X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FColumnSelection.java;h=94e26422a5d29c857f706d1353959072db4424b6;hb=f5f5806de6923a8a62906c5a62c6276ba56ae0da;hp=26dba83bd36d44c00093efbe57d37d7959e00e31;hpb=ab2005eb4fd46c5d9f2df238f2cf20bcb35bf1f3;p=jalview.git

diff --git a/src/jalview/gui/ColumnSelection.java b/src/jalview/gui/ColumnSelection.java
index 26dba83..94e2642 100755
--- a/src/jalview/gui/ColumnSelection.java
+++ b/src/jalview/gui/ColumnSelection.java
@@ -171,6 +171,23 @@ public class ColumnSelection
                 selected.setElementAt(new Integer(temp - change), i);
             }
         }
+
+        if(hiddenColumns!=null)
+        {
+          for(int i=0; i<hiddenColumns.size(); i++)
+          {
+            int[] region = (int[]) hiddenColumns.elementAt(i);
+            if(region[0] > start)
+            {
+              region[0] -= change;
+              region[1] -= change;
+            }
+            if(region[0]<0)
+              region[0] = 0;
+            if(region[1] <0)
+             region[1] = 0;
+          }
+        }
     }
 
     /**
@@ -267,7 +284,7 @@ public class ColumnSelection
      * In otherwords, the next hidden column.
      * @param index int
      */
-    public int getHiddenRegionBoundary(int alPos)
+    public int getHiddenBoundaryRight(int alPos)
     {
       if (hiddenColumns != null)
       {
@@ -286,9 +303,35 @@ public class ColumnSelection
       return alPos;
 
     }
+    /**
+     * THis method returns the rightmost limit of a
+     * region of an alignment with hidden columns.
+     * In otherwords, the next hidden column.
+     * @param index int
+     */
+    public int getHiddenBoundaryLeft(int alPos)
+    {
+      if (hiddenColumns != null)
+      {
+        int index = hiddenColumns.size()-1;
+        do
+        {
+          int[] region = (int[]) hiddenColumns.elementAt(index);
+          if(alPos > region[1])
+            return region[1];
 
+          index--;
+        }
+        while(index >-1);
+      }
+
+      return alPos;
+
+    }
 
-    public void hideColumns(int res, AlignViewport av)
+
+
+    public void hideColumns(int res)
     {
       if(hiddenColumns==null)
         hiddenColumns = new Vector();
@@ -318,13 +361,21 @@ public class ColumnSelection
       if(!added)
         hiddenColumns.addElement(new int[]{min, max});
 
-
-      av.setSelectionGroup(null);
-      av.hasHiddenColumns = true;
     }
 
     public void revealAllHiddenColumns(AlignViewport av)
     {
+      if(hiddenColumns!=null)
+      {
+        for (int i = 0; i < hiddenColumns.size(); i++)
+        {
+          int[] region = (int[]) hiddenColumns.elementAt(i);
+          for (int j = region[0]; j < region[1]; j++)
+          {
+            addElement(j);
+          }
+        }
+      }
       av.hasHiddenColumns = false;
       hiddenColumns = null;
     }
@@ -336,6 +387,11 @@ public class ColumnSelection
         int [] region = (int[])hiddenColumns.elementAt(i);
         if( res == region[0])
         {
+          for (int j = region[0]; j < region[1]; j++)
+          {
+            addElement(j);
+          }
+
           hiddenColumns.remove(region);
           break;
         }