JAL-2446 merged to spike branch

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

diff --git a/src/jalview/datamodel/CigarArray.java b/src/jalview/datamodel/CigarArray.java
index 61f3c33..837a10b 100644 (file)
--- a/src/jalview/datamodel/CigarArray.java
+++ b/src/jalview/datamodel/CigarArray.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
- * Copyright (C) 2015 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -85,12 +85,12 @@ public class CigarArray extends CigarBase
    * @param columnSelection
    * @param selectionGroup
    */
-  public CigarArray(AlignmentI alignment, ColumnSelection columnSelection,
+  public CigarArray(AlignmentI alignment, HiddenColumns hidden,
           SequenceGroup selectionGroup)
   {
     this(constructSeqCigarArray(alignment, selectionGroup));
     constructFromAlignment(alignment,
-            columnSelection != null ? columnSelection.getHiddenColumns()
+            hidden != null ? hidden.getHiddenRegions()
                     : null, selectionGroup);
   }
 
@@ -218,7 +218,7 @@ public class CigarArray extends CigarBase
   }
 
   /**
-   * @see Cigar.getSequenceAndDeletions
+   * @see CigarBase.getSequenceAndDeletions
    * @param GapChar
    *          char
    * @return Object[][]