Merge branch 'JAL-1397' into develop

diff --combined src/jalview/appletgui/AlignFrame.java
index 2e39b10,40999c6..da43281
--- 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;
@@@ -159,7 -158,8 +159,8 @@@ public class AlignFrame extends Embmenu
      showConsensusHistogram.setState(viewport.isShowConsensusHistogram());
      showSequenceLogo.setState(viewport.isShowSequenceLogo());
      normSequenceLogo.setState(viewport.isNormaliseSequenceLogo());
- 
+     applyToAllGroups.setState(viewport.getColourAppliesToAllGroups());
+     
      seqLimits.setState(viewport.showJVSuffix);
  
      if (applet != null)
@@@ -1045,10 -1045,6 +1046,10 @@@
      {
        changeColour(new PurinePyrimidineColourScheme());
      }
 +    else if (source == RNAInteractionColour)\r
 +    {\r
 +      changeColour(new RNAInteractionColourScheme());\r
 +    }\r
      else if (source == RNAHelixColour)
      {
        new RNAHelicesColourChooser(viewport, alignPanel);
@@@ -2332,42 -2328,20 +2333,20 @@@
      {
        if (viewport.getAbovePIDThreshold())
        {
-         threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,
-                 "Background");
- 
-         cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
- 
-         viewport.setGlobalColourScheme(cs);
-       }
-       else
-       {
-         cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
-       }
+         viewport.setThreshold(SliderPanel.setPIDSliderSource(alignPanel, cs,
+                 "Background"));
+       } 
  
        if (viewport.getConservationSelected())
        {
- 
-         Alignment al = (Alignment) viewport.getAlignment();
-         Conservation c = new Conservation("All",
-                 ResidueProperties.propHash, 3, al.getSequences(), 0,
-                 al.getWidth() - 1);
- 
-         c.calculate();
-         c.verdict(false, viewport.getConsPercGaps());
- 
-         cs.setConservation(c);
- 
-         cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel,
+         cs.setConservationApplied(true);
+         viewport.setIncrement(SliderPanel.setConservationSlider(alignPanel,
                  cs, "Background"));
        }
        else
        {
-         cs.setConservation(null);
+         cs.setConservationApplied(false);
        }
- 
-       cs.setConsensus(viewport.getSequenceConsensusHash());
- 
      }
      viewport.setGlobalColourScheme(cs);
  
@@@ -2836,8 -2810,6 +2815,8 @@@
  
    MenuItem purinePyrimidineColour = new MenuItem();
  
 +  MenuItem RNAInteractionColour = new MenuItem();\r
 +\r
    MenuItem RNAHelixColour = new MenuItem();
  
    MenuItem userDefinedColour = new MenuItem();
@@@ -3045,8 -3017,6 +3024,8 @@@
      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"));
@@@ -3273,7 -3243,6 +3252,7 @@@
      colourMenu.add(buriedColour);
      colourMenu.add(nucleotideColour);
      colourMenu.add(purinePyrimidineColour);
 +    //    colourMenu.add(RNAInteractionColour);\r
      colourMenu.add(tcoffeeColour);
      colourMenu.add(userDefinedColour);
      colourMenu.addSeparator();