Package org.biojava.bio.seq

Class SimpleFeatureHolder

java.lang.Object

org.biojava.utils.AbstractChangeable

org.biojava.bio.seq.AbstractFeatureHolder

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:

RichFeatureRelationshipHolder, 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

Constructors

Constructor	Description
SimpleFeatureHolder()	Construct a new SimpleFeatureHolder with a non-informative schema.
SimpleFeatureHolder(FeatureFilter schema)	Construct a new SimpleFeatureHolder with the specified schema.

Method Summary

Modifier and Type	Method	Description
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<Feature>	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<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

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