderer.processMouseEvent
(FeatureHolder holder, SequenceRenderContext context, MouseEvent mEvent) Methods in org.biojava.bio.gui.sequence with parameters of type FeatureHolderModifier and TypeMethodDescriptionAbstractBeadRenderer.processMouseEvent
(FeatureHolder holder, SequenceRenderContext context, MouseEvent mEvent) processMouseEvent
defines the behaviour on revieving a mouse event.ArrowedFeatureRenderer.processMouseEvent
(FeatureHolder hits, SequenceRenderContext src, MouseEvent me) BasicFeatureRenderer.processMouseEvent
(FeatureHolder hits, SequenceRenderContext src, MouseEvent me) BasicImapRenderer.processMouseEvent
(FeatureHolder holder, SequenceRenderContext context, MouseEvent mEvent) FeatureLabelRenderer.processMouseEvent
(FeatureHolder hits, SequenceRenderContext src, MouseEvent me) FeatureRenderer.processMouseEvent
(FeatureHolder hits, SequenceRenderContext src, MouseEvent me) GlyphFeatureRenderer.processMouseEvent
(FeatureHolder fh, SequenceRenderContext src, MouseEvent me) RectangularImapRenderer.processMouseEvent
(FeatureHolder holder, SequenceRenderContext context, MouseEvent mEvent) SixFrameZiggyRenderer.processMouseEvent
(FeatureHolder hits, SequenceRenderContext src, MouseEvent me) StackedFeatureRenderer.processMouseEvent
(FeatureHolder hits, SequenceRenderContext src, MouseEvent me) TickFeatureRenderer.processMouseEvent
(FeatureHolder hits, SequenceRenderContext src, MouseEvent me) ZiggyFeatureRenderer.processMouseEvent
(FeatureHolder hits, SequenceRenderContext src, MouseEvent me) ZiggyImapRenderer.processMouseEvent
(FeatureHolder holder, SequenceRenderContext context, MouseEvent mEvent) Constructors in org.biojava.bio.gui.sequence with parameters of type FeatureHolderModifierConstructorDescriptionSubCircularRendererContext
(CircularRendererContext delegate, SymbolList symbols, FeatureHolder features, double radius) Create a new sub context.SubPairwiseRenderContext
(PairwiseRenderContext context, SymbolList symbols, SymbolList secondarySymbols, FeatureHolder features, FeatureHolder secondaryFeatures, RangeLocation range, RangeLocation secondaryRange) Creates a newSubPairwiseRenderContext
.SubSequenceRenderContext
(SequenceRenderContext src, SymbolList symbols, FeatureHolder features, RangeLocation range) SubSequenceRenderContext
(SequenceRenderContext src, SymbolList symbols, FeatureHolder features, RangeLocation range, int symOffset) -
Uses of FeatureHolder in org.biojava.bio.molbio
Subinterfaces of FeatureHolder in org.biojava.bio.molbioModifier and TypeInterfaceDescriptioninterface
RestrictionSite
represents the recognition site of a restriction enzyme. -
Uses of FeatureHolder in org.biojava.bio.program.phred
Classes in org.biojava.bio.program.phred that implement FeatureHolderModifier and TypeClassDescriptionclass
PhredSequence is an extension of SimpleSequence that implements Qualitative to hold Phred quality scores. -
Uses of FeatureHolder in org.biojava.bio.program.xff
Methods in org.biojava.bio.program.xff with parameters of type FeatureHolderModifier and TypeMethodDescriptionvoid
XFFWriter.writeFeatureSet
(FeatureHolder fh, XMLWriter xw) static void
XFFTools.writeXFF
(File xffFile, FeatureHolder features) static void
XFFTools.writeXFF
(PrintWriter xffPR, FeatureHolder features) -
Uses of FeatureHolder in org.biojava.bio.seq
Subinterfaces of FeatureHolder in org.biojava.bio.seqModifier and TypeInterfaceDescriptioninterface
Feature which represents a component in an assembly (contig).interface
A feature within a sequence, or nested within another feature.interface
Title: FramedFeature.interface
Extension of GappedSymbolList which also projects features into the gapped coordinate system.interface
Interface forFeatureHolder
objects which know how to instantiate new child Features.interface
A feature that indicates that there is some remote feature that can't be represented entirely on a single Sequence.interface
A biological sequence.interface
Adds the concept of 'strand' to features.Classes in org.biojava.bio.seq that implement FeatureHolderModifier and TypeClassDescriptionclass
An abstract implementation of FeatureHolder.class
A circular view onto another Sequence object.static final class
class
Wrapper implementation of FeatureHolder which calls a method to create a contained FeatureHolder on demand.class
FeatureHolder which exposes all the features in a set of sub-FeatureHolders.class
A Sequence which is assembled from other sequences contained in a set of ComponentFeature objects.class
A Sequence which is assembled from other sequences contained in a set of ComponentFeature objects.class
A no-frills implementation of FeatureHolder.Fields in org.biojava.bio.seq declared as FeatureHolderMethods in org.biojava.bio.seq that return FeatureHolderModifier and TypeMethodDescriptionprotected abstract FeatureHolder
LazyFeatureHolder.createFeatureHolder()
AbstractFeatureHolder.filter
(FeatureFilter filter) AbstractFeatureHolder.filter
(FeatureFilter ff, boolean recurse) FeatureHolder.EmptyFeatureHolder.filter
(FeatureFilter fc) FeatureHolder.EmptyFeatureHolder.filter
(FeatureFilter fc, boolean recurse) FeatureHolder.filter
(FeatureFilter filter) Query this set of features using a suppliedFeatureFilter
.FeatureHolder.filter
(FeatureFilter fc, boolean recurse) Return a new FeatureHolder that contains all of the children of this one that passed the filter fc.LazyFeatureHolder.filter
(FeatureFilter ff) LazyFeatureHolder.filter
(FeatureFilter ff, boolean recurse) MergeFeatureHolder.filter
(FeatureFilter ff, boolean recurse) When applied to a MergeFeatureHolder, this filters each child FeatureHolder independently.NewSimpleAssembly.filter
(FeatureFilter ff) NewSimpleAssembly.filter
(FeatureFilter ff, boolean recurse) SimpleAssembly.filter
(FeatureFilter ff) SimpleAssembly.filter
(FeatureFilter ff, boolean recurse) Feature.getParent()
Return theFeatureHolder
to which this feature has been attached.static FeatureHolder
FeatureHolderUtils.intersect
(FeatureHolder fh1, FeatureHolder fh2) Operator: Intersect FeatureHolder1 with FeatureHolder2static FeatureHolder
FeatureHolderUtils.not
(FeatureHolder fh1, FeatureHolder fh2) Operator: FeatureHolder 1 NOT FeatureHolder2static FeatureHolder
FeatureHolderUtils.union
(FeatureHolder fh1, FeatureHolder fh2) Operator: Union of FeatureHolder1 and FeatureHolder2Methods in org.biojava.bio.seq with parameters of type FeatureHolderModifier and TypeMethodDescriptionstatic void
SequenceTools.addAllFeatures
(Sequence seq, FeatureHolder fh) Add features to a sequence that contain the same information as all those in a feature holder.void
MergeFeatureHolder.addFeatureHolder
(FeatureHolder fh) Add an extra FeatureHolder to the set of FeatureHolders which are merged.static Set
FeatureHolderUtils.featureHolderAsSet
(FeatureHolder fh) Returns a FeatureHolder as a Set of Featuresstatic FeatureHolder
FeatureHolderUtils.intersect
(FeatureHolder fh1, FeatureHolder fh2) Operator: Intersect FeatureHolder1 with FeatureHolder2static FeatureHolder
FeatureHolderUtils.not
(FeatureHolder fh1, FeatureHolder fh2) Operator: FeatureHolder 1 NOT FeatureHolder2FeatureRealizer.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) void
MergeFeatureHolder.removeFeatureHolder
(FeatureHolder fh) Remove a FeatureHolder from the set of FeatureHolders which are merged.static FeatureHolder
FeatureHolderUtils.union
(FeatureHolder fh1, FeatureHolder fh2) Operator: Union of FeatureHolder1 and FeatureHolder2 -
Uses of FeatureHolder in org.biojava.bio.seq.db
Methods in org.biojava.bio.seq.db that return FeatureHolderModifier and TypeMethodDescriptionAbstractSequenceDB.filter
(FeatureFilter ff) SequenceDB.filter
(FeatureFilter filter) Query features attached to all sequences in this database. -
Uses of FeatureHolder in org.biojava.bio.seq.db.biosql
Methods in org.biojava.bio.seq.db.biosql that return FeatureHolder -
Uses of FeatureHolder in org.biojava.bio.seq.distributed
Methods in org.biojava.bio.seq.distributed that return FeatureHolderModifier and TypeMethodDescriptionDistDataSource.getFeatures
(String id, FeatureFilter ff, boolean recurse) Get all features matching a FeatureFilter on a Sequence with an ID and recurse flats.DistDataSource.getFeatures
(FeatureFilter ff) Get all features matching a FeatureFilter provided by this DistDataSource.GFFDataSource.getFeatures
(String id, FeatureFilter ff, boolean recurse) GFFDataSource.getFeatures
(FeatureFilter ff) SequenceDBDataSource.getFeatures
(String id, FeatureFilter ff, boolean recurse) SequenceDBDataSource.getFeatures
(FeatureFilter ff) -
Uses of FeatureHolder in org.biojava.bio.seq.homol
Subinterfaces of FeatureHolder in org.biojava.bio.seq.homolModifier and TypeInterfaceDescriptioninterface
interface
SimilarityPairFeature
describes a pairwise similarity between two nucleotide sequences (as it extendsStrandedFeature
).Methods in org.biojava.bio.seq.homol that return FeatureHolderModifier and TypeMethodDescriptionHomology.getFeatures()
Retrieve the set of features that mark homologous regions.SimpleHomology.getFeatures()
getFeatures
returns the constituentHomologyFeature
s which are also used as the keys in the alignment. -
Uses of FeatureHolder in org.biojava.bio.seq.impl
Classes in org.biojava.bio.seq.impl that implement FeatureHolderModifier and TypeClassDescriptionfinal class
A Sequence implementation that has a name and URI but no features, and a zero length symbol list.class
FeatureHolder which lazily applies a specified filter to another FeatureHolder.class
A reverse complement view ontoSequence
interface.class
A no-frills implementation of a feature.class
Title: SimpleFramedFeature.class
Simple implementation of GappedSequence.class
class
A no-frills implementation of a remote feature.class
SimpleRestrictionSite
represents the recognition site of a restriction enzyme.class
A basic implementation of theSequence
interface.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.class
View a sub-section of a given sequence object, including all the features intersecting that region.class
A view onto another Sequence object.Methods in org.biojava.bio.seq.impl that return FeatureHolderModifier and TypeMethodDescriptionDummySequence.filter
(FeatureFilter ff) DummySequence.filter
(FeatureFilter ff, boolean recurse) LazyFilterFeatureHolder.filter
(FeatureFilter ff) LazyFilterFeatureHolder.filter
(FeatureFilter ff, boolean recurse) RevCompSequence.filter
(FeatureFilter ff) RevCompSequence.filter
(FeatureFilter ff, boolean recurse) SimpleFeature.filter
(FeatureFilter ff) SimpleFeature.filter
(FeatureFilter ff, boolean recurse) SimpleGappedSequence.filter
(FeatureFilter ff) SimpleGappedSequence.filter
(FeatureFilter ff, boolean recurse) SimpleSequence.filter
(FeatureFilter filter) SimpleSequence.filter
(FeatureFilter ff, boolean recurse) SubSequence.filter
(FeatureFilter ff) SubSequence.filter
(FeatureFilter ff, boolean recurse) ViewSequence.filter
(FeatureFilter fc) ViewSequence.filter
(FeatureFilter fc, boolean recurse) ViewSequence.getAddedFeatures()
SimpleFeature.getParent()
SubSequence.SubProjectedFeatureContext.projectChildFeatures
(Feature f, FeatureHolder parent) Methods in org.biojava.bio.seq.impl with parameters of type FeatureHolderModifier and TypeMethodDescriptionSimpleSequence.createFeature
(FeatureHolder fh, Feature.Template template) Deprecated.Please use new 1-arg createFeature instead.SubSequence.SubProjectedFeatureContext.projectChildFeatures
(Feature f, FeatureHolder parent) SimpleFeature.realizeFeature
(FeatureHolder fh, Feature.Template templ) SimpleSequence.realizeFeature
(FeatureHolder parent, Feature.Template template) ViewSequence.realizeFeature
(FeatureHolder parent, Feature.Template template) Constructors in org.biojava.bio.seq.impl with parameters of type FeatureHolderModifierConstructorDescriptionSimpleFeature
(Sequence sourceSeq, FeatureHolder parent, Feature.Template template) Create aSimpleFeature
on the given sequence.SimpleFramedFeature
(Sequence sourceSeq, FeatureHolder parent, FramedFeature.Template template) SimpleHomologyFeature
(Sequence sourceSeq, FeatureHolder parent, HomologyFeature.Template template) SimpleRemoteFeature
(Sequence sourceSeq, FeatureHolder parent, RemoteFeature.Template template) SimpleRestrictionSite
(Sequence sourceSeq, FeatureHolder parent, RestrictionSite.Template template) Creates a newSimpleRestrictionSite
.SimpleSimilarityPairFeature
(Sequence sourceSeq, FeatureHolder parent, SimilarityPairFeature.Template template) Creates a newSimpleSimilarityPairFeature
.SimpleStrandedFeature
(Sequence sourceSeq, FeatureHolder parent, StrandedFeature.Template template) -
Uses of FeatureHolder in org.biojava.bio.seq.io.agave
Methods in org.biojava.bio.seq.io.agave with parameters of type FeatureHolder -
Uses of FeatureHolder in org.biojava.bio.seq.projection
Classes in org.biojava.bio.seq.projection that implement FeatureHolderModifier and TypeClassDescriptionclass
Internal class used by ProjectionEngine to wrap Feature objects.final class
Helper class for projecting Feature objects into an alternative coordinate system.Methods in org.biojava.bio.seq.projection that return FeatureHolderModifier and TypeMethodDescriptionProjectedFeature.filter
(FeatureFilter ff) ProjectedFeature.filter
(FeatureFilter ff, boolean recurse) ProjectedFeatureHolder.filter
(FeatureFilter ff) ProjectedFeatureHolder.filter
(FeatureFilter ff, boolean recurse) ProjectedFeature.getParent()
final FeatureHolder
ReparentContext.getParent()
final FeatureHolder
protected FeatureHolder
ProjectedFeature.getProjectedFeatures()
ProjectionContext.getUnprojectedFeatures()
Get the features before projection.final FeatureHolder
ReparentContext.getUnprojectedFeatures()
protected FeatureHolder
ProjectedFeatureHolder.makeProjectionSet
(FeatureHolder fh) Called internally to construct a lightweight projected view of a set of featuresProjectionContext.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.projectFeatures
(FeatureHolder features) Project all of the features in a FeatureHolder.final FeatureHolder
ReparentContext.projectFeatures
(FeatureHolder fh) Methods in org.biojava.bio.seq.projection with parameters of type FeatureHolderModifier and TypeMethodDescriptionprotected FeatureHolder
ProjectedFeatureHolder.makeProjectionSet
(FeatureHolder fh) Called internally to construct a lightweight projected view of a set of featuresProjectionContext.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.projectFeatures
(FeatureHolder features) Project all of the features in a FeatureHolder.final FeatureHolder
ReparentContext.projectFeatures
(FeatureHolder fh) Constructors in org.biojava.bio.seq.projection with parameters of type FeatureHolderModifierConstructorDescriptionReparentContext
(FeatureHolder parent, FeatureHolder wrapped) TranslateFlipContext
(FeatureHolder parent, FeatureHolder wrapped, int translation) Create a new TranslateFlipContext with translation only.TranslateFlipContext
(FeatureHolder parent, FeatureHolder wrapped, int translate, boolean oppositeStrand) Create a new TranslateFlipContext with explicit translation and flip.TranslateFlipContext
(FeatureHolder parent, FeatureHolder wrapped, int min, int max) Create a new TranslateFlipContext that flips all featurs arround min and max. -
Uses of FeatureHolder in org.biojavax.bio.db
Methods in org.biojavax.bio.db that return FeatureHolder -
Uses of FeatureHolder in org.biojavax.bio.db.biosql
Methods in org.biojavax.bio.db.biosql that return FeatureHolderModifier and TypeMethodDescriptionBioSQLRichSequenceDB.filter
(FeatureFilter ff) BioSQLRichSequenceDB.processFeatureFilter
(FeatureFilter ff) -
Uses of FeatureHolder in org.biojavax.bio.seq
Subinterfaces of FeatureHolder 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.interface
A rich sequence is a combination of a org.biojavax.bio.Bioentry and a Sequence.Classes in org.biojavax.bio.seq that implement FeatureHolderModifier and TypeClassDescriptionclass
A simple implementation of RichFeature.class
A simple implementation of RichSequence.class
A simple implementation of RichSequence.Methods in org.biojavax.bio.seq that return FeatureHolderModifier and TypeMethodDescriptionSimpleRichFeature.filter
(FeatureFilter filter) Query this set of features using a suppliedFeatureFilter
.SimpleRichFeature.filter
(FeatureFilter fc, boolean recurse) Return a new FeatureHolder that contains all of the children of this one that passed the filter fc.ThinRichSequence.filter
(FeatureFilter filter) Query this set of features using a suppliedFeatureFilter
.ThinRichSequence.filter
(FeatureFilter fc, boolean recurse) Return a new FeatureHolder that contains all of the children of this one that passed the filter fc.SimpleRichFeature.getParent()
Return theFeatureHolder
to which this feature has been attached.Methods in org.biojavax.bio.seq with parameters of type FeatureHolderModifier and TypeMethodDescriptionvoid
RichFeature.setParent
(FeatureHolder parent) Sets the parent of this feature.void
SimpleRichFeature.setParent
(FeatureHolder parent) Sets the parent of this feature.Constructors in org.biojavax.bio.seq with parameters of type FeatureHolderModifierConstructorDescriptionSimpleRichFeature
(FeatureHolder parent, Feature.Template templ) Creates a new instance of SimpleRichFeature based on a template.