org.biojava.bio.seq

Interface FeatureFilter

All Superinterfaces:

Serializable

All Known Subinterfaces:

BioSQLFeatureFilter, OptimizableFilter

All Known Implementing Classes:

BioSQLAcceptAllFilter, BioSQLAcceptNoneFilter, BioSQLFeatureFilter.And, BioSQLFeatureFilter.ByName, BioSQLFeatureFilter.ByNote, BioSQLFeatureFilter.ByNoteTermOnly, BioSQLFeatureFilter.ByRank, BioSQLFeatureFilter.BySequenceName, BioSQLFeatureFilter.BySourceTerm, BioSQLFeatureFilter.BySourceTermName, BioSQLFeatureFilter.ByStrand, BioSQLFeatureFilter.ByTypeTerm, BioSQLFeatureFilter.ByTypeTermName, BioSQLFeatureFilter.ContainedByRichLocation, BioSQLFeatureFilter.HibernateFeatureFilter, BioSQLFeatureFilter.Not, BioSQLFeatureFilter.Or, BioSQLFeatureFilter.OverlapsRichLocation, FeatureFilter.And, FeatureFilter.AnnotationContains, FeatureFilter.ByAncestor, FeatureFilter.ByAnnotation, FeatureFilter.ByAnnotationType, FeatureFilter.ByChild, FeatureFilter.ByClass, FeatureFilter.ByComponentName, FeatureFilter.ByDescendant, FeatureFilter.ByFeature, FeatureFilter.ByPairwiseScore, FeatureFilter.ByParent, FeatureFilter.BySequenceName, FeatureFilter.BySource, FeatureFilter.ByType, FeatureFilter.ContainedByLocation, FeatureFilter.FrameFilter, FeatureFilter.HasAnnotation, FeatureFilter.Not, FeatureFilter.OnlyChildren, FeatureFilter.OnlyDescendants, FeatureFilter.Or, FeatureFilter.OverlapsLocation, FeatureFilter.ShadowContainedByLocation, FeatureFilter.ShadowOverlapsLocation, FeatureFilter.StrandFilter

public interface FeatureFilter
extends Serializable

A filter for accepting or rejecting a feature.

It is possible to write custom FeatureFilters by implementing this interface. There are also a wide range of built-in features, and it is possible to build complex queries using FeatureFilter.And, FeatureFilter.Or, and FeatureFilter.Not. Where possible, use of the built-in filters is preferable to writing new filters, since the methods in the FilterUtils class have access to special knowledge about the built-in filter types and how they relate to one another.

If the filter is to be used in a remote process, it is recognized that it may be serialized and sent over to run remotely, rather than each feature being retrieved locally.

Since:

1.0

Author:

Matthew Pocock, Thomas Down

Nested Class Summary

Nested Classes

Modifier and Type	Interface 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 SimilarityPairFeatures by their score.
static class	FeatureFilter.ByParent Filter by applying a nested FeatureFilter to the parent feature.
static class	FeatureFilter.BySequenceName Accept features that reside on a sequence with a particular name.
static class	FeatureFilter.BySource Construct one of these to filter features by source.
static class	FeatureFilter.ByType Construct one of these to filter features by type.
static class	FeatureFilter.ContainedByLocation A filter that returns all features contained within a location.
static class	FeatureFilter.FrameFilter Accept features with a given reading frame.
static class	FeatureFilter.HasAnnotation Retrieve features that contain a given annotation with any value.
static class	FeatureFilter.Not A filter that returns all features not accepted by a child filter.
static class	FeatureFilter.OnlyChildren Accepts features where all immediate children meet the supplied filter.
static class	FeatureFilter.OnlyDescendants Accepts features where all descendants meet the supplied filter.
static class	FeatureFilter.Or A filter that returns all features accepted by at least one child filter.
static class	FeatureFilter.OverlapsLocation A filter that returns all features overlapping a location.
static class	FeatureFilter.ShadowContainedByLocation A filter that accepts all features whose shadow is contained by a specified Location.
static class	FeatureFilter.ShadowOverlapsLocation A filter that accepts all features whose shadow overlaps a specified Location.
static class	FeatureFilter.StrandFilter Accept features with a given strandedness.

Field Summary

Fields

Modifier and Type	Field and Description
static FeatureFilter	all All features are selected by this filter.
static FeatureFilter	leaf A filter which accepts features with no children
static FeatureFilter	none No features are selected by this filter.
static FeatureFilter	top_level A filter which accepts only top-level Features.

Method Summary

Methods

Modifier and Type	Method and Description
boolean	accept(Feature f) This method determines whether a feature is to be accepted.

Field Detail

all

static final FeatureFilter all

All features are selected by this filter.

none

static final FeatureFilter none

No features are selected by this filter.

top_level

static final FeatureFilter top_level

A filter which accepts only top-level Features. This is true is getParent() returns a Sequence instance.

Since:

1.3

leaf

static final FeatureFilter leaf

A filter which accepts features with no children

Since:

1.3

Method Detail

accept

boolean accept(Feature f)

This method determines whether a feature is to be accepted.

Parameters:

f - the Feature to evaluate

Returns:

true if this feature is to be selected in, or false if it is to be ignored