org.biojava.bio.seq
Class FeatureFilter.ByAnnotationType

java.lang.Object
  extended byorg.biojava.bio.seq.FeatureFilter.ByAnnotationType
All Implemented Interfaces:
FeatureFilter, OptimizableFilter, java.io.Serializable
Direct Known Subclasses:
FeatureFilter.AnnotationContains, FeatureFilter.ByAnnotation, FeatureFilter.HasAnnotation
Enclosing class:
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 inherited from class 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
protected FeatureFilter.ByAnnotationType()
           
  FeatureFilter.ByAnnotationType(AnnotationType type)
           
 
Method Summary
 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)

hashCode

public int hashCode()

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()