org.biojava.bio.seq
Class FeatureFilter.ByPairwiseScore

java.lang.Object
  extended byorg.biojava.bio.seq.FeatureFilter.ByPairwiseScore
All Implemented Interfaces:
FeatureFilter, OptimizableFilter, java.io.Serializable
Enclosing class:
FeatureFilter

public static final class FeatureFilter.ByPairwiseScore
extends java.lang.Object
implements OptimizableFilter

ByPairwiseScore is used to filter SimilarityPairFeatures 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 not SimilarityPairFeatures. The minimum value accepted must be less than the maximum value.

Since:
1.3
Author:
Keith James
See Also:
Serialized Form

Nested Class Summary
 
Nested classes inherited from class 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
 
Field Summary
 
Fields inherited from interface org.biojava.bio.seq.FeatureFilter
all, leaf, none, top_level
 
Constructor Summary
FeatureFilter.ByPairwiseScore(double minScore, double maxScore)
          Creates a new ByPairwiseScore.
 
Method Summary
 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(java.lang.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.
 java.lang.String toString()
           
 
Methods inherited from class java.lang.Object
clone, finalize, getClass, notify, notifyAll, wait, wait, wait
 

Constructor Detail

FeatureFilter.ByPairwiseScore

public FeatureFilter.ByPairwiseScore(double minScore,
                                     double maxScore)
Creates a new ByPairwiseScore.

Parameters:
minScore - a double.
maxScore - a double.
Method Detail

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 interface FeatureFilter
Parameters:
f - a Feature.
Returns:
a boolean.

getMinScore

public double getMinScore()
getMinScore returns the minimum score accepted.

Returns:
a double.

getMaxScore

public double getMaxScore()
getMaxScore returns the maximum score accepted.

Returns:
a double.

equals

public boolean equals(java.lang.Object o)

hashCode

public int hashCode()

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 interface OptimizableFilter
Parameters:
sup - the potential super set
Returns:
true if sup contains all features contained by this filter

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 interface OptimizableFilter

toString

public java.lang.String toString()