X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FCigarArray.java;h=b6224c2d803579c04b8e6b8edc8769581acae8d4;hb=be762d8d9c71a7aa3121e845c45911c7192b7827;hp=a48a178179221382a27a44a595a374e222af900c;hpb=d1707d4c26db76cfeb640f0dbeb3e3427fd40eb7;p=jalview.git

diff --git a/src/jalview/datamodel/CigarArray.java b/src/jalview/datamodel/CigarArray.java
index a48a178..b6224c2 100644
--- a/src/jalview/datamodel/CigarArray.java
+++ b/src/jalview/datamodel/CigarArray.java
@@ -20,8 +20,6 @@
  */
 package jalview.datamodel;
 
-import htsjdk.samtools.Cigar;
-
 import java.util.List;
 
 public class CigarArray extends CigarBase
@@ -70,7 +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;
         }
@@ -92,8 +91,8 @@ public class CigarArray extends CigarBase
   {
     this(constructSeqCigarArray(alignment, selectionGroup));
     constructFromAlignment(alignment,
-            hidden != null ? hidden.getListOfCols()
-                    : null, selectionGroup);
+            hidden != null ? hidden.getHiddenColumnsCopy() : null,
+            selectionGroup);
   }
 
   private static int[] _calcStartEndBounds(AlignmentI alignment,
@@ -220,7 +219,7 @@ public class CigarArray extends CigarBase
   }
 
   /**
-   * @see Cigar.getSequenceAndDeletions
+   * @see CigarBase.getSequenceAndDeletions
    * @param GapChar
    *          char
    * @return Object[][]