Interface FeatureHolder

All Superinterfaces:
Changeable
All Known Subinterfaces:
ComponentFeature, Feature, FramedFeature, GappedSequence, HomologyFeature, RealizingFeatureHolder, RemoteFeature, RestrictionSite, RichFeature, RichSequence, Sequence, SimilarityPairFeature, StrandedFeature
All Known Implementing Classes:
AbstractFeatureHolder, CircularView, DummySequence, FeatureHolder.EmptyFeatureHolder, LazyFeatureHolder, LazyFilterFeatureHolder, MergeFeatureHolder, NewSimpleAssembly, PhredSequence, ProjectedFeature, ProjectedFeatureHolder, RevCompSequence, SimpleAssembly, SimpleFeature, SimpleFeatureHolder, SimpleFramedFeature, SimpleGappedSequence, SimpleHomologyFeature, SimpleRemoteFeature, SimpleRestrictionSite, SimpleRichFeature, SimpleRichSequence, SimpleSequence, SimpleSimilarityPairFeature, SimpleStrandedFeature, SubSequence, ThinRichSequence, ViewSequence

public interface FeatureHolder extends Changeable
The interface for objects that contain features.

Feature holders abstract the containment of a feature from the objects that implements both the real container or the features. FeatureHolders are like sets of features.

Author:
Matthew Pocock, Thomas Down
See Also:
  • Field Details

  • Method Details

    • countFeatures

      Count how many features are contained.
      Returns:
      a positive integer or zero, equal to the number of features contained
    • features

      Iterate over the features in no well defined order.
      Returns:
      an Iterator
    • filter

      FeatureHolder filter(FeatureFilter fc, boolean recurse)
      Return a new FeatureHolder that contains all of the children of this one that passed the filter fc. This method is scheduled for deprecation. Use the 1-arg filter instead.
      Parameters:
      fc - the FeatureFilter to apply
      recurse - true if all features-of-features should be scanned, and a single flat collection of features returned, or false if just immediate children should be filtered.
    • filter

      Query this set of features using a supplied FeatureFilter.
      Parameters:
      filter - the FeatureFilter to apply.
      Returns:
      all features in this container which match filter.
    • createFeature

      Create a new Feature, and add it to this FeatureHolder. This method will generally only work on Sequences, and on some Features which have been attached to Sequences.
      Throws:
      BioException - if something went wrong during creating the feature
      ChangeVetoException - if this FeatureHolder does not support creation of new features, or if the change was vetoed
    • removeFeature

      Remove a feature from this FeatureHolder.
      Throws:
      ChangeVetoException - if this FeatureHolder does not support feature removal or if the change was vetoed
      BioException - if there was an error removing the feature
    • containsFeature

      Check if the feature is present in this holder.
      Parameters:
      f - the Feature to check
      Returns:
      true if f is in this set
      Since:
      1.2
    • getSchema

      Return a schema-filter for this FeatureHolder. This is a filter which all Features immediately contained by this FeatureHolder will match. It need not directly match their child features, but it can (and should!) provide information about them using FeatureFilter.OnlyChildren filters. In cases where there is no feature hierarchy, this can be indicated by including FeatureFilter.leaf in the schema filter.

      For the truly non-informative case, it is possible to return FeatureFilter.all. However, it is almost always possible to provide slightly more information that this. For example, Sequence objects should, at a minimum, return FeatureFilter.top_level. Feature objects should, as a minimum, return FeatureFilter.ByParent(new FeatureFilter.ByFeature(this)).

      Returns:
      the schema filter
      Since:
      1.3