Uses of Interface
org.biojava.bio.seq.FeatureFilter
Packages that use FeatureFilter
Package
Description
Graphical displays of biological sequences and associated annotations.
GFF manipulation.
Classes and interfaces for defining biological sequences and informatics
objects.
Collections of biological sequence data.
General purpose Sequence storage in a relational database.
Sequences and SequenceDBs which are composed from data taken
from a number of data sources.
Standard in-memory implementations of
Sequence
and
Feature
.Tools for reading and writing an XML representation of BioJava's FeatureFilter language.
Code for projecting Feature objects and systematically altering their
properties.
Interactions between biojavax objects and a DB.
Interface between biojava and biosql databases
Rich implementations of Sequences, Locations and Features.
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Uses of FeatureFilter in org.biojava.bio.gui.sequence
Fields in org.biojava.bio.gui.sequence declared as FeatureFilterModifier and TypeFieldDescriptionprotected FeatureFilter
FilteringRenderer.filter
protected FeatureFilter
PairwiseFilteringRenderer.filter
filter
is the filter applied to bothFeatureHolder
s.Fields in org.biojava.bio.gui.sequence with type parameters of type FeatureFilterMethods in org.biojava.bio.gui.sequence that return FeatureFilterModifier and TypeMethodDescriptionGlyphFeatureRenderer.getFeatureFilter
(int i) Returns the ithFeatureFilter
in this renderer.AbstractPeptideDigestRenderer.getFilter()
FilteringRenderer.getFilter()
PairwiseFilteringRenderer.getFilter()
getFilter
returns the current filter.Methods in org.biojava.bio.gui.sequence with parameters of type FeatureFilterModifier and TypeMethodDescriptionvoid
GlyphFeatureRenderer.addFilterAndGlyph
(FeatureFilter ff, Glyph g) boolean
GlyphFeatureRenderer.containsFilter
(FeatureFilter ff) Returns true if the givenFeatureFilter
is already contained in this renderer.protected List
BumpedRenderer.doLayer
(SequenceRenderContext src, FeatureFilter filt) GlyphFeatureRenderer.getGlyphForFilter
(FeatureFilter ff) Returns theGlyph
object which is assigned to the given feature filter.void
GlyphFeatureRenderer.removeFilterWithGlyph
(FeatureFilter ff) void
AbstractPeptideDigestRenderer.setFilter
(FeatureFilter filter) void
FilteringRenderer.setFilter
(FeatureFilter filter) void
PairwiseFilteringRenderer.setFilter
(FeatureFilter filter) setFilter
sets the filter.void
GlyphFeatureRenderer.setGlyphForFilter
(FeatureFilter ff, Glyph glyph) Allows setting anotherGlyph
object to be painted for the given FeatureFilter.Constructors in org.biojava.bio.gui.sequence with parameters of type FeatureFilterModifierConstructorDescriptionAbstractPeptideDigestRenderer
(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 newPairwiseFilteringRenderer
.PeptideDigestRenderer
(FeatureSource source, FeatureFilter filter) PeptideDigestRenderer
(FeatureSource source, FeatureFilter filter, int distanceBetweenFeatures) -
Uses of FeatureFilter in org.biojava.bio.program.gff
Methods in org.biojava.bio.program.gff that return FeatureFilterModifier and TypeMethodDescriptionSequencesAsGFF.getFeatureFilter()
Return the current FeatureFilter.Methods in org.biojava.bio.program.gff with parameters of type FeatureFilterModifier and TypeMethodDescriptionvoid
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.seqModifier and TypeInterfaceDescriptioninterface
The interface for filters that can potentialy optimize themselves, and compare themselves with other filters.Classes in org.biojava.bio.seq that implement FeatureFilterModifier and TypeClassDescriptionstatic final class
A filter that returns all features accepted by both child filter.static final class
Retrieve features that contain a given annotation, and that the set of values contains the value given.static class
Filter by applying a nestedFeatureFilter
to all ancestor features.static final class
Retrieve features that contain a given annotation with a given value.static class
A filter that returns all features that have an annotation bundle that is of a given annotation type.static class
Filter by applying a nestedFeatureFilter
to the child features.static final class
Filter which accepts only those filters which are an instance of a specific Java classstatic final class
Accepts features which are ComponentFeatures and have acomponentSequenceName
property of the specified value.static class
Filter by applying a nestedFeatureFilter
to all descendant features.static final class
Accept only features which are equal to the specified featurestatic final class
ByPairwiseScore
is used to filterSimilarityPairFeature
s by their score.static class
Filter by applying a nestedFeatureFilter
to the parent feature.static final class
Accept features that reside on a sequence with a particular name.static final class
Construct one of these to filter features by source.static final class
Construct one of these to filter features by type.static final class
A filter that returns all features contained within a location.static final class
Accept features with a given reading frame.static final class
Retrieve features that contain a given annotation with any value.static final class
A filter that returns all features not accepted by a child filter.static class
Accepts features where all immediate children meet the supplied filter.static class
Accepts features where all descendants meet the supplied filter.static final class
A filter that returns all features accepted by at least one child filter.static final class
A filter that returns all features overlapping a location.static final class
A filter that accepts all features whose shadow is contained by a specifiedLocation
.static final class
A filter that accepts all features whose shadow overlaps a specifiedLocation
.static final class
Accept features with a given strandedness.Fields in org.biojava.bio.seq declared as FeatureFilterModifier and TypeFieldDescriptionstatic final FeatureFilter
FeatureFilter.all
All features are selected by this filter.static final FeatureFilter
FeatureFilter.leaf
A filter which accepts features with no childrenstatic final FeatureFilter
FeatureFilter.none
No features are selected by this filter.static final FeatureFilter
FeatureFilter.top_level
A filter which accepts only top-level Features.Methods in org.biojava.bio.seq that return FeatureFilterModifier and TypeMethodDescriptionstatic final FeatureFilter
FilterUtils.all()
Return a filter which matches all features.static final FeatureFilter
FilterUtils.and
(FeatureFilter[] filters) Constructs a new filter which matches the intersection of a set of filters.static final FeatureFilter
FilterUtils.and
(FeatureFilter c1, FeatureFilter c2) Construct a new filter which matches the intersection of two other filters.static final FeatureFilter
FilterUtils.byAncestor
(FeatureFilter ancestorFilter) Match features where at least one of the ancestors matches the specified filter.static final FeatureFilter
FilterUtils.byAnnotation
(Object key, Object value) Match features where the annotation property namedkey
is equal tovalue
.static final FeatureFilter
FilterUtils.byAnnotationType
(Object key, Class valClass) Match features where the annotation property namedkey
is an instance ofvalClass
.static final FeatureFilter
FilterUtils.byAnnotationType
(AnnotationType type) Match features with annotations matching the specifiedAnnotationType
static final FeatureFilter
FilterUtils.byChild
(FeatureFilter childFilter) Match features where at least one child feature matches the supplied filter.static final FeatureFilter
Construct a filter which matches features which are assignable to the specified class or interface.static final FeatureFilter
FilterUtils.byComponentName
(String compName) Construct a filter which matches all features which implement theComponentFeature
interface and have acomponentName
property equal to the specified valuestatic final 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 final FeatureFilter
FilterUtils.byFrame
(FramedFeature.ReadingFrame frame) Construct a filter which matches FramedFeatures with the specified reading frame.static final FeatureFilter
FilterUtils.byPairwiseScore
(double minScore, double maxScore) Match SeqSimilaritiy features with scores in the specified range.static final FeatureFilter
FilterUtils.byParent
(FeatureFilter parentFilter) Match features where the parent feature matches the specified filter.static final FeatureFilter
FilterUtils.bySequenceName
(String name) Match features attached to sequences with a specified name.static final FeatureFilter
Construct a filter which matches features with a specificsource
value.static final FeatureFilter
FilterUtils.byStrand
(StrandedFeature.Strand strand) Match StrandedFeatures on the specified strand.static final FeatureFilter
Construct a filter which matches features with a specifictype
value.static final FeatureFilter
FilterUtils.containedByLocation
(Location loc) Construct a filter which matches features with locations wholly contained by the specifiedLocation
.FeatureFilter.Not.getChild()
FeatureFilter.And.getChild1()
FeatureFilter.Or.getChild1()
FeatureFilter.And.getChild2()
FeatureFilter.Or.getChild2()
FeatureFilter.ByAncestor.getFilter()
FeatureFilter.ByChild.getFilter()
FeatureFilter.ByDescendant.getFilter()
FeatureFilter.ByParent.getFilter()
FeatureFilter.OnlyChildren.getFilter()
FeatureFilter.OnlyDescendants.getFilter()
FeatureHolder.EmptyFeatureHolder.getSchema()
FeatureHolder.getSchema()
Return a schema-filter for thisFeatureHolder
.FeatureTypes.Type.getSchema()
Get the schema for this type.LazyFeatureHolder.getSchema()
MergeFeatureHolder.getSchema()
NewSimpleAssembly.getSchema()
SimpleAssembly.getSchema()
SimpleFeatureHolder.getSchema()
static final FeatureFilter
FilterUtils.hasAnnotation
(Object key) Match features where the propertykey
has been defined as having some value, regardless of the exact value.static final FeatureFilter
FilterUtils.leaf()
Return a filter which matches features with zero children.static final FeatureFilter
FilterUtils.none()
Return a filter which matches no features.static final FeatureFilter
FilterUtils.not
(FeatureFilter filter) Construct a new filter which is the negation offilter
.static final FeatureFilter
FilterUtils.onlyChildren
(FeatureFilter child) Construct a filter which matches features whose children all match the specified filter.static final FeatureFilter
FilterUtils.onlyDescendants
(FeatureFilter desc) Construct a filter which matches features whose decendants all match the specified filter.static final FeatureFilter
FilterUtils.optimize
(FeatureFilter filter) Attempts to reduce a FeatureFilter to an equivalent FeatureFilter with fewer terms.static final FeatureFilter
FilterUtils.or
(FeatureFilter[] filters) Construct a new filter which matches the intersection of two filters.static final FeatureFilter
FilterUtils.or
(FeatureFilter c1, FeatureFilter c2) Construct a new filter which matches the union of two filters.static final FeatureFilter
FilterUtils.overlapsLocation
(Location loc) Construct a filter which matches features with locations contained by or overlapping the specifiedLocation
.static final FeatureFilter
FilterUtils.shadowContainedByLocation
(Location loc) Construct a filter which matches features with locations where the interval between themin
andmax
positions are contained by the specifiedLocation
.static final FeatureFilter
FilterUtils.shadowOverlapsLocation
(Location loc) Construct a filter which matches features with locations where the interval between themin
andmax
positions are contained by or overlap the specifiedLocation
.static final FeatureFilter
FilterUtils.topLevel()
Return a filter which matches all top-level features.FilterUtils.DelegatingTransformer.transform
(FeatureFilter ff) 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 FeatureFilterModifier and TypeMethodDescriptionstatic final FeatureFilter
FilterUtils.and
(FeatureFilter[] filters) Constructs a new filter which matches the intersection of a set of filters.static final 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 final 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 beproven
to be a proper subset of the features matched by sup.static final FeatureFilter
FilterUtils.byAncestor
(FeatureFilter ancestorFilter) Match features where at least one of the ancestors matches the specified filter.static final FeatureFilter
FilterUtils.byChild
(FeatureFilter childFilter) Match features where at least one child feature matches the supplied filter.static final 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 final FeatureFilter
FilterUtils.byParent
(FeatureFilter parentFilter) Match features where the parent feature matches the specified filter.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.AbstractFeatureHolder.filter
(FeatureFilter filter) AbstractFeatureHolder.filter
(FeatureFilter ff, boolean recurse) FeatureHolder.EmptyFeatureHolder.filter
(FeatureFilter fc) FeatureHolder.EmptyFeatureHolder.filter
(FeatureFilter fc, boolean recurse) FeatureHolder.filter
(FeatureFilter filter) Query this set of features using a suppliedFeatureFilter
.FeatureHolder.filter
(FeatureFilter fc, boolean recurse) Return a new FeatureHolder that contains all of the children of this one that passed the filter fc.LazyFeatureHolder.filter
(FeatureFilter ff) LazyFeatureHolder.filter
(FeatureFilter ff, boolean recurse) MergeFeatureHolder.filter
(FeatureFilter ff, boolean recurse) When applied to a MergeFeatureHolder, this filters each child FeatureHolder independently.NewSimpleAssembly.filter
(FeatureFilter ff) NewSimpleAssembly.filter
(FeatureFilter ff, boolean recurse) SimpleAssembly.filter
(FeatureFilter ff) 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 final FeatureFilter
FilterUtils.not
(FeatureFilter filter) Construct a new filter which is the negation offilter
.static final FeatureFilter
FilterUtils.onlyChildren
(FeatureFilter child) Construct a filter which matches features whose children all match the specified filter.static final FeatureFilter
FilterUtils.onlyDescendants
(FeatureFilter desc) Construct a filter which matches features whose decendants all match the specified filter.static final FeatureFilter
FilterUtils.optimize
(FeatureFilter filter) Attempts to reduce a FeatureFilter to an equivalent FeatureFilter with fewer terms.static final FeatureFilter
FilterUtils.or
(FeatureFilter[] filters) Construct a new filter which matches the intersection of two filters.static final FeatureFilter
FilterUtils.or
(FeatureFilter c1, FeatureFilter c2) Construct a new filter which matches the union of two filters.FilterUtils.DelegatingTransformer.transform
(FeatureFilter ff) 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 FeatureFilterModifierConstructorDescriptionAnd
(FeatureFilter c1, FeatureFilter c2) ByChild
(FeatureFilter ff) protected
LazyFeatureHolder
(FeatureFilter schema) Construct a LazyFeatureHolder with the specified schemaNot
(FeatureFilter child) 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 FeatureFilterModifier and TypeMethodDescriptionAbstractSequenceDB.filter
(FeatureFilter ff) SequenceDB.filter
(FeatureFilter filter) Query features attached to all sequences in this database. -
Uses of FeatureFilter in org.biojava.bio.seq.db.biosql
Methods in org.biojava.bio.seq.db.biosql with parameters of type FeatureFilter -
Uses of FeatureFilter in org.biojava.bio.seq.distributed
Methods in org.biojava.bio.seq.distributed with parameters of type FeatureFilterModifier and TypeMethodDescriptionDistDataSource.getFeatures
(String id, FeatureFilter ff, boolean recurse) Get all features matching a FeatureFilter on a Sequence with an ID and recurse flats.DistDataSource.getFeatures
(FeatureFilter ff) Get all features matching a FeatureFilter provided by this DistDataSource.GFFDataSource.getFeatures
(String id, FeatureFilter ff, boolean recurse) GFFDataSource.getFeatures
(FeatureFilter ff) SequenceDBDataSource.getFeatures
(String id, FeatureFilter ff, boolean recurse) SequenceDBDataSource.getFeatures
(FeatureFilter ff) -
Uses of FeatureFilter in org.biojava.bio.seq.filter
Methods in org.biojava.bio.seq.filter that return FeatureFilterModifier and TypeMethodDescriptionFilterTransformer.and
(FeatureFilter.And and, FeatureFilter c1, FeatureFilter c2) FilterTransformer.byAncestor
(FeatureFilter.ByAncestor ancestor, FeatureFilter c) FilterTransformer.byChild
(FeatureFilter.ByChild child, FeatureFilter c) FilterTransformer.byDescendant
(FeatureFilter.ByDescendant desc, FeatureFilter c) FilterTransformer.byParent
(FeatureFilter.ByParent parent, FeatureFilter c) FilterTransformer.featureFilter
(FeatureFilter filter) FilterTransformer.not
(FeatureFilter.Not not, FeatureFilter c) FilterTransformer.onlyChildren
(FeatureFilter.OnlyChildren child, FeatureFilter c) FilterTransformer.onlyDescendants
(FeatureFilter.OnlyDescendants desc, FeatureFilter c) FilterTransformer.or
(FeatureFilter.Or or, FeatureFilter c1, FeatureFilter c2) Methods in org.biojava.bio.seq.filter with parameters of type FeatureFilterModifier and TypeMethodDescriptionFilterTransformer.and
(FeatureFilter.And and, FeatureFilter c1, FeatureFilter c2) FilterTransformer.byAncestor
(FeatureFilter.ByAncestor ancestor, FeatureFilter c) FilterTransformer.byChild
(FeatureFilter.ByChild child, FeatureFilter c) FilterTransformer.byDescendant
(FeatureFilter.ByDescendant desc, FeatureFilter c) FilterTransformer.byParent
(FeatureFilter.ByParent parent, FeatureFilter c) FilterTransformer.featureFilter
(FeatureFilter filter) FilterTransformer.not
(FeatureFilter.Not not, FeatureFilter c) FilterTransformer.onlyChildren
(FeatureFilter.OnlyChildren child, FeatureFilter c) FilterTransformer.onlyDescendants
(FeatureFilter.OnlyDescendants desc, FeatureFilter c) 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 FeatureFilterModifier and TypeMethodDescriptionDummySequence.getSchema()
LazyFilterFeatureHolder.getSchema()
SimpleFeature.getSchema()
SimpleGappedSequence.getSchema()
SimpleSequence.getSchema()
SubSequence.getSchema()
ViewSequence.getSchema()
Methods in org.biojava.bio.seq.impl with parameters of type FeatureFilterModifier and TypeMethodDescriptionDummySequence.filter
(FeatureFilter ff) DummySequence.filter
(FeatureFilter ff, boolean recurse) LazyFilterFeatureHolder.filter
(FeatureFilter ff) LazyFilterFeatureHolder.filter
(FeatureFilter ff, boolean recurse) RevCompSequence.filter
(FeatureFilter ff) RevCompSequence.filter
(FeatureFilter ff, boolean recurse) SimpleFeature.filter
(FeatureFilter ff) SimpleFeature.filter
(FeatureFilter ff, boolean recurse) SimpleGappedSequence.filter
(FeatureFilter ff) SimpleGappedSequence.filter
(FeatureFilter ff, boolean recurse) SimpleSequence.filter
(FeatureFilter filter) SimpleSequence.filter
(FeatureFilter ff, boolean recurse) SubSequence.filter
(FeatureFilter ff) SubSequence.filter
(FeatureFilter ff, boolean recurse) ViewSequence.filter
(FeatureFilter fc) ViewSequence.filter
(FeatureFilter fc, boolean recurse) Constructors in org.biojava.bio.seq.impl with parameters of type FeatureFilter -
Uses of FeatureFilter in org.biojava.bio.seq.io.filterxml
Methods in org.biojava.bio.seq.io.filterxml that return FeatureFilterMethods in org.biojava.bio.seq.io.filterxml with parameters of type FeatureFilterModifier and TypeMethodDescriptionvoid
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 FeatureFilterModifier and TypeMethodDescriptionProjectedFeatureHolder.getSchema()
final FeatureFilter
ProjectionContext.projectFilter
(FeatureFilter filt) Transform a filter on unprojected features so that it applies to projected features.final FeatureFilter
ReparentContext.projectFilter
(FeatureFilter ff) ProjectionContext.revertFilter
(FeatureFilter filt) Transform a filter on projected features so that it applies to unprojected features.final FeatureFilter
ReparentContext.revertFilter
(FeatureFilter ff) Methods in org.biojava.bio.seq.projection with parameters of type FeatureFilterModifier and TypeMethodDescriptionProjectedFeature.filter
(FeatureFilter ff) ProjectedFeature.filter
(FeatureFilter ff, boolean recurse) ProjectedFeatureHolder.filter
(FeatureFilter ff) ProjectedFeatureHolder.filter
(FeatureFilter ff, boolean recurse) ProjectionContext.projectFilter
(FeatureFilter filt) Transform a filter on unprojected features so that it applies to projected features.final FeatureFilter
ReparentContext.projectFilter
(FeatureFilter ff) ProjectionContext.revertFilter
(FeatureFilter filt) Transform a filter on projected features so that it applies to unprojected features.final FeatureFilter
ReparentContext.revertFilter
(FeatureFilter ff) -
Uses of FeatureFilter in org.biojavax.bio.db
Methods in org.biojavax.bio.db with parameters of type FeatureFilter -
Uses of FeatureFilter in org.biojavax.bio.db.biosql
Subinterfaces of FeatureFilter in org.biojavax.bio.db.biosqlModifier and TypeInterfaceDescriptioninterface
A filter for accepting or rejecting a feature.Classes in org.biojavax.bio.db.biosql that implement FeatureFilterModifier and TypeClassDescriptionclass
The class that accepts all features.class
The class that accepts no features.static final class
A filter that returns all features accepted by both child filter.static final class
Construct one of these to filter features by display name.static final class
A filter that returns all features that have the given note, and the value and rank is checked as well.static final class
A filter that returns all features that have a note with the given term.static final class
Construct one of these to filter features by rank.static final class
Accept features that reside on a sequence with a particular name.static final class
Construct one of these to filter features by source.static final class
Construct one of these to filter features by source (name only - parent ontology is ignored).static final class
A filter that returns all features having locations on a given strand.static final class
Construct one of these to filter features by type.static final class
Construct one of these to filter features by type (name only - parent ontology is ignored).static final class
A filter that returns all features contained within a location.static class
A filter for Hibernate-BioSQL filters to extend.static final class
A filter that returns all features not accepted by a child filter.static final class
A filter that returns all features accepted by at least one child filter.static final class
A filter that returns all features overlapping a location.Methods in org.biojavax.bio.db.biosql with parameters of type FeatureFilterModifier and TypeMethodDescriptionstatic BioSQLFeatureFilter
BioSQLFeatureFilter.Tools.convert
(FeatureFilter ff) Convert a non-BioSQL FeatureFilter into a BioSQL one.BioSQLRichSequenceDB.filter
(FeatureFilter ff) BioSQLRichSequenceDB.processFeatureFilter
(FeatureFilter ff) -
Uses of FeatureFilter in org.biojavax.bio.seq
Methods in org.biojavax.bio.seq that return FeatureFilterModifier and TypeMethodDescriptionSimpleRichFeature.getSchema()
Return a schema-filter for thisFeatureHolder
.ThinRichSequence.getSchema()
Return a schema-filter for thisFeatureHolder
.Methods in org.biojavax.bio.seq with parameters of type FeatureFilterModifier and TypeMethodDescriptionSimpleRichFeature.filter
(FeatureFilter filter) Query this set of features using a suppliedFeatureFilter
.SimpleRichFeature.filter
(FeatureFilter fc, boolean recurse) Return a new FeatureHolder that contains all of the children of this one that passed the filter fc.ThinRichSequence.filter
(FeatureFilter filter) Query this set of features using a suppliedFeatureFilter
.ThinRichSequence.filter
(FeatureFilter fc, boolean recurse) Return a new FeatureHolder that contains all of the children of this one that passed the filter fc.