JAL-2591 More HiddenColumns refactoring. Tests passing.

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

diff --git a/src/jalview/datamodel/CigarArray.java b/src/jalview/datamodel/CigarArray.java
index aab82a1..31af5f8 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
@@ -92,7 +90,7 @@ public class CigarArray extends CigarBase
   {
     this(constructSeqCigarArray(alignment, selectionGroup));
     constructFromAlignment(alignment,
-            hidden != null ? hidden.getHiddenRegions()
+            hidden != null ? hidden.getHiddenColumnsCopyAsList()
                     : null, selectionGroup);
   }
 
@@ -220,7 +218,7 @@ public class CigarArray extends CigarBase
   }
 
   /**
-   * @see Cigar.getSequenceAndDeletions
+   * @see CigarBase.getSequenceAndDeletions
    * @param GapChar
    *          char
    * @return Object[][]