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java.lang.Objectorg.biojava.bio.seq.projection.ReparentContext
org.biojava.bio.seq.impl.SubSequence.SubProjectedFeatureContext
public static class SubSequence.SubProjectedFeatureContext
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.
Method Summary | |
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protected FilterUtils.FilterTransformer |
getReverter()
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protected FilterUtils.FilterTransformer |
getTransformer()
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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)
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Feature |
revertFeature(Feature projFeat)
Unproject a feature. |
Methods inherited from class org.biojava.bio.seq.projection.ReparentContext |
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addChangeListener, createFeature, createFeature, getParent, getParent, getSchema, getSequence, getUnprojectedFeatures, projectFeatures, projectFilter, removeChangeListener, removeFeature, removeFeature, revertFilter |
Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Method Detail |
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public Location projectLocation(Location toTransform)
public Feature projectFeature(Feature origFeat)
ReparentContext
ProjectedFeatureHolder
.
projectFeature
in interface ProjectionContext
projectFeature
in class ReparentContext
origFeat
- the Feature to project
public Feature revertFeature(Feature projFeat)
ProjectionContext
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.
revertFeature
in interface ProjectionContext
revertFeature
in class ReparentContext
projFeat
- the Feature to un-project
public FeatureHolder projectChildFeatures(Feature f, FeatureHolder parent)
ProjectionContext
projectChildFeatures
in interface ProjectionContext
projectChildFeatures
in class ReparentContext
f
- the Feature to project all children ofparent
- the new parent feature holder
protected FilterUtils.FilterTransformer getReverter()
getReverter
in class ReparentContext
protected FilterUtils.FilterTransformer getTransformer()
getTransformer
in class ReparentContext
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