X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSeqCigar.java;h=9cc7b4a35ff054f5a6a3a48728216f0eaa197105;hb=refs%2Fheads%2Fbug%2FJAL-2491;hp=9dbdf6f59ad8bee3850b904d2ca1db3275c21703;hpb=db93a1adcbe0a4eaaf06e0a70ade0d6c5c1961c3;p=jalview.git

diff --git a/src/jalview/datamodel/SeqCigar.java b/src/jalview/datamodel/SeqCigar.java
index 9dbdf6f..9cc7b4a 100644
--- a/src/jalview/datamodel/SeqCigar.java
+++ b/src/jalview/datamodel/SeqCigar.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
- * 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.
  * 
@@ -494,18 +494,18 @@ public class SeqCigar extends CigarSimple
   /**
    * create an alignment from the given array of cigar sequences and gap
    * character, and marking the given segments as visible in the given
-   * columselection.
+   * hiddenColumns.
    * 
    * @param alseqs
    * @param gapCharacter
-   * @param colsel
-   *          - columnSelection where hidden regions are marked
+   * @param hidden
+   *          - hiddenColumns where hidden regions are marked
    * @param segments
    *          - visible regions of alignment
    * @return SequenceI[]
    */
   public static SequenceI[] createAlignmentSequences(SeqCigar[] alseqs,
-          char gapCharacter, ColumnSelection colsel, int[] segments)
+          char gapCharacter, HiddenColumns hidden, int[] segments)
   {
     SequenceI[] seqs = new SequenceI[alseqs.length];
     StringBuffer[] g_seqs = new StringBuffer[alseqs.length];
@@ -577,7 +577,7 @@ public class SeqCigar extends CigarSimple
           if (segments == null)
           {
             // add a hidden column for this deletion
-            colsel.hideColumns(inspos, inspos + insert.length - 1);
+            hidden.hideColumns(inspos, inspos + insert.length - 1);
           }
         }
       }
@@ -598,7 +598,7 @@ public class SeqCigar extends CigarSimple
       {
         // int start=shifts.shift(segments[i]-1)+1;
         // int end=shifts.shift(segments[i]+segments[i+1]-1)-1;
-        colsel.hideColumns(segments[i + 1], segments[i + 1]
+        hidden.hideColumns(segments[i + 1], segments[i + 1]
                 + segments[i + 2] - 1);
       }
     }