X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FCigarArray.java;h=b6224c2d803579c04b8e6b8edc8769581acae8d4;hb=refs%2Fheads%2Ffeature%2FJAL-2611;hp=837a10bd3942df6240aa9ebc2e98492cae1f5ea1;hpb=c3b3dc0d34e9da7507211ba332c35d3791a481c5;p=jalview.git

diff --git a/src/jalview/datamodel/CigarArray.java b/src/jalview/datamodel/CigarArray.java
index 837a10b..b6224c2 100644
--- a/src/jalview/datamodel/CigarArray.java
+++ b/src/jalview/datamodel/CigarArray.java
@@ -68,7 +68,8 @@ public class CigarArray extends CigarBase
       for (int c = 0; c < cigars.length; c++)
       {
         refCigars[c] = cigars[c];
-        if (!((cigars[c] instanceof SeqCigar) || cigars[c] instanceof CigarCigar))
+        if (!((cigars[c] instanceof SeqCigar)
+                || cigars[c] instanceof CigarCigar))
         {
           seqcigararray = false;
         }
@@ -90,8 +91,8 @@ public class CigarArray extends CigarBase
   {
     this(constructSeqCigarArray(alignment, selectionGroup));
     constructFromAlignment(alignment,
-            hidden != null ? hidden.getHiddenRegions()
-                    : null, selectionGroup);
+            hidden != null ? hidden.getHiddenColumnsCopy() : null,
+            selectionGroup);
   }
 
   private static int[] _calcStartEndBounds(AlignmentI alignment,