Package org.biojava.bio.seq
Class FeatureFilter.ByPairwiseScore
- java.lang.Object
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- org.biojava.bio.seq.FeatureFilter.ByPairwiseScore
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- All Implemented Interfaces:
Serializable
,FeatureFilter
,OptimizableFilter
- Enclosing interface:
- FeatureFilter
public static final class FeatureFilter.ByPairwiseScore extends Object implements OptimizableFilter
ByPairwiseScore
is used to filterSimilarityPairFeature
s by their score. Features are accepted if their score falls between the filter's minimum and maximum values, inclusive. Features are rejected if they are notSimilarityPairFeature
s. The minimum value accepted must be less than the maximum value.- Since:
- 1.3
- Author:
- Keith James
- 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 Constructor Description ByPairwiseScore(double minScore, double maxScore)
Creates a newByPairwiseScore
.
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description boolean
accept(Feature f)
Accept a Feature if it is an instance of SimilarityPairFeature and its score is <= filter's minimum score and >= filter's maximum score.boolean
equals(Object o)
double
getMaxScore()
getMaxScore
returns the maximum score accepted.double
getMinScore()
getMinScore
returns the minimum score accepted.int
hashCode()
boolean
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
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.String
toString()
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Constructor Detail
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ByPairwiseScore
public ByPairwiseScore(double minScore, double maxScore)
Creates a newByPairwiseScore
.- Parameters:
minScore
- adouble
.maxScore
- adouble
.
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Method Detail
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accept
public boolean accept(Feature f)
Accept a Feature if it is an instance of SimilarityPairFeature and its score is <= filter's minimum score and >= filter's maximum score.- Specified by:
accept
in interfaceFeatureFilter
- Parameters:
f
- aFeature
.- Returns:
- a
boolean
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getMinScore
public double getMinScore()
getMinScore
returns the minimum score accepted.- Returns:
- a
double
.
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getMaxScore
public double getMaxScore()
getMaxScore
returns the maximum score accepted.- Returns:
- a
double
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isProperSubset
public boolean isProperSubset(FeatureFilter sup)
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:
sup
- the potential super set- Returns:
- true if sup contains all features contained by this filter
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isDisjoint
public boolean isDisjoint(FeatureFilter filt)
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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