X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FColumnSelection.java;h=eb6cafe3fb9283b4d1af2ab3400c43c6fb833caa;hb=ef6291f17491f1c426e2cad44021c31f609e2808;hp=26dba83bd36d44c00093efbe57d37d7959e00e31;hpb=ab2005eb4fd46c5d9f2df238f2cf20bcb35bf1f3;p=jalview.git

diff --git a/src/jalview/gui/ColumnSelection.java b/src/jalview/gui/ColumnSelection.java
index 26dba83..eb6cafe 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)
       {
@@ -286,6 +303,31 @@ 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)
@@ -325,6 +367,14 @@ public class ColumnSelection
 
     public void revealAllHiddenColumns(AlignViewport av)
     {
+      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 +386,11 @@ 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;
         }