Merge branch 'bug/JAL-2541cutWithFeatures' into features/JAL-2446NCList

diff --cc src/jalview/commands/EditCommand.java
index 98ac2d5,21ff841..388c533
--- 1/src/jalview/commands/EditCommand.java
--- 2/src/jalview/commands/EditCommand.java
+++ b/src/jalview/commands/EditCommand.java
@@@ -555,6 -555,6 +555,7 @@@ public class EditCommand implements Com
                command.oldds = new SequenceI[command.seqs.length];
              }
              command.oldds[i] = oldds;
++            // FIXME JAL-2541 JAL-2526 get correct positions if on a gap
              adjustFeatures(
                      command,
                      i,
@@@ -1101,8 -1101,8 +1102,8 @@@
      }
    }
  
--  final static void adjustFeatures(Edit command, int index, int i, int j,
--          boolean insert)
++  final static void adjustFeatures(Edit command, int index, final int i,
++          final int j, boolean insert)
    {
      SequenceI seq = command.seqs[index];
      SequenceI sequence = seq.getDatasetSequence();

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

diff --cc test/jalview/datamodel/SequenceTest.java
index 586cc5d,739ef5d..ebf4857
--- 1/test/jalview/datamodel/SequenceTest.java
--- 2/test/jalview/datamodel/SequenceTest.java
+++ b/test/jalview/datamodel/SequenceTest.java
@@@ -40,6 -41,6 +41,8 @@@ import java.util.Vector
  
  import junit.extensions.PA;
  
++import junit.extensions.PA;
++
  import org.testng.Assert;
  import org.testng.annotations.BeforeClass;
  import org.testng.annotations.BeforeMethod;