Merge branch 'releases/Release_2_10_2b1_Branch'

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

diff --git a/src/jalview/datamodel/CigarArray.java b/src/jalview/datamodel/CigarArray.java
index aab82a1..b6224c2 100644 (file)
--- 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.getHiddenRegions()
-                    : 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[][]