org.biojava.bio.seq

Class FeatureFilter.ByAnnotationType

java.lang.Object

org.biojava.bio.seq.FeatureFilter.ByAnnotationType

All Implemented Interfaces:

java.io.Serializable, FeatureFilter, OptimizableFilter

Direct Known Subclasses:

FeatureFilter.AnnotationContains, FeatureFilter.ByAnnotation, FeatureFilter.HasAnnotation

Enclosing interface:

FeatureFilter

public static class FeatureFilter.ByAnnotationType
extends java.lang.Object
implements OptimizableFilter

A filter that returns all features that have an annotation bundle that is of a given annotation type.

Since:

1.3

Author:

Matthew Pocock, 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

Modifier	Constructor and Description
protected	FeatureFilter.ByAnnotationType()
	FeatureFilter.ByAnnotationType(AnnotationType type)

Method Summary

Methods

Modifier and Type	Method and Description
boolean	accept(Feature f) This method determines whether a feature is to be accepted.
boolean	equals(java.lang.Object o)
AnnotationType	getType()
int	hashCode()
boolean	isDisjoint(FeatureFilter filter) Returns true if this filter is disjoint from filt - that is, there is no Feature that is accepted by both filters.
boolean	isProperSubset(FeatureFilter filter) Returns true if this filter is a proper subset of sup - that is, for every feature that matches this, it also matches sup.
protected void	setType(AnnotationType type)
java.lang.String	toString()

Methods inherited from class java.lang.Object

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

Constructor Detail

FeatureFilter.ByAnnotationType

protected FeatureFilter.ByAnnotationType()

FeatureFilter.ByAnnotationType

public FeatureFilter.ByAnnotationType(AnnotationType type)

Method Detail

getType

public AnnotationType getType()

setType

protected void setType(AnnotationType type)

accept

public boolean accept(Feature f)

Description copied from interface: FeatureFilter

This method determines whether a feature is to be accepted.

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(java.lang.Object o)

Overrides:

equals in class java.lang.Object

hashCode

public int hashCode()

Overrides:

hashCode in class java.lang.Object

isDisjoint

public boolean isDisjoint(FeatureFilter filter)

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

isProperSubset

public boolean isProperSubset(FeatureFilter filter)

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:

filter - the potential super set

Returns:

true if sup contains all features contained by this filter

toString

public java.lang.String toString()

Overrides:

toString in class java.lang.Object