Fix overviewPanel bugs

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