Package org.biojava.bio.seq.projection

Class ReparentContext

java.lang.Object

org.biojava.bio.seq.projection.ReparentContext

All Implemented Interfaces:

Serializable, ProjectionContext

Direct Known Subclasses:

SimpleGappedSequence.GappedContext, SubSequence.SubProjectedFeatureContext, TranslateFlipContext

public class ReparentContext
extends Object
implements ProjectionContext, Serializable

A good base class to implement ProjectionContext from.

ReparentContext takes care of much of the ugliness of implementing ProjectionContext, such as handling listeners and grafting features onto a new parent. It also sets up a framework for mutating feature filters. Think carefully before overriding methods in this class.

Author:

Matthew Pocock, Thomas Down

See Also:

Serialized Form

Constructor Summary

Constructors

Constructor	Description
ReparentContext(FeatureHolder parent, FeatureHolder wrapped)

Method Summary

Modifier and Type	Method	Description
void	addChangeListener(Feature f, ChangeListener cl, ChangeType ct)	Add a ChangeListener to a projected feature.
Feature	createFeature(Feature.Template projTempl)	Create a projected feature with properties matching the template.
Feature	createFeature(Feature f, Feature.Template projTempl)	Create a new projected feature.
FeatureHolder	getParent()
FeatureHolder	getParent(Feature f)
protected FilterUtils.FilterTransformer	getReverter()
FeatureFilter	getSchema(Feature f)
Sequence	getSequence(Feature f)	Get the sequence for a feature.
protected FilterUtils.FilterTransformer	getTransformer()
FeatureHolder	getUnprojectedFeatures()	Get the features before projection.
FeatureHolder	projectChildFeatures(Feature f, FeatureHolder parent)	Project all features that are children of feature so that they become children of parent.
Feature	projectFeature(Feature feat)	Create a single projected feature using the rules of this ProjectedFeatureHolder.
FeatureHolder	projectFeatures(FeatureHolder fh)	Project all of the features in a FeatureHolder.
FeatureFilter	projectFilter(FeatureFilter ff)	Transform a filter on unprojected features so that it applies to projected features.
void	removeChangeListener(Feature f, ChangeListener cl, ChangeType ct)	Remove a ChangeListener from a projected feature.
void	removeFeature(Feature dyingChild)	Remove the dying child.
void	removeFeature(Feature f, Feature f2)	Remove the dying child.
Feature	revertFeature(Feature feat)	Unproject a feature.
FeatureFilter	revertFilter(FeatureFilter ff)	Transform a filter on projected features so that it applies to unprojected features.

Methods inherited from class java.lang.Object

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

Constructor Detail

ReparentContext

public ReparentContext(FeatureHolder parent,
                       FeatureHolder wrapped)

Method Detail

getParent

public final FeatureHolder getParent()

getUnprojectedFeatures

public final FeatureHolder getUnprojectedFeatures()

Description copied from interface: ProjectionContext

Get the features before projection.

If you are projecting all the features in some feature holder, that is what this method should return.

Specified by:

getUnprojectedFeatures in interface ProjectionContext

Returns:

the features before projection

projectFeature

public Feature projectFeature(Feature feat)

Create a single projected feature using the rules of this ProjectedFeatureHolder.

Specified by:

projectFeature in interface ProjectionContext

Parameters:

feat - the Feature to project

Returns:

a Feature representing feat after being transformed by this context

revertFeature

public Feature revertFeature(Feature feat)

Description copied from interface: ProjectionContext

Unproject a feature.

This is the inverse opperation to @link projectFeature().

Note: The result of calling this method for a feature that is not projected through this context is not specified by this API, but it is reasonable to assume that bad things will happen.

Specified by:

revertFeature in interface ProjectionContext

Parameters:

feat - the Feature to un-project

Returns:

the unprojected feature

projectFilter

public final FeatureFilter projectFilter(FeatureFilter ff)

Description copied from interface: ProjectionContext

Transform a filter on unprojected features so that it applies to projected features.

Specified by:

projectFilter in interface ProjectionContext

Parameters:

ff - the FeatureFilter to transform

Returns:

the transformed FeatureFilter

revertFilter

public final FeatureFilter revertFilter(FeatureFilter ff)

Description copied from interface: ProjectionContext

Transform a filter on projected features so that it applies to unprojected features.

Specified by:

revertFilter in interface ProjectionContext

Parameters:

ff - the FeatureFilter to transform

Returns:

the transformed FeatureFilter

getTransformer

protected FilterUtils.FilterTransformer getTransformer()

getReverter

protected FilterUtils.FilterTransformer getReverter()

getParent

public final FeatureHolder getParent(Feature f)

Specified by:

getParent in interface ProjectionContext

getSequence

public final Sequence getSequence(Feature f)

Description copied from interface: ProjectionContext

Get the sequence for a feature.

This will be the return value of projFeat.getParent().

Specified by:

getSequence in interface ProjectionContext

Parameters:

f - the projected Feature

Returns:

the Sequence of the Feature

projectChildFeatures

public FeatureHolder projectChildFeatures(Feature f,
                                          FeatureHolder parent)

Description copied from interface: ProjectionContext

Project all features that are children of feature so that they become children of parent.

Specified by:

projectChildFeatures in interface ProjectionContext

Parameters:

f - the Feature to project all children of

parent - the new parent feature holder

Returns:

a FeatureHolder containing projections of all children of feature so that f.getParent() is equal to parent

createFeature

public final Feature createFeature(Feature.Template projTempl)
                            throws BioException,
                                   ChangeVetoException

Description copied from interface: ProjectionContext

Create a projected feature with properties matching the template.

You will probably implement this by delegating to the unprojected feature holder. It is imperative that the template properties are unprojected first so that when the newly created feature is projected, the properties match up.

Not every projection context has fully reversible semantics. Use your discression and come up with a reasonable plan that causes least supprise to the user.

Specified by:

createFeature in interface ProjectionContext

Parameters:

projTempl - the Feature.Template to instantiate

Returns:

a new projected Feature matching the template as closely as possible

Throws:

BioException - if there was a problem instantiating the template

ChangeVetoException - if the feature creation was vetoed

removeFeature

public final void removeFeature(Feature dyingChild)
                         throws BioException,
                                ChangeVetoException

Description copied from interface: ProjectionContext

Remove the dying child.

Specified by:

removeFeature in interface ProjectionContext

Parameters:

dyingChild - a projected feature to remove

Throws:

BioException - if there is an error removing the feature

ChangeVetoException - if the removal of the feature was vetoed

createFeature

public final Feature createFeature(Feature f,
                                   Feature.Template projTempl)
                            throws BioException,
                                   ChangeVetoException

Description copied from interface: ProjectionContext

Create a new projected feature.

See the notes for @link createFeature(Feature.Template) for implementation advice.

Specified by:

createFeature in interface ProjectionContext

Parameters:

f - the parent for the newly created feature

projTempl - the Feature.Template specifying the new feature

Returns:

a new ProjectedFeature that is a child of projParent

Throws:

BioException - if there was a problem creating the feature

ChangeVetoException - if the creation of the feature was vetoed

removeFeature

public final void removeFeature(Feature f,
                                Feature f2)
                         throws ChangeVetoException,
                                BioException

Description copied from interface: ProjectionContext

Remove the dying child.

Specified by:

removeFeature in interface ProjectionContext

Parameters:

f - the projected parent Feature

f2 - the child Feature to remove

Throws:

ChangeVetoException - if the removal of the feature was vetoed

BioException

getSchema

public final FeatureFilter getSchema(Feature f)

addChangeListener

public final void addChangeListener(Feature f,
                                    ChangeListener cl,
                                    ChangeType ct)

Description copied from interface: ProjectionContext

Add a ChangeListener to a projected feature.

Specified by:

addChangeListener in interface ProjectionContext

Parameters:

f - the projected Feature to add the listener for

cl - the ChangeListener to add

ct - the ChangeType to register it for

removeChangeListener

public final void removeChangeListener(Feature f,
                                       ChangeListener cl,
                                       ChangeType ct)

Description copied from interface: ProjectionContext

Remove a ChangeListener from a projected feature.

Specified by:

removeChangeListener in interface ProjectionContext

Parameters:

f - the projected Feature to remove the listener for

cl - the ChangeListener to remove

ct - the ChangeType it is registered for

projectFeatures

public final FeatureHolder projectFeatures(FeatureHolder fh)

Description copied from interface: ProjectionContext

Project all of the features in a FeatureHolder.

Warning: The results of calling this method for features that are not in getUnprojectedFeatures() is not specified by this API, but it is reasonable to assume that bad things will happen.

Specified by:

projectFeatures in interface ProjectionContext

Parameters:

fh - the FeatureHolder containing the features to project

Returns:

a FeatureHolder containing all the features projected