Package org.biojava.bio.seq

Class AbstractFeatureHolder

java.lang.Object

org.biojava.utils.AbstractChangeable

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

Constructors

Constructor	Description
AbstractFeatureHolder()

Method Summary

Modifier and Type	Method	Description
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.utils.Changeable

addChangeListener, addChangeListener, isUnchanging, removeChangeListener, removeChangeListener

Methods inherited from interface org.biojava.bio.seq.FeatureHolder

containsFeature, countFeatures, features, getSchema

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