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

Packages that use FeatureFilter
org.biojava.bio.gui.sequence: Graphical displays of biological sequences and associated annotations.
org.biojava.bio.program.das: Development client for the Distributed Annotation System.
org.biojava.bio.program.gff: GFF manipulation.
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.impl: Standard in-memory implementations of `Sequence` and `Feature`.
org.biojava.bio.seq.io.filterxml: Tools for reading and writing an XML representation of BioJava's FeatureFilter language.
org.biojava.bio.seq.projection: Code for projecting Feature objects into alternate coordinate systems.

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

Fields in org.biojava.bio.gui.sequence declared as FeatureFilter
`protected FeatureFilter` `FilteringRenderer.filter`
`protected FeatureFilter` `PairwiseFilteringRenderer.filter` `filter` is the filter applied to both `FeatureHolder`s.

Methods in org.biojava.bio.gui.sequence that return FeatureFilter
`FeatureFilter` `FilteringRenderer.getFilter()`
`FeatureFilter` `PairwiseFilteringRenderer.getFilter()` `getFilter` returns the current filter.

Methods in org.biojava.bio.gui.sequence with parameters of type FeatureFilter
`void` `FilteringRenderer.setFilter(FeatureFilter filter)`
`void` `PairwiseFilteringRenderer.setFilter(FeatureFilter filter)` `setFilter` sets the filter.
`protected java.util.List` `BumpedRenderer.doLayer(SequenceRenderContext src, FeatureFilter filt)`

Constructors in org.biojava.bio.gui.sequence with parameters of type FeatureFilter
`FilteringRenderer(SequenceRenderer renderer, FeatureFilter filter, boolean recurse)`
`PairwiseFilteringRenderer(PairwiseSequenceRenderer renderer, FeatureFilter filter, boolean recurse)` Creates a new `PairwiseFilteringRenderer`.

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

Methods in org.biojava.bio.program.das that return FeatureFilter
`FeatureFilter` `DASSequence.getSchema()`

Methods in org.biojava.bio.program.das with parameters of type FeatureFilter
`FeatureHolder` `DASSequenceDB.filter(FeatureFilter ff)`
`FeatureHolder` `DASSequence.filter(FeatureFilter ff)`
`FeatureHolder` `DASSequence.filter(FeatureFilter ff, boolean recurse)`

Uses of FeatureFilter in org.biojava.bio.program.gff

Methods in org.biojava.bio.program.gff that return FeatureFilter
`FeatureFilter` `SequencesAsGFF.getFeatureFilter()` Return the current FeatureFilter.

Methods in org.biojava.bio.program.gff with parameters of type FeatureFilter
`void` `SequencesAsGFF.setFeatureFilter(FeatureFilter filter)` Replace the current FeatureFilter with filter.

Uses of FeatureFilter in org.biojava.bio.seq

Subinterfaces of FeatureFilter in org.biojava.bio.seq
`interface` `OptimizableFilter` The interface for filters that can potentialy optimize themselves, and compare themselves with other filters.

Classes in org.biojava.bio.seq that implement FeatureFilter
`static class` `FeatureFilter.And` A filter that returns all features accepted by both child filter.
`static class` `FeatureFilter.AnnotationContains` Retrieve features that contain a given annotation, and that the set of values contains the value given.
`static class` `FeatureFilter.ByAncestor` Filter by applying a nested `FeatureFilter` to all ancestor features.
`static class` `FeatureFilter.ByAnnotation` Retrieve features that contain a given annotation with a given value.
`static class` `FeatureFilter.ByAnnotationType` A filter that returns all features that have an annotation bundle that is of a given annotation type.
`static class` `FeatureFilter.ByChild` Filter by applying a nested `FeatureFilter` to the child features.
`static class` `FeatureFilter.ByClass` Filter which accepts only those filters which are an instance of a specific Java class
`static class` `FeatureFilter.ByComponentName` Accepts features which are ComponentFeatures and have a `componentSequenceName` property of the specified value.
`static class` `FeatureFilter.ByDescendant` Filter by applying a nested `FeatureFilter` to all descendant features.
`static class` `FeatureFilter.ByFeature` Accept only features which are equal to the specified feature
`static class` `FeatureFilter.ByPairwiseScore` `ByPairwiseScore` is used to filter `SimilarityPairFeature`s by their score.
`static class` `FeatureFilter.ByParent` Filter by applying a nested `FeatureFilter` to the parent feature.
`static class` `FeatureFilter.BySequenceName` Accept features that reside on a sequence with a particular name.
`static class` `FeatureFilter.BySource` Construct one of these to filter features by source.
`static class` `FeatureFilter.ByType` Construct one of these to filter features by type.
`static class` `FeatureFilter.ContainedByLocation` A filter that returns all features contained within a location.
`static class` `FeatureFilter.FrameFilter` Accept features with a given reading frame.
`static class` `FeatureFilter.HasAnnotation` Retrieve features that contain a given annotation with any value.
`static class` `FeatureFilter.Not` A filter that returns all features not accepted by a child filter.
`static class` `FeatureFilter.OnlyChildren` Accepts features where all immediate children meet the supplied filter.
`static class` `FeatureFilter.OnlyDescendants` Accepts features where all descendants meet the supplied filter.
`static class` `FeatureFilter.Or` A filter that returns all features accepted by at least one child filter.
`static class` `FeatureFilter.OverlapsLocation` A filter that returns all features overlapping a location.
`static class` `FeatureFilter.ShadowContainedByLocation` A filter that accepts all features whose shadow is contained by a specified `Location`.
`static class` `FeatureFilter.ShadowOverlapsLocation` A filter that accepts all features whose shadow overlaps a specified `Location`.
`static class` `FeatureFilter.StrandFilter` Accept features with a given strandedness.

Fields in org.biojava.bio.seq declared as FeatureFilter
`static FeatureFilter` `FeatureFilter.all` All features are selected by this filter.
`static FeatureFilter` `FeatureFilter.none` No features are selected by this filter.
`static FeatureFilter` `FeatureFilter.top_level` A filter which accepts only top-level Features.
`static FeatureFilter` `FeatureFilter.leaf` A filter which accepts features with no children

Methods in org.biojava.bio.seq that return FeatureFilter
`FeatureFilter` `FeatureTypes.Type.getSchema()` Get the schema for this type.
`FeatureFilter` `SimpleFeatureHolder.getSchema()`
`FeatureFilter` `FeatureFilter.Not.getChild()`
`FeatureFilter` `FeatureFilter.And.getChild1()`
`FeatureFilter` `FeatureFilter.And.getChild2()`
`FeatureFilter` `FeatureFilter.Or.getChild1()`
`FeatureFilter` `FeatureFilter.Or.getChild2()`
`FeatureFilter` `FeatureFilter.ByParent.getFilter()`
`FeatureFilter` `FeatureFilter.ByAncestor.getFilter()`
`FeatureFilter` `FeatureFilter.OnlyChildren.getFilter()`
`FeatureFilter` `FeatureFilter.OnlyDescendants.getFilter()`
`FeatureFilter` `FeatureFilter.ByChild.getFilter()`
`FeatureFilter` `FeatureFilter.ByDescendant.getFilter()`
`static FeatureFilter` `FilterUtils.byType(java.lang.String type)`
`static FeatureFilter` `FilterUtils.bySource(java.lang.String source)`
`static FeatureFilter` `FilterUtils.byClass(java.lang.Class clazz)`
`static FeatureFilter` `FilterUtils.containedByLocation(Location loc)`
`static FeatureFilter` `FilterUtils.overlapsLocation(Location loc)`
`static FeatureFilter` `FilterUtils.bySequenceName(java.lang.String name)`
`static FeatureFilter` `FilterUtils.not(FeatureFilter filter)`
`static FeatureFilter` `FilterUtils.and(FeatureFilter c1, FeatureFilter c2)`
`static FeatureFilter` `FilterUtils.and(FeatureFilter[] filters)`
`static FeatureFilter` `FilterUtils.or(FeatureFilter c1, FeatureFilter c2)`
`static FeatureFilter` `FilterUtils.or(FeatureFilter[] filters)`
`static FeatureFilter` `FilterUtils.byAnnotationType(AnnotationType type)`
`static FeatureFilter` `FilterUtils.byAnnotation(java.lang.Object key, java.lang.Object value)`
`static FeatureFilter` `FilterUtils.byAnnotationType(java.lang.Object key, java.lang.Class valClass)`
`static FeatureFilter` `FilterUtils.hasAnnotation(java.lang.Object key)`
`static FeatureFilter` `FilterUtils.byStrand(StrandedFeature.Strand strand)`
`static FeatureFilter` `FilterUtils.byParent(FeatureFilter parentFilter)`
`static FeatureFilter` `FilterUtils.byAncestor(FeatureFilter ancestorFilter)`
`static FeatureFilter` `FilterUtils.byChild(FeatureFilter childFilter)`
`static FeatureFilter` `FilterUtils.byDescendant(FeatureFilter descFilter)`
`static FeatureFilter` `FilterUtils.byFrame(FramedFeature.ReadingFrame frame)`
`static FeatureFilter` `FilterUtils.byPairwiseScore(double minScore, double maxScore)`
`static FeatureFilter` `FilterUtils.byComponentName(java.lang.String compName)`
`static FeatureFilter` `FilterUtils.topLevel()`
`static FeatureFilter` `FilterUtils.leaf()`
`static FeatureFilter` `FilterUtils.all()`
`static FeatureFilter` `FilterUtils.none()`
`static FeatureFilter` `FilterUtils.optimize(FeatureFilter filter)`
`static FeatureFilter` `FilterUtils.transformFilter(FeatureFilter ff, FilterUtils.FilterTransformer trans)` This is a general framework method for transforming one filter into another.
`FeatureFilter` `FilterUtils.FilterTransformer.transform(FeatureFilter filt)` Transform a filter, or return null if it can not be transformed.
`FeatureFilter` `FilterUtils.DelegatingTransformer.transform(FeatureFilter ff)`
`FeatureFilter` `ViewSequence.getSchema()`
`FeatureFilter` `SimpleAssembly.getSchema()`
`FeatureFilter` `MergeFeatureHolder.getSchema()`
`FeatureFilter` `FeatureHolder.getSchema()` Return a schema-filter for this `FeatureHolder`.
`FeatureFilter` `FeatureHolder.EmptyFeatureHolder.getSchema()`
`FeatureFilter` `SimpleGappedSequence.getSchema()`
`FeatureFilter` `ProjectedFeatureHolder.getSchema()`
`protected FeatureFilter` `ProjectedFeatureHolder.untransformFilter(FeatureFilter ff)` Called to transform a FeatureFilter applying to our projections into a corresponding filter on the parent FeatureHolder.
`protected FeatureFilter` `ProjectedFeatureHolder.transformFilter(FeatureFilter ff)` Called to transform a FeatureFilter applying to our parent FeatureHolder into the coordinate system of our parent.
`FeatureFilter` `ProjectedFeatureHolder.getSchema(Feature f)`
`FeatureFilter` `SubSequence.getSchema()`
`FeatureFilter` `DummySequence.getSchema()`
`FeatureFilter` `LazyFeatureHolder.getSchema()`

Methods in org.biojava.bio.seq with parameters of type FeatureFilter
`FeatureTypes.Type` `FeatureTypes.RepositoryImpl.createType(java.lang.String name, FeatureFilter schema, java.util.Set parents)` Create a new type in this repository.
`boolean` `FeatureFilter.ByType.isProperSubset(FeatureFilter sup)`
`boolean` `FeatureFilter.ByType.isDisjoint(FeatureFilter filt)`
`boolean` `FeatureFilter.BySource.isProperSubset(FeatureFilter sup)`
`boolean` `FeatureFilter.BySource.isDisjoint(FeatureFilter filt)`
`boolean` `FeatureFilter.ByClass.isProperSubset(FeatureFilter sup)`
`boolean` `FeatureFilter.ByClass.isDisjoint(FeatureFilter feat)`
`boolean` `FeatureFilter.StrandFilter.isProperSubset(FeatureFilter sup)`
`boolean` `FeatureFilter.StrandFilter.isDisjoint(FeatureFilter filt)`
`boolean` `FeatureFilter.BySequenceName.isProperSubset(FeatureFilter sup)`
`boolean` `FeatureFilter.BySequenceName.isDisjoint(FeatureFilter filt)`
`boolean` `FeatureFilter.ContainedByLocation.isProperSubset(FeatureFilter sup)`
`boolean` `FeatureFilter.ContainedByLocation.isDisjoint(FeatureFilter filt)`
`boolean` `FeatureFilter.OverlapsLocation.isProperSubset(FeatureFilter sup)`
`boolean` `FeatureFilter.OverlapsLocation.isDisjoint(FeatureFilter filt)`
`boolean` `FeatureFilter.ShadowOverlapsLocation.isProperSubset(FeatureFilter sup)`
`boolean` `FeatureFilter.ShadowOverlapsLocation.isDisjoint(FeatureFilter filt)`
`boolean` `FeatureFilter.ShadowContainedByLocation.isProperSubset(FeatureFilter sup)`
`boolean` `FeatureFilter.ShadowContainedByLocation.isDisjoint(FeatureFilter filt)`
`boolean` `FeatureFilter.ByAnnotationType.isDisjoint(FeatureFilter filter)`
`boolean` `FeatureFilter.ByAnnotationType.isProperSubset(FeatureFilter filter)`
`boolean` `FeatureFilter.ByParent.isProperSubset(FeatureFilter ff)`
`boolean` `FeatureFilter.ByParent.isDisjoint(FeatureFilter ff)`
`boolean` `FeatureFilter.ByAncestor.isProperSubset(FeatureFilter ff)`
`boolean` `FeatureFilter.ByAncestor.isDisjoint(FeatureFilter ff)`
`boolean` `FeatureFilter.OnlyChildren.isProperSubset(FeatureFilter ff)`
`boolean` `FeatureFilter.OnlyChildren.isDisjoint(FeatureFilter ff)`
`boolean` `FeatureFilter.OnlyDescendants.isProperSubset(FeatureFilter ff)`
`boolean` `FeatureFilter.OnlyDescendants.isDisjoint(FeatureFilter ff)`
`boolean` `FeatureFilter.ByChild.isProperSubset(FeatureFilter ff)`
`boolean` `FeatureFilter.ByChild.isDisjoint(FeatureFilter ff)`
`boolean` `FeatureFilter.ByDescendant.isProperSubset(FeatureFilter ff)`
`boolean` `FeatureFilter.ByDescendant.isDisjoint(FeatureFilter ff)`
`boolean` `FeatureFilter.FrameFilter.isProperSubset(FeatureFilter sup)`
`boolean` `FeatureFilter.FrameFilter.isDisjoint(FeatureFilter filt)`
`boolean` `FeatureFilter.ByPairwiseScore.isProperSubset(FeatureFilter sup)`
`boolean` `FeatureFilter.ByPairwiseScore.isDisjoint(FeatureFilter filt)`
`boolean` `FeatureFilter.ByComponentName.isProperSubset(FeatureFilter sup)`
`boolean` `FeatureFilter.ByComponentName.isDisjoint(FeatureFilter feat)`
`boolean` `FeatureFilter.ByFeature.isProperSubset(FeatureFilter ff)`
`boolean` `FeatureFilter.ByFeature.isDisjoint(FeatureFilter ff)`
`static boolean` `FilterUtils.areProperSubset(FeatureFilter sub, FeatureFilter sup)` Determines if the set of features matched by sub can be `proven` to be a proper subset of the features matched by sup.
`static boolean` `FilterUtils.areDisjoint(FeatureFilter a, FeatureFilter b)` Determines is two queries can be proven to be disjoint.
`static Location` `FilterUtils.extractOverlappingLocation(FeatureFilter ff)` Try to determine the minimal location which all features matching a given filter must overlap.
`static boolean` `FilterUtils.areEqual(FeatureFilter f1, FeatureFilter f2)`
`static FeatureFilter` `FilterUtils.not(FeatureFilter filter)`
`static FeatureFilter` `FilterUtils.and(FeatureFilter c1, FeatureFilter c2)`
`static FeatureFilter` `FilterUtils.and(FeatureFilter[] filters)`
`static FeatureFilter` `FilterUtils.or(FeatureFilter c1, FeatureFilter c2)`
`static FeatureFilter` `FilterUtils.or(FeatureFilter[] filters)`
`static FeatureFilter` `FilterUtils.byParent(FeatureFilter parentFilter)`
`static FeatureFilter` `FilterUtils.byAncestor(FeatureFilter ancestorFilter)`
`static FeatureFilter` `FilterUtils.byChild(FeatureFilter childFilter)`
`static FeatureFilter` `FilterUtils.byDescendant(FeatureFilter descFilter)`
`static FeatureFilter` `FilterUtils.optimize(FeatureFilter filter)`
`static FeatureFilter` `FilterUtils.transformFilter(FeatureFilter ff, FilterUtils.FilterTransformer trans)` This is a general framework method for transforming one filter into another.
`FeatureFilter` `FilterUtils.FilterTransformer.transform(FeatureFilter filt)` Transform a filter, or return null if it can not be transformed.
`FeatureFilter` `FilterUtils.DelegatingTransformer.transform(FeatureFilter ff)`
`FeatureHolder` `ViewSequence.filter(FeatureFilter fc, boolean recurse)`
`FeatureHolder` `ViewSequence.filter(FeatureFilter fc)`
`FeatureHolder` `SimpleAssembly.filter(FeatureFilter ff, boolean recurse)`
`FeatureHolder` `SimpleAssembly.filter(FeatureFilter ff)`
`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.filter(FeatureFilter filter)` Query this set of features using a supplied `FeatureFilter`.
`FeatureHolder` `FeatureHolder.EmptyFeatureHolder.filter(FeatureFilter fc, boolean recurse)`
`FeatureHolder` `FeatureHolder.EmptyFeatureHolder.filter(FeatureFilter fc)`
`FeatureHolder` `SimpleGappedSequence.filter(FeatureFilter ff)`
`FeatureHolder` `SimpleGappedSequence.filter(FeatureFilter ff, boolean recurse)`
`FeatureHolder` `ProjectedFeatureHolder.filter(FeatureFilter ff)`
`FeatureHolder` `ProjectedFeatureHolder.filter(FeatureFilter ff, boolean recurse)`
`protected FeatureFilter` `ProjectedFeatureHolder.untransformFilter(FeatureFilter ff)` Called to transform a FeatureFilter applying to our projections into a corresponding filter on the parent FeatureHolder.
`protected FeatureFilter` `ProjectedFeatureHolder.transformFilter(FeatureFilter ff)` Called to transform a FeatureFilter applying to our parent FeatureHolder into the coordinate system of our parent.
`FeatureHolder` `AbstractFeatureHolder.filter(FeatureFilter filter)`
`FeatureHolder` `AbstractFeatureHolder.filter(FeatureFilter ff, boolean recurse)`
`FeatureHolder` `SubSequence.filter(FeatureFilter ff, boolean recurse)`
`FeatureHolder` `SubSequence.filter(FeatureFilter ff)`
`FeatureHolder` `DummySequence.filter(FeatureFilter ff, boolean recurse)`
`FeatureHolder` `DummySequence.filter(FeatureFilter ff)`
`boolean` `OptimizableFilter.isProperSubset(FeatureFilter sup)` Returns true if this filter is a proper subset of sup - that is, for every feature that matches this, it also matches sup.
`boolean` `OptimizableFilter.isDisjoint(FeatureFilter filt)` Returns true if this filter is disjoint from filt - that is, there is no Feature that is accepted by both filters.
`FeatureHolder` `LazyFeatureHolder.filter(FeatureFilter ff)`
`FeatureHolder` `LazyFeatureHolder.filter(FeatureFilter ff, boolean recurse)`

Constructors in org.biojava.bio.seq with parameters of type FeatureFilter
`SimpleFeatureHolder(FeatureFilter schema)` Construct a new SimpleFeatureHolder with the specified schema.
`FeatureFilter.Not(FeatureFilter child)`
`FeatureFilter.And(FeatureFilter c1, FeatureFilter c2)`
`FeatureFilter.Or(FeatureFilter c1, FeatureFilter c2)`
`FeatureFilter.ByParent(FeatureFilter ff)`
`FeatureFilter.ByAncestor(FeatureFilter ff)`
`FeatureFilter.OnlyChildren(FeatureFilter ff)`
`FeatureFilter.OnlyDescendants(FeatureFilter ff)`
`FeatureFilter.ByChild(FeatureFilter ff)`
`FeatureFilter.ByDescendant(FeatureFilter ff)`
`ProjectedFeatureHolder(FeatureHolder fh, FeatureFilter filter, FeatureHolder parent, int translation, boolean oppositeStrand)` Deprecated. Now just wraps up a LazyFilterFeatureHolder
`SubSequence(Sequence seq, int start, int end, FeatureFilter ff, boolean recurse)` Construct a new SubSequence of the specified sequence.
`SubSequence(Sequence seq, int start, int end, FeatureFilter ff, boolean recurse, java.lang.String name)` Construct a new SubSequence of the specified sequence with a new name.
`LazyFeatureHolder(FeatureFilter schema)` Construct a LazyFeatureHolder with the specified schema

Uses of FeatureFilter in org.biojava.bio.seq.db

Methods in org.biojava.bio.seq.db with parameters of type FeatureFilter
`FeatureHolder` `SequenceDB.filter(FeatureFilter filter)` Query features attached to all sequences in this database.
`FeatureHolder` `AbstractSequenceDB.filter(FeatureFilter ff)`

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

Methods in org.biojava.bio.seq.db.biosql with parameters of type FeatureFilter
`FeatureHolder` `BioSQLSequenceDB.filter(FeatureFilter ff)`

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

Methods in org.biojava.bio.seq.distributed with parameters of type FeatureFilter
`FeatureHolder` `GFFDataSource.getFeatures(FeatureFilter ff)`
`FeatureHolder` `GFFDataSource.getFeatures(java.lang.String id, FeatureFilter ff, boolean recurse)`
`FeatureHolder` `SequenceDBDataSource.getFeatures(FeatureFilter ff)`
`FeatureHolder` `SequenceDBDataSource.getFeatures(java.lang.String id, FeatureFilter ff, boolean recurse)`
`FeatureHolder` `DistDataSource.getFeatures(FeatureFilter ff)` Get all features matching a FeatureFilter provided by this DistDataSource.
`FeatureHolder` `DistDataSource.getFeatures(java.lang.String id, FeatureFilter ff, boolean recurse)` Get all features matching a FeatureFilter on a Sequence with an ID and recurse flats.
`FeatureHolder` `DistributedSequenceDB.filter(FeatureFilter ff)`

Uses of FeatureFilter in org.biojava.bio.seq.impl

Methods in org.biojava.bio.seq.impl that return FeatureFilter
`FeatureFilter` `SimpleSequence.getSchema()`
`FeatureFilter` `LazyFilterFeatureHolder.getSchema()`
`FeatureFilter` `SimpleFeature.getSchema()`

Methods in org.biojava.bio.seq.impl with parameters of type FeatureFilter
`FeatureHolder` `SimpleSequence.filter(FeatureFilter filter)`
`FeatureHolder` `SimpleSequence.filter(FeatureFilter ff, boolean recurse)`
`FeatureHolder` `LazyFilterFeatureHolder.filter(FeatureFilter ff)`
`FeatureHolder` `LazyFilterFeatureHolder.filter(FeatureFilter ff, boolean recurse)`
`FeatureHolder` `SimpleFeature.filter(FeatureFilter ff)`
`FeatureHolder` `SimpleFeature.filter(FeatureFilter ff, boolean recurse)`

Constructors in org.biojava.bio.seq.impl with parameters of type FeatureFilter
`LazyFilterFeatureHolder(FeatureHolder fh, FeatureFilter ff)`

Uses of FeatureFilter in org.biojava.bio.seq.io.filterxml

Methods in org.biojava.bio.seq.io.filterxml that return FeatureFilter
`FeatureFilter` `XMLFilterHandler.FilterHandler.getFeatureFilter()`

Methods in org.biojava.bio.seq.io.filterxml with parameters of type FeatureFilter
`void` `XMLFilterWriter.addXMLFilterWriter(FeatureFilter ff, XMLFilterWriter.FilterWriter xfw)` Add a writer for a singleton filter.
`void` `XMLFilterWriter.writeFilter(FeatureFilter ff, XMLWriter xw)` Write a FeatureFilter to the supplied XMLWriter
`void` `XMLFilterWriter.FilterWriter.writeFilter(FeatureFilter ff, XMLWriter xw, XMLFilterWriter config)`

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

Methods in org.biojava.bio.seq.projection that return FeatureFilter
`FeatureFilter` `ProjectedFeature.getSchema()`
`FeatureFilter` `ProjectionContext.getSchema(Feature f)` Delegate for getSchema

Methods in org.biojava.bio.seq.projection with parameters of type FeatureFilter
`FeatureHolder` `ProjectedFeature.filter(FeatureFilter ff)`
`FeatureHolder` `ProjectedFeature.filter(FeatureFilter ff, boolean recurse)`