JAL-1807 explicit imports (jalview.datamodel)

[jalview.git] / src / jalview / datamodel / AlignmentView.java

diff --git a/src/jalview/datamodel/AlignmentView.java b/src/jalview/datamodel/AlignmentView.java
index f73fb74..5457fbc 100644 (file)
--- a/src/jalview/datamodel/AlignmentView.java
+++ b/src/jalview/datamodel/AlignmentView.java
@@ -109,7 +109,7 @@ public class AlignmentView
           boolean recordGroups)
   {
     // refactored from AlignViewport.getAlignmentView(selectedOnly);
-    this(new jalview.datamodel.CigarArray(alignment,
+    this(new CigarArray(alignment,
             (hasHiddenColumns ? columnSelection : null),
             (selectedRegionOnly ? selection : null)),
             (selectedRegionOnly && selection != null) ? selection
@@ -179,7 +179,9 @@ public class AlignmentView
         sgrps[g] = new ScGroup();
         sgrps[g].sg = new SequenceGroup(sg);
         addedgps[g] = false;
-        seqsets.set(g, sg.getSequences(null));
+        // can't set entry 0 in an empty list
+        // seqsets.set(g, sg.getSequences(null));
+        seqsets.add(sg.getSequences());
       }
       // seqsets now contains vectors (should be sets) for each group, so we can
       // track when we've done with the group