X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FColumnSelection.java;h=63a5700efb39182eaeab2e37140a5caa55a7a0e5;hb=bd248212fee44557d973432f42666780530db8ed;hp=afa2e07103b168f6a73756ecb62f44240c1aebdd;hpb=4bc692b7e0ccca12c362bcb6ee9b4c88f431bd22;p=jalview.git

diff --git a/src/jalview/datamodel/ColumnSelection.java b/src/jalview/datamodel/ColumnSelection.java
index afa2e07..63a5700 100644
--- a/src/jalview/datamodel/ColumnSelection.java
+++ b/src/jalview/datamodel/ColumnSelection.java
@@ -1,20 +1,19 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)
- * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
+ * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
  * 
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
+ * This file is part of Jalview.
  * 
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
  * 
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  */
 package jalview.datamodel;
 
@@ -509,8 +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
@@ -522,21 +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.
   }
 
   /**
@@ -1060,7 +1059,9 @@ public class ColumnSelection
   }
 
   /**
-   * add in any unselected columns from the given column selection, excluding any that are hidden.
+   * add in any unselected columns from the given column selection, excluding
+   * any that are hidden.
+   * 
    * @param colsel
    */
   public void addElementsFrom(ColumnSelection colsel)
@@ -1071,7 +1072,8 @@ public class ColumnSelection
       while (e.hasMoreElements())
       {
         Object eo = e.nextElement();
-        if (hiddenColumns!=null && isVisible(((Integer) eo).intValue())) {
+        if (hiddenColumns != null && isVisible(((Integer) eo).intValue()))
+        {
           if (!selected.contains(eo))
           {
             selected.addElement(eo);
@@ -1080,27 +1082,33 @@ public class ColumnSelection
       }
     }
   }
-/**
- * set the selected columns the given column selection, excluding any columns that are hidden. 
- * @param colsel
- */
+
+  /**
+   * set the selected columns the given column selection, excluding any columns
+   * that are hidden.
+   * 
+   * @param colsel
+   */
   public void setElementsFrom(ColumnSelection colsel)
   {
+    selected = new Vector();
     if (colsel.selected != null && colsel.selected.size() > 0)
     {
-      if (hiddenColumns!=null && hiddenColumns.size()>0)
+      if (hiddenColumns != null && hiddenColumns.size() > 0)
       {
         // only select visible columns in this columns selection
         selected = new Vector();
         addElementsFrom(colsel);
-      } else {
-        // be quick
-        selected = new Vector(colsel.selected);
       }
-    }
-    else
-    {
-      selected = new Vector();
+      else
+      {
+        // add everything regardless
+        Enumeration en = colsel.selected.elements();
+        while (en.hasMoreElements())
+        {
+          selected.addElement(en.nextElement());
+        }
+      }
     }
   }
 }