Package 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
A filter for accepting or rejecting a feature.
It is possible to write custom FeatureFilter
s 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 ClassesModifier and TypeInterfaceDescriptionstatic final class
A filter that returns all features accepted by both child filter.static final class
Retrieve features that contain a given annotation, and that the set of values contains the value given.static class
Filter by applying a nestedFeatureFilter
to all ancestor features.static final class
Retrieve features that contain a given annotation with a given value.static class
A filter that returns all features that have an annotation bundle that is of a given annotation type.static class
Filter by applying a nestedFeatureFilter
to the child features.static final class
Filter which accepts only those filters which are an instance of a specific Java classstatic final class
Accepts features which are ComponentFeatures and have acomponentSequenceName
property of the specified value.static class
Filter by applying a nestedFeatureFilter
to all descendant features.static final class
Accept only features which are equal to the specified featurestatic final class
ByPairwiseScore
is used to filterSimilarityPairFeature
s by their score.static class
Filter by applying a nestedFeatureFilter
to the parent feature.static final class
Accept features that reside on a sequence with a particular name.static final class
Construct one of these to filter features by source.static final class
Construct one of these to filter features by type.static final class
A filter that returns all features contained within a location.static final class
Accept features with a given reading frame.static final class
Retrieve features that contain a given annotation with any value.static final class
A filter that returns all features not accepted by a child filter.static class
Accepts features where all immediate children meet the supplied filter.static class
Accepts features where all descendants meet the supplied filter.static final class
A filter that returns all features accepted by at least one child filter.static final class
A filter that returns all features overlapping a location.static final class
A filter that accepts all features whose shadow is contained by a specifiedLocation
.static final class
A filter that accepts all features whose shadow overlaps a specifiedLocation
.static final class
Accept features with a given strandedness. -
Field Summary
FieldsModifier and TypeFieldDescriptionstatic final FeatureFilter
All features are selected by this filter.static final FeatureFilter
A filter which accepts features with no childrenstatic final FeatureFilter
No features are selected by this filter.static final FeatureFilter
A filter which accepts only top-level Features. -
Method Summary
-
Field Details
-
all
All features are selected by this filter. -
none
No features are selected by this filter. -
top_level
A filter which accepts only top-level Features. This is true isgetParent()
returns aSequence
instance.- Since:
- 1.3
-
leaf
A filter which accepts features with no children- Since:
- 1.3
-
-
Method Details
-
accept
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
-