Jalview 2.6 source licence

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

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