Package org.biojava.bio.seq

Class FeatureFilter.StrandFilter

java.lang.Object

org.biojava.bio.seq.FeatureFilter.StrandFilter

All Implemented Interfaces:

Serializable, FeatureFilter, OptimizableFilter

Enclosing interface:

FeatureFilter

public static final class FeatureFilter.StrandFilter
extends Object
implements OptimizableFilter

Accept features with a given strandedness.

Since:

1.1

Author:

Matthew Pocock

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	Description
StrandFilter(StrandedFeature.Strand strand)	Build a new filter that matches all features of a given strand.

Method Summary

Modifier and Type	Method	Description
boolean	accept(Feature f)	Accept the Feature if it is an instance of StrandedFeature and matches the value of getStrand().
boolean	equals(Object o)
StrandedFeature.Strand	getStrand()	Retrieve the strand this matches.
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()

Methods inherited from class java.lang.Object

clone, finalize, getClass, notify, notifyAll, wait, wait, wait

Constructor Detail

StrandFilter

public StrandFilter(StrandedFeature.Strand strand)

Build a new filter that matches all features of a given strand.

Parameters:

strand - the Strand to match

Method Detail

getStrand

public StrandedFeature.Strand getStrand()

Retrieve the strand this matches.

Returns:

the Strand matched

accept

public boolean accept(Feature f)

Accept the Feature if it is an instance of StrandedFeature and matches the value of getStrand().

Specified by:

accept in interface FeatureFilter

Parameters:

f - the Feature to check

Returns:

true if the strand matches, or false otherwise

equals

public boolean equals(Object o)

Overrides:

equals in class Object

hashCode

public int hashCode()

Overrides:

hashCode in class Object

toString

public String toString()

Overrides:

toString in class 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