org.biojava.bio.seq
Class AbstractFeatureHolder

java.lang.Object
  extended by org.biojava.utils.AbstractChangeable
      extended by org.biojava.bio.seq.AbstractFeatureHolder
All Implemented Interfaces:
FeatureHolder, Changeable
Direct Known Subclasses:
MergeFeatureHolder, ProjectedFeatureHolder, SimpleFeatureHolder

public abstract class AbstractFeatureHolder
extends AbstractChangeable
implements FeatureHolder

An abstract implementation of FeatureHolder. This provides the filter method, but who wants to code that more than once? It also has support for the ChangeEvents.

Author:
Matthew Pocock, Thomas Down

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
AbstractFeatureHolder()
           
 
Method Summary
 Feature createFeature(Feature.Template temp)
          Create a new Feature, and add it to this FeatureHolder.
 FeatureHolder filter(FeatureFilter filter)
          Query this set of features using a supplied FeatureFilter.
 FeatureHolder filter(FeatureFilter ff, boolean recurse)
          Return a new FeatureHolder that contains all of the children of this one that passed the filter fc.
 void removeFeature(Feature f)
          Remove a feature from this FeatureHolder.
 
Methods inherited from class org.biojava.utils.AbstractChangeable
addChangeListener, addChangeListener, generateChangeSupport, getChangeSupport, hasListeners, hasListeners, isUnchanging, removeChangeListener, removeChangeListener
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 
Methods inherited from interface org.biojava.bio.seq.FeatureHolder
containsFeature, countFeatures, features, getSchema
 
Methods inherited from interface org.biojava.utils.Changeable
addChangeListener, addChangeListener, isUnchanging, removeChangeListener, removeChangeListener
 

Constructor Detail

AbstractFeatureHolder

public AbstractFeatureHolder()
Method Detail

filter

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

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

filter

public FeatureHolder filter(FeatureFilter ff,
                            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:
ff - 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.

createFeature

public Feature createFeature(Feature.Template temp)
                      throws BioException,
                             ChangeVetoException
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
Throws:
BioException - if something went wrong during creating the feature
ChangeVetoException - if this FeatureHolder does not support creation of new features, or if the change was vetoed

removeFeature

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

Specified by:
removeFeature in interface FeatureHolder
Throws:
ChangeVetoException - if this FeatureHolder does not support feature removal or if the change was vetoed
BioException - if there was an error removing the feature