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 FeatureFilterFilteringRenderer.filterprotected FeatureFilterPairwiseFilteringRenderer.filterfilteris the filter applied to bothFeatureHolders.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 ithFeatureFilterin this renderer.AbstractPeptideDigestRenderer.getFilter()FilteringRenderer.getFilter()PairwiseFilteringRenderer.getFilter()getFilterreturns the current filter.Methods in org.biojava.bio.gui.sequence with parameters of type FeatureFilterModifier and TypeMethodDescriptionvoidGlyphFeatureRenderer.addFilterAndGlyph(FeatureFilter ff, Glyph g) booleanGlyphFeatureRenderer.containsFilter(FeatureFilter ff) Returns true if the givenFeatureFilteris already contained in this renderer.protected ListBumpedRenderer.doLayer(SequenceRenderContext src, FeatureFilter filt) GlyphFeatureRenderer.getGlyphForFilter(FeatureFilter ff) Returns theGlyphobject which is assigned to the given feature filter.voidGlyphFeatureRenderer.removeFilterWithGlyph(FeatureFilter ff) voidAbstractPeptideDigestRenderer.setFilter(FeatureFilter filter) voidFilteringRenderer.setFilter(FeatureFilter filter) voidPairwiseFilteringRenderer.setFilter(FeatureFilter filter) setFiltersets the filter.voidGlyphFeatureRenderer.setGlyphForFilter(FeatureFilter ff, Glyph glyph) Allows setting anotherGlyphobject 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 TypeMethodDescriptionvoidSequencesAsGFF.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 TypeInterfaceDescriptioninterfaceThe 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 classA filter that returns all features accepted by both child filter.static final classRetrieve features that contain a given annotation, and that the set of values contains the value given.static classFilter by applying a nestedFeatureFilterto all ancestor features.static final classRetrieve features that contain a given annotation with a given value.static classA filter that returns all features that have an annotation bundle that is of a given annotation type.static classFilter by applying a nestedFeatureFilterto the child features.static final classFilter which accepts only those filters which are an instance of a specific Java classstatic final classAccepts features which are ComponentFeatures and have acomponentSequenceNameproperty of the specified value.static classFilter by applying a nestedFeatureFilterto all descendant features.static final classAccept only features which are equal to the specified featurestatic final classByPairwiseScoreis used to filterSimilarityPairFeatures by their score.static classFilter by applying a nestedFeatureFilterto the parent feature.static final classAccept features that reside on a sequence with a particular name.static final classConstruct one of these to filter features by source.static final classConstruct one of these to filter features by type.static final classA filter that returns all features contained within a location.static final classAccept features with a given reading frame.static final classRetrieve features that contain a given annotation with any value.static final classA filter that returns all features not accepted by a child filter.static classAccepts features where all immediate children meet the supplied filter.static classAccepts features where all descendants meet the supplied filter.static final classA filter that returns all features accepted by at least one child filter.static final classA filter that returns all features overlapping a location.static final classA filter that accepts all features whose shadow is contained by a specifiedLocation.static final classA filter that accepts all features whose shadow overlaps a specifiedLocation.static final classAccept features with a given strandedness.Fields in org.biojava.bio.seq declared as FeatureFilterModifier and TypeFieldDescriptionstatic final FeatureFilterFeatureFilter.allAll features are selected by this filter.static final FeatureFilterFeatureFilter.leafA filter which accepts features with no childrenstatic final FeatureFilterFeatureFilter.noneNo features are selected by this filter.static final FeatureFilterFeatureFilter.top_levelA filter which accepts only top-level Features.Methods in org.biojava.bio.seq that return FeatureFilterModifier and TypeMethodDescriptionstatic final FeatureFilterFilterUtils.all()Return a filter which matches all features.static final FeatureFilterFilterUtils.and(FeatureFilter[] filters) Constructs a new filter which matches the intersection of a set of filters.static final FeatureFilterFilterUtils.and(FeatureFilter c1, FeatureFilter c2) Construct a new filter which matches the intersection of two other filters.static final FeatureFilterFilterUtils.byAncestor(FeatureFilter ancestorFilter) Match features where at least one of the ancestors matches the specified filter.static final FeatureFilterFilterUtils.byAnnotation(Object key, Object value) Match features where the annotation property namedkeyis equal tovalue.static final FeatureFilterFilterUtils.byAnnotationType(Object key, Class valClass) Match features where the annotation property namedkeyis an instance ofvalClass.static final FeatureFilterFilterUtils.byAnnotationType(AnnotationType type) Match features with annotations matching the specifiedAnnotationTypestatic final FeatureFilterFilterUtils.byChild(FeatureFilter childFilter) Match features where at least one child feature matches the supplied filter.static final FeatureFilterConstruct a filter which matches features which are assignable to the specified class or interface.static final FeatureFilterFilterUtils.byComponentName(String compName) Construct a filter which matches all features which implement theComponentFeatureinterface and have acomponentNameproperty equal to the specified valuestatic final FeatureFilterFilterUtils.byDescendant(FeatureFilter descFilter) Match features where at least one decendant feature -- possibly but not necessarily an immediate child -- matches the specified filter.static final FeatureFilterFilterUtils.byFrame(FramedFeature.ReadingFrame frame) Construct a filter which matches FramedFeatures with the specified reading frame.static final FeatureFilterFilterUtils.byPairwiseScore(double minScore, double maxScore) Match SeqSimilaritiy features with scores in the specified range.static final FeatureFilterFilterUtils.byParent(FeatureFilter parentFilter) Match features where the parent feature matches the specified filter.static final FeatureFilterFilterUtils.bySequenceName(String name) Match features attached to sequences with a specified name.static final FeatureFilterConstruct a filter which matches features with a specificsourcevalue.static final FeatureFilterFilterUtils.byStrand(StrandedFeature.Strand strand) Match StrandedFeatures on the specified strand.static final FeatureFilterConstruct a filter which matches features with a specifictypevalue.static final FeatureFilterFilterUtils.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 FeatureFilterFilterUtils.hasAnnotation(Object key) Match features where the propertykeyhas been defined as having some value, regardless of the exact value.static final FeatureFilterFilterUtils.leaf()Return a filter which matches features with zero children.static final FeatureFilterFilterUtils.none()Return a filter which matches no features.static final FeatureFilterFilterUtils.not(FeatureFilter filter) Construct a new filter which is the negation offilter.static final FeatureFilterFilterUtils.onlyChildren(FeatureFilter child) Construct a filter which matches features whose children all match the specified filter.static final FeatureFilterFilterUtils.onlyDescendants(FeatureFilter desc) Construct a filter which matches features whose decendants all match the specified filter.static final FeatureFilterFilterUtils.optimize(FeatureFilter filter) Attempts to reduce a FeatureFilter to an equivalent FeatureFilter with fewer terms.static final FeatureFilterFilterUtils.or(FeatureFilter[] filters) Construct a new filter which matches the intersection of two filters.static final FeatureFilterFilterUtils.or(FeatureFilter c1, FeatureFilter c2) Construct a new filter which matches the union of two filters.static final FeatureFilterFilterUtils.overlapsLocation(Location loc) Construct a filter which matches features with locations contained by or overlapping the specifiedLocation.static final FeatureFilterFilterUtils.shadowContainedByLocation(Location loc) Construct a filter which matches features with locations where the interval between theminandmaxpositions are contained by the specifiedLocation.static final FeatureFilterFilterUtils.shadowOverlapsLocation(Location loc) Construct a filter which matches features with locations where the interval between theminandmaxpositions are contained by or overlap the specifiedLocation.static final FeatureFilterFilterUtils.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 FeatureFilterFilterUtils.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 FeatureFilterFilterUtils.and(FeatureFilter[] filters) Constructs a new filter which matches the intersection of a set of filters.static final FeatureFilterFilterUtils.and(FeatureFilter c1, FeatureFilter c2) Construct a new filter which matches the intersection of two other filters.static booleanFilterUtils.areDisjoint(FeatureFilter a, FeatureFilter b) Determines if two queries can be proven to be disjoint.static final booleanFilterUtils.areEqual(FeatureFilter f1, FeatureFilter f2) Decide if two feature filters accept exactly the same set of features.static booleanFilterUtils.areProperSubset(FeatureFilter sub, FeatureFilter sup) Determines if the set of features matched by sub can beprovento be a proper subset of the features matched by sup.static final FeatureFilterFilterUtils.byAncestor(FeatureFilter ancestorFilter) Match features where at least one of the ancestors matches the specified filter.static final FeatureFilterFilterUtils.byChild(FeatureFilter childFilter) Match features where at least one child feature matches the supplied filter.static final FeatureFilterFilterUtils.byDescendant(FeatureFilter descFilter) Match features where at least one decendant feature -- possibly but not necessarily an immediate child -- matches the specified filter.static final FeatureFilterFilterUtils.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 LocationFilterUtils.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) booleanFeatureFilter.ByAncestor.isDisjoint(FeatureFilter ff) booleanFeatureFilter.ByAnnotationType.isDisjoint(FeatureFilter filter) booleanFeatureFilter.ByChild.isDisjoint(FeatureFilter ff) booleanFeatureFilter.ByClass.isDisjoint(FeatureFilter feat) booleanFeatureFilter.ByComponentName.isDisjoint(FeatureFilter feat) booleanFeatureFilter.ByDescendant.isDisjoint(FeatureFilter ff) booleanFeatureFilter.ByFeature.isDisjoint(FeatureFilter ff) booleanFeatureFilter.ByPairwiseScore.isDisjoint(FeatureFilter filt) booleanFeatureFilter.ByParent.isDisjoint(FeatureFilter ff) booleanFeatureFilter.BySequenceName.isDisjoint(FeatureFilter filt) booleanFeatureFilter.BySource.isDisjoint(FeatureFilter filt) booleanFeatureFilter.ByType.isDisjoint(FeatureFilter filt) booleanFeatureFilter.ContainedByLocation.isDisjoint(FeatureFilter filt) booleanFeatureFilter.FrameFilter.isDisjoint(FeatureFilter filt) booleanFeatureFilter.OnlyChildren.isDisjoint(FeatureFilter ff) booleanFeatureFilter.OnlyDescendants.isDisjoint(FeatureFilter ff) booleanFeatureFilter.OverlapsLocation.isDisjoint(FeatureFilter filt) booleanFeatureFilter.ShadowContainedByLocation.isDisjoint(FeatureFilter filt) booleanFeatureFilter.ShadowOverlapsLocation.isDisjoint(FeatureFilter filt) booleanFeatureFilter.StrandFilter.isDisjoint(FeatureFilter filt) booleanOptimizableFilter.isDisjoint(FeatureFilter filt) Returns true if this filter is disjoint from filt - that is, there is no Feature that is accepted by both filters.booleanFeatureFilter.ByAncestor.isProperSubset(FeatureFilter ff) booleanFeatureFilter.ByAnnotationType.isProperSubset(FeatureFilter filter) booleanFeatureFilter.ByChild.isProperSubset(FeatureFilter ff) booleanFeatureFilter.ByClass.isProperSubset(FeatureFilter sup) booleanFeatureFilter.ByComponentName.isProperSubset(FeatureFilter sup) booleanFeatureFilter.ByDescendant.isProperSubset(FeatureFilter ff) booleanFeatureFilter.ByFeature.isProperSubset(FeatureFilter ff) booleanFeatureFilter.ByPairwiseScore.isProperSubset(FeatureFilter sup) booleanFeatureFilter.ByParent.isProperSubset(FeatureFilter ff) booleanFeatureFilter.BySequenceName.isProperSubset(FeatureFilter sup) booleanFeatureFilter.BySource.isProperSubset(FeatureFilter sup) booleanFeatureFilter.ByType.isProperSubset(FeatureFilter sup) booleanFeatureFilter.ContainedByLocation.isProperSubset(FeatureFilter sup) booleanFeatureFilter.FrameFilter.isProperSubset(FeatureFilter sup) booleanFeatureFilter.OnlyChildren.isProperSubset(FeatureFilter ff) booleanFeatureFilter.OnlyDescendants.isProperSubset(FeatureFilter ff) booleanFeatureFilter.OverlapsLocation.isProperSubset(FeatureFilter sup) booleanFeatureFilter.ShadowContainedByLocation.isProperSubset(FeatureFilter sup) booleanFeatureFilter.ShadowOverlapsLocation.isProperSubset(FeatureFilter sup) booleanFeatureFilter.StrandFilter.isProperSubset(FeatureFilter sup) booleanOptimizableFilter.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 FeatureFilterFilterUtils.not(FeatureFilter filter) Construct a new filter which is the negation offilter.static final FeatureFilterFilterUtils.onlyChildren(FeatureFilter child) Construct a filter which matches features whose children all match the specified filter.static final FeatureFilterFilterUtils.onlyDescendants(FeatureFilter desc) Construct a filter which matches features whose decendants all match the specified filter.static final FeatureFilterFilterUtils.optimize(FeatureFilter filter) Attempts to reduce a FeatureFilter to an equivalent FeatureFilter with fewer terms.static final FeatureFilterFilterUtils.or(FeatureFilter[] filters) Construct a new filter which matches the intersection of two filters.static final FeatureFilterFilterUtils.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 FeatureFilterFilterUtils.transformFilter(FeatureFilter ff, FilterUtils.FilterTransformer trans) This is a general framework method for transforming one filter into another.static ObjectFilterUtils.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) protectedLazyFeatureHolder(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 TypeMethodDescriptionvoidXMLFilterWriter.addXMLFilterWriter(FeatureFilter ff, XMLFilterWriter.FilterWriter xfw) Add a writer for a singleton filter.voidXMLFilterWriter.FilterWriter.writeFilter(FeatureFilter ff, XMLWriter xw, XMLFilterWriter config) voidXMLFilterWriter.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 FeatureFilterProjectionContext.projectFilter(FeatureFilter filt) Transform a filter on unprojected features so that it applies to projected features.final FeatureFilterReparentContext.projectFilter(FeatureFilter ff) ProjectionContext.revertFilter(FeatureFilter filt) Transform a filter on projected features so that it applies to unprojected features.final FeatureFilterReparentContext.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 FeatureFilterReparentContext.projectFilter(FeatureFilter ff) ProjectionContext.revertFilter(FeatureFilter filt) Transform a filter on projected features so that it applies to unprojected features.final FeatureFilterReparentContext.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 TypeInterfaceDescriptioninterfaceA filter for accepting or rejecting a feature.Classes in org.biojavax.bio.db.biosql that implement FeatureFilterModifier and TypeClassDescriptionclassThe class that accepts all features.classThe class that accepts no features.static final classA filter that returns all features accepted by both child filter.static final classConstruct one of these to filter features by display name.static final classA filter that returns all features that have the given note, and the value and rank is checked as well.static final classA filter that returns all features that have a note with the given term.static final classConstruct one of these to filter features by rank.static final classAccept features that reside on a sequence with a particular name.static final classConstruct one of these to filter features by source.static final classConstruct one of these to filter features by source (name only - parent ontology is ignored).static final classA filter that returns all features having locations on a given strand.static final classConstruct one of these to filter features by type.static final classConstruct one of these to filter features by type (name only - parent ontology is ignored).static final classA filter that returns all features contained within a location.static classA filter for Hibernate-BioSQL filters to extend.static final classA filter that returns all features not accepted by a child filter.static final classA filter that returns all features accepted by at least one child filter.static final classA filter that returns all features overlapping a location.Methods in org.biojavax.bio.db.biosql with parameters of type FeatureFilterModifier and TypeMethodDescriptionstatic BioSQLFeatureFilterBioSQLFeatureFilter.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.