Merge branch 'develop' into features/JAL-2446NCList

Conflicts:
	src/jalview/datamodel/SequenceI.java

diff --cc src/jalview/datamodel/Sequence.java
Simple merge

diff --cc src/jalview/datamodel/SequenceI.java
index dbf3ed3,12ddf60..cf9d6ad
--- 1/src/jalview/datamodel/SequenceI.java
--- 2/src/jalview/datamodel/SequenceI.java
+++ b/src/jalview/datamodel/SequenceI.java
@@@ -20,8 -20,7 +20,9 @@@
   */
  package jalview.datamodel;
  
 +import jalview.datamodel.features.SequenceFeaturesI;
 +
+ import java.util.BitSet;
  import java.util.List;
  import java.util.Vector;
  
@@@ -510,14 -479,9 +511,21 @@@ public interface SequenceI extends ASeq
    public List<DBRefEntry> getPrimaryDBRefs();
  
    /**
 +   * Returns a (possibly empty) list of sequence features that overlap the range
 +   * from-to (inclusive), optionally restricted to one or more specified feature
 +   * types
 +   * 
 +   * @param from
 +   * @param to
 +   * @param types
 +   * @return
 +   */
 +  List<SequenceFeature> findFeatures(int from, int to, String... types);
++  
++  /**
+    * 
+    * @return BitSet corresponding to index [0,length) where Comparison.isGap()
+    *         returns true.
+    */
+   BitSet getInsertionsAsBits();
  }

diff --cc src/jalview/ext/ensembl/EnsemblGene.java
Simple merge

diff --cc src/jalview/gui/PopupMenu.java
Simple merge

diff --cc test/jalview/datamodel/SequenceTest.java
Simple merge