JAL-1492 JAL-1397 JAL-643 JAL-969 pull up global and group colourscheme logic and...

[jalview.git] / src / jalview / appletgui / AlignFrame.java

diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java
index 5e6df04..40999c6 100644 (file)
--- a/src/jalview/appletgui/AlignFrame.java
+++ b/src/jalview/appletgui/AlignFrame.java
@@ -158,7 +158,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     showConsensusHistogram.setState(viewport.isShowConsensusHistogram());
     showSequenceLogo.setState(viewport.isShowSequenceLogo());
     normSequenceLogo.setState(viewport.isNormaliseSequenceLogo());
-
+    applyToAllGroups.setState(viewport.getColourAppliesToAllGroups());
+    
     seqLimits.setState(viewport.showJVSuffix);
 
     if (applet != null)
@@ -2327,42 +2328,20 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     {
       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);