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 FilteringRenderer.filter
           
protected  FeatureFilter PairwiseFilteringRenderer.filter
          filter is the filter applied to both FeatureHolders.
 

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 FilteringRenderer.getFilter()
           
 FeatureFilter AbstractPeptideDigestRenderer.getFilter()
           
 FeatureFilter PairwiseFilteringRenderer.getFilter()
          getFilter returns the current filter.
 

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 FilteringRenderer.setFilter(FeatureFilter filter)
           
 void AbstractPeptideDigestRenderer.setFilter(FeatureFilter filter)
           
 void PairwiseFilteringRenderer.setFilter(FeatureFilter filter)
          setFilter sets the 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 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
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 NewSimpleAssembly.getSchema()
           
 FeatureFilter SimpleAssembly.getSchema()
           
 FeatureFilter SimpleFeatureHolder.getSchema()
           
 FeatureFilter LazyFeatureHolder.getSchema()
           
 FeatureFilter FeatureTypes.Type.getSchema()
          Get the schema for this type.
 FeatureFilter MergeFeatureHolder.getSchema()
           
 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 NewSimpleAssembly.filter(FeatureFilter ff)
           
 FeatureHolder SimpleAssembly.filter(FeatureFilter ff)
           
 FeatureHolder LazyFeatureHolder.filter(FeatureFilter ff)
           
 FeatureHolder AbstractFeatureHolder.filter(FeatureFilter filter)
           
 FeatureHolder FeatureHolder.filter(FeatureFilter filter)
          Query this set of features using a supplied FeatureFilter.
 FeatureHolder FeatureHolder.EmptyFeatureHolder.filter(FeatureFilter fc)
           
 FeatureHolder NewSimpleAssembly.filter(FeatureFilter ff, boolean recurse)
           
 FeatureHolder SimpleAssembly.filter(FeatureFilter ff, boolean recurse)
           
 FeatureHolder LazyFeatureHolder.filter(FeatureFilter ff, boolean recurse)
           
 FeatureHolder AbstractFeatureHolder.filter(FeatureFilter ff, boolean recurse)
           
 FeatureHolder MergeFeatureHolder.filter(FeatureFilter ff, boolean recurse)
          When applied to a MergeFeatureHolder, this filters each child FeatureHolder independently.
 FeatureHolder FeatureHolder.filter(FeatureFilter fc, boolean recurse)
          Return a new FeatureHolder that contains all of the children of this one that passed the filter fc.
 FeatureHolder FeatureHolder.EmptyFeatureHolder.filter(FeatureFilter fc, boolean recurse)
           
 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 GFFDataSource.getFeatures(FeatureFilter ff)
           
 FeatureHolder SequenceDBDataSource.getFeatures(FeatureFilter ff)
           
 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 SequenceDBDataSource.getFeatures(String id, FeatureFilter ff, boolean recurse)
           
 FeatureHolder DistDataSource.getFeatures(String id, FeatureFilter ff, boolean recurse)
          Get all features matching a FeatureFilter on a Sequence with an ID and recurse flats.
 

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 LazyFilterFeatureHolder.getSchema()
           
 FeatureFilter ViewSequence.getSchema()
           
 FeatureFilter SimpleSequence.getSchema()
           
 FeatureFilter SimpleFeature.getSchema()
           
 FeatureFilter SimpleGappedSequence.getSchema()
           
 FeatureFilter SubSequence.getSchema()
           
 FeatureFilter DummySequence.getSchema()
           
 

Methods in org.biojava.bio.seq.impl with parameters of type FeatureFilter
 FeatureHolder LazyFilterFeatureHolder.filter(FeatureFilter ff)
           
 FeatureHolder ViewSequence.filter(FeatureFilter fc)
           
 FeatureHolder SimpleSequence.filter(FeatureFilter filter)
           
 FeatureHolder SimpleFeature.filter(FeatureFilter ff)
           
 FeatureHolder RevCompSequence.filter(FeatureFilter ff)
           
 FeatureHolder SimpleGappedSequence.filter(FeatureFilter ff)
           
 FeatureHolder SubSequence.filter(FeatureFilter ff)
           
 FeatureHolder DummySequence.filter(FeatureFilter ff)
           
 FeatureHolder LazyFilterFeatureHolder.filter(FeatureFilter ff, boolean recurse)
           
 FeatureHolder ViewSequence.filter(FeatureFilter fc, boolean recurse)
           
 FeatureHolder SimpleSequence.filter(FeatureFilter ff, boolean recurse)
           
 FeatureHolder SimpleFeature.filter(FeatureFilter ff, boolean recurse)
           
 FeatureHolder RevCompSequence.filter(FeatureFilter ff, boolean recurse)
           
 FeatureHolder SimpleGappedSequence.filter(FeatureFilter ff, boolean recurse)
           
 FeatureHolder SubSequence.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 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
 FeatureHolder SimpleRichFeature.filter(FeatureFilter filter)
          Query this set of features using a supplied FeatureFilter.
 FeatureHolder ThinRichSequence.filter(FeatureFilter filter)
          Query this set of features using a supplied FeatureFilter.
 FeatureHolder SimpleRichFeature.filter(FeatureFilter fc, boolean recurse)
          Return a new FeatureHolder that contains all of the children of this one that passed the filter fc.
 FeatureHolder ThinRichSequence.filter(FeatureFilter fc, boolean recurse)
          Return a new FeatureHolder that contains all of the children of this one that passed the filter fc.