X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FColumnSelection.java;h=546ba1a7dbe4443e0e40da5929f4d07585b6dea5;hb=153dd62dc91da13ae732600e6ea55ddbe15eab39;hp=4371994e0d3593a5594b07d2bd89e86895aee9a9;hpb=d423f22792e47dbc800ae220a58677f988971d06;p=jalview.git

diff --git a/src/jalview/datamodel/ColumnSelection.java b/src/jalview/datamodel/ColumnSelection.java
index 4371994..546ba1a 100644
--- a/src/jalview/datamodel/ColumnSelection.java
+++ b/src/jalview/datamodel/ColumnSelection.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
  * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
  * 
  * This file is part of Jalview.
@@ -508,8 +508,8 @@ public class ColumnSelection
   }
 
   /**
-   * Use this method to find out where a visible column is in the alignment when
-   * hidden columns exist
+   * Use this method to find out where a column will appear in the visible alignment when
+   * hidden columns exist. If the column is not visible, then the left-most visible column will always be returned.
    * 
    * @param hiddenColumn
    *          int
@@ -521,21 +521,21 @@ public class ColumnSelection
     if (hiddenColumns != null)
     {
       int index = 0;
-      int gaps = 0;
+      int[] region;
       do
       {
-        int[] region = (int[]) hiddenColumns.elementAt(index);
+        region = (int[]) hiddenColumns.elementAt(index++);
         if (hiddenColumn > region[1])
         {
           result -= region[1] + 1 - region[0];
         }
-        index++;
-      } while (index < hiddenColumns.size());
-
-      result -= gaps;
+      } while ((hiddenColumn > region[1]) && (index < hiddenColumns.size()));
+      if (hiddenColumn>region[0] && hiddenColumn<region[1])
+      {
+        return region[0]+hiddenColumn-result;
+      }
     }
-
-    return result;
+    return result; // return the shifted position after removing hidden columns.
   }
 
   /**