org.biojava.bio.seq.impl
Class LazyFilterFeatureHolder

java.lang.Object
  org.biojava.bio.seq.impl.LazyFilterFeatureHolder

All Implemented Interfaces:

FeatureHolder, Changeable

public class LazyFilterFeatureHolder
extends Object
implements FeatureHolder

FeatureHolder which lazily applies a specified filter to another FeatureHolder. This means that when you use a second filter to query the LazyFilterFeatureHolder, the underlying holder receives a single filter request with the two queries ANDed together.

Since:

1.3

Author:

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

LazyFilterFeatureHolder(FeatureHolder fh, FeatureFilter ff)

Method Summary

void	addChangeListener(ChangeListener cl) Add a listener that will be informed of all changes.
void	addChangeListener(ChangeListener cl, ChangeType ct) Add a listener that will be informed of changes of a given type.
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 temp) Create a new Feature, and add it to this FeatureHolder.
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 ChangeSupport	getChangeSupport()
FeatureFilter	getSchema() Return a schema-filter for this FeatureHolder.
protected boolean	hasListeners()
boolean	isUnchanging(ChangeType ct) A particular ChangeType can never be raised by this Changeable.
void	removeChangeListener(ChangeListener cl) Remove a listener that was interested in all types of changes.
void	removeChangeListener(ChangeListener cl, ChangeType ct) Remove a listener that was interested in a specific types of changes.
void	removeFeature(Feature f) Remove a feature from this FeatureHolder.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

LazyFilterFeatureHolder

public LazyFilterFeatureHolder(FeatureHolder fh,
                               FeatureFilter ff)

Method Detail

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

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

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 temp)
                      throws ChangeVetoException,
                             BioException

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:

ChangeVetoException - if this FeatureHolder does not support creation of new features, or if the change was vetoed

BioException - if something went wrong during creating the feature

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

hasListeners

protected boolean hasListeners()

getChangeSupport

protected ChangeSupport getChangeSupport()

addChangeListener

public final void addChangeListener(ChangeListener cl)

Description copied from interface: Changeable

Add a listener that will be informed of all changes.

Specified by:

addChangeListener in interface Changeable

Parameters:

cl - the ChangeListener to add

addChangeListener

public final void addChangeListener(ChangeListener cl,
                                    ChangeType ct)

Description copied from interface: Changeable

Add a listener that will be informed of changes of a given type.

Specified by:

addChangeListener in interface Changeable

Parameters:

cl - the ChangeListener

ct - the ChangeType it is to be informed of

removeChangeListener

public final void removeChangeListener(ChangeListener cl)

Description copied from interface: Changeable

Remove a listener that was interested in all types of changes.

Specified by:

removeChangeListener in interface Changeable

Parameters:

cl - a ChangeListener to remove

removeChangeListener

public final void removeChangeListener(ChangeListener cl,
                                       ChangeType ct)

Description copied from interface: Changeable

Remove a listener that was interested in a specific types of changes.

Specified by:

removeChangeListener in interface Changeable

Parameters:

cl - a ChangeListener to remove

ct - the ChangeType that it was interested in

isUnchanging

public boolean isUnchanging(ChangeType ct)

Description copied from interface: Changeable

A particular ChangeType can never be raised by this Changeable.

If this returns true, then it is guaranteed that change events of this type (and all child types) can never under any circumstances be fired by this Changeable instance. If it returns false, that does not mean that this type of event will or even can be raised, but that it is worth registering listeners incase.

Specified by:

isUnchanging in interface Changeable

Parameters:

ct - the ChangeType to check

Returns:

true if ChangeEvents of this type are guaranteed to never be fired

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