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

Packages that use FeatureFilter

Package	Description
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.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.seq	Rich implementations of Sequences, Locations and Features.

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

Methods in org.biojava.bio.program.gff that return FeatureFilter

Modifier and Type	Method	Description
FeatureFilter	SequencesAsGFF.getFeatureFilter()	Return the current FeatureFilter.

Methods in org.biojava.bio.program.gff with parameters of type FeatureFilter

Modifier and Type	Method	Description
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

Modifier and Type	Interface	Description
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

Modifier and Type	Class	Description
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 SimilarityPairFeatures 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

Modifier and Type	Field	Description
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

Modifier and Type	Method	Description
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(Object key, Class valClass)	Match features where the annotation property named key is an instance of valClass.
static FeatureFilter	FilterUtils.byAnnotationType(AnnotationType type)	Match features with annotations matching the specified AnnotationType
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.ByAncestor.getFilter()
FeatureFilter	FeatureFilter.ByChild.getFilter()
FeatureFilter	FeatureFilter.ByDescendant.getFilter()
FeatureFilter	FeatureFilter.ByParent.getFilter()
FeatureFilter	FeatureFilter.OnlyChildren.getFilter()
FeatureFilter	FeatureFilter.OnlyDescendants.getFilter()
FeatureFilter	FeatureHolder.EmptyFeatureHolder.getSchema()
FeatureFilter	FeatureHolder.getSchema()	Return a schema-filter for this FeatureHolder.
FeatureFilter	FeatureTypes.Type.getSchema()	Get the schema for this type.
FeatureFilter	LazyFeatureHolder.getSchema()
FeatureFilter	MergeFeatureHolder.getSchema()
FeatureFilter	NewSimpleAssembly.getSchema()
FeatureFilter	SimpleAssembly.getSchema()
FeatureFilter	SimpleFeatureHolder.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.DelegatingTransformer.transform(FeatureFilter ff)
FeatureFilter	FilterUtils.FilterTransformer.transform(FeatureFilter filter)	Transform a filter, or return null if it can not be transformed.
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

Modifier and Type	Method	Description
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	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)
boolean	FeatureFilter.ByAncestor.isDisjoint(FeatureFilter ff)
boolean	FeatureFilter.ByAnnotationType.isDisjoint(FeatureFilter filter)
boolean	FeatureFilter.ByChild.isDisjoint(FeatureFilter ff)
boolean	FeatureFilter.ByClass.isDisjoint(FeatureFilter feat)
boolean	FeatureFilter.ByComponentName.isDisjoint(FeatureFilter feat)
boolean	FeatureFilter.ByDescendant.isDisjoint(FeatureFilter ff)
boolean	FeatureFilter.ByFeature.isDisjoint(FeatureFilter ff)
boolean	FeatureFilter.ByPairwiseScore.isDisjoint(FeatureFilter filt)
boolean	FeatureFilter.ByParent.isDisjoint(FeatureFilter ff)
boolean	FeatureFilter.BySequenceName.isDisjoint(FeatureFilter filt)
boolean	FeatureFilter.BySource.isDisjoint(FeatureFilter filt)
boolean	FeatureFilter.ByType.isDisjoint(FeatureFilter filt)
boolean	FeatureFilter.ContainedByLocation.isDisjoint(FeatureFilter filt)
boolean	FeatureFilter.FrameFilter.isDisjoint(FeatureFilter filt)
boolean	FeatureFilter.OnlyChildren.isDisjoint(FeatureFilter ff)
boolean	FeatureFilter.OnlyDescendants.isDisjoint(FeatureFilter ff)
boolean	FeatureFilter.OverlapsLocation.isDisjoint(FeatureFilter filt)
boolean	FeatureFilter.ShadowContainedByLocation.isDisjoint(FeatureFilter filt)
boolean	FeatureFilter.ShadowOverlapsLocation.isDisjoint(FeatureFilter filt)
boolean	FeatureFilter.StrandFilter.isDisjoint(FeatureFilter filt)
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.ByAncestor.isProperSubset(FeatureFilter ff)
boolean	FeatureFilter.ByAnnotationType.isProperSubset(FeatureFilter filter)
boolean	FeatureFilter.ByChild.isProperSubset(FeatureFilter ff)
boolean	FeatureFilter.ByClass.isProperSubset(FeatureFilter sup)
boolean	FeatureFilter.ByComponentName.isProperSubset(FeatureFilter sup)
boolean	FeatureFilter.ByDescendant.isProperSubset(FeatureFilter ff)
boolean	FeatureFilter.ByFeature.isProperSubset(FeatureFilter ff)
boolean	FeatureFilter.ByPairwiseScore.isProperSubset(FeatureFilter sup)
boolean	FeatureFilter.ByParent.isProperSubset(FeatureFilter ff)
boolean	FeatureFilter.BySequenceName.isProperSubset(FeatureFilter sup)
boolean	FeatureFilter.BySource.isProperSubset(FeatureFilter sup)
boolean	FeatureFilter.ByType.isProperSubset(FeatureFilter sup)
boolean	FeatureFilter.ContainedByLocation.isProperSubset(FeatureFilter sup)
boolean	FeatureFilter.FrameFilter.isProperSubset(FeatureFilter sup)
boolean	FeatureFilter.OnlyChildren.isProperSubset(FeatureFilter ff)
boolean	FeatureFilter.OnlyDescendants.isProperSubset(FeatureFilter ff)
boolean	FeatureFilter.OverlapsLocation.isProperSubset(FeatureFilter sup)
boolean	FeatureFilter.ShadowContainedByLocation.isProperSubset(FeatureFilter sup)
boolean	FeatureFilter.ShadowOverlapsLocation.isProperSubset(FeatureFilter sup)
boolean	FeatureFilter.StrandFilter.isProperSubset(FeatureFilter sup)
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.
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.DelegatingTransformer.transform(FeatureFilter ff)
FeatureFilter	FilterUtils.FilterTransformer.transform(FeatureFilter filter)	Transform a filter, or return null if it can not be transformed.
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

Constructor	Description
And(FeatureFilter c1, FeatureFilter c2)
ByAncestor(FeatureFilter ff)
ByChild(FeatureFilter ff)
ByDescendant(FeatureFilter ff)
ByParent(FeatureFilter ff)
LazyFeatureHolder(FeatureFilter schema)	Construct a LazyFeatureHolder with the specified schema
Not(FeatureFilter child)
OnlyChildren(FeatureFilter ff)
OnlyDescendants(FeatureFilter ff)
Or(FeatureFilter c1, FeatureFilter c2)
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

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 FeatureFilter in org.biojava.bio.seq.distributed

Methods in org.biojava.bio.seq.distributed with parameters of type FeatureFilter

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 FeatureFilter in org.biojava.bio.seq.filter

Methods in org.biojava.bio.seq.filter that return FeatureFilter

Modifier and Type	Method	Description
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

Modifier and Type	Method	Description
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

Modifier and Type	Method	Description
FeatureFilter	DummySequence.getSchema()
FeatureFilter	LazyFilterFeatureHolder.getSchema()
FeatureFilter	SimpleFeature.getSchema()
FeatureFilter	SimpleGappedSequence.getSchema()
FeatureFilter	SimpleSequence.getSchema()
FeatureFilter	SubSequence.getSchema()
FeatureFilter	ViewSequence.getSchema()

Methods in org.biojava.bio.seq.impl with parameters of type FeatureFilter

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)

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

Constructor	Description
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

Modifier and Type	Method	Description
FeatureFilter	XMLFilterHandler.FilterHandler.getFeatureFilter()

Methods in org.biojava.bio.seq.io.filterxml with parameters of type FeatureFilter

Modifier and Type	Method	Description
void	XMLFilterWriter.addXMLFilterWriter(FeatureFilter ff, XMLFilterWriter.FilterWriter xfw)	Add a writer for a singleton filter.
void	XMLFilterWriter.FilterWriter.writeFilter(FeatureFilter ff, XMLWriter xw, XMLFilterWriter config)
void	XMLFilterWriter.writeFilter(FeatureFilter ff, XMLWriter xw)	Write a FeatureFilter to the supplied XMLWriter

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

Methods in org.biojava.bio.seq.projection that return FeatureFilter

Modifier and Type	Method	Description
FeatureFilter	ProjectedFeatureHolder.getSchema()
FeatureFilter	ReparentContext.getSchema(Feature f)
FeatureFilter	ProjectionContext.projectFilter(FeatureFilter filt)	Transform a filter on unprojected features so that it applies to projected features.
FeatureFilter	ReparentContext.projectFilter(FeatureFilter ff)
FeatureFilter	ProjectionContext.revertFilter(FeatureFilter filt)	Transform a filter on projected features so that it applies to unprojected features.
FeatureFilter	ReparentContext.revertFilter(FeatureFilter ff)

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

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)
FeatureFilter	ProjectionContext.projectFilter(FeatureFilter filt)	Transform a filter on unprojected features so that it applies to projected features.
FeatureFilter	ReparentContext.projectFilter(FeatureFilter ff)
FeatureFilter	ProjectionContext.revertFilter(FeatureFilter filt)	Transform a filter on projected features so that it applies to unprojected features.
FeatureFilter	ReparentContext.revertFilter(FeatureFilter ff)

Uses of FeatureFilter in org.biojavax.bio.db

Methods in org.biojavax.bio.db with parameters of type FeatureFilter

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

Uses of FeatureFilter in org.biojavax.bio.seq

Methods in org.biojavax.bio.seq that return FeatureFilter

Modifier and Type	Method	Description
FeatureFilter	SimpleRichFeature.getSchema()	Return a schema-filter for this FeatureHolder.
FeatureFilter	ThinRichSequence.getSchema()	Return a schema-filter for this FeatureHolder.

Methods in org.biojavax.bio.seq with parameters of type FeatureFilter

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.