JAL-1517 update copyright to version 2.8.2

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

diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java
index 6ea4b94..16602c8 100644 (file)
--- a/src/jalview/appletgui/AlignFrame.java
+++ b/src/jalview/appletgui/AlignFrame.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
@@ -159,7 +159,8 @@ 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)
@@ -2332,42 +2333,20 @@ 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);
 
@@ -3164,7 +3143,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     menu1.setLabel(MessageManager.getString("action.show"));
     showColumns.setLabel(MessageManager.getString("label.all_columns"));
     showSeqs.setLabel(MessageManager.getString("label.all_sequences"));
-    menu2.setLabel(MessageManager.getString("aciton.hide"));
+    menu2.setLabel(MessageManager.getString("action.hide"));
     hideColumns.setLabel(MessageManager.getString("label.selected_columns"));
     hideSequences.setLabel(MessageManager.getString("label.selected_sequences"));
     hideAllButSelection.setLabel(MessageManager.getString("label.all_but_selected_region"));
@@ -3393,7 +3372,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
       fileMenu.remove(closeMenuItem);
       fileMenu.remove(3); // Remove Seperator
       embeddedMenu = makeEmbeddedPopupMenu(alignFrameMenuBar, "Arial",
-              Font.PLAIN, 10, false); // use our own fonts.
+              Font.PLAIN, 11, false); // use our own fonts.
       // and actually add the components to the applet area
       viewport.applet.setLayout(new BorderLayout());
       viewport.applet.add(embeddedMenu, BorderLayout.NORTH);