org.biojava.bio.seq

Class FeatureFilter.ByPairwiseScore

java.lang.Object

org.biojava.bio.seq.FeatureFilter.ByPairwiseScore

All Implemented Interfaces:

java.io.Serializable, FeatureFilter, OptimizableFilter

Enclosing interface:

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/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

Field Summary

Fields inherited from interface org.biojava.bio.seq.FeatureFilter

all, leaf, none, top_level

Constructor Summary

Constructors

Constructor and Description
FeatureFilter.ByPairwiseScore(double minScore, double maxScore) Creates a new ByPairwiseScore.

Method Summary

Methods

Modifier and Type	Method and 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(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)

Overrides:

equals in class java.lang.Object

hashCode

public int hashCode()

Overrides:

hashCode in class java.lang.Object

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()

Overrides:

toString in class java.lang.Object