Merge branch 'r281_JAL-1211' into develop

diff --combined src/jalview/appletgui/AlignFrame.java
index fd426d3,51df8b9..6ea4b94
--- 1/src/jalview/appletgui/AlignFrame.java
--- 2/src/jalview/appletgui/AlignFrame.java
+++ b/src/jalview/appletgui/AlignFrame.java
@@@ -53,7 -53,6 +53,7 @@@ import jalview.schemes.NucleotideColour
  import jalview.schemes.PIDColourScheme;
  import jalview.schemes.PurinePyrimidineColourScheme;
  import jalview.schemes.RNAHelicesColourChooser;
 +import jalview.schemes.RNAInteractionColourScheme;\r
  import jalview.schemes.ResidueProperties;
  import jalview.schemes.StrandColourScheme;
  import jalview.schemes.TCoffeeColourScheme;
@@@ -123,7 -122,28 +123,28 @@@ public class AlignFrame extends Embmenu
      {
        ex.printStackTrace();
      }
- 
+     // need to get window geometry before we calculate alignment layout
+     if (applet != null)
+     {
+       String param;
+       try
+       {
+         param = applet.getParameter("windowWidth");
+         if (param != null)
+         {
+           int width = Integer.parseInt(param);
+           DEFAULT_WIDTH = width;
+         }
+         param = applet.getParameter("windowHeight");
+         if (param != null)
+         {
+           int height = Integer.parseInt(param);
+           DEFAULT_HEIGHT = height;
+         }
+       } catch (Exception ex)
+       {
+       }
+     }
      viewport = new AlignViewport(al, applet);
      alignPanel = new AlignmentPanel(this, viewport);
      avc = new jalview.controller.AlignViewController(this, viewport, alignPanel);
@@@ -175,23 -195,6 +196,6 @@@
          centreColumnLabelFlag.setState(true);
          centreColumnLabelFlag_stateChanged();
        }
-       try
-       {
-         param = applet.getParameter("windowWidth");
-         if (param != null)
-         {
-           int width = Integer.parseInt(param);
-           DEFAULT_WIDTH = width;
-         }
-         param = applet.getParameter("windowHeight");
-         if (param != null)
-         {
-           int height = Integer.parseInt(param);
-           DEFAULT_HEIGHT = height;
-         }
-       } catch (Exception ex)
-       {
-       }
  
      }
      if (viewport.getAlignment().isNucleotide())
@@@ -1041,10 -1044,6 +1045,10 @@@
      {
        changeColour(new PurinePyrimidineColourScheme());
      }
 +    else if (source == RNAInteractionColour)\r
 +    {\r
 +      changeColour(new RNAInteractionColourScheme());\r
 +    }\r
      else if (source == RNAHelixColour)
      {
        new RNAHelicesColourChooser(viewport, alignPanel);
@@@ -2832,8 -2831,6 +2836,8 @@@
  
    MenuItem purinePyrimidineColour = new MenuItem();
  
 +  MenuItem RNAInteractionColour = new MenuItem();\r
 +\r
    MenuItem RNAHelixColour = new MenuItem();
  
    MenuItem userDefinedColour = new MenuItem();
@@@ -3041,8 -3038,6 +3045,8 @@@
      buriedColour.addActionListener(this);
      purinePyrimidineColour.setLabel(MessageManager.getString("label.purine_pyrimidine"));
      purinePyrimidineColour.addActionListener(this);
 +    RNAInteractionColour.setLabel(MessageManager.getString("label.rna_interaction"));\r
 +    RNAInteractionColour.addActionListener(this);\r
      RNAHelixColour.setLabel(MessageManager.getString("action.by_rna_helixes"));
      RNAHelixColour.addActionListener(this);
      userDefinedColour.setLabel(MessageManager.getString("action.user_defined"));
@@@ -3269,7 -3264,6 +3273,7 @@@
      colourMenu.add(buriedColour);
      colourMenu.add(nucleotideColour);
      colourMenu.add(purinePyrimidineColour);
 +    //    colourMenu.add(RNAInteractionColour);\r
      colourMenu.add(tcoffeeColour);
      colourMenu.add(userDefinedColour);
      colourMenu.addSeparator();