org.biojava.bio.seq
Class SimpleFeatureHolder

java.lang.Object
  extended by org.biojava.utils.AbstractChangeable
      extended by org.biojava.bio.seq.AbstractFeatureHolder
          extended by org.biojava.bio.seq.SimpleFeatureHolder
All Implemented Interfaces:
Serializable, FeatureHolder, Changeable

public class SimpleFeatureHolder
extends AbstractFeatureHolder
implements Serializable

A no-frills implementation of FeatureHolder.

Author:
Matthew Pocock, Thomas Down
See Also:
RichFeatureHolder, Serialized Form

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
SimpleFeatureHolder()
          Construct a new SimpleFeatureHolder with a non-informative schema.
SimpleFeatureHolder(FeatureFilter schema)
          Construct a new SimpleFeatureHolder with the specified schema.
 
Method Summary
 void addFeature(Feature f)
          Add a feature to the featureholder
 boolean containsFeature(Feature f)
          Check if the feature is present in this holder.
 int countFeatures()
          Count how many features are contained.
 Iterator features()
          Iterate over the features in no well defined order.
protected  List getFeatures()
          Returns the list of features in this featureholder.
 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.bio.seq.AbstractFeatureHolder
createFeature, filter, filter
 
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
 

Constructor Detail

SimpleFeatureHolder

public SimpleFeatureHolder()
Construct a new SimpleFeatureHolder with a non-informative schema.


SimpleFeatureHolder

public SimpleFeatureHolder(FeatureFilter schema)
Construct a new SimpleFeatureHolder with the specified schema.

Method Detail

getFeatures

protected List getFeatures()
Returns the list of features in this featureholder.


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 features()
Description copied from interface: FeatureHolder
Iterate over the features in no well defined order.

Specified by:
features in interface FeatureHolder
Returns:
an Iterator

addFeature

public void addFeature(Feature f)
                throws ChangeVetoException
Add a feature to the featureholder

Throws:
ChangeVetoException

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
Overrides:
removeFeature in class AbstractFeatureHolder
Throws:
ChangeVetoException - if this FeatureHolder does not support feature removal or if the change was vetoed

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