Uses of Interface
org.biojava.bio.seq.FeatureFilter
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Packages that use FeatureFilter Package Description org.biojava.bio.gui.sequence Graphical displays of biological sequences and associated annotations.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 ofSequence
andFeature
.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 databasesorg.biojavax.bio.seq 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 FeatureFilter Modifier and Type Field Description protected 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 FeatureFilter Modifier and Type Field Description protected List<FeatureFilter>
GlyphFeatureRenderer. fList
Methods in org.biojava.bio.gui.sequence that return FeatureFilter Modifier and Type Method Description FeatureFilter
GlyphFeatureRenderer. getFeatureFilter(int i)
Returns the ithFeatureFilter
in this renderer.FeatureFilter
AbstractPeptideDigestRenderer. getFilter()
FeatureFilter
FilteringRenderer. getFilter()
FeatureFilter
PairwiseFilteringRenderer. getFilter()
getFilter
returns the current filter.Methods in org.biojava.bio.gui.sequence with parameters of type FeatureFilter Modifier and Type Method Description void
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)
Glyph
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 FeatureFilter Constructor Description 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 newPairwiseFilteringRenderer
.PeptideDigestRenderer(FeatureSource source, FeatureFilter filter)
PeptideDigestRenderer(FeatureSource source, FeatureFilter filter, int distanceBetweenFeatures)
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Uses of FeatureFilter in org.biojava.bio.program.gff
Methods in org.biojava.bio.program.gff that return FeatureFilter Modifier and Type Method Description FeatureFilter
SequencesAsGFF. getFeatureFilter()
Return the current FeatureFilter.Methods in org.biojava.bio.program.gff with parameters of type FeatureFilter Modifier and Type Method Description void
SequencesAsGFF. setFeatureFilter(FeatureFilter filter)
Replace the current FeatureFilter with filter. -
Uses of FeatureFilter in org.biojava.bio.seq
Subinterfaces of FeatureFilter in org.biojava.bio.seq Modifier and Type Interface Description interface
OptimizableFilter
The interface for filters that can potentialy optimize themselves, and compare themselves with other filters.Classes in org.biojava.bio.seq that implement FeatureFilter Modifier and Type Class Description static class
FeatureFilter.And
A filter that returns all features accepted by both child filter.static class
FeatureFilter.AnnotationContains
Retrieve features that contain a given annotation, and that the set of values contains the value given.static class
FeatureFilter.ByAncestor
Filter by applying a nestedFeatureFilter
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 nestedFeatureFilter
to the child features.static class
FeatureFilter.ByClass
Filter which accepts only those filters which are an instance of a specific Java classstatic class
FeatureFilter.ByComponentName
Accepts features which are ComponentFeatures and have acomponentSequenceName
property of the specified value.static class
FeatureFilter.ByDescendant
Filter by applying a nestedFeatureFilter
to all descendant features.static class
FeatureFilter.ByFeature
Accept only features which are equal to the specified featurestatic class
FeatureFilter.ByPairwiseScore
ByPairwiseScore
is used to filterSimilarityPairFeature
s by their score.static class
FeatureFilter.ByParent
Filter by applying a nestedFeatureFilter
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 specifiedLocation
.static class
FeatureFilter.ShadowOverlapsLocation
A filter that accepts all features whose shadow overlaps a specifiedLocation
.static class
FeatureFilter.StrandFilter
Accept features with a given strandedness.Fields in org.biojava.bio.seq declared as FeatureFilter Modifier and Type Field Description static FeatureFilter
FeatureFilter. all
All features are selected by this filter.static FeatureFilter
FeatureFilter. leaf
A filter which accepts features with no childrenstatic FeatureFilter
FeatureFilter. none
No features are selected by this filter.static FeatureFilter
FeatureFilter. top_level
A filter which accepts only top-level Features.Methods in org.biojava.bio.seq that return FeatureFilter Modifier and Type Method Description static FeatureFilter
FilterUtils. all()
Return a filter which matches all features.static FeatureFilter
FilterUtils. and(FeatureFilter[] filters)
Constructs a new filter which matches the intersection of a set of filters.static FeatureFilter
FilterUtils. and(FeatureFilter c1, FeatureFilter c2)
Construct a new filter which matches the intersection of two other filters.static FeatureFilter
FilterUtils. byAncestor(FeatureFilter ancestorFilter)
Match features where at least one of the ancestors matches the specified filter.static FeatureFilter
FilterUtils. byAnnotation(Object key, Object value)
Match features where the annotation property namedkey
is equal tovalue
.static FeatureFilter
FilterUtils. byAnnotationType(Object key, Class valClass)
Match features where the annotation property namedkey
is an instance ofvalClass
.static FeatureFilter
FilterUtils. byAnnotationType(AnnotationType type)
Match features with annotations matching the specifiedAnnotationType
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 theComponentFeature
interface and have acomponentName
property equal to the specified valuestatic 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 specificsource
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 specifictype
value.static FeatureFilter
FilterUtils. containedByLocation(Location loc)
Construct a filter which matches features with locations wholly contained by the specifiedLocation
.FeatureFilter
FeatureFilter.Not. getChild()
FeatureFilter
FeatureFilter.And. getChild1()
FeatureFilter
FeatureFilter.Or. getChild1()
FeatureFilter
FeatureFilter.And. getChild2()
FeatureFilter
FeatureFilter.Or. getChild2()
FeatureFilter
FeatureFilter.ByAncestor. getFilter()
FeatureFilter
FeatureFilter.ByChild. getFilter()
FeatureFilter
FeatureFilter.ByDescendant. getFilter()
FeatureFilter
FeatureFilter.ByParent. getFilter()
FeatureFilter
FeatureFilter.OnlyChildren. getFilter()
FeatureFilter
FeatureFilter.OnlyDescendants. getFilter()
FeatureFilter
FeatureHolder.EmptyFeatureHolder. getSchema()
FeatureFilter
FeatureHolder. getSchema()
Return a schema-filter for thisFeatureHolder
.FeatureFilter
FeatureTypes.Type. getSchema()
Get the schema for this type.FeatureFilter
LazyFeatureHolder. getSchema()
FeatureFilter
MergeFeatureHolder. getSchema()
FeatureFilter
NewSimpleAssembly. getSchema()
FeatureFilter
SimpleAssembly. getSchema()
FeatureFilter
SimpleFeatureHolder. getSchema()
static FeatureFilter
FilterUtils. hasAnnotation(Object key)
Match features where the propertykey
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 offilter
.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 specifiedLocation
.static 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 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 FeatureFilter
FilterUtils. topLevel()
Return a filter which matches all top-level features.FeatureFilter
FilterUtils.DelegatingTransformer. transform(FeatureFilter ff)
FeatureFilter
FilterUtils.FilterTransformer. transform(FeatureFilter filter)
Transform a filter, or return null if it can not be transformed.static FeatureFilter
FilterUtils. transformFilter(FeatureFilter ff, FilterUtils.FilterTransformer trans)
This is a general framework method for transforming one filter into another.Methods in org.biojava.bio.seq with parameters of type FeatureFilter Modifier and Type Method Description static FeatureFilter
FilterUtils. and(FeatureFilter[] filters)
Constructs a new filter which matches the intersection of a set of filters.static FeatureFilter
FilterUtils. and(FeatureFilter c1, FeatureFilter c2)
Construct a new filter which matches the intersection of two other filters.static boolean
FilterUtils. areDisjoint(FeatureFilter a, FeatureFilter b)
Determines if two queries can be proven to be disjoint.static boolean
FilterUtils. areEqual(FeatureFilter f1, FeatureFilter f2)
Decide if two feature filters accept exactly the same set of features.static boolean
FilterUtils. areProperSubset(FeatureFilter sub, FeatureFilter sup)
Determines if the set of features matched by sub can beproven
to be a proper subset of the features matched by sup.static FeatureFilter
FilterUtils. byAncestor(FeatureFilter ancestorFilter)
Match features where at least one of the ancestors matches the specified filter.static FeatureFilter
FilterUtils. byChild(FeatureFilter childFilter)
Match features where at least one child feature matches the supplied filter.static FeatureFilter
FilterUtils. byDescendant(FeatureFilter descFilter)
Match features where at least one decendant feature -- possibly but not necessarily an immediate child -- matches the specified filter.static FeatureFilter
FilterUtils. byParent(FeatureFilter parentFilter)
Match features where the parent feature matches the specified filter.FeatureTypes.Type
FeatureTypes.RepositoryImpl. createType(String name, FeatureFilter schema, Set parents)
Create a new type in this repository.static Location
FilterUtils. extractOverlappingLocation(FeatureFilter ff)
Try to determine the minimal location which all features matching a given filter must overlap.FeatureHolder
AbstractFeatureHolder. filter(FeatureFilter filter)
FeatureHolder
AbstractFeatureHolder. filter(FeatureFilter ff, boolean recurse)
FeatureHolder
FeatureHolder.EmptyFeatureHolder. filter(FeatureFilter fc)
FeatureHolder
FeatureHolder.EmptyFeatureHolder. filter(FeatureFilter fc, boolean recurse)
FeatureHolder
FeatureHolder. filter(FeatureFilter filter)
Query this set of features using a suppliedFeatureFilter
.FeatureHolder
FeatureHolder. filter(FeatureFilter fc, boolean recurse)
Return a new FeatureHolder that contains all of the children of this one that passed the filter fc.FeatureHolder
LazyFeatureHolder. filter(FeatureFilter ff)
FeatureHolder
LazyFeatureHolder. filter(FeatureFilter ff, boolean recurse)
FeatureHolder
MergeFeatureHolder. filter(FeatureFilter ff, boolean recurse)
When applied to a MergeFeatureHolder, this filters each child FeatureHolder independently.FeatureHolder
NewSimpleAssembly. filter(FeatureFilter ff)
FeatureHolder
NewSimpleAssembly. filter(FeatureFilter ff, boolean recurse)
FeatureHolder
SimpleAssembly. filter(FeatureFilter ff)
FeatureHolder
SimpleAssembly. filter(FeatureFilter ff, boolean recurse)
boolean
FeatureFilter.ByAncestor. isDisjoint(FeatureFilter ff)
boolean
FeatureFilter.ByAnnotationType. isDisjoint(FeatureFilter filter)
boolean
FeatureFilter.ByChild. isDisjoint(FeatureFilter ff)
boolean
FeatureFilter.ByClass. isDisjoint(FeatureFilter feat)
boolean
FeatureFilter.ByComponentName. isDisjoint(FeatureFilter feat)
boolean
FeatureFilter.ByDescendant. isDisjoint(FeatureFilter ff)
boolean
FeatureFilter.ByFeature. isDisjoint(FeatureFilter ff)
boolean
FeatureFilter.ByPairwiseScore. isDisjoint(FeatureFilter filt)
boolean
FeatureFilter.ByParent. isDisjoint(FeatureFilter ff)
boolean
FeatureFilter.BySequenceName. isDisjoint(FeatureFilter filt)
boolean
FeatureFilter.BySource. isDisjoint(FeatureFilter filt)
boolean
FeatureFilter.ByType. isDisjoint(FeatureFilter filt)
boolean
FeatureFilter.ContainedByLocation. isDisjoint(FeatureFilter filt)
boolean
FeatureFilter.FrameFilter. isDisjoint(FeatureFilter filt)
boolean
FeatureFilter.OnlyChildren. isDisjoint(FeatureFilter ff)
boolean
FeatureFilter.OnlyDescendants. isDisjoint(FeatureFilter ff)
boolean
FeatureFilter.OverlapsLocation. isDisjoint(FeatureFilter filt)
boolean
FeatureFilter.ShadowContainedByLocation. isDisjoint(FeatureFilter filt)
boolean
FeatureFilter.ShadowOverlapsLocation. isDisjoint(FeatureFilter filt)
boolean
FeatureFilter.StrandFilter. isDisjoint(FeatureFilter filt)
boolean
OptimizableFilter. isDisjoint(FeatureFilter filt)
Returns true if this filter is disjoint from filt - that is, there is no Feature that is accepted by both filters.boolean
FeatureFilter.ByAncestor. isProperSubset(FeatureFilter ff)
boolean
FeatureFilter.ByAnnotationType. isProperSubset(FeatureFilter filter)
boolean
FeatureFilter.ByChild. isProperSubset(FeatureFilter ff)
boolean
FeatureFilter.ByClass. isProperSubset(FeatureFilter sup)
boolean
FeatureFilter.ByComponentName. isProperSubset(FeatureFilter sup)
boolean
FeatureFilter.ByDescendant. isProperSubset(FeatureFilter ff)
boolean
FeatureFilter.ByFeature. isProperSubset(FeatureFilter ff)
boolean
FeatureFilter.ByPairwiseScore. isProperSubset(FeatureFilter sup)
boolean
FeatureFilter.ByParent. isProperSubset(FeatureFilter ff)
boolean
FeatureFilter.BySequenceName. isProperSubset(FeatureFilter sup)
boolean
FeatureFilter.BySource. isProperSubset(FeatureFilter sup)
boolean
FeatureFilter.ByType. isProperSubset(FeatureFilter sup)
boolean
FeatureFilter.ContainedByLocation. isProperSubset(FeatureFilter sup)
boolean
FeatureFilter.FrameFilter. isProperSubset(FeatureFilter sup)
boolean
FeatureFilter.OnlyChildren. isProperSubset(FeatureFilter ff)
boolean
FeatureFilter.OnlyDescendants. isProperSubset(FeatureFilter ff)
boolean
FeatureFilter.OverlapsLocation. isProperSubset(FeatureFilter sup)
boolean
FeatureFilter.ShadowContainedByLocation. isProperSubset(FeatureFilter sup)
boolean
FeatureFilter.ShadowOverlapsLocation. isProperSubset(FeatureFilter sup)
boolean
FeatureFilter.StrandFilter. isProperSubset(FeatureFilter sup)
boolean
OptimizableFilter. isProperSubset(FeatureFilter sup)
Returns true if this filter is a proper subset of sup - that is, for every feature that matches this, it also matches sup.static FeatureFilter
FilterUtils. not(FeatureFilter filter)
Construct a new filter which is the negation offilter
.static FeatureFilter
FilterUtils. onlyChildren(FeatureFilter child)
Construct a filter which matches features whose children all match the specified filter.static FeatureFilter
FilterUtils. onlyDescendants(FeatureFilter desc)
Construct a filter which matches features whose decendants all match the specified filter.static FeatureFilter
FilterUtils. optimize(FeatureFilter filter)
Attempts to reduce a FeatureFilter to an equivalent FeatureFilter with fewer terms.static FeatureFilter
FilterUtils. or(FeatureFilter[] filters)
Construct a new filter which matches the intersection of two filters.static FeatureFilter
FilterUtils. or(FeatureFilter c1, FeatureFilter c2)
Construct a new filter which matches the union of two filters.FeatureFilter
FilterUtils.DelegatingTransformer. transform(FeatureFilter ff)
FeatureFilter
FilterUtils.FilterTransformer. transform(FeatureFilter filter)
Transform a filter, or return null if it can not be transformed.static FeatureFilter
FilterUtils. transformFilter(FeatureFilter ff, FilterUtils.FilterTransformer trans)
This is a general framework method for transforming one filter into another.static Object
FilterUtils. visitFilter(FeatureFilter filter, Visitor visitor)
Applies a visitor to a filter, and returns the visitor's result or null.Constructors in org.biojava.bio.seq with parameters of type FeatureFilter Constructor Description And(FeatureFilter c1, FeatureFilter c2)
ByAncestor(FeatureFilter ff)
ByChild(FeatureFilter ff)
ByDescendant(FeatureFilter ff)
ByParent(FeatureFilter ff)
LazyFeatureHolder(FeatureFilter schema)
Construct a LazyFeatureHolder with the specified schemaNot(FeatureFilter child)
OnlyChildren(FeatureFilter ff)
OnlyDescendants(FeatureFilter ff)
Or(FeatureFilter c1, FeatureFilter c2)
SimpleFeatureHolder(FeatureFilter schema)
Construct a new SimpleFeatureHolder with the specified schema. -
Uses of FeatureFilter in org.biojava.bio.seq.db
Methods in org.biojava.bio.seq.db with parameters of type FeatureFilter Modifier and Type Method Description FeatureHolder
AbstractSequenceDB. filter(FeatureFilter ff)
FeatureHolder
SequenceDB. filter(FeatureFilter filter)
Query features attached to all sequences in this database. -
Uses of FeatureFilter in org.biojava.bio.seq.db.biosql
Methods in org.biojava.bio.seq.db.biosql with parameters of type FeatureFilter Modifier and Type Method Description 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 Modifier and Type Method Description FeatureHolder
DistDataSource. getFeatures(String id, FeatureFilter ff, boolean recurse)
Get all features matching a FeatureFilter on a Sequence with an ID and recurse flats.FeatureHolder
DistDataSource. getFeatures(FeatureFilter ff)
Get all features matching a FeatureFilter provided by this DistDataSource.FeatureHolder
GFFDataSource. getFeatures(String id, FeatureFilter ff, boolean recurse)
FeatureHolder
GFFDataSource. getFeatures(FeatureFilter ff)
FeatureHolder
SequenceDBDataSource. getFeatures(String id, FeatureFilter ff, boolean recurse)
FeatureHolder
SequenceDBDataSource. getFeatures(FeatureFilter ff)
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Uses of FeatureFilter in org.biojava.bio.seq.filter
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Uses of FeatureFilter in org.biojava.bio.seq.impl
Methods in org.biojava.bio.seq.impl that return FeatureFilter Modifier and Type Method Description FeatureFilter
DummySequence. getSchema()
FeatureFilter
LazyFilterFeatureHolder. getSchema()
FeatureFilter
SimpleFeature. getSchema()
FeatureFilter
SimpleGappedSequence. getSchema()
FeatureFilter
SimpleSequence. getSchema()
FeatureFilter
SubSequence. getSchema()
FeatureFilter
ViewSequence. getSchema()
Methods in org.biojava.bio.seq.impl with parameters of type FeatureFilter Modifier and Type Method Description FeatureHolder
DummySequence. filter(FeatureFilter ff)
FeatureHolder
DummySequence. filter(FeatureFilter ff, boolean recurse)
FeatureHolder
LazyFilterFeatureHolder. filter(FeatureFilter ff)
FeatureHolder
LazyFilterFeatureHolder. filter(FeatureFilter ff, boolean recurse)
FeatureHolder
RevCompSequence. filter(FeatureFilter ff)
FeatureHolder
RevCompSequence. filter(FeatureFilter ff, boolean recurse)
FeatureHolder
SimpleFeature. filter(FeatureFilter ff)
FeatureHolder
SimpleFeature. filter(FeatureFilter ff, boolean recurse)
FeatureHolder
SimpleGappedSequence. filter(FeatureFilter ff)
FeatureHolder
SimpleGappedSequence. filter(FeatureFilter ff, boolean recurse)
FeatureHolder
SimpleSequence. filter(FeatureFilter filter)
FeatureHolder
SimpleSequence. filter(FeatureFilter ff, boolean recurse)
FeatureHolder
SubSequence. filter(FeatureFilter ff)
FeatureHolder
SubSequence. filter(FeatureFilter ff, boolean recurse)
FeatureHolder
ViewSequence. filter(FeatureFilter fc)
FeatureHolder
ViewSequence. filter(FeatureFilter fc, boolean recurse)
Constructors in org.biojava.bio.seq.impl with parameters of type FeatureFilter Constructor Description LazyFilterFeatureHolder(FeatureHolder fh, FeatureFilter ff)
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Uses of FeatureFilter in org.biojava.bio.seq.io.filterxml
Methods in org.biojava.bio.seq.io.filterxml that return FeatureFilter Modifier and Type Method Description FeatureFilter
XMLFilterHandler.FilterHandler. getFeatureFilter()
Methods in org.biojava.bio.seq.io.filterxml with parameters of type FeatureFilter Modifier and Type Method Description void
XMLFilterWriter. addXMLFilterWriter(FeatureFilter ff, XMLFilterWriter.FilterWriter xfw)
Add a writer for a singleton filter.void
XMLFilterWriter.FilterWriter. writeFilter(FeatureFilter ff, XMLWriter xw, XMLFilterWriter config)
void
XMLFilterWriter. writeFilter(FeatureFilter ff, XMLWriter xw)
Write a FeatureFilter to the supplied XMLWriter -
Uses of FeatureFilter in org.biojava.bio.seq.projection
Methods in org.biojava.bio.seq.projection that return FeatureFilter Modifier and Type Method Description FeatureFilter
ProjectedFeatureHolder. getSchema()
FeatureFilter
ReparentContext. getSchema(Feature f)
FeatureFilter
ProjectionContext. projectFilter(FeatureFilter filt)
Transform a filter on unprojected features so that it applies to projected features.FeatureFilter
ReparentContext. projectFilter(FeatureFilter ff)
FeatureFilter
ProjectionContext. revertFilter(FeatureFilter filt)
Transform a filter on projected features so that it applies to unprojected features.FeatureFilter
ReparentContext. revertFilter(FeatureFilter ff)
Methods in org.biojava.bio.seq.projection with parameters of type FeatureFilter Modifier and Type Method Description FeatureHolder
ProjectedFeature. filter(FeatureFilter ff)
FeatureHolder
ProjectedFeature. filter(FeatureFilter ff, boolean recurse)
FeatureHolder
ProjectedFeatureHolder. filter(FeatureFilter ff)
FeatureHolder
ProjectedFeatureHolder. filter(FeatureFilter ff, boolean recurse)
FeatureFilter
ProjectionContext. projectFilter(FeatureFilter filt)
Transform a filter on unprojected features so that it applies to projected features.FeatureFilter
ReparentContext. projectFilter(FeatureFilter ff)
FeatureFilter
ProjectionContext. revertFilter(FeatureFilter filt)
Transform a filter on projected features so that it applies to unprojected features.FeatureFilter
ReparentContext. revertFilter(FeatureFilter ff)
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Uses of FeatureFilter in org.biojavax.bio.db
Methods in org.biojavax.bio.db with parameters of type FeatureFilter Modifier and Type Method Description FeatureHolder
AbstractRichSequenceDB. filter(FeatureFilter ff)
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Uses of FeatureFilter in org.biojavax.bio.db.biosql
Subinterfaces of FeatureFilter in org.biojavax.bio.db.biosql Modifier and Type Interface Description interface
BioSQLFeatureFilter
A filter for accepting or rejecting a feature.Classes in org.biojavax.bio.db.biosql that implement FeatureFilter Modifier and Type Class Description 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 Modifier and Type Method Description 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)
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Uses of FeatureFilter in org.biojavax.bio.seq
Methods in org.biojavax.bio.seq that return FeatureFilter Modifier and Type Method Description FeatureFilter
SimpleRichFeature. getSchema()
Return a schema-filter for thisFeatureHolder
.FeatureFilter
ThinRichSequence. getSchema()
Return a schema-filter for thisFeatureHolder
.Methods in org.biojavax.bio.seq with parameters of type FeatureFilter Modifier and Type Method Description FeatureHolder
SimpleRichFeature. filter(FeatureFilter filter)
Query this set of features using a suppliedFeatureFilter
.FeatureHolder
SimpleRichFeature. filter(FeatureFilter fc, boolean recurse)
Return a new FeatureHolder that contains all of the children of this one that passed the filter fc.FeatureHolder
ThinRichSequence. filter(FeatureFilter filter)
Query this set of features using a suppliedFeatureFilter
.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.
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