org.biojava.bio.seq

Class LazyFeatureHolder

java.lang.Object

org.biojava.utils.AbstractChangeable

org.biojava.bio.seq.LazyFeatureHolder

All Implemented Interfaces:

FeatureHolder, Changeable

public abstract class LazyFeatureHolder
extends AbstractChangeable
implements FeatureHolder

Wrapper implementation of FeatureHolder which calls a method to create a contained FeatureHolder on demand. This is an abstract class and is normally used like: FeatureHolder fh = new LazyFeatureHolder() { protected FeatureHolder createFeatureHolder() { SimpleFeatureHolder features = new SimpleFeatureHolder(); // Create some features in here... return features; } } ;

Since:

1.2

Author:

Thomas Down, Matthew Pocock

See Also:

RichFeatureRelationshipHolder

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

Modifier	Constructor and Description
protected	LazyFeatureHolder() Construct a LazyFeatureHolder with the schema of its contained featureholder
protected	LazyFeatureHolder(FeatureFilter schema) Construct a LazyFeatureHolder with the specified schema

Method Summary

Modifier and Type	Method and Description
boolean	containsFeature(Feature f) Check if the feature is present in this holder.
int	countFeatures() Count how many features are contained.
Feature	createFeature(Feature.Template template) Create a new Feature, and add it to this FeatureHolder.
protected abstract FeatureHolder	createFeatureHolder()
Iterator	features() Iterate over the features in no well defined order.
FeatureHolder	filter(FeatureFilter ff) 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.
protected void	flushFeatures()
protected ChangeSupport	getChangeSupport(ChangeType ct) Called to retrieve the ChangeSupport for this object.
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.utils.AbstractChangeable

addChangeListener, addChangeListener, generateChangeSupport, 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

LazyFeatureHolder

protected LazyFeatureHolder()

Construct a LazyFeatureHolder with the schema of its contained featureholder

LazyFeatureHolder

protected LazyFeatureHolder(FeatureFilter schema)

Construct a LazyFeatureHolder with the specified schema

Method Detail

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

createFeatureHolder

protected abstract FeatureHolder createFeatureHolder()

flushFeatures

protected void flushFeatures()

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

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

filter

public FeatureHolder filter(FeatureFilter ff)

Description copied from interface: FeatureHolder

Query this set of features using a supplied FeatureFilter.

Specified by:

filter in interface FeatureHolder

Parameters:

ff - 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 template)
                      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

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

getChangeSupport

protected ChangeSupport getChangeSupport(ChangeType ct)

Description copied from class: AbstractChangeable

Called to retrieve the ChangeSupport for this object.

Your implementation of this method should have the following structure:

 ChangeSupport cs = super.getChangeSupport(ct);

 if(someForwarder == null && ct.isMatching(SomeInterface.SomeChangeType)) {
   someForwarder = new ChangeForwarder(...

   this.stateVariable.addChangeListener(someForwarder, VariableInterface.AChange);
 }

 return cs;
 

It is usual for the forwarding listeners (someForwarder in this example) to be transient and lazily instantiated. Be sure to register & unregister the forwarder in the code that does the ChangeEvent handling in setter methods.

Overrides:

getChangeSupport in class AbstractChangeable