org.biojava.bio.seq.projection

Class ProjectionEngine

java.lang.Object

org.biojava.bio.seq.projection.ProjectionEngine

public class ProjectionEngine
extends Object

Factory for proxy objects which project BioJava features into alternate coordinate systems. This class binds together a feature and a ProjectionContext object, and returns the resulting projected feature. New feature-projection wrapper classes are generated automatically as they are required. Don't use this class directly. This class contains deep voodoo code. Run away while you still can. You may find that for some bizaare reason you need to manually project a feature through a ProjectionContext. You should be using @link ProjectionContext.projectFeature(). If this is not practical for some reason, use this class. However, this probably indicates that you are doing something mad. Projected feature classes will be named as org.biojava.bio.seq.projection.{$ctxt}.{$feat} where $ctxt and $feat are the full class names of the context and feature respectively with each "." character replaced with "_". Delegate into this from your ProjectionContext to do the dirty work of actually projecting features from the underlying data. This factory generate a new class that is unique to the combination of your projection context and the Feature interface that the projected feature implements. Then, it will instantiate that class with your context and the underlying feature. The returned feature will currently be an implementation of the package-private class org.biojava.bio.seq.projection.ProjectedFeature, but this is implementation detail and should not be relied upon.

Since:

1.2

Author:

Thomas Down

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static interface	ProjectionEngine.Instantiator Internal helper class.
static interface	ProjectionEngine.TemplateProjector This is an interface for things that project feature templates.

Field Summary

Fields

Modifier and Type	Field and Description
static ProjectionEngine	DEFAULT The standard projection engine object.

Method Summary

Methods

Modifier and Type	Method and Description
Feature	projectFeature(Feature f, ProjectionContext ctx) Return a projection of Feature f into the system defined by a given ProjectionContext.
Feature.Template	revertTemplate(Feature.Template templ, ProjectionContext ctxt) Revert a template so that it can be used on the original feature-space.

Methods inherited from class java.lang.Object

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

Field Detail

DEFAULT

public static final ProjectionEngine DEFAULT

The standard projection engine object.

Method Detail

projectFeature

public Feature projectFeature(Feature f,
                     ProjectionContext ctx)

Return a projection of Feature f into the system defined by a given ProjectionContext. The returned object will implement the same Feature interface (sub-interface of Feature as the underlying feature, and will also implement the Projection interface.

revertTemplate

public Feature.Template revertTemplate(Feature.Template templ,
                              ProjectionContext ctxt)

Revert a template so that it can be used on the original feature-space.

This will use the revertFoo methods defined in the context to revert all of the transformed properties.

Parameters:

templ - the template to revert

ctxt - the context defining the reversion

Returns:

a new template of the same type as templ, with reverted fields