Package org.biojava.bio.seq

Class MergeFeatureHolder

java.lang.Object

org.biojava.utils.AbstractChangeable

org.biojava.bio.seq.AbstractFeatureHolder

org.biojava.bio.seq.MergeFeatureHolder

All Implemented Interfaces:

Serializable, FeatureHolder, Changeable

public class MergeFeatureHolder
extends AbstractFeatureHolder
implements Serializable

FeatureHolder which exposes all the features in a set of sub-FeatureHolders. This is provided primarily as a support class for ViewSequence. It may also be useful for other applications, such as simple distributed annotation systems.

Author:

Thomas Down, Matthew Pocock

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
MergeFeatureHolder()	Create a new, empty, MergeFeatureHolder.

Method Summary

Modifier and Type	Method	Description
void	addFeatureHolder(FeatureHolder fh)	Add an extra FeatureHolder to the set of FeatureHolders which are merged.
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 all the features in all child FeatureHolders.
FeatureHolder	filter(FeatureFilter ff, boolean recurse)	When applied to a MergeFeatureHolder, this filters each child FeatureHolder independently.
FeatureFilter	getSchema()	Return a schema-filter for this FeatureHolder.
void	removeFeatureHolder(FeatureHolder fh)	Remove a FeatureHolder from the set of FeatureHolders which are merged.

Methods inherited from class org.biojava.bio.seq.AbstractFeatureHolder

createFeature, filter, removeFeature

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

MergeFeatureHolder

public MergeFeatureHolder()

Create a new, empty, MergeFeatureHolder.

Method Detail

addFeatureHolder

public void addFeatureHolder(FeatureHolder fh)
                      throws ChangeVetoException

Add an extra FeatureHolder to the set of FeatureHolders which are merged. This method is provided for backward compatibility, and is equivalent to:

     mfh.addFeatureHolder(fh, FeatureFilter.all);
 

You should always use the two-arg version in preference if you are able to define the membership of a FeatureHolder.

Throws:

ChangeVetoException

removeFeatureHolder

public void removeFeatureHolder(FeatureHolder fh)
                         throws ChangeVetoException

Remove a FeatureHolder from the set of FeatureHolders which are merged.

Throws:

ChangeVetoException

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

features

public Iterator features()

Iterate over all the features in all child FeatureHolders. The Iterator may throw ConcurrantModificationException if there is a change in the underlying collections during iteration.

Specified by:

features in interface FeatureHolder

Returns:

an Iterator

filter

public FeatureHolder filter(FeatureFilter ff,
                            boolean recurse)

When applied to a MergeFeatureHolder, this filters each child FeatureHolder independently.

Specified by:

filter in interface FeatureHolder

Overrides:

filter in class AbstractFeatureHolder

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.

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