From 3ad2eb8f66c9b73fb80b2c8e957e81b0e4969e3c Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Tue, 14 Jun 2005 11:33:41 +0000
Subject: [PATCH] PaintRefresher must be sent alignment

---
 src/jalview/gui/AlignFrame.java |   11 ++++++++---
 1 file changed, 8 insertions(+), 3 deletions(-)

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index ad350cc..5fe31da 100755
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -563,7 +563,7 @@ public class AlignFrame
 
     sg.setEndRes(viewport.alignment.getWidth());
     viewport.setSelectionGroup(sg);
-    PaintRefresher.Refresh(null);
+    PaintRefresher.Refresh(null, viewport.alignment);
   }
 
   public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
@@ -571,12 +571,17 @@ public class AlignFrame
     viewport.setSelectionGroup(null);
     viewport.getColumnSelection().clear();
     viewport.setSelectionGroup(null);
-    PaintRefresher.Refresh(null);
+    PaintRefresher.Refresh(null, viewport.alignment);
   }
 
   public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
   {
     SequenceGroup sg = viewport.getSelectionGroup();
+    if(sg==null)
+    {
+      selectAllSequenceMenuItem_actionPerformed(null);
+      return;
+    }
 
     for (int i = 0; i < viewport.getAlignment().getSequences().size();
          i++)
@@ -584,7 +589,7 @@ public class AlignFrame
       sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
     }
 
-    PaintRefresher.Refresh(null);
+    PaintRefresher.Refresh(null, viewport.alignment);
   }
 
   public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
-- 
1.7.10.2