Package org.biojava.bio.seq

Class FeatureHolder.EmptyFeatureHolder

java.lang.Object

org.biojava.utils.Unchangeable

org.biojava.bio.seq.FeatureHolder.EmptyFeatureHolder

All Implemented Interfaces:

FeatureHolder, Changeable

Enclosing interface:

FeatureHolder

public static final class FeatureHolder.EmptyFeatureHolder
extends Unchangeable
implements FeatureHolder

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
EmptyFeatureHolder()

Method Summary

Modifier and Type	Method	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 f)	Create a new Feature, and add it to this FeatureHolder.
Iterator<Feature>	features()	Iterate over the features in no well defined order.
FeatureHolder	filter(FeatureFilter fc)	Query this set of features using a supplied FeatureFilter.
FeatureHolder	filter(FeatureFilter fc, boolean recurse)	Return a new FeatureHolder that contains all of the children of this one that passed the filter fc.
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.Unchangeable

addChangeListener, addChangeListener, addForwarder, getForwarders, getListeners, isUnchanging, removeChangeListener, removeChangeListener, removeForwarder

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

EmptyFeatureHolder

public EmptyFeatureHolder()

Method Detail

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

filter

public FeatureHolder filter(FeatureFilter fc,
                            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:

fc - 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.

filter

public FeatureHolder filter(FeatureFilter fc)

Description copied from interface: FeatureHolder

Query this set of features using a supplied FeatureFilter.

Specified by:

filter in interface FeatureHolder

Parameters:

fc - the FeatureFilter to apply.

Returns:

all features in this container which match filter.

createFeature

public Feature createFeature(Feature.Template f)

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

removeFeature

public void removeFeature(Feature f)

Description copied from interface: FeatureHolder

Remove a feature from this FeatureHolder.

Specified by:

removeFeature in interface FeatureHolder

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