X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FCigarArray.java;h=aab82a1e0cd02d5c8237e75271c42c3341f7544d;hb=f2779aae6cd89facf15b81e053179e15e0315546;hp=a55f676c593639a3d825e3111f4459ebe9a85d6e;hpb=c1a4229bd662c4299301ee8827b36096d015c075;p=jalview.git

diff --git a/src/jalview/datamodel/CigarArray.java b/src/jalview/datamodel/CigarArray.java
index a55f676..aab82a1 100644
--- a/src/jalview/datamodel/CigarArray.java
+++ b/src/jalview/datamodel/CigarArray.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 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.
  * 
@@ -20,6 +20,8 @@
  */
 package jalview.datamodel;
 
+import htsjdk.samtools.Cigar;
+
 import java.util.List;
 
 public class CigarArray extends CigarBase
@@ -85,20 +87,19 @@ 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);
   }
 
   private static int[] _calcStartEndBounds(AlignmentI alignment,
           SequenceGroup selectionGroup)
   {
-    int[] startend = new int[]
-    { 0, 0, 0 };
+    int[] startend = new int[] { 0, 0, 0 };
     if (selectionGroup != null)
     {
       startend[0] = selectionGroup.getSize();
@@ -343,8 +344,11 @@ public class CigarArray extends CigarBase
           delpos = new java.util.Vector();
         }
         int delstart = cursor, delend = cursor + range[i] - 1; // inclusive
-        delpos.addElement(new int[]
-        { vcursor + offset, range[i] }); // index of right hand column after
+        delpos.addElement(new int[] { vcursor + offset, range[i] }); // index of
+                                                                     // right
+                                                                     // hand
+                                                                     // column
+                                                                     // after
         // hidden region boundary
         offset += range[i] - 1; // shift in visible column coordinates
         System.arraycopy(operation, i + 1, operation, i, length - i);