Package org.biojava.bio.seq

Class FeatureHolder.EmptyFeatureHolder

java.lang.Object
org.biojava.utils.Unchangeable
org.biojava.bio.seq.FeatureHolder.EmptyFeatureHolder
All Implemented Interfaces:
FeatureHolder, Changeable
Enclosing interface:
FeatureHolder
public static final class FeatureHolder.EmptyFeatureHolder extends Unchangeable implements FeatureHolder

  • Constructor Details

  • Method Details

    • countFeatures

      public int countFeatures()
      Description copied from interface: FeatureHolder
      Count how many features are contained.
      Specified by:
      countFeatures in interface FeatureHolder
      Returns:
      a positive integer or zero, equal to the number of features contained

    • features

      public Iterator<Feature> features()
      Description copied from interface: FeatureHolder
      Iterate over the features in no well defined order.
      Specified by:
      features in interface FeatureHolder
      Returns:
      an Iterator

    • filter

      public FeatureHolder filter(FeatureFilter fc, boolean recurse)
      Description copied from interface: FeatureHolder
      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.
      Specified by:
      filter in interface FeatureHolder
      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

      public FeatureHolder filter(FeatureFilter fc)
      Description copied from interface: FeatureHolder
      Query this set of features using a supplied FeatureFilter.
      Specified by:
      filter in interface FeatureHolder
      Parameters:
      fc - the FeatureFilter to apply.
      Returns:
      all features in this container which match filter.

    • createFeature

      public Feature createFeature(Feature.Template f)
      Description copied from interface: FeatureHolder
      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.
      Specified by:
      createFeature in interface FeatureHolder

    • removeFeature

      public void removeFeature(Feature f)
      Description copied from interface: FeatureHolder
      Remove a feature from this FeatureHolder.
      Specified by:
      removeFeature in interface FeatureHolder

    • containsFeature

      public boolean containsFeature(Feature f)
      Description copied from interface: FeatureHolder
      Check if the feature is present in this holder.
      Specified by:
      containsFeature in interface FeatureHolder
      Parameters:
      f - the Feature to check
      Returns:
      true if f is in this set

    • getSchema

      public FeatureFilter getSchema()
      Description copied from interface: FeatureHolder
      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)).

      Specified by:
      getSchema in interface FeatureHolder
      Returns:
      the schema filter