org.biojava.bio.seq
Class AbstractFeatureHolder
java.lang.Object
org.biojava.utils.AbstractChangeable
org.biojava.bio.seq.AbstractFeatureHolder
- All Implemented Interfaces:
- Changeable, FeatureHolder
- 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
Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
AbstractFeatureHolder
public AbstractFeatureHolder()
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 applyrecurse
- 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
- 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