- Enclosing class:
public static class SubSequence.SubProjectedFeatureContext extends ReparentContextTargetContext 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.
- Matthew Pocock, Thomas Down
- See Also:
- Serialized Form
All Methods Instance Methods Concrete Methods Modifier and Type Method Description
projectChildFeatures(Feature f, FeatureHolder parent)Project all features that are children of feature so that they become children of parent.
projectFeature(Feature origFeat)Create a single projected feature using the rules of this
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
public Feature projectFeature(Feature origFeat)Description copied from class:
ReparentContextCreate a single projected feature using the rules of this
public Feature revertFeature(Feature projFeat)Description copied from interface:
ProjectionContextUnproject 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.
public FeatureHolder projectChildFeatures(Feature f, FeatureHolder parent)Description copied from interface:
ProjectionContextProject all features that are children of feature so that they become children of parent.
- Specified by:
f- the Feature to project all children of
parent- the new parent feature holder
- a FeatureHolder containing projections of all children of feature so that f.getParent() is equal to parent
protected FilterUtils.FilterTransformer getReverter()