SelectMenu.java

    }
  }

  /**
   *  If there are some selected bases or features select the features that are
   *  fully contained within that selection.
   **/
  private void selectContainedFeatures () {
    final MarkerRange selected_marker_range =
      getSelection ().getMarkerRange ();

    final FeatureVector featuresContainedByRange;
    try
    {
      if (selected_marker_range == null) {
        final FeatureVector selected_features = getSelection ().getAllFeatures ();
        if (selected_features.size () == 0) {
          new MessageDialog (getParentFrame (), "nothing selected");
          return;
        }

        featuresContainedByRange = new FeatureVector();
        for(int i=0; i<selected_features.size(); i++) {
          Range r = selected_features.elementAt(i).getMaxRawRange();
          final FeatureVector featuresContained = getFeaturesContainedByRange(r);
          for(int j=0; j<featuresContained.size(); j++) {
            final Feature f = featuresContained.elementAt(j);
            if(!featuresContainedByRange.contains(f) && !selected_features.contains(f))
              featuresContainedByRange.add(f);
          }
        }
      } else {
        featuresContainedByRange = getFeaturesContainedByRange(
            selected_marker_range.getRawRange());
      }
    } catch (OutOfRangeException e) {
      throw new Error ("internal error - unexpected exception: " + e);
    }
    getSelection ().set (featuresContainedByRange);
  }

  /**
   * Return the features that are contained by a given range
   * @param r
   * @return
   * @throws OutOfRangeException
   */
  private FeatureVector getFeaturesContainedByRange(Range r) throws OutOfRangeException
  {
    final FeatureVector featuresInRange =
        getEntryGroup ().getFeaturesInRange (r);
    final FeatureVector featuresContainedByRange = new FeatureVector();
    for(int i=0; i<featuresInRange.size(); i++)
    {
      Feature f = featuresInRange.elementAt(i);
      Range maxR =  f.getMaxRawRange(); 
      if(r.getStart() <= maxR.getStart() &&
         r.getEnd()   >= maxR.getEnd())
        featuresContainedByRange.add(f);
    }
    return featuresContainedByRange;
  }

  /**
   *  This method sends an GotoEvent to all the GotoEvent listeners that will
   *  make the given base visible.
   **/
  private void makeBaseVisible (final Marker base_marker) {
    goto_event_source.gotoBase (base_marker);
  }

  /**
   *  Return the EntryGroup that was passed to the constructor.
   **/
  private EntryGroup getEntryGroup () {
    return entry_group;
  }

}