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	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.

Field Summary

Fields
Modifier and Type	Field	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

All Methods Instance Methods Abstract Methods
Modifier and Type Method 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

Interface FeatureFilter

Nested Class Summary

Field Summary

Method Summary

Field Detail

all

none

top_level

leaf

Method Detail

accept