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

Packages that use FeatureHolder

Package	Description
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.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	Interface between biojava and biosql databases
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

Modifier and Type	Method	Description
FeatureHolder	FeatureSource.getFeatureHolder()
FeatureHolder	CircularRendererContext.getFeatures()	The features to render.
FeatureHolder	HeadlessRenderContext.getFeatures()
FeatureHolder	PairwiseSequencePanel.getFeatures()	getFeatures returns all of the Features belonging to the currently rendered Sequence.
FeatureHolder	SequencePanel.getFeatures()
FeatureHolder	SequencePoster.getFeatures()	Deprecated.
FeatureHolder	SequenceRenderContext.getFeatures()	The features to render.
FeatureHolder	SubCircularRendererContext.getFeatures()
FeatureHolder	SubPairwiseRenderContext.getFeatures()
FeatureHolder	SubSequenceRenderContext.getFeatures()
FeatureHolder	TranslatedSequencePanel.getFeatures()	getFeatures returns all of the Features belonging to the currently rendered Sequence.
FeatureHolder	PairwiseRenderContext.getSecondaryFeatures()	getSecondaryFeatures returns the features on the secondary sequence.
FeatureHolder	PairwiseSequencePanel.getSecondaryFeatures()	getSecondaryFeatures returns all of the Features belonging to the currently rendered secondary Sequence.
FeatureHolder	SubPairwiseRenderContext.getSecondaryFeatures()
FeatureHolder	AbstractBeadRenderer.processMouseEvent(FeatureHolder holder, SequenceRenderContext context, MouseEvent mEvent)	processMouseEvent defines the behaviour on revieving a mouse event.
FeatureHolder	ArrowedFeatureRenderer.processMouseEvent(FeatureHolder hits, SequenceRenderContext src, MouseEvent me)
FeatureHolder	BasicFeatureRenderer.processMouseEvent(FeatureHolder hits, SequenceRenderContext src, MouseEvent me)
FeatureHolder	BasicImapRenderer.processMouseEvent(FeatureHolder holder, SequenceRenderContext context, MouseEvent mEvent)
FeatureHolder	FeatureLabelRenderer.processMouseEvent(FeatureHolder hits, SequenceRenderContext src, MouseEvent me)
FeatureHolder	FeatureRenderer.processMouseEvent(FeatureHolder hits, SequenceRenderContext src, MouseEvent me)
FeatureHolder	GlyphFeatureRenderer.processMouseEvent(FeatureHolder fh, SequenceRenderContext src, MouseEvent me)
FeatureHolder	RectangularImapRenderer.processMouseEvent(FeatureHolder holder, SequenceRenderContext context, MouseEvent mEvent)
FeatureHolder	SixFrameZiggyRenderer.processMouseEvent(FeatureHolder hits, SequenceRenderContext src, MouseEvent me)
FeatureHolder	StackedFeatureRenderer.processMouseEvent(FeatureHolder hits, SequenceRenderContext src, MouseEvent me)
FeatureHolder	TickFeatureRenderer.processMouseEvent(FeatureHolder hits, SequenceRenderContext src, MouseEvent me)
FeatureHolder	ZiggyFeatureRenderer.processMouseEvent(FeatureHolder hits, 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

Modifier and Type	Method	Description
FeatureHolder	AbstractBeadRenderer.processMouseEvent(FeatureHolder holder, SequenceRenderContext context, MouseEvent mEvent)	processMouseEvent defines the behaviour on revieving a mouse event.
FeatureHolder	ArrowedFeatureRenderer.processMouseEvent(FeatureHolder hits, SequenceRenderContext src, MouseEvent me)
FeatureHolder	BasicFeatureRenderer.processMouseEvent(FeatureHolder hits, SequenceRenderContext src, MouseEvent me)
FeatureHolder	BasicImapRenderer.processMouseEvent(FeatureHolder holder, SequenceRenderContext context, MouseEvent mEvent)
FeatureHolder	FeatureLabelRenderer.processMouseEvent(FeatureHolder hits, SequenceRenderContext src, MouseEvent me)
FeatureHolder	FeatureRenderer.processMouseEvent(FeatureHolder hits, SequenceRenderContext src, MouseEvent me)
FeatureHolder	GlyphFeatureRenderer.processMouseEvent(FeatureHolder fh, SequenceRenderContext src, MouseEvent me)
FeatureHolder	RectangularImapRenderer.processMouseEvent(FeatureHolder holder, SequenceRenderContext context, MouseEvent mEvent)
FeatureHolder	SixFrameZiggyRenderer.processMouseEvent(FeatureHolder hits, SequenceRenderContext src, MouseEvent me)
FeatureHolder	StackedFeatureRenderer.processMouseEvent(FeatureHolder hits, SequenceRenderContext src, MouseEvent me)
FeatureHolder	TickFeatureRenderer.processMouseEvent(FeatureHolder hits, SequenceRenderContext src, MouseEvent me)
FeatureHolder	ZiggyFeatureRenderer.processMouseEvent(FeatureHolder hits, 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

Constructor	Description
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

Modifier and Type	Interface	Description
interface	RestrictionSite	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 FeatureHolder

Modifier and Type	Class	Description
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

Modifier and Type	Method	Description
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

Modifier and Type	Interface	Description
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

Modifier and Type	Class	Description
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

Modifier and Type	Field	Description
static FeatureHolder	FeatureHolder.EMPTY_FEATURE_HOLDER

Methods in org.biojava.bio.seq that return FeatureHolder

Modifier and Type	Method	Description
protected abstract FeatureHolder	LazyFeatureHolder.createFeatureHolder()
FeatureHolder	AbstractFeatureHolder.filter(FeatureFilter filter)
FeatureHolder	AbstractFeatureHolder.filter(FeatureFilter ff, boolean recurse)
FeatureHolder	FeatureHolder.EmptyFeatureHolder.filter(FeatureFilter fc)
FeatureHolder	FeatureHolder.EmptyFeatureHolder.filter(FeatureFilter fc, boolean recurse)
FeatureHolder	FeatureHolder.filter(FeatureFilter filter)	Query this set of features using a supplied FeatureFilter.
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	LazyFeatureHolder.filter(FeatureFilter ff)
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	NewSimpleAssembly.filter(FeatureFilter ff)
FeatureHolder	NewSimpleAssembly.filter(FeatureFilter ff, boolean recurse)
FeatureHolder	SimpleAssembly.filter(FeatureFilter ff)
FeatureHolder	SimpleAssembly.filter(FeatureFilter ff, 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

Modifier and Type	Method	Description
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	FeatureRealizer.realizeFeature(Sequence seq, FeatureHolder parent, Feature.Template template)	Install a feature on the specified sequence.
Feature	NewSimpleAssembly.realizeFeature(FeatureHolder fh, Feature.Template temp)
Feature	RealizingFeatureHolder.realizeFeature(FeatureHolder parent, Feature.Template template)	Realize a feature template.
Feature	SimpleAssembly.realizeFeature(FeatureHolder fh, Feature.Template temp)
Feature	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 FeatureHolder

Modifier and Type	Method	Description
FeatureHolder	AbstractSequenceDB.filter(FeatureFilter ff)
FeatureHolder	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

Modifier and Type	Method	Description
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

Modifier and Type	Method	Description
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	DistDataSource.getFeatures(FeatureFilter ff)	Get all features matching a FeatureFilter provided by this DistDataSource.
FeatureHolder	GFFDataSource.getFeatures(String id, FeatureFilter ff, boolean recurse)
FeatureHolder	GFFDataSource.getFeatures(FeatureFilter ff)
FeatureHolder	SequenceDBDataSource.getFeatures(String id, FeatureFilter ff, boolean recurse)
FeatureHolder	SequenceDBDataSource.getFeatures(FeatureFilter ff)

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

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

Modifier and Type	Interface	Description
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

Modifier and Type	Method	Description
FeatureHolder	Homology.getFeatures()	Retrieve the set of features that mark homologous regions.
FeatureHolder	SimpleHomology.getFeatures()	getFeatures returns the constituent HomologyFeatures 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

Modifier and Type	Class	Description
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

Modifier and Type	Method	Description
FeatureHolder	DummySequence.filter(FeatureFilter ff)
FeatureHolder	DummySequence.filter(FeatureFilter ff, boolean recurse)
FeatureHolder	LazyFilterFeatureHolder.filter(FeatureFilter ff)
FeatureHolder	LazyFilterFeatureHolder.filter(FeatureFilter ff, boolean recurse)
FeatureHolder	RevCompSequence.filter(FeatureFilter ff)
FeatureHolder	RevCompSequence.filter(FeatureFilter ff, boolean recurse)
FeatureHolder	SimpleFeature.filter(FeatureFilter ff)
FeatureHolder	SimpleFeature.filter(FeatureFilter ff, boolean recurse)
FeatureHolder	SimpleGappedSequence.filter(FeatureFilter ff)
FeatureHolder	SimpleGappedSequence.filter(FeatureFilter ff, boolean recurse)
FeatureHolder	SimpleSequence.filter(FeatureFilter filter)
FeatureHolder	SimpleSequence.filter(FeatureFilter ff, boolean recurse)
FeatureHolder	SubSequence.filter(FeatureFilter ff)
FeatureHolder	SubSequence.filter(FeatureFilter ff, boolean recurse)
FeatureHolder	ViewSequence.filter(FeatureFilter fc)
FeatureHolder	ViewSequence.filter(FeatureFilter fc, 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

Modifier and Type	Method	Description
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	SimpleFeature.realizeFeature(FeatureHolder fh, Feature.Template templ)
Feature	SimpleSequence.realizeFeature(FeatureHolder parent, Feature.Template template)
Feature	ViewSequence.realizeFeature(FeatureHolder parent, Feature.Template template)

Constructors in org.biojava.bio.seq.impl with parameters of type FeatureHolder

Constructor	Description
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

Modifier and Type	Method	Description
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

Modifier and Type	Class	Description
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

Modifier and Type	Method	Description
FeatureHolder	ProjectedFeature.filter(FeatureFilter ff)
FeatureHolder	ProjectedFeature.filter(FeatureFilter ff, boolean recurse)
FeatureHolder	ProjectedFeatureHolder.filter(FeatureFilter ff)
FeatureHolder	ProjectedFeatureHolder.filter(FeatureFilter ff, boolean recurse)
FeatureHolder	ProjectedFeature.getParent()
FeatureHolder	ProjectionContext.getParent(Feature projFeat)
FeatureHolder	ReparentContext.getParent()
FeatureHolder	ReparentContext.getParent(Feature f)
protected FeatureHolder	ProjectedFeature.getProjectedFeatures()
FeatureHolder	ProjectionContext.getUnprojectedFeatures()	Get the features before projection.
FeatureHolder	ReparentContext.getUnprojectedFeatures()
protected FeatureHolder	ProjectedFeatureHolder.makeProjectionSet(FeatureHolder fh)	Called internally to construct a lightweight projected view of a set of features
FeatureHolder	ProjectionContext.projectChildFeatures(Feature feature, FeatureHolder parent)	Project all features that are children of feature so that they become children of parent.
FeatureHolder	ReparentContext.projectChildFeatures(Feature f, FeatureHolder parent)
FeatureHolder	ProjectionContext.projectFeatures(FeatureHolder features)	Project all of the features in a FeatureHolder.
FeatureHolder	ReparentContext.projectFeatures(FeatureHolder fh)

Methods in org.biojava.bio.seq.projection with parameters of type FeatureHolder

Modifier and Type	Method	Description
protected FeatureHolder	ProjectedFeatureHolder.makeProjectionSet(FeatureHolder fh)	Called internally to construct a lightweight projected view of a set of features
FeatureHolder	ProjectionContext.projectChildFeatures(Feature feature, FeatureHolder parent)	Project all features that are children of feature so that they become children of parent.
FeatureHolder	ReparentContext.projectChildFeatures(Feature f, FeatureHolder parent)
FeatureHolder	ProjectionContext.projectFeatures(FeatureHolder features)	Project all of the features in a FeatureHolder.
FeatureHolder	ReparentContext.projectFeatures(FeatureHolder fh)

Constructors in org.biojava.bio.seq.projection with parameters of type FeatureHolder

Constructor	Description
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

Modifier and Type	Method	Description
FeatureHolder	AbstractRichSequenceDB.filter(FeatureFilter ff)

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

Methods in org.biojavax.bio.db.biosql that return FeatureHolder

Modifier and Type	Method	Description
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

Modifier and Type	Interface	Description
interface	RichFeature	Represents a feature that can be given name and rank and be moved from one sequence to another.
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

Modifier and Type	Class	Description
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

Modifier and Type	Method	Description
FeatureHolder	SimpleRichFeature.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 filter)	Query this set of features using a supplied FeatureFilter.
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

Modifier and Type	Method	Description
void	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 FeatureHolder

Constructor	Description
SimpleRichFeature(FeatureHolder parent, Feature.Template templ)	Creates a new instance of SimpleRichFeature based on a template.