org.biojava.bio.seq.projection

Class ProjectedFeatureHolder

java.lang.Object

org.biojava.utils.AbstractChangeable

org.biojava.bio.seq.AbstractFeatureHolder

org.biojava.bio.seq.projection.ProjectedFeatureHolder

All Implemented Interfaces:

Serializable, FeatureHolder, Changeable

public final class ProjectedFeatureHolder
extends AbstractFeatureHolder
implements FeatureHolder, Serializable

Helper class for projecting Feature objects into an alternative coordinate system. This class offers a view onto a set of features, projecting them into a different coordinate system, and also changing their parent property. The destination coordinate system can run in the opposite direction from the source, in which case the strand property of StrandedFeatures is flipped.

The projected features returned by this class are small proxy objects. Proxy classes are autogenerated on demand for any sub-interface of Feature by the ProjectionEngine class.

Since:

1.1

Author:

Thomas Down, Matthew Pocock

See Also:

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 and Description
ProjectedFeatureHolder(ProjectionContext context)

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 templ) 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 ChangeEvent	forwardChangeEvent(ChangeEvent cev) Called internally to generate a forwarded version of a ChangeEvent from our underlying FeatureHolder
ProjectionContext	getContext()
FeatureFilter	getSchema() Return a schema-filter for this FeatureHolder.
protected FeatureHolder	makeProjectionSet(FeatureHolder fh) Called internally to construct a lightweight projected view of a set of features
void	removeFeature(Feature dyingChild) Remove a feature from this FeatureHolder.

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

ProjectedFeatureHolder

public ProjectedFeatureHolder(ProjectionContext context)

Method Detail

getContext

public ProjectionContext getContext()

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

Overrides:

filter in class AbstractFeatureHolder

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

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.

createFeature

public Feature createFeature(Feature.Template templ)
                      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

Overrides:

createFeature in class AbstractFeatureHolder

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 dyingChild)
                   throws ChangeVetoException,
                          BioException

Description copied from interface: FeatureHolder

Remove a feature from this FeatureHolder.

Specified by:

removeFeature in interface FeatureHolder

Overrides:

removeFeature in class AbstractFeatureHolder

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

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

makeProjectionSet

protected FeatureHolder makeProjectionSet(FeatureHolder fh)

Called internally to construct a lightweight projected view of a set of features

forwardChangeEvent

protected ChangeEvent forwardChangeEvent(ChangeEvent cev)

Called internally to generate a forwarded version of a ChangeEvent from our underlying FeatureHolder