org.biojava.bio.seq.impl

Class SubSequence.SubProjectedFeatureContext

java.lang.Object

org.biojava.bio.seq.projection.ReparentContext

org.biojava.bio.seq.impl.SubSequence.SubProjectedFeatureContext

All Implemented Interfaces:

Serializable, ProjectionContext

Enclosing class:

SubSequence

public static class SubSequence.SubProjectedFeatureContext
extends ReparentContext

TargetContext that implements the mapping between the parent sequence and this sub-sequence.

This context is public because all contexts must be public, and not because it is usefull to you or part of the API. Don't use it directly.

The context extends TranslateFlipContext so that it can translate all features within the parent location to being from index 1 in the projection. It also transforms and reverts locations so that locations falling outside the parent location are trunchated and replaced by fuzzy locations. Lastly, features with fuzzy locations are replaced by RemoteFeature instances.

Since:

1.4

Author:

Matthew Pocock, Thomas Down

See Also:

Serialized Form

Method Summary

Modifier and Type	Method and Description
protected FilterUtils.FilterTransformer	getReverter()
protected FilterUtils.FilterTransformer	getTransformer()
FeatureHolder	projectChildFeatures(Feature f, FeatureHolder parent) Project all features that are children of feature so that they become children of parent.
Feature	projectFeature(Feature origFeat) Create a single projected feature using the rules of this ProjectedFeatureHolder.
Location	projectLocation(Location toTransform)
Feature	revertFeature(Feature projFeat) Unproject a feature.

Methods inherited from class org.biojava.bio.seq.projection.ReparentContext

addChangeListener, createFeature, createFeature, getParent, getParent, getSchema, getSequence, getUnprojectedFeatures, projectFeatures, projectFilter, removeChangeListener, removeFeature, removeFeature, revertFilter

Methods inherited from class java.lang.Object

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

Method Detail

projectLocation

public Location projectLocation(Location toTransform)

projectFeature

public Feature projectFeature(Feature origFeat)

Description copied from class: ReparentContext

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

Specified by:

projectFeature in interface ProjectionContext

Overrides:

projectFeature in class ReparentContext

Parameters:

origFeat - the Feature to project

Returns:

a Feature representing feat after being transformed by this context

revertFeature

public Feature revertFeature(Feature projFeat)

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

Overrides:

revertFeature in class ReparentContext

Parameters:

projFeat - the Feature to un-project

Returns:

the unprojected 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

Overrides:

projectChildFeatures in class ReparentContext

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

getReverter

protected FilterUtils.FilterTransformer getReverter()

Overrides:

getReverter in class ReparentContext

getTransformer

protected FilterUtils.FilterTransformer getTransformer()

Overrides:

getTransformer in class ReparentContext