org.biojava.bio.seq

Class FeatureFilter.ShadowContainedByLocation

java.lang.Object

org.biojava.bio.seq.FeatureFilter.ShadowContainedByLocation

All Implemented Interfaces:

Serializable, FeatureFilter, OptimizableFilter

Enclosing interface:

FeatureFilter

public static final class FeatureFilter.ShadowContainedByLocation
extends Object
implements OptimizableFilter

A filter that accepts all features whose shadow is contained by a specified Location. The shadow is defined as the interval between the minimum and maximum positions of the feature's location. For features with contiguous locations, this filter is equivalent to FeatureFilter.ContainedByLocation.

Since:

1.3

Author:

Thomas Down

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.ShadowContainedByLocation(Location loc) Creates a filter that returns everything contained within loc.

Method Summary

Methods

Modifier and Type	Method and Description
boolean	accept(Feature f) Returns true if the feature is within this filter's location.
boolean	equals(Object o)
Location	getLocation()
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

FeatureFilter.ShadowContainedByLocation

public FeatureFilter.ShadowContainedByLocation(Location loc)

Creates a filter that returns everything contained within loc.

Parameters:

loc - the location that will contain the accepted features

Method Detail

getLocation

public Location getLocation()

accept

public boolean accept(Feature f)

Returns true if the feature is within this filter's location.

Specified by:

accept in interface FeatureFilter

Parameters:

f - the Feature to evaluate

Returns:

true if this feature is to be selected in, or false if it is to be ignored

equals

public boolean equals(Object o)

Overrides:

equals in class Object

hashCode

public int hashCode()

Overrides:

hashCode 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

toString

public String toString()

Overrides:

toString in class Object