org.biojava.bio.seq
Class FeatureHolder.EmptyFeatureHolder

java.lang.Object
  extended by org.biojava.utils.Unchangeable
      extended by org.biojava.bio.seq.FeatureHolder.EmptyFeatureHolder
All Implemented Interfaces:
FeatureHolder, Changeable
Enclosing interface:
FeatureHolder

public static final class FeatureHolder.EmptyFeatureHolder
extends Unchangeable
implements FeatureHolder


Nested Class Summary
 
Nested classes/interfaces inherited from interface org.biojava.bio.seq.FeatureHolder
FeatureHolder.EmptyFeatureHolder
 
Field Summary
 
Fields inherited from interface org.biojava.bio.seq.FeatureHolder
EMPTY_FEATURE_HOLDER, FEATURES, SCHEMA
 
Constructor Summary
FeatureHolder.EmptyFeatureHolder()
           
 
Method Summary
 boolean containsFeature(Feature f)
          Check if the feature is present in this holder.
 int countFeatures()
          Count how many features are contained.
 Feature createFeature(Feature.Template f)
          Create a new Feature, and add it to this FeatureHolder.
 Iterator<Feature> features()
          Iterate over the features in no well defined order.
 FeatureHolder filter(FeatureFilter fc)
          Query this set of features using a supplied FeatureFilter.
 FeatureHolder filter(FeatureFilter fc, boolean recurse)
          Return a new FeatureHolder that contains all of the children of this one that passed the filter fc.
 FeatureFilter getSchema()
          Return a schema-filter for this FeatureHolder.
 void removeFeature(Feature f)
          Remove a feature from this FeatureHolder.
 
Methods inherited from class org.biojava.utils.Unchangeable
addChangeListener, addChangeListener, addForwarder, getForwarders, getListeners, isUnchanging, removeChangeListener, removeChangeListener, removeForwarder
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 
Methods inherited from interface org.biojava.utils.Changeable
addChangeListener, addChangeListener, isUnchanging, removeChangeListener, removeChangeListener
 

Constructor Detail

FeatureHolder.EmptyFeatureHolder

public FeatureHolder.EmptyFeatureHolder()
Method Detail

countFeatures

public int countFeatures()
Description copied from interface: FeatureHolder
Count how many features are contained.

Specified by:
countFeatures in interface FeatureHolder
Returns:
a positive integer or zero, equal to the number of features contained

features

public Iterator<Feature> features()
Description copied from interface: FeatureHolder
Iterate over the features in no well defined order.

Specified by:
features in interface FeatureHolder
Returns:
an Iterator

filter

public FeatureHolder filter(FeatureFilter fc,
                            boolean recurse)
Description copied from interface: FeatureHolder
Return a new FeatureHolder that contains all of the children of this one that passed the filter fc. This method is scheduled for deprecation. Use the 1-arg filter instead.

Specified by:
filter in interface FeatureHolder
Parameters:
fc - the FeatureFilter to apply
recurse - true if all features-of-features should be scanned, and a single flat collection of features returned, or false if just immediate children should be filtered.

filter

public FeatureHolder filter(FeatureFilter fc)
Description copied from interface: FeatureHolder
Query this set of features using a supplied FeatureFilter.

Specified by:
filter in interface FeatureHolder
Parameters:
fc - the FeatureFilter to apply.
Returns:
all features in this container which match filter.

createFeature

public Feature createFeature(Feature.Template f)
Description copied from interface: FeatureHolder
Create a new Feature, and add it to this FeatureHolder. This method will generally only work on Sequences, and on some Features which have been attached to Sequences.

Specified by:
createFeature in interface FeatureHolder

removeFeature

public void removeFeature(Feature f)
Description copied from interface: FeatureHolder
Remove a feature from this FeatureHolder.

Specified by:
removeFeature in interface FeatureHolder

containsFeature

public boolean containsFeature(Feature f)
Description copied from interface: FeatureHolder
Check if the feature is present in this holder.

Specified by:
containsFeature in interface FeatureHolder
Parameters:
f - the Feature to check
Returns:
true if f is in this set

getSchema

public FeatureFilter getSchema()
Description copied from interface: FeatureHolder
Return a schema-filter for this FeatureHolder. This is a filter which all Features immediately contained by this FeatureHolder will match. It need not directly match their child features, but it can (and should!) provide information about them using FeatureFilter.OnlyChildren filters. In cases where there is no feature hierarchy, this can be indicated by including FeatureFilter.leaf in the schema filter.

For the truly non-informative case, it is possible to return FeatureFilter.all. However, it is almost always possible to provide slightly more information that this. For example, Sequence objects should, at a minimum, return FeatureFilter.top_level. Feature objects should, as a minimum, return FeatureFilter.ByParent(new FeatureFilter.ByFeature(this)).

Specified by:
getSchema in interface FeatureHolder
Returns:
the schema filter