org.biojava.bio.seq

Interface FeatureHolder

All Superinterfaces:

Changeable

All Known Subinterfaces:

ComponentFeature, Feature, FramedFeature, GappedSequence, HomologyFeature, RealizingFeatureHolder, RemoteFeature, RestrictionSite, RichFeature, RichSequence, Sequence, SimilarityPairFeature, StrandedFeature

All Known Implementing Classes:

AbstractFeatureHolder, CircularView, DummySequence, FeatureHolder.EmptyFeatureHolder, LazyFeatureHolder, LazyFilterFeatureHolder, MergeFeatureHolder, NewSimpleAssembly, PhredSequence, ProjectedFeature, ProjectedFeatureHolder, RevCompSequence, SimpleAssembly, SimpleFeature, SimpleFeatureHolder, SimpleFramedFeature, SimpleGappedSequence, SimpleHomologyFeature, SimpleRemoteFeature, SimpleRestrictionSite, SimpleRichFeature, SimpleRichSequence, SimpleSequence, SimpleSimilarityPairFeature, SimpleStrandedFeature, SubSequence, ThinRichSequence, ViewSequence

public interface FeatureHolder
extends Changeable

The interface for objects that contain features.

Feature holders abstract the containment of a feature from the objects that implements both the real container or the features. FeatureHolders are like sets of features.

Author:

Matthew Pocock, Thomas Down

See Also:

RichFeatureRelationshipHolder

Nested Class Summary

Nested Classes

Modifier and Type	Interface and Description
static class	FeatureHolder.EmptyFeatureHolder

Field Summary

Fields

Modifier and Type	Field and Description
static FeatureHolder	EMPTY_FEATURE_HOLDER
static ChangeType	FEATURES Signals that features have been added or removed directly within this FeatureHolder.
static ChangeType	SCHEMA Signals that the schema of this FeatureHolder has changed.

Method Summary

Methods

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 ft) 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 filter) 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 interface org.biojava.utils.Changeable

addChangeListener, addChangeListener, isUnchanging, removeChangeListener, removeChangeListener

Field Detail

FEATURES

static final ChangeType FEATURES

Signals that features have been added or removed directly within this FeatureHolder.

SCHEMA

static final ChangeType SCHEMA

Signals that the schema of this FeatureHolder has changed.

Since:

1.3

EMPTY_FEATURE_HOLDER

static final FeatureHolder EMPTY_FEATURE_HOLDER

Method Detail

countFeatures

int countFeatures()

Count how many features are contained.

Returns:

a positive integer or zero, equal to the number of features contained

features

Iterator<Feature> features()

Iterate over the features in no well defined order.

Returns:

an Iterator

filter

FeatureHolder filter(FeatureFilter fc,
                   boolean recurse)

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.

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

FeatureHolder filter(FeatureFilter filter)

Query this set of features using a supplied FeatureFilter.

Parameters:

filter - the FeatureFilter to apply.

Returns:

all features in this container which match filter.

createFeature

Feature createFeature(Feature.Template ft)
                      throws BioException,
                             ChangeVetoException

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.

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

void removeFeature(Feature f)
                   throws ChangeVetoException,
                          BioException

Remove a feature from this 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

boolean containsFeature(Feature f)

Check if the feature is present in this holder.

Parameters:

f - the Feature to check

Returns:

true if f is in this set

Since:

1.2

getSchema

FeatureFilter getSchema()

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)).

Returns:

the schema filter

Since:

1.3