Package org.biojava.bio.seq

Class MergeFeatureHolder

java.lang.Object
org.biojava.utils.AbstractChangeable
org.biojava.bio.seq.AbstractFeatureHolder
org.biojava.bio.seq.MergeFeatureHolder
All Implemented Interfaces:
Serializable, FeatureHolder, Changeable
public class MergeFeatureHolder extends AbstractFeatureHolder implements Serializable
FeatureHolder which exposes all the features in a set of sub-FeatureHolders. This is provided primarily as a support class for ViewSequence. It may also be useful for other applications, such as simple distributed annotation systems.
Author:
Thomas Down, Matthew Pocock
See Also:

  • Constructor Details

    • MergeFeatureHolder

      public MergeFeatureHolder()
      Create a new, empty, MergeFeatureHolder.

  • Method Details

    • addFeatureHolder

      public void addFeatureHolder(FeatureHolder fh) throws ChangeVetoException
      Add an extra FeatureHolder to the set of FeatureHolders which are merged. This method is provided for backward compatibility, and is equivalent to: 
           mfh.addFeatureHolder(fh, FeatureFilter.all);

      You should always use the two-arg version in preference if you are able to define the membership of a FeatureHolder.

      Throws:
      ChangeVetoException

    • removeFeatureHolder

      public void removeFeatureHolder(FeatureHolder fh) throws ChangeVetoException
      Remove a FeatureHolder from the set of FeatureHolders which are merged.
      Throws:
      ChangeVetoException

    • 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

    • 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

    • features

      public Iterator features()
      Iterate over all the features in all child FeatureHolders. The Iterator may throw ConcurrantModificationException if there is a change in the underlying collections during iteration.
      Specified by:
      features in interface FeatureHolder
      Returns:
      an Iterator

    • filter

      public FeatureHolder filter(FeatureFilter ff, boolean recurse)
      When applied to a MergeFeatureHolder, this filters each child FeatureHolder independently.
      Specified by:
      filter in interface FeatureHolder
      Overrides:
      filter in class AbstractFeatureHolder
      Parameters:
      ff - 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.

    • 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