Package org.biojava.bio.seq

Class FeatureFilter.FrameFilter

java.lang.Object

org.biojava.bio.seq.FeatureFilter.FrameFilter

All Implemented Interfaces:

Serializable, FeatureFilter, OptimizableFilter

Enclosing interface:

FeatureFilter

public static final class FeatureFilter.FrameFilter
extends Object
implements OptimizableFilter

Accept features with a given reading frame.

Since:

1.2

Author:

Mark Schreiber

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
FrameFilter(FramedFeature.ReadingFrame frame)	Build a new filter that matches all features of a reading frame.

Method Summary

Modifier and Type	Method	Description
boolean	accept(Feature f)	Accept the Feature if it is an instance of FramedFeature and matches the value of getFrame().
boolean	equals(Object o)
FramedFeature.ReadingFrame	getFrame()	Retrieve the reading frame this filter 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.

Methods inherited from class java.lang.Object

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

Constructor Detail

FrameFilter

public FrameFilter(FramedFeature.ReadingFrame frame)

Build a new filter that matches all features of a reading frame.

Parameters:

frame - the ReadingFrame to match

Method Detail

getFrame

public FramedFeature.ReadingFrame getFrame()

Retrieve the reading frame this filter matches.

accept

public boolean accept(Feature f)

Accept the Feature if it is an instance of FramedFeature and matches the value of getFrame().

Specified by:

accept in interface FeatureFilter

Parameters:

f - the Feature to check

Returns:

true if the frame matches, or false otherwise

hashCode

public int hashCode()

Overrides:

hashCode in class Object

equals

public boolean equals(Object o)

Overrides:

equals 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