Uses of Interface org.biojava.bio.seq.FeatureHolder (BioJava-1.5-beta API)

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## Uses of Interface
org.biojava.bio.seq.FeatureHolder

Packages that use FeatureHolder
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.phred | Parser for Phred output
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.db | Collections of biological sequence data.
org.biojava.bio.seq.db.biosql | General purpose Sequence storage in a relational database.
org.biojava.bio.seq.distributed | Sequences and SequenceDBs which are composed from data taken from a number of data sources.
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.agave | Classes for converting between AGAVE XML and BioJava objects.
org.biojava.bio.seq.projection | Code for projecting Feature objects and systematically altering their properties.
org.biojavax.bio.db | Interactions between biojavax objects and a DB.
org.biojavax.bio.db.biosql |
org.biojavax.bio.seq | Rich implementations of Sequences, Locations and Features.

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

Methods in org.biojava.bio.gui.sequence that return FeatureHolder
`FeatureHolder` | `FeatureSource.getFeatureHolder()`
`FeatureHolder` | `SubCircularRendererContext.getFeatures()`
`FeatureHolder` | `SubSequenceRenderContext.getFeatures()`
`FeatureHolder` | `SequencePanel.getFeatures()`
`FeatureHolder` | `HeadlessRenderContext.getFeatures()`
`FeatureHolder` | `PairwiseSequencePanel.getFeatures()` `getFeatures` returns all of the `Feature`s belonging to the currently rendered `Sequence`.
`FeatureHolder` | `SequenceRenderContext.getFeatures()` The features to render.
`FeatureHolder` | `SequencePoster.getFeatures()` Deprecated.
`FeatureHolder` | `CircularRendererContext.getFeatures()` The features to render.
`FeatureHolder` | `TranslatedSequencePanel.getFeatures()` `getFeatures` returns all of the `Feature`s belonging to the currently rendered `Sequence`.
`FeatureHolder` | `SubPairwiseRenderContext.getFeatures()`
`FeatureHolder` | `PairwiseRenderContext.getSecondaryFeatures()` `getSecondaryFeatures` returns the features on the secondary sequence.
`FeatureHolder` | `PairwiseSequencePanel.getSecondaryFeatures()` `getSecondaryFeatures` returns all of the `Feature`s belonging to the currently rendered secondary `Sequence`.
`FeatureHolder` | `SubPairwiseRenderContext.getSecondaryFeatures()`
`FeatureHolder` | `SixFrameZiggyRenderer.processMouseEvent(FeatureHolder hits, SequenceRenderContext src, MouseEvent me)`
`FeatureHolder` | `BasicImapRenderer.processMouseEvent(FeatureHolder holder, SequenceRenderContext context, MouseEvent mEvent)`
`FeatureHolder` | `RectangularImapRenderer.processMouseEvent(FeatureHolder holder, SequenceRenderContext context, MouseEvent mEvent)`
`FeatureHolder` | `BasicFeatureRenderer.processMouseEvent(FeatureHolder hits, SequenceRenderContext src, MouseEvent me)`
`FeatureHolder` | `ZiggyFeatureRenderer.processMouseEvent(FeatureHolder hits, SequenceRenderContext src, MouseEvent me)`
`FeatureHolder` | `FeatureLabelRenderer.processMouseEvent(FeatureHolder hits, SequenceRenderContext src, MouseEvent me)`
`FeatureHolder` | `FeatureRenderer.processMouseEvent(FeatureHolder hits, SequenceRenderContext src, MouseEvent me)`
`FeatureHolder` | `ArrowedFeatureRenderer.processMouseEvent(FeatureHolder hits, SequenceRenderContext src, MouseEvent me)`
`FeatureHolder` | `AbstractBeadRenderer.processMouseEvent(FeatureHolder holder, SequenceRenderContext context, MouseEvent mEvent)` `processMouseEvent` defines the behaviour on revieving a mouse event.
`FeatureHolder` | `TickFeatureRenderer.processMouseEvent(FeatureHolder hits, SequenceRenderContext src, MouseEvent me)`
`FeatureHolder` | `StackedFeatureRenderer.processMouseEvent(FeatureHolder hits, SequenceRenderContext src, MouseEvent me)`
`FeatureHolder` | `GlyphFeatureRenderer.processMouseEvent(FeatureHolder fh, SequenceRenderContext src, MouseEvent me)`
`FeatureHolder` | `ZiggyImapRenderer.processMouseEvent(FeatureHolder holder, SequenceRenderContext context, MouseEvent mEvent)`

Methods in org.biojava.bio.gui.sequence with parameters of type FeatureHolder
`FeatureHolder` | `SixFrameZiggyRenderer.processMouseEvent(FeatureHolder hits, SequenceRenderContext src, MouseEvent me)`
`FeatureHolder` | `BasicImapRenderer.processMouseEvent(FeatureHolder holder, SequenceRenderContext context, MouseEvent mEvent)`
`FeatureHolder` | `RectangularImapRenderer.processMouseEvent(FeatureHolder holder, SequenceRenderContext context, MouseEvent mEvent)`
`FeatureHolder` | `BasicFeatureRenderer.processMouseEvent(FeatureHolder hits, SequenceRenderContext src, MouseEvent me)`
`FeatureHolder` | `ZiggyFeatureRenderer.processMouseEvent(FeatureHolder hits, SequenceRenderContext src, MouseEvent me)`
`FeatureHolder` | `FeatureLabelRenderer.processMouseEvent(FeatureHolder hits, SequenceRenderContext src, MouseEvent me)`
`FeatureHolder` | `FeatureRenderer.processMouseEvent(FeatureHolder hits, SequenceRenderContext src, MouseEvent me)`
`FeatureHolder` | `ArrowedFeatureRenderer.processMouseEvent(FeatureHolder hits, SequenceRenderContext src, MouseEvent me)`
`FeatureHolder` | `AbstractBeadRenderer.processMouseEvent(FeatureHolder holder, SequenceRenderContext context, MouseEvent mEvent)` `processMouseEvent` defines the behaviour on revieving a mouse event.
`FeatureHolder` | `TickFeatureRenderer.processMouseEvent(FeatureHolder hits, SequenceRenderContext src, MouseEvent me)`
`FeatureHolder` | `StackedFeatureRenderer.processMouseEvent(FeatureHolder hits, SequenceRenderContext src, MouseEvent me)`
`FeatureHolder` | `GlyphFeatureRenderer.processMouseEvent(FeatureHolder fh, SequenceRenderContext src, MouseEvent me)`
`FeatureHolder` | `ZiggyImapRenderer.processMouseEvent(FeatureHolder holder, SequenceRenderContext context, MouseEvent mEvent)`

Constructors in org.biojava.bio.gui.sequence with parameters of type FeatureHolder
`SubCircularRendererContext(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 new `SubPairwiseRenderContext`.
`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.molbio
`interface` | `RestrictionSite` `RestrictionSite` represents the recognition site of a restriction enzyme.

Uses of FeatureHolder in org.biojava.bio.program.das

Methods in org.biojava.bio.program.das that return FeatureHolder
`FeatureHolder` | `DASSequenceDB.filter(FeatureFilter ff)`
`FeatureHolder` | `DASSequence.filter(FeatureFilter ff)`
`FeatureHolder` | `DASSequence.filter(FeatureFilter ff, boolean recurse)`

Methods in org.biojava.bio.program.das with parameters of type FeatureHolder
`Feature` | `DASSequence.realizeFeature(FeatureHolder dest, Feature.Template temp)`

Uses of FeatureHolder in org.biojava.bio.program.phred

Classes in org.biojava.bio.program.phred that implement FeatureHolder
`class` | `PhredSequence` 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 FeatureHolder
`void` | `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.seq
`interface` | `ComponentFeature` Feature which represents a component in an assembly (contig).
`interface` | `Feature` A feature within a sequence, or nested within another feature.
`interface` | `FramedFeature` Title: FramedFeature.
`interface` | `GappedSequence` Extension of GappedSymbolList which also projects features into the gapped coordinate system.
`interface` | `RealizingFeatureHolder` Interface for `FeatureHolder` objects which know how to instantiate new child Features.
`interface` | `RemoteFeature` A feature that indicates that there is some remote feature that can't be represented entirely on a single Sequence.
`interface` | `Sequence` A biological sequence.
`interface` | `StrandedFeature` Adds the concept of 'strand' to features.

Classes in org.biojava.bio.seq that implement FeatureHolder
`class` | `AbstractFeatureHolder` An abstract implementation of FeatureHolder.
`class` | `CircularView` A circular view onto another Sequence object.
`static class` | `FeatureHolder.EmptyFeatureHolder`
`class` | `LazyFeatureHolder` Wrapper implementation of FeatureHolder which calls a method to create a contained FeatureHolder on demand.
`class` | `MergeFeatureHolder` FeatureHolder which exposes all the features in a set of sub-FeatureHolders.
`class` | `NewSimpleAssembly` A Sequence which is assembled from other sequences contained in a set of ComponentFeature objects.
`class` | `SimpleAssembly` A Sequence which is assembled from other sequences contained in a set of ComponentFeature objects.
`class` | `SimpleFeatureHolder` A no-frills implementation of FeatureHolder.

Fields in org.biojava.bio.seq declared as FeatureHolder
`static FeatureHolder` | `FeatureHolder.EMPTY_FEATURE_HOLDER`

Methods in org.biojava.bio.seq that return FeatureHolder
`protected abstract FeatureHolder` | `LazyFeatureHolder.createFeatureHolder()`
`FeatureHolder` | `SimpleAssembly.filter(FeatureFilter ff)`
`FeatureHolder` | `AbstractFeatureHolder.filter(FeatureFilter filter)`
`FeatureHolder` | `NewSimpleAssembly.filter(FeatureFilter ff)`
`FeatureHolder` | `LazyFeatureHolder.filter(FeatureFilter ff)`
`FeatureHolder` | `FeatureHolder.filter(FeatureFilter filter)` Query this set of features using a supplied `FeatureFilter`.
`FeatureHolder` | `FeatureHolder.EmptyFeatureHolder.filter(FeatureFilter fc)`
`FeatureHolder` | `SimpleAssembly.filter(FeatureFilter ff, boolean recurse)`
`FeatureHolder` | `AbstractFeatureHolder.filter(FeatureFilter ff, boolean recurse)`
`FeatureHolder` | `NewSimpleAssembly.filter(FeatureFilter ff, boolean recurse)`
`FeatureHolder` | `LazyFeatureHolder.filter(FeatureFilter ff, boolean recurse)`
`FeatureHolder` | `MergeFeatureHolder.filter(FeatureFilter ff, boolean recurse)` When applied to a MergeFeatureHolder, this filters each child FeatureHolder independently.
`FeatureHolder` | `FeatureHolder.filter(FeatureFilter fc, boolean recurse)` Return a new FeatureHolder that contains all of the children of this one that passed the filter fc.
`FeatureHolder` | `FeatureHolder.EmptyFeatureHolder.filter(FeatureFilter fc, boolean recurse)`
`FeatureHolder` | `Feature.getParent()` Return the `FeatureHolder` to which this feature has been attached.
`static FeatureHolder` | `FeatureHolderUtils.intersect(FeatureHolder fh1, FeatureHolder fh2)` Operator: Intersect FeatureHolder1 with FeatureHolder2
`static FeatureHolder` | `FeatureHolderUtils.not(FeatureHolder fh1, FeatureHolder fh2)` Operator: FeatureHolder 1 NOT FeatureHolder2
`static FeatureHolder` | `FeatureHolderUtils.union(FeatureHolder fh1, FeatureHolder fh2)` Operator: Union of FeatureHolder1 and FeatureHolder2

Methods in org.biojava.bio.seq with parameters of type FeatureHolder
`static 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 Features
`static FeatureHolder` | `FeatureHolderUtils.intersect(FeatureHolder fh1, FeatureHolder fh2)` Operator: Intersect FeatureHolder1 with FeatureHolder2
`static FeatureHolder` | `FeatureHolderUtils.not(FeatureHolder fh1, FeatureHolder fh2)` Operator: FeatureHolder 1 NOT FeatureHolder2
`Feature` | `SimpleAssembly.realizeFeature(FeatureHolder fh, Feature.Template temp)`
`Feature` | `NewSimpleAssembly.realizeFeature(FeatureHolder fh, Feature.Template temp)`
`Feature` | `RealizingFeatureHolder.realizeFeature(FeatureHolder parent, Feature.Template template)` Realize a feature template.
`Feature` | `SimpleFeatureRealizer.realizeFeature(Sequence seq, FeatureHolder parent, Feature.Template temp)`
`Feature` | `FeatureRealizer.realizeFeature(Sequence seq, FeatureHolder parent, Feature.Template template)` Install a feature on the specified sequence.
`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 FeatureHolder
`FeatureHolder` | `SequenceDB.filter(FeatureFilter filter)` Query features attached to all sequences in this database.
`FeatureHolder` | `AbstractSequenceDB.filter(FeatureFilter ff)`

Uses of FeatureHolder in org.biojava.bio.seq.db.biosql

Methods in org.biojava.bio.seq.db.biosql that return FeatureHolder
`FeatureHolder` | `BioSQLSequenceDB.filter(FeatureFilter ff)` Deprecated.

Uses of FeatureHolder in org.biojava.bio.seq.distributed

Methods in org.biojava.bio.seq.distributed that return FeatureHolder
`FeatureHolder` | `SequenceDBDataSource.getFeatures(FeatureFilter ff)`
`FeatureHolder` | `DistDataSource.getFeatures(FeatureFilter ff)` Get all features matching a FeatureFilter provided by this DistDataSource.
`FeatureHolder` | `GFFDataSource.getFeatures(FeatureFilter ff)`
`FeatureHolder` | `SequenceDBDataSource.getFeatures(String id, FeatureFilter ff, boolean recurse)`
`FeatureHolder` | `DistDataSource.getFeatures(String id, FeatureFilter ff, boolean recurse)` Get all features matching a FeatureFilter on a Sequence with an ID and recurse flats.
`FeatureHolder` | `GFFDataSource.getFeatures(String id, FeatureFilter ff, boolean recurse)`

Uses of FeatureHolder in org.biojava.bio.seq.homol

Subinterfaces of FeatureHolder in org.biojava.bio.seq.homol
`interface` | `HomologyFeature`
`interface` | `SimilarityPairFeature` `SimilarityPairFeature` describes a pairwise similarity between two nucleotide sequences (as it extends `StrandedFeature`).

Methods in org.biojava.bio.seq.homol that return FeatureHolder
`FeatureHolder` | `Homology.getFeatures()` Retrieve the set of features that mark homologous regions.
`FeatureHolder` | `SimpleHomology.getFeatures()` `getFeatures` returns the constituent `HomologyFeature`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 FeatureHolder
`class` | `DummySequence` A Sequence implementation that has a name and URI but no features, and a zero length symbol list.
`class` | `LazyFilterFeatureHolder` FeatureHolder which lazily applies a specified filter to another FeatureHolder.
`class` | `RevCompSequence` A reverse complement view onto `Sequence` interface.
`class` | `SimpleFeature` A no-frills implementation of a feature.
`class` | `SimpleFramedFeature` Title: SimpleFramedFeature.
`class` | `SimpleGappedSequence` Simple implementation of GappedSequence.
`class` | `SimpleHomologyFeature`
`class` | `SimpleRemoteFeature` A no-frills implementation of a remote feature.
`class` | `SimpleRestrictionSite` `SimpleRestrictionSite` represents the recognition site of a restriction enzyme.
`class` | `SimpleSequence` A basic implementation of the `Sequence` interface.
`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.
`class` | `SubSequence` View a sub-section of a given sequence object, including all the features intersecting that region.
`class` | `ViewSequence` A view onto another Sequence object.

Methods in org.biojava.bio.seq.impl that return FeatureHolder
`FeatureHolder` | `SimpleGappedSequence.filter(FeatureFilter ff)`
`FeatureHolder` | `RevCompSequence.filter(FeatureFilter ff)`
`FeatureHolder` | `SimpleSequence.filter(FeatureFilter filter)`
`FeatureHolder` | `SimpleFeature.filter(FeatureFilter ff)`
`FeatureHolder` | `DummySequence.filter(FeatureFilter ff)`
`FeatureHolder` | `ViewSequence.filter(FeatureFilter fc)`
`FeatureHolder` | `SubSequence.filter(FeatureFilter ff)`
`FeatureHolder` | `LazyFilterFeatureHolder.filter(FeatureFilter ff)`
`FeatureHolder` | `SimpleGappedSequence.filter(FeatureFilter ff, boolean recurse)`
`FeatureHolder` | `RevCompSequence.filter(FeatureFilter ff, boolean recurse)`
`FeatureHolder` | `SimpleSequence.filter(FeatureFilter ff, boolean recurse)`
`FeatureHolder` | `SimpleFeature.filter(FeatureFilter ff, boolean recurse)`
`FeatureHolder` | `DummySequence.filter(FeatureFilter ff, boolean recurse)`
`FeatureHolder` | `ViewSequence.filter(FeatureFilter fc, boolean recurse)`
`FeatureHolder` | `SubSequence.filter(FeatureFilter ff, boolean recurse)`
`FeatureHolder` | `LazyFilterFeatureHolder.filter(FeatureFilter ff, boolean recurse)`
`FeatureHolder` | `ViewSequence.getAddedFeatures()`
`FeatureHolder` | `SimpleFeature.getParent()`
`FeatureHolder` | `SubSequence.SubProjectedFeatureContext.projectChildFeatures(Feature f, FeatureHolder parent)`

Methods in org.biojava.bio.seq.impl with parameters of type FeatureHolder
`Feature` | `SimpleSequence.createFeature(FeatureHolder fh, Feature.Template template)` Deprecated. Please use new 1-arg createFeature instead.
`FeatureHolder` | `SubSequence.SubProjectedFeatureContext.projectChildFeatures(Feature f, FeatureHolder parent)`
`Feature` | `SimpleSequence.realizeFeature(FeatureHolder parent, Feature.Template template)`
`Feature` | `SimpleFeature.realizeFeature(FeatureHolder fh, Feature.Template templ)`
`Feature` | `ViewSequence.realizeFeature(FeatureHolder parent, Feature.Template template)`

Constructors in org.biojava.bio.seq.impl with parameters of type FeatureHolder
`LazyFilterFeatureHolder(FeatureHolder fh, FeatureFilter ff)`
`SimpleFeature(Sequence sourceSeq, FeatureHolder parent, Feature.Template template)` Create a `SimpleFeature` 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 new `SimpleRestrictionSite`.
`SimpleSimilarityPairFeature(Sequence sourceSeq, FeatureHolder parent, SimilarityPairFeature.Template template)` Creates a new `SimpleSimilarityPairFeature`.
`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
`protected void` | `AgaveWriter.writeAnnotations(FeatureHolder f)`

Uses of FeatureHolder in org.biojava.bio.seq.projection

Classes in org.biojava.bio.seq.projection that implement FeatureHolder
`class` | `ProjectedFeature` Internal class used by ProjectionEngine to wrap Feature objects.
`class` | `ProjectedFeatureHolder` Helper class for projecting Feature objects into an alternative coordinate system.

Methods in org.biojava.bio.seq.projection that return FeatureHolder
`FeatureHolder` | `ProjectedFeature.filter(FeatureFilter ff)`
`FeatureHolder` | `ProjectedFeatureHolder.filter(FeatureFilter ff)`
`FeatureHolder` | `ProjectedFeature.filter(FeatureFilter ff, boolean recurse)`
`FeatureHolder` | `ProjectedFeatureHolder.filter(FeatureFilter ff, boolean recurse)`
`FeatureHolder` | `ProjectedFeature.getParent()`
`FeatureHolder` | `ReparentContext.getParent()`
`FeatureHolder` | `ReparentContext.getParent(Feature f)`
`FeatureHolder` | `ProjectionContext.getParent(Feature projFeat)`
`protected FeatureHolder` | `ProjectedFeature.getProjectedFeatures()`
`FeatureHolder` | `ReparentContext.getUnprojectedFeatures()`
`FeatureHolder` | `ProjectionContext.getUnprojectedFeatures()` Get the features before projection.
`protected FeatureHolder` | `ProjectedFeatureHolder.makeProjectionSet(FeatureHolder fh)` Called internally to construct a lightweight projected view of a set of features
`FeatureHolder` | `ReparentContext.projectChildFeatures(Feature f, FeatureHolder parent)`
`FeatureHolder` | `ProjectionContext.projectChildFeatures(Feature feature, FeatureHolder parent)` Project all features that are children of feature so that they become children of parent.
`FeatureHolder` | `ReparentContext.projectFeatures(FeatureHolder fh)`
`FeatureHolder` | `ProjectionContext.projectFeatures(FeatureHolder features)` Project all of the features in a FeatureHolder.

Methods in org.biojava.bio.seq.projection with parameters of type FeatureHolder
`protected FeatureHolder` | `ProjectedFeatureHolder.makeProjectionSet(FeatureHolder fh)` Called internally to construct a lightweight projected view of a set of features
`FeatureHolder` | `ReparentContext.projectChildFeatures(Feature f, FeatureHolder parent)`
`FeatureHolder` | `ProjectionContext.projectChildFeatures(Feature feature, FeatureHolder parent)` Project all features that are children of feature so that they become children of parent.
`FeatureHolder` | `ReparentContext.projectFeatures(FeatureHolder fh)`
`FeatureHolder` | `ProjectionContext.projectFeatures(FeatureHolder features)` Project all of the features in a FeatureHolder.

Constructors in org.biojava.bio.seq.projection with parameters of type FeatureHolder
`ReparentContext(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
`FeatureHolder` | `AbstractRichSequenceDB.filter(FeatureFilter ff)`

Uses of FeatureHolder in org.biojavax.bio.db.biosql

Methods in org.biojavax.bio.db.biosql that return FeatureHolder
`FeatureHolder` | `BioSQLRichSequenceDB.filter(FeatureFilter ff)`
`FeatureHolder` | `BioSQLRichSequenceDB.processFeatureFilter(FeatureFilter ff)`

Uses of FeatureHolder in org.biojavax.bio.seq

Subinterfaces of FeatureHolder in org.biojavax.bio.seq
`interface` | `RichFeature` Represents a feature that can be given name and rank and be moved from one sequence to another.
`interface` | `RichFeatureHolder` Holds feature relationships.
`interface` | `RichSequence` A rich sequence is a combination of a org.biojavax.bio.Bioentry and a Sequence.

Classes in org.biojavax.bio.seq that implement FeatureHolder
`class` | `SimpleRichFeature` A simple implementation of RichFeature.
`class` | `SimpleRichSequence` A simple implementation of RichSequence.
`class` | `ThinRichSequence` A simple implementation of RichSequence.

Methods in org.biojavax.bio.seq that return FeatureHolder
`FeatureHolder` | `SimpleRichFeature.filter(FeatureFilter filter)` Query this set of features using a supplied `FeatureFilter`.
`FeatureHolder` | `ThinRichSequence.filter(FeatureFilter filter)` Query this set of features using a supplied `FeatureFilter`.
`FeatureHolder` | `SimpleRichFeature.filter(FeatureFilter fc, boolean recurse)` Return a new FeatureHolder that contains all of the children of this one that passed the filter fc.
`FeatureHolder` | `ThinRichSequence.filter(FeatureFilter fc, boolean recurse)` Return a new FeatureHolder that contains all of the children of this one that passed the filter fc.
`FeatureHolder` | `SimpleRichFeature.getParent()` Return the `FeatureHolder` to which this feature has been attached.

Methods in org.biojavax.bio.seq with parameters of type FeatureHolder
`void` | `SimpleRichFeature.setParent(FeatureHolder parent)` Sets the parent of this feature.
`void` | `RichFeature.setParent(FeatureHolder parent)` Sets the parent of this feature.

Constructors in org.biojavax.bio.seq with parameters of type FeatureHolder
`SimpleRichFeature(FeatureHolder parent, Feature.Template templ)` Creates a new instance of SimpleRichFeature based on a template.

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