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 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.
|
Modifier and Type | Field and Description |
---|---|
protected FeatureFilter |
PairwiseFilteringRenderer.filter
filter is the filter applied to both
FeatureHolder s. |
protected FeatureFilter |
FilteringRenderer.filter |
Modifier and Type | Field and Description |
---|---|
protected List<FeatureFilter> |
GlyphFeatureRenderer.fList |
Modifier and Type | Method and Description |
---|---|
FeatureFilter |
GlyphFeatureRenderer.getFeatureFilter(int i)
Returns the ith
FeatureFilter in this renderer. |
FeatureFilter |
PairwiseFilteringRenderer.getFilter()
getFilter returns the current filter. |
FeatureFilter |
FilteringRenderer.getFilter() |
FeatureFilter |
AbstractPeptideDigestRenderer.getFilter() |
Modifier and Type | Method and Description |
---|---|
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 |
PairwiseFilteringRenderer.setFilter(FeatureFilter filter)
setFilter sets the filter. |
void |
FilteringRenderer.setFilter(FeatureFilter filter) |
void |
AbstractPeptideDigestRenderer.setFilter(FeatureFilter filter) |
void |
GlyphFeatureRenderer.setGlyphForFilter(FeatureFilter ff,
Glyph glyph)
Allows setting another
Glyph object to be painted for the given
FeatureFilter. |
Constructor and 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 new
PairwiseFilteringRenderer . |
PeptideDigestRenderer(FeatureSource source,
FeatureFilter filter) |
PeptideDigestRenderer(FeatureSource source,
FeatureFilter filter,
int distanceBetweenFeatures) |
Modifier and Type | Method and Description |
---|---|
FeatureFilter |
SequencesAsGFF.getFeatureFilter()
Return the current FeatureFilter.
|
Modifier and Type | Method and Description |
---|---|
void |
SequencesAsGFF.setFeatureFilter(FeatureFilter filter)
Replace the current FeatureFilter with
filter.
|
Modifier and Type | Interface and Description |
---|---|
interface |
OptimizableFilter
The interface for filters that can potentialy optimize themselves, and
compare themselves with other filters.
|
Modifier and Type | Class and Description |
---|---|
static class |
FeatureFilter.And
A filter that returns all features accepted by both child filter.
|
static class |
FeatureFilter.AnnotationContains
Retrieve features that contain a given annotation, and that the set of values
contains the value given.
|
static class |
FeatureFilter.ByAncestor
Filter by applying a nested
FeatureFilter to all
ancestor features. |
static class |
FeatureFilter.ByAnnotation
Retrieve features that contain a given annotation with a given value.
|
static class |
FeatureFilter.ByAnnotationType
A filter that returns all features that have an annotation bundle that is of a given
annotation type.
|
static class |
FeatureFilter.ByChild
Filter by applying a nested
FeatureFilter to the
child features. |
static class |
FeatureFilter.ByClass
Filter which accepts only those filters which are an instance
of a specific Java class
|
static class |
FeatureFilter.ByComponentName
Accepts features which are ComponentFeatures and have a
componentSequenceName
property of the specified value. |
static class |
FeatureFilter.ByDescendant
Filter by applying a nested
FeatureFilter to all
descendant features. |
static class |
FeatureFilter.ByFeature
Accept only features which are equal to the specified feature
|
static class |
FeatureFilter.ByPairwiseScore
ByPairwiseScore is used to filter
SimilarityPairFeature s 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.
|
Modifier and Type | Field and Description |
---|---|
static FeatureFilter |
FeatureFilter.all
All features are selected by this filter.
|
static FeatureFilter |
FeatureFilter.leaf
A filter which accepts features with no children
|
static FeatureFilter |
FeatureFilter.none
No features are selected by this filter.
|
static FeatureFilter |
FeatureFilter.top_level
A filter which accepts only top-level Features.
|
Modifier and Type | Method and Description |
---|---|
static FeatureFilter |
FilterUtils.all()
Return a filter which matches all features.
|
static FeatureFilter |
FilterUtils.and(FeatureFilter[] filters)
Constructs a new filter which matches the intersection of a set of filters.
|
static FeatureFilter |
FilterUtils.and(FeatureFilter c1,
FeatureFilter c2)
Construct a new filter which matches the intersection of two other
filters.
|
static FeatureFilter |
FilterUtils.byAncestor(FeatureFilter ancestorFilter)
Match features where at least one of the ancestors matches the specified
filter.
|
static FeatureFilter |
FilterUtils.byAnnotation(Object key,
Object value)
Match features where the annotation property named
key is
equal to value . |
static FeatureFilter |
FilterUtils.byAnnotationType(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 |
SimpleFeatureHolder.getSchema() |
FeatureFilter |
SimpleAssembly.getSchema() |
FeatureFilter |
NewSimpleAssembly.getSchema() |
FeatureFilter |
MergeFeatureHolder.getSchema() |
FeatureFilter |
LazyFeatureHolder.getSchema() |
FeatureFilter |
FeatureTypes.Type.getSchema()
Get the schema for this type.
|
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.
|
Modifier and Type | Method and Description |
---|---|
static FeatureFilter |
FilterUtils.and(FeatureFilter[] filters)
Constructs a new filter which matches the intersection of a set of filters.
|
static FeatureFilter |
FilterUtils.and(FeatureFilter c1,
FeatureFilter c2)
Construct a new filter which matches the intersection of two other
filters.
|
static boolean |
FilterUtils.areDisjoint(FeatureFilter a,
FeatureFilter b)
Determines if two queries can be proven to be disjoint.
|
static boolean |
FilterUtils.areEqual(FeatureFilter f1,
FeatureFilter f2)
Decide if two feature filters accept exactly the same set of features.
|
static boolean |
FilterUtils.areProperSubset(FeatureFilter sub,
FeatureFilter sup)
Determines if the set of features matched by sub can be
proven to be a
proper subset of the features matched by sup. |
static FeatureFilter |
FilterUtils.byAncestor(FeatureFilter ancestorFilter)
Match features where at least one of the ancestors matches the specified
filter.
|
static FeatureFilter |
FilterUtils.byChild(FeatureFilter childFilter)
Match features where at least one child feature matches the supplied filter.
|
static FeatureFilter |
FilterUtils.byDescendant(FeatureFilter descFilter)
Match features where at least one decendant feature -- possibly but not necessarily an
immediate child -- matches the specified filter.
|
static FeatureFilter |
FilterUtils.byParent(FeatureFilter parentFilter)
Match features where the parent feature matches the specified filter.
|
FeatureTypes.Type |
FeatureTypes.RepositoryImpl.createType(String name,
FeatureFilter schema,
Set parents)
Create a new type in this repository.
|
static Location |
FilterUtils.extractOverlappingLocation(FeatureFilter ff)
Try to determine the minimal location which all features matching a given
filter must overlap.
|
FeatureHolder |
SimpleAssembly.filter(FeatureFilter ff) |
FeatureHolder |
NewSimpleAssembly.filter(FeatureFilter ff) |
FeatureHolder |
LazyFeatureHolder.filter(FeatureFilter ff) |
FeatureHolder |
FeatureHolder.filter(FeatureFilter filter)
Query this set of features using a supplied
FeatureFilter . |
FeatureHolder |
FeatureHolder.EmptyFeatureHolder.filter(FeatureFilter fc) |
FeatureHolder |
AbstractFeatureHolder.filter(FeatureFilter filter) |
FeatureHolder |
SimpleAssembly.filter(FeatureFilter ff,
boolean recurse) |
FeatureHolder |
NewSimpleAssembly.filter(FeatureFilter ff,
boolean recurse) |
FeatureHolder |
MergeFeatureHolder.filter(FeatureFilter ff,
boolean recurse)
When applied to a MergeFeatureHolder, this filters each child
FeatureHolder independently.
|
FeatureHolder |
LazyFeatureHolder.filter(FeatureFilter ff,
boolean recurse) |
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) |
FeatureHolder |
AbstractFeatureHolder.filter(FeatureFilter ff,
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.
|
Constructor and Description |
---|
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.
|
Modifier and Type | Method and Description |
---|---|
FeatureHolder |
SequenceDB.filter(FeatureFilter filter)
Query features attached to all sequences in this database.
|
FeatureHolder |
AbstractSequenceDB.filter(FeatureFilter ff) |
Modifier and Type | Method and Description |
---|---|
FeatureHolder |
BioSQLSequenceDB.filter(FeatureFilter ff)
Deprecated.
|
Modifier and Type | Method and Description |
---|---|
FeatureHolder |
SequenceDBDataSource.getFeatures(FeatureFilter ff) |
FeatureHolder |
GFFDataSource.getFeatures(FeatureFilter ff) |
FeatureHolder |
DistDataSource.getFeatures(FeatureFilter ff)
Get all features matching a FeatureFilter provided by this DistDataSource.
|
FeatureHolder |
SequenceDBDataSource.getFeatures(String id,
FeatureFilter ff,
boolean recurse) |
FeatureHolder |
GFFDataSource.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.
|
Modifier and Type | Method and Description |
---|---|
FeatureFilter |
FilterTransformer.and(FeatureFilter.And and,
FeatureFilter c1,
FeatureFilter c2) |
FeatureFilter |
FilterTransformer.byAncestor(FeatureFilter.ByAncestor ancestor,
FeatureFilter c) |
FeatureFilter |
FilterTransformer.byChild(FeatureFilter.ByChild child,
FeatureFilter c) |
FeatureFilter |
FilterTransformer.byDescendant(FeatureFilter.ByDescendant desc,
FeatureFilter c) |
FeatureFilter |
FilterTransformer.byParent(FeatureFilter.ByParent parent,
FeatureFilter c) |
FeatureFilter |
FilterTransformer.featureFilter(FeatureFilter filter) |
FeatureFilter |
FilterTransformer.not(FeatureFilter.Not not,
FeatureFilter c) |
FeatureFilter |
FilterTransformer.onlyChildren(FeatureFilter.OnlyChildren child,
FeatureFilter c) |
FeatureFilter |
FilterTransformer.onlyDescendants(FeatureFilter.OnlyDescendants desc,
FeatureFilter c) |
FeatureFilter |
FilterTransformer.or(FeatureFilter.Or or,
FeatureFilter c1,
FeatureFilter c2) |
Modifier and Type | Method and Description |
---|---|
FeatureFilter |
ViewSequence.getSchema() |
FeatureFilter |
SubSequence.getSchema() |
FeatureFilter |
SimpleSequence.getSchema() |
FeatureFilter |
SimpleGappedSequence.getSchema() |
FeatureFilter |
SimpleFeature.getSchema() |
FeatureFilter |
LazyFilterFeatureHolder.getSchema() |
FeatureFilter |
DummySequence.getSchema() |
Modifier and Type | Method and Description |
---|---|
FeatureHolder |
ViewSequence.filter(FeatureFilter fc) |
FeatureHolder |
SubSequence.filter(FeatureFilter ff) |
FeatureHolder |
SimpleSequence.filter(FeatureFilter filter) |
FeatureHolder |
SimpleGappedSequence.filter(FeatureFilter ff) |
FeatureHolder |
SimpleFeature.filter(FeatureFilter ff) |
FeatureHolder |
RevCompSequence.filter(FeatureFilter ff) |
FeatureHolder |
LazyFilterFeatureHolder.filter(FeatureFilter ff) |
FeatureHolder |
DummySequence.filter(FeatureFilter ff) |
FeatureHolder |
ViewSequence.filter(FeatureFilter fc,
boolean recurse) |
FeatureHolder |
SubSequence.filter(FeatureFilter ff,
boolean recurse) |
FeatureHolder |
SimpleSequence.filter(FeatureFilter ff,
boolean recurse) |
FeatureHolder |
SimpleGappedSequence.filter(FeatureFilter ff,
boolean recurse) |
FeatureHolder |
SimpleFeature.filter(FeatureFilter ff,
boolean recurse) |
FeatureHolder |
RevCompSequence.filter(FeatureFilter ff,
boolean recurse) |
FeatureHolder |
LazyFilterFeatureHolder.filter(FeatureFilter ff,
boolean recurse) |
FeatureHolder |
DummySequence.filter(FeatureFilter ff,
boolean recurse) |
Constructor and Description |
---|
LazyFilterFeatureHolder(FeatureHolder fh,
FeatureFilter ff) |
Modifier and Type | Method and Description |
---|---|
FeatureFilter |
XMLFilterHandler.FilterHandler.getFeatureFilter() |
Modifier and Type | Method and Description |
---|---|
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) |
Modifier and Type | Method and Description |
---|---|
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.
|
Modifier and Type | Method and Description |
---|---|
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.
|
Modifier and Type | Method and Description |
---|---|
FeatureHolder |
AbstractRichSequenceDB.filter(FeatureFilter ff) |
Modifier and Type | Interface and Description |
---|---|
interface |
BioSQLFeatureFilter
A filter for accepting or rejecting a feature.
|
Modifier and Type | Class and 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.
|
Modifier and Type | Method and 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) |
Modifier and Type | Method and Description |
---|---|
FeatureFilter |
ThinRichSequence.getSchema()
Return a schema-filter for this
FeatureHolder . |
FeatureFilter |
SimpleRichFeature.getSchema()
Return a schema-filter for this
FeatureHolder . |
Modifier and Type | Method and Description |
---|---|
FeatureHolder |
ThinRichSequence.filter(FeatureFilter filter)
Query this set of features using a supplied
FeatureFilter . |
FeatureHolder |
SimpleRichFeature.filter(FeatureFilter filter)
Query this set of features using a supplied
FeatureFilter . |
FeatureHolder |
ThinRichSequence.filter(FeatureFilter fc,
boolean recurse)
Return a new FeatureHolder that contains all of the children of this one
that passed the filter fc.
|
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.
|
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