X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAppJmol.java;h=f71cd3077ee666176e11d98e472016cd44b2d9cb;hb=f8efe615d1c7d5c23fd838c1abcd77be542b154c;hp=9d68c1bcb047b2a1e3860422b350c48b379fdd2b;hpb=a65993fd311b1a53617c5df3c84abfb78740a900;p=jalview.git

diff --git a/src/jalview/gui/AppJmol.java b/src/jalview/gui/AppJmol.java
index 9d68c1b..f71cd30 100644
--- a/src/jalview/gui/AppJmol.java
+++ b/src/jalview/gui/AppJmol.java
@@ -153,6 +153,15 @@ public class AppJmol extends GStructureViewer implements Runnable,
   {
     seqColour.setSelected(jmb.isColourBySequence());
     jmolColour.setSelected(!jmb.isColourBySequence());
+    if (_colourwith==null)
+    {
+      _colourwith=new Vector<AlignmentPanel>();
+    }
+    if (_alignwith==null)
+    {
+      _alignwith=new Vector<AlignmentPanel>();
+    }
+    
     seqColourBy = new ViewSelectionMenu("Colour by ..", this, _colourwith,
             new ItemListener()
             {
@@ -210,30 +219,7 @@ public class AppJmol extends GStructureViewer implements Runnable,
 
       }
     });
-    colourMenu.addMenuListener(new MenuListener()
-    {
-      
-      @Override
-      public void menuSelected(MenuEvent arg0)
-      {
-        
-        handlingGuiEvents=true;
-      }
-      
-      @Override
-      public void menuDeselected(MenuEvent arg0)
-      {
-        handlingGuiEvents=false;
-      }
-      
-      @Override
-      public void menuCanceled(MenuEvent arg0)
-      {
-        handlingGuiEvents=false;
-      }
-    });
   }
-
   IProgressIndicator progressBar = null;
 
   public AppJmol(PDBEntry pdbentry, SequenceI[] seq, String[] chains,
@@ -374,13 +360,13 @@ public class AppJmol extends GStructureViewer implements Runnable,
   /**
    * list of alignment panels to use for superposition
    */
-  ArrayList<AlignmentPanel> _alignwith = new ArrayList();
+  Vector<AlignmentPanel> _alignwith = new Vector<AlignmentPanel>();
 
   /**
    * list of alignment panels that are used for colouring structures by aligned
    * sequences
    */
-  ArrayList<AlignmentPanel> _colourwith = new ArrayList();
+  Vector<AlignmentPanel> _colourwith = new Vector<AlignmentPanel>();
 
   /**
    * set the primary alignmentPanel reference and add another alignPanel to the
@@ -658,13 +644,6 @@ public class AppJmol extends GStructureViewer implements Runnable,
    */
   private boolean _started = false;
 
-  /**
-   * state flag indicating if the GUI is active when a particular button event
-   * takes place (e.g. when a stateChange occurs on a checkbox - this could be
-   * programmatic or due to the user doing something)
-   */
-  private boolean handlingGuiEvents=false;
-
   public void run()
   {
     _started = true;
@@ -954,15 +933,15 @@ public class AppJmol extends GStructureViewer implements Runnable,
     jmb.setColourBySequence(seqColour.isSelected());
     if (_colourwith == null)
     {
-      _colourwith = new ArrayList<AlignmentPanel>();
+      _colourwith = new Vector<AlignmentPanel>();
     }
     if (jmb.isColourBySequence())
     {
-      if (!jmb.isLoadingFromArchive() && handlingGuiEvents)
+      if (!jmb.isLoadingFromArchive())
       {
-        if (ap!=null) {
-        	// Make the currently displayed alignment panel the associated view
-        	_colourwith.add(ap.alignFrame.alignPanel);
+        if (_colourwith.size()==0 && ap!=null) {
+          // Make the currently displayed alignment panel the associated view
+          _colourwith.add(ap.alignFrame.alignPanel);
         }
       }
       // Set the colour using the current view for the associated alignframe
@@ -1173,7 +1152,7 @@ public class AppJmol extends GStructureViewer implements Runnable,
   {
     if (_alignwith == null)
     {
-      _alignwith = new ArrayList<AlignmentPanel>();
+      _alignwith = new Vector<AlignmentPanel>();
     }
     if (_alignwith.size() == 0 && ap != null)
     {