From 6b792c2d7f4113eb52518b69dff3d6a59f003462 Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Mon, 17 Jan 2005 16:12:55 +0000
Subject: [PATCH] Fix overviewPanel bugs

---
 src/jalview/gui/AlignFrame.java |   22 ++++++++++++++--------
 1 file changed, 14 insertions(+), 8 deletions(-)

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 96ba962..a41491a 100755
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -416,6 +416,10 @@ public class AlignFrame extends GAlignFrame
     alignPanel.RefreshPanels();
   }
 
+  public void secondaryStructure_actionPerformed(ActionEvent evt)
+  {
+    alignPanel.setSecondaryStructureVisible(secondaryStructure.isSelected());
+  }
 
   public void consensusGraphMenuItem_actionPerformed(ActionEvent e)
   {
@@ -424,6 +428,8 @@ public class AlignFrame extends GAlignFrame
 
   public void overviewMenuItem_actionPerformed(ActionEvent e)
   {
+    if (alignPanel.overviewPanel != null)
+      return;
 
     JInternalFrame frame = new JInternalFrame();
     OverviewPanel overview = alignPanel.getOverviewPanel();
@@ -519,8 +525,8 @@ public class AlignFrame extends GAlignFrame
     else if(conservationMenuItem.isSelected())
       conservationMenuItem_actionPerformed(null);
 
-     alignPanel.seqPanel.seqCanvas.paintFlag = true;
-     alignPanel.repaint();
+
+     alignPanel.RefreshPanels();
   }
 
   void addConservationOrPIDColour()
@@ -612,8 +618,6 @@ public class AlignFrame extends GAlignFrame
        scs.setThreshold(threshold);
      }
 
-     alignPanel.seqPanel.seqCanvas.paintFlag = true;
-     alignPanel.repaint();
 
   }
 
@@ -795,12 +799,13 @@ public class AlignFrame extends GAlignFrame
 
 
 
+
   public void clustalAlignMenuItem_actionPerformed(ActionEvent e)
   {
     // JBPNote
     // Should check to see if the server settings are valid
     // Need visual-delay indication here.
-    Jemboss jemboss = new Jemboss();
+     jalview.ws.Jemboss jemboss = new jalview.ws.Jemboss();
 
     Vector sv = viewport.getAlignment().getSequences();
     SequenceI[] seqs = new SequenceI[sv.size()];
@@ -816,15 +821,16 @@ public class AlignFrame extends GAlignFrame
     if (alignment != null)
     {
       AlignFrame af = new AlignFrame(new Alignment(alignment));
-      Desktop.addInternalFrame(af, getTitle().concat(" - ClustalW Alignment"), 
+      Desktop.addInternalFrame(af, getTitle().concat(" - ClustalW Alignment"),
                                700, 500); // JBPNote - is there a new window geom. property ?
     }
   }
 
+
   public void pdbTest_actionPerformed(ActionEvent e)
   {
-   String reply = 
-       JOptionPane.showInternalInputDialog(this, "Enter pdb code", 
+   String reply =
+       JOptionPane.showInternalInputDialog(this, "Enter pdb code",
                                            "PDB test viewer", JOptionPane.QUESTION_MESSAGE);
 
    String url = "http://www.ebi.ac.uk/cgi-bin/pdbfetch?id=1a4u";
-- 
1.7.10.2