Class SubSequence.SubProjectedFeatureContext
- All Implemented Interfaces:
Serializable
,ProjectionContext
- Enclosing class:
SubSequence
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:
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Method Summary
Modifier and TypeMethodDescriptionprotected FilterUtils.FilterTransformer
protected FilterUtils.FilterTransformer
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 thisProjectedFeatureHolder
.projectLocation
(Location toTransform) 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
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Method Details
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projectLocation
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projectFeature
Description copied from class:ReparentContext
Create a single projected feature using the rules of thisProjectedFeatureHolder
.- Specified by:
projectFeature
in interfaceProjectionContext
- Overrides:
projectFeature
in classReparentContext
- Parameters:
origFeat
- the Feature to project- Returns:
- a Feature representing feat after being transformed by this context
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revertFeature
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 interfaceProjectionContext
- Overrides:
revertFeature
in classReparentContext
- Parameters:
projFeat
- the Feature to un-project- Returns:
- the unprojected feature
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projectChildFeatures
Description copied from interface:ProjectionContext
Project all features that are children of feature so that they become children of parent.- Specified by:
projectChildFeatures
in interfaceProjectionContext
- Overrides:
projectChildFeatures
in classReparentContext
- Parameters:
f
- the Feature to project all children ofparent
- the new parent feature holder- Returns:
- a FeatureHolder containing projections of all children of feature so that f.getParent() is equal to parent
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getReverter
- Overrides:
getReverter
in classReparentContext
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getTransformer
- Overrides:
getTransformer
in classReparentContext
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