Package org.biojava.bio.seq
Class FeatureFilter.ByAnnotationType
- java.lang.Object
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- org.biojava.bio.seq.FeatureFilter.ByAnnotationType
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- All Implemented Interfaces:
Serializable
,FeatureFilter
,OptimizableFilter
- Direct Known Subclasses:
FeatureFilter.AnnotationContains
,FeatureFilter.ByAnnotation
,FeatureFilter.HasAnnotation
- Enclosing interface:
- FeatureFilter
public static class FeatureFilter.ByAnnotationType extends Object implements OptimizableFilter
A filter that returns all features that have an annotation bundle that is of a given annotation type.- Since:
- 1.3
- Author:
- Matthew Pocock, Thomas Down
- See Also:
- Serialized Form
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Nested Class Summary
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Nested classes/interfaces inherited from interface org.biojava.bio.seq.FeatureFilter
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
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Field Summary
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Fields inherited from interface org.biojava.bio.seq.FeatureFilter
all, leaf, none, top_level
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Constructor Summary
Constructors Modifier Constructor Description protected
ByAnnotationType()
ByAnnotationType(AnnotationType type)
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description boolean
accept(Feature f)
This method determines whether a feature is to be accepted.boolean
equals(Object o)
AnnotationType
getType()
int
hashCode()
boolean
isDisjoint(FeatureFilter filter)
Returns true if this filter is disjoint from filt - that is, there is no Feature that is accepted by both filters.boolean
isProperSubset(FeatureFilter filter)
Returns true if this filter is a proper subset of sup - that is, for every feature that matches this, it also matches sup.protected void
setType(AnnotationType type)
String
toString()
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Constructor Detail
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ByAnnotationType
protected ByAnnotationType()
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ByAnnotationType
public ByAnnotationType(AnnotationType type)
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Method Detail
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getType
public AnnotationType getType()
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setType
protected void setType(AnnotationType type)
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accept
public boolean accept(Feature f)
Description copied from interface:FeatureFilter
This method determines whether a feature is to be accepted.- Specified by:
accept
in interfaceFeatureFilter
- Parameters:
f
- the Feature to evaluate- Returns:
- true if this feature is to be selected in, or false if it is to be ignored
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isDisjoint
public boolean isDisjoint(FeatureFilter filter)
Description copied from interface:OptimizableFilter
Returns true if this filter is disjoint from filt - that is, there is no Feature that is accepted by both filters. The empty filter is disjoint from all other filters. The all filter is disjoint from none.- Specified by:
isDisjoint
in interfaceOptimizableFilter
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isProperSubset
public boolean isProperSubset(FeatureFilter filter)
Description copied from interface:OptimizableFilter
Returns true if this filter is a proper subset of sup - that is, for every feature that matches this, it also matches sup. The empty filter is a proper subset of all filters. All filters are a proper subset of the all filter. All filters are proper subsets of themselves.- Specified by:
isProperSubset
in interfaceOptimizableFilter
- Parameters:
filter
- the potential super set- Returns:
- true if sup contains all features contained by this filter
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