## 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.filter
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 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 FeatureFilter in org.biojava.bio.gui.sequence

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

Fields in org.biojava.bio.gui.sequence with type parameters of type FeatureFilter
`protected List<FeatureFilter>` `GlyphFeatureRenderer.fList`

Methods in org.biojava.bio.gui.sequence that return FeatureFilter
`FeatureFilter` `GlyphFeatureRenderer.getFeatureFilter(int i)` Returns the ith `FeatureFilter` in this renderer.
`FeatureFilter` `PairwiseFilteringRenderer.getFilter()` `getFilter` returns the current filter.
`FeatureFilter` `FilteringRenderer.getFilter()`
`FeatureFilter` `AbstractPeptideDigestRenderer.getFilter()`

Methods in org.biojava.bio.gui.sequence with parameters of type FeatureFilter
`void` `GlyphFeatureRenderer.addFilterAndGlyph(FeatureFilter ff, Glyph g)`
`boolean` `GlyphFeatureRenderer.containsFilter(FeatureFilter ff)` Returns true if the given `FeatureFilter` is already contained in this renderer.
`protected List` `BumpedRenderer.doLayer(SequenceRenderContext src, FeatureFilter filt)`
`Glyph` `GlyphFeatureRenderer.getGlyphForFilter(FeatureFilter ff)` Returns the `Glyph` object which is assigned to the given feature filter.
`void` `GlyphFeatureRenderer.removeFilterWithGlyph(FeatureFilter ff)`
`void` `PairwiseFilteringRenderer.setFilter(FeatureFilter filter)` `setFilter` sets the filter.
`void` `FilteringRenderer.setFilter(FeatureFilter filter)`
`void` `AbstractPeptideDigestRenderer.setFilter(FeatureFilter filter)`
`void` `GlyphFeatureRenderer.setGlyphForFilter(FeatureFilter ff, Glyph glyph)` Allows setting another `Glyph` object to be painted for the given FeatureFilter.

Constructors in org.biojava.bio.gui.sequence with parameters of type FeatureFilter
`AbstractPeptideDigestRenderer(FeatureSource source, FeatureFilter filter)`
`AbstractPeptideDigestRenderer(FeatureSource source, FeatureFilter filter, int distanceBetweenFeatures)`
`CircularFeatureFilteringRenderer(CircularRenderer renderer, FeatureFilter filter, boolean recurse)`
`FilteringRenderer(SequenceRenderer renderer, FeatureFilter filter, boolean recurse)`
`PairwiseFilteringRenderer(PairwiseSequenceRenderer renderer, FeatureFilter filter, boolean recurse)` Creates a new `PairwiseFilteringRenderer`.
`PeptideDigestRenderer(FeatureSource source, FeatureFilter filter)`
`PeptideDigestRenderer(FeatureSource source, FeatureFilter filter, int distanceBetweenFeatures)`

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.leaf` A filter which accepts features with no children
`static FeatureFilter` `FeatureFilter.none` No features are selected by this filter.
`static FeatureFilter` `FeatureFilter.top_level` A filter which accepts only top-level Features.

Methods in org.biojava.bio.seq that return FeatureFilter
`static FeatureFilter` `FilterUtils.all()` Return a filter which matches all features.
`static FeatureFilter` `FilterUtils.and(FeatureFilter[] filters)` Constructs a new filter which matches the intersection of a set of filters.
`static FeatureFilter` `FilterUtils.and(FeatureFilter c1, FeatureFilter c2)` Construct a new filter which matches the intersection of two other filters.
`static FeatureFilter` `FilterUtils.byAncestor(FeatureFilter ancestorFilter)` Match features where at least one of the ancestors matches the specified filter.
`static FeatureFilter` `FilterUtils.byAnnotation(Object key, Object value)` Match features where the annotation property named `key` is equal to `value`.
`static FeatureFilter` `FilterUtils.byAnnotationType(AnnotationType type)` Match features with annotations matching the specified `AnnotationType`
`static FeatureFilter` `FilterUtils.byAnnotationType(Object key, Class valClass)` Match features where the annotation property named `key` is an instance of `valClass`.
`static FeatureFilter` `FilterUtils.byChild(FeatureFilter childFilter)` Match features where at least one child feature matches the supplied filter.
`static FeatureFilter` `FilterUtils.byClass(Class clazz)` Construct a filter which matches features which are assignable to the specified class or interface.
`static FeatureFilter` `FilterUtils.byComponentName(String compName)` Construct a filter which matches all features which implement the `ComponentFeature` interface and have a `componentName` property equal to the specified value
`static FeatureFilter` `FilterUtils.byDescendant(FeatureFilter descFilter)` Match features where at least one decendant feature -- possibly but not necessarily an immediate child -- matches the specified filter.
`static FeatureFilter` `FilterUtils.byFrame(FramedFeature.ReadingFrame frame)` Construct a filter which matches FramedFeatures with the specified reading frame.
`static FeatureFilter` `FilterUtils.byPairwiseScore(double minScore, double maxScore)` Match SeqSimilaritiy features with scores in the specified range.
`static FeatureFilter` `FilterUtils.byParent(FeatureFilter parentFilter)` Match features where the parent feature matches the specified filter.
`static FeatureFilter` `FilterUtils.bySequenceName(String name)` Match features attached to sequences with a specified name.
`static FeatureFilter` `FilterUtils.bySource(String source)` Construct a filter which matches features with a specific `source` value.
`static FeatureFilter` `FilterUtils.byStrand(StrandedFeature.Strand strand)` Match StrandedFeatures on the specified strand.
`static FeatureFilter` `FilterUtils.byType(String type)` Construct a filter which matches features with a specific `type` value.
`static FeatureFilter` `FilterUtils.containedByLocation(Location loc)` Construct a filter which matches features with locations wholly contained by the specified `Location`.
`FeatureFilter` `FeatureFilter.Not.getChild()`
`FeatureFilter` `FeatureFilter.And.getChild1()`
`FeatureFilter` `FeatureFilter.Or.getChild1()`
`FeatureFilter` `FeatureFilter.And.getChild2()`
`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()`
`FeatureFilter` `SimpleFeatureHolder.getSchema()`
`FeatureFilter` `SimpleAssembly.getSchema()`
`FeatureFilter` `NewSimpleAssembly.getSchema()`
`FeatureFilter` `MergeFeatureHolder.getSchema()`
`FeatureFilter` `LazyFeatureHolder.getSchema()`
`FeatureFilter` `FeatureTypes.Type.getSchema()` Get the schema for this type.
`FeatureFilter` `FeatureHolder.getSchema()` Return a schema-filter for this `FeatureHolder`.
`FeatureFilter` `FeatureHolder.EmptyFeatureHolder.getSchema()`
`static FeatureFilter` `FilterUtils.hasAnnotation(Object key)` Match features where the property `key` has been defined as having some value, regardless of the exact value.
`static FeatureFilter` `FilterUtils.leaf()` Return a filter which matches features with zero children.
`static FeatureFilter` `FilterUtils.none()` Return a filter which matches no features.
`static FeatureFilter` `FilterUtils.not(FeatureFilter filter)` Construct a new filter which is the negation of `filter`.
`static FeatureFilter` `FilterUtils.onlyChildren(FeatureFilter child)` Construct a filter which matches features whose children all match the specified filter.
`static FeatureFilter` `FilterUtils.onlyDescendants(FeatureFilter desc)` Construct a filter which matches features whose decendants all match the specified filter.
`static FeatureFilter` `FilterUtils.optimize(FeatureFilter filter)` Attempts to reduce a FeatureFilter to an equivalent FeatureFilter with fewer terms.
`static FeatureFilter` `FilterUtils.or(FeatureFilter[] filters)` Construct a new filter which matches the intersection of two filters.
`static FeatureFilter` `FilterUtils.or(FeatureFilter c1, FeatureFilter c2)` Construct a new filter which matches the union of two filters.
`static FeatureFilter` `FilterUtils.overlapsLocation(Location loc)` Construct a filter which matches features with locations contained by or overlapping the specified `Location`.
`static FeatureFilter` `FilterUtils.shadowContainedByLocation(Location loc)` Construct a filter which matches features with locations where the interval between the `min` and `max` positions are contained by the specified `Location`.
`static FeatureFilter` `FilterUtils.shadowOverlapsLocation(Location loc)` Construct a filter which matches features with locations where the interval between the `min` and `max` positions are contained by or overlap the specified `Location`.
`static FeatureFilter` `FilterUtils.topLevel()` Return a filter which matches all top-level features.
`FeatureFilter` `FilterUtils.FilterTransformer.transform(FeatureFilter filter)` Transform a filter, or return null if it can not be transformed.
`FeatureFilter` `FilterUtils.DelegatingTransformer.transform(FeatureFilter ff)`
`static FeatureFilter` `FilterUtils.transformFilter(FeatureFilter ff, FilterUtils.FilterTransformer trans)` This is a general framework method for transforming one filter into another.

Methods in org.biojava.bio.seq with parameters of type FeatureFilter
`static FeatureFilter` `FilterUtils.and(FeatureFilter[] filters)` Constructs a new filter which matches the intersection of a set of filters.
`static FeatureFilter` `FilterUtils.and(FeatureFilter c1, FeatureFilter c2)` Construct a new filter which matches the intersection of two other filters.
`static boolean` `FilterUtils.areDisjoint(FeatureFilter a, FeatureFilter b)` Determines if two queries can be proven to be disjoint.
`static boolean` `FilterUtils.areEqual(FeatureFilter f1, FeatureFilter f2)` Decide if two feature filters accept exactly the same set of features.
`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 FeatureFilter` `FilterUtils.byAncestor(FeatureFilter ancestorFilter)` Match features where at least one of the ancestors matches the specified filter.
`static FeatureFilter` `FilterUtils.byChild(FeatureFilter childFilter)` Match features where at least one child feature matches the supplied filter.
`static FeatureFilter` `FilterUtils.byDescendant(FeatureFilter descFilter)` Match features where at least one decendant feature -- possibly but not necessarily an immediate child -- matches the specified filter.
`static FeatureFilter` `FilterUtils.byParent(FeatureFilter parentFilter)` Match features where the parent feature matches the specified filter.
`FeatureTypes.Type` `FeatureTypes.RepositoryImpl.createType(String name, FeatureFilter schema, Set parents)` Create a new type in this repository.
`static Location` `FilterUtils.extractOverlappingLocation(FeatureFilter ff)` Try to determine the minimal location which all features matching a given filter must overlap.
`FeatureHolder` `SimpleAssembly.filter(FeatureFilter ff)`
`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` `AbstractFeatureHolder.filter(FeatureFilter filter)`
`FeatureHolder` `SimpleAssembly.filter(FeatureFilter ff, boolean recurse)`
`FeatureHolder` `NewSimpleAssembly.filter(FeatureFilter ff, boolean recurse)`
`FeatureHolder` `MergeFeatureHolder.filter(FeatureFilter ff, boolean recurse)` When applied to a MergeFeatureHolder, this filters each child FeatureHolder independently.
`FeatureHolder` `LazyFeatureHolder.filter(FeatureFilter ff, boolean recurse)`
`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` `AbstractFeatureHolder.filter(FeatureFilter ff, boolean recurse)`
`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.
`boolean` `FeatureFilter.ByType.isDisjoint(FeatureFilter filt)`
`boolean` `FeatureFilter.BySource.isDisjoint(FeatureFilter filt)`
`boolean` `FeatureFilter.ByClass.isDisjoint(FeatureFilter feat)`
`boolean` `FeatureFilter.StrandFilter.isDisjoint(FeatureFilter filt)`
`boolean` `FeatureFilter.BySequenceName.isDisjoint(FeatureFilter filt)`
`boolean` `FeatureFilter.ContainedByLocation.isDisjoint(FeatureFilter filt)`
`boolean` `FeatureFilter.OverlapsLocation.isDisjoint(FeatureFilter filt)`
`boolean` `FeatureFilter.ShadowOverlapsLocation.isDisjoint(FeatureFilter filt)`
`boolean` `FeatureFilter.ShadowContainedByLocation.isDisjoint(FeatureFilter filt)`
`boolean` `FeatureFilter.ByAnnotationType.isDisjoint(FeatureFilter filter)`
`boolean` `FeatureFilter.ByParent.isDisjoint(FeatureFilter ff)`
`boolean` `FeatureFilter.ByAncestor.isDisjoint(FeatureFilter ff)`
`boolean` `FeatureFilter.OnlyChildren.isDisjoint(FeatureFilter ff)`
`boolean` `FeatureFilter.OnlyDescendants.isDisjoint(FeatureFilter ff)`
`boolean` `FeatureFilter.ByChild.isDisjoint(FeatureFilter ff)`
`boolean` `FeatureFilter.ByDescendant.isDisjoint(FeatureFilter ff)`
`boolean` `FeatureFilter.FrameFilter.isDisjoint(FeatureFilter filt)`
`boolean` `FeatureFilter.ByPairwiseScore.isDisjoint(FeatureFilter filt)`
`boolean` `FeatureFilter.ByComponentName.isDisjoint(FeatureFilter feat)`
`boolean` `FeatureFilter.ByFeature.isDisjoint(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` `FeatureFilter.ByType.isProperSubset(FeatureFilter sup)`
`boolean` `FeatureFilter.BySource.isProperSubset(FeatureFilter sup)`
`boolean` `FeatureFilter.ByClass.isProperSubset(FeatureFilter sup)`
`boolean` `FeatureFilter.StrandFilter.isProperSubset(FeatureFilter sup)`
`boolean` `FeatureFilter.BySequenceName.isProperSubset(FeatureFilter sup)`
`boolean` `FeatureFilter.ContainedByLocation.isProperSubset(FeatureFilter sup)`
`boolean` `FeatureFilter.OverlapsLocation.isProperSubset(FeatureFilter sup)`
`boolean` `FeatureFilter.ShadowOverlapsLocation.isProperSubset(FeatureFilter sup)`
`boolean` `FeatureFilter.ShadowContainedByLocation.isProperSubset(FeatureFilter sup)`
`boolean` `FeatureFilter.ByAnnotationType.isProperSubset(FeatureFilter filter)`
`boolean` `FeatureFilter.ByParent.isProperSubset(FeatureFilter ff)`
`boolean` `FeatureFilter.ByAncestor.isProperSubset(FeatureFilter ff)`
`boolean` `FeatureFilter.OnlyChildren.isProperSubset(FeatureFilter ff)`
`boolean` `FeatureFilter.OnlyDescendants.isProperSubset(FeatureFilter ff)`
`boolean` `FeatureFilter.ByChild.isProperSubset(FeatureFilter ff)`
`boolean` `FeatureFilter.ByDescendant.isProperSubset(FeatureFilter ff)`
`boolean` `FeatureFilter.FrameFilter.isProperSubset(FeatureFilter sup)`
`boolean` `FeatureFilter.ByPairwiseScore.isProperSubset(FeatureFilter sup)`
`boolean` `FeatureFilter.ByComponentName.isProperSubset(FeatureFilter sup)`
`boolean` `FeatureFilter.ByFeature.isProperSubset(FeatureFilter ff)`
`static FeatureFilter` `FilterUtils.not(FeatureFilter filter)` Construct a new filter which is the negation of `filter`.
`static FeatureFilter` `FilterUtils.onlyChildren(FeatureFilter child)` Construct a filter which matches features whose children all match the specified filter.
`static FeatureFilter` `FilterUtils.onlyDescendants(FeatureFilter desc)` Construct a filter which matches features whose decendants all match the specified filter.
`static FeatureFilter` `FilterUtils.optimize(FeatureFilter filter)` Attempts to reduce a FeatureFilter to an equivalent FeatureFilter with fewer terms.
`static FeatureFilter` `FilterUtils.or(FeatureFilter[] filters)` Construct a new filter which matches the intersection of two filters.
`static FeatureFilter` `FilterUtils.or(FeatureFilter c1, FeatureFilter c2)` Construct a new filter which matches the union of two filters.
`FeatureFilter` `FilterUtils.FilterTransformer.transform(FeatureFilter filter)` Transform a filter, or return null if it can not be transformed.
`FeatureFilter` `FilterUtils.DelegatingTransformer.transform(FeatureFilter ff)`
`static FeatureFilter` `FilterUtils.transformFilter(FeatureFilter ff, FilterUtils.FilterTransformer trans)` This is a general framework method for transforming one filter into another.
`static Object` `FilterUtils.visitFilter(FeatureFilter filter, Visitor visitor)` Applies a visitor to a filter, and returns the visitor's result or null.

Constructors in org.biojava.bio.seq with parameters of type FeatureFilter
`FeatureFilter.And(FeatureFilter c1, FeatureFilter c2)`
`FeatureFilter.ByAncestor(FeatureFilter ff)`
`FeatureFilter.ByChild(FeatureFilter ff)`
`FeatureFilter.ByDescendant(FeatureFilter ff)`
`FeatureFilter.ByParent(FeatureFilter ff)`
`FeatureFilter.Not(FeatureFilter child)`
`FeatureFilter.OnlyChildren(FeatureFilter ff)`
`FeatureFilter.OnlyDescendants(FeatureFilter ff)`
`FeatureFilter.Or(FeatureFilter c1, FeatureFilter c2)`
`LazyFeatureHolder(FeatureFilter schema)` Construct a LazyFeatureHolder with the specified schema
`SimpleFeatureHolder(FeatureFilter schema)` Construct a new SimpleFeatureHolder 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)` Deprecated.

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

Methods in org.biojava.bio.seq.distributed with parameters of type FeatureFilter
`FeatureHolder` `SequenceDBDataSource.getFeatures(FeatureFilter ff)`
`FeatureHolder` `GFFDataSource.getFeatures(FeatureFilter ff)`
`FeatureHolder` `DistDataSource.getFeatures(FeatureFilter ff)` Get all features matching a FeatureFilter provided by this DistDataSource.
`FeatureHolder` `SequenceDBDataSource.getFeatures(String id, FeatureFilter ff, boolean recurse)`
`FeatureHolder` `GFFDataSource.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.

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

Methods in org.biojava.bio.seq.filter that return FeatureFilter
`FeatureFilter` `FilterTransformer.and(FeatureFilter.And and, FeatureFilter c1, FeatureFilter c2)`
`FeatureFilter` `FilterTransformer.byAncestor(FeatureFilter.ByAncestor ancestor, FeatureFilter c)`
`FeatureFilter` `FilterTransformer.byChild(FeatureFilter.ByChild child, FeatureFilter c)`
`FeatureFilter` `FilterTransformer.byDescendant(FeatureFilter.ByDescendant desc, FeatureFilter c)`
`FeatureFilter` `FilterTransformer.byParent(FeatureFilter.ByParent parent, FeatureFilter c)`
`FeatureFilter` `FilterTransformer.featureFilter(FeatureFilter filter)`
`FeatureFilter` `FilterTransformer.not(FeatureFilter.Not not, FeatureFilter c)`
`FeatureFilter` `FilterTransformer.onlyChildren(FeatureFilter.OnlyChildren child, FeatureFilter c)`
`FeatureFilter` `FilterTransformer.onlyDescendants(FeatureFilter.OnlyDescendants desc, FeatureFilter c)`
`FeatureFilter` `FilterTransformer.or(FeatureFilter.Or or, FeatureFilter c1, FeatureFilter c2)`

Methods in org.biojava.bio.seq.filter with parameters of type FeatureFilter
`FeatureFilter` `FilterTransformer.and(FeatureFilter.And and, FeatureFilter c1, FeatureFilter c2)`
`FeatureFilter` `FilterTransformer.byAncestor(FeatureFilter.ByAncestor ancestor, FeatureFilter c)`
`FeatureFilter` `FilterTransformer.byChild(FeatureFilter.ByChild child, FeatureFilter c)`
`FeatureFilter` `FilterTransformer.byDescendant(FeatureFilter.ByDescendant desc, FeatureFilter c)`
`FeatureFilter` `FilterTransformer.byParent(FeatureFilter.ByParent parent, FeatureFilter c)`
`FeatureFilter` `FilterTransformer.featureFilter(FeatureFilter filter)`
`FeatureFilter` `FilterTransformer.not(FeatureFilter.Not not, FeatureFilter c)`
`FeatureFilter` `FilterTransformer.onlyChildren(FeatureFilter.OnlyChildren child, FeatureFilter c)`
`FeatureFilter` `FilterTransformer.onlyDescendants(FeatureFilter.OnlyDescendants desc, FeatureFilter c)`
`FeatureFilter` `FilterTransformer.or(FeatureFilter.Or or, FeatureFilter c1, FeatureFilter c2)`

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

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

Methods in org.biojava.bio.seq.impl with parameters of type FeatureFilter
`FeatureHolder` `ViewSequence.filter(FeatureFilter fc)`
`FeatureHolder` `SubSequence.filter(FeatureFilter ff)`
`FeatureHolder` `SimpleSequence.filter(FeatureFilter filter)`
`FeatureHolder` `SimpleGappedSequence.filter(FeatureFilter ff)`
`FeatureHolder` `SimpleFeature.filter(FeatureFilter ff)`
`FeatureHolder` `RevCompSequence.filter(FeatureFilter ff)`
`FeatureHolder` `LazyFilterFeatureHolder.filter(FeatureFilter ff)`
`FeatureHolder` `DummySequence.filter(FeatureFilter ff)`
`FeatureHolder` `ViewSequence.filter(FeatureFilter fc, boolean recurse)`
`FeatureHolder` `SubSequence.filter(FeatureFilter ff, boolean recurse)`
`FeatureHolder` `SimpleSequence.filter(FeatureFilter ff, boolean recurse)`
`FeatureHolder` `SimpleGappedSequence.filter(FeatureFilter ff, boolean recurse)`
`FeatureHolder` `SimpleFeature.filter(FeatureFilter ff, boolean recurse)`
`FeatureHolder` `RevCompSequence.filter(FeatureFilter ff, boolean recurse)`
`FeatureHolder` `LazyFilterFeatureHolder.filter(FeatureFilter ff, boolean recurse)`
`FeatureHolder` `DummySequence.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` `ProjectedFeatureHolder.getSchema()`
`FeatureFilter` `ReparentContext.getSchema(Feature f)`
`FeatureFilter` `ReparentContext.projectFilter(FeatureFilter ff)`
`FeatureFilter` `ProjectionContext.projectFilter(FeatureFilter filt)` Transform a filter on unprojected features so that it applies to projected features.
`FeatureFilter` `ReparentContext.revertFilter(FeatureFilter ff)`
`FeatureFilter` `ProjectionContext.revertFilter(FeatureFilter filt)` Transform a filter on projected features so that it applies to unprojected features.

Methods in org.biojava.bio.seq.projection with parameters of type FeatureFilter
`FeatureHolder` `ProjectedFeatureHolder.filter(FeatureFilter ff)`
`FeatureHolder` `ProjectedFeature.filter(FeatureFilter ff)`
`FeatureHolder` `ProjectedFeatureHolder.filter(FeatureFilter ff, boolean recurse)`
`FeatureHolder` `ProjectedFeature.filter(FeatureFilter ff, boolean recurse)`
`FeatureFilter` `ReparentContext.projectFilter(FeatureFilter ff)`
`FeatureFilter` `ProjectionContext.projectFilter(FeatureFilter filt)` Transform a filter on unprojected features so that it applies to projected features.
`FeatureFilter` `ReparentContext.revertFilter(FeatureFilter ff)`
`FeatureFilter` `ProjectionContext.revertFilter(FeatureFilter filt)` Transform a filter on projected features so that it applies to unprojected features.

Uses of FeatureFilter in org.biojavax.bio.db

Methods in org.biojavax.bio.db with parameters of type FeatureFilter
`FeatureHolder` `AbstractRichSequenceDB.filter(FeatureFilter ff)`

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

Subinterfaces of FeatureFilter in org.biojavax.bio.db.biosql
`interface` `BioSQLFeatureFilter` A filter for accepting or rejecting a feature.

Classes in org.biojavax.bio.db.biosql that implement FeatureFilter
`class` `BioSQLAcceptAllFilter` The class that accepts all features.
`class` `BioSQLAcceptNoneFilter` The class that accepts no features.
`static class` `BioSQLFeatureFilter.And` A filter that returns all features accepted by both child filter.
`static class` `BioSQLFeatureFilter.ByName` Construct one of these to filter features by display name.
`static class` `BioSQLFeatureFilter.ByNote` A filter that returns all features that have the given note, and the value and rank is checked as well.
`static class` `BioSQLFeatureFilter.ByNoteTermOnly` A filter that returns all features that have a note with the given term.
`static class` `BioSQLFeatureFilter.ByRank` Construct one of these to filter features by rank.
`static class` `BioSQLFeatureFilter.BySequenceName` Accept features that reside on a sequence with a particular name.
`static class` `BioSQLFeatureFilter.BySourceTerm` Construct one of these to filter features by source.
`static class` `BioSQLFeatureFilter.BySourceTermName` Construct one of these to filter features by source (name only - parent ontology is ignored).
`static class` `BioSQLFeatureFilter.ByStrand` A filter that returns all features having locations on a given strand.
`static class` `BioSQLFeatureFilter.ByTypeTerm` Construct one of these to filter features by type.
`static class` `BioSQLFeatureFilter.ByTypeTermName` Construct one of these to filter features by type (name only - parent ontology is ignored).
`static class` `BioSQLFeatureFilter.ContainedByRichLocation` A filter that returns all features contained within a location.
`static class` `BioSQLFeatureFilter.HibernateFeatureFilter` A filter for Hibernate-BioSQL filters to extend.
`static class` `BioSQLFeatureFilter.Not` A filter that returns all features not accepted by a child filter.
`static class` `BioSQLFeatureFilter.Or` A filter that returns all features accepted by at least one child filter.
`static class` `BioSQLFeatureFilter.OverlapsRichLocation` A filter that returns all features overlapping a location.

Methods in org.biojavax.bio.db.biosql with parameters of type FeatureFilter
`static BioSQLFeatureFilter` `BioSQLFeatureFilter.Tools.convert(FeatureFilter ff)` Convert a non-BioSQL FeatureFilter into a BioSQL one.
`FeatureHolder` `BioSQLRichSequenceDB.filter(FeatureFilter ff)`
`FeatureHolder` `BioSQLRichSequenceDB.processFeatureFilter(FeatureFilter ff)`

Uses of FeatureFilter in org.biojavax.bio.seq

Methods in org.biojavax.bio.seq that return FeatureFilter
`FeatureFilter` `ThinRichSequence.getSchema()` Return a schema-filter for this `FeatureHolder`.
`FeatureFilter` `SimpleRichFeature.getSchema()` Return a schema-filter for this `FeatureHolder`.

Methods in org.biojavax.bio.seq with parameters of type FeatureFilter
`FeatureHolder` `ThinRichSequence.filter(FeatureFilter filter)` Query this set of features using a supplied `FeatureFilter`.
`FeatureHolder` `SimpleRichFeature.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.filter(FeatureFilter fc, boolean recurse)` Return a new FeatureHolder that contains all of the children of this one that passed the filter fc.