X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignViewport.java;fp=src%2Fjalview%2Fgui%2FAlignViewport.java;h=4e1fcab04fda7ee5f0acfa6a6158fd86795e6fca;hb=e83ce5d8ef826fc0b509a51f154abdf734501077;hp=5613f1672c007ca19ce800db6ccd10506bd75226;hpb=786475501a15799d7c4058dbf74e4bf896d03736;p=jalview.git

diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index 5613f16..4e1fcab 100644
--- a/src/jalview/gui/AlignViewport.java
+++ b/src/jalview/gui/AlignViewport.java
@@ -45,7 +45,6 @@ import jalview.bin.Console;
 import jalview.commands.CommandI;
 import jalview.datamodel.AlignedCodonFrame;
 import jalview.datamodel.Alignment;
-import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.ColumnSelection;
 import jalview.datamodel.ContactMatrixI;
@@ -282,11 +281,15 @@ public class AlignViewport extends AlignmentViewport
       }
       showConsensusHistogram = Cache.getDefault("SHOW_CONSENSUS_HISTOGRAM",
               true);
-      showSequenceLogo = Cache.getDefault("SHOW_CONSENSUS_LOGO", false);
+      showSSConsensusHistogram = Cache.getDefault("SHOW_SSCONSENSUS_HISTOGRAM",
+              true);
+      showSequenceLogo = Cache.getDefault("SHOW_CONSENSUS_LOGO", true);
       normaliseSequenceLogo = Cache.getDefault("NORMALISE_CONSENSUS_LOGO",
               false);
       showGroupConsensus = Cache.getDefault("SHOW_GROUP_CONSENSUS", false);
       showConsensus = Cache.getDefault("SHOW_IDENTITY", true);
+      
+      showSSConsensus = Cache.getDefault("SHOW_SS_CONSENSUS", false);
 
       showOccupancy = Cache.getDefault(Preferences.SHOW_OCCUPANCY, true);
     }
@@ -315,6 +318,7 @@ public class AlignViewport extends AlignmentViewport
     if (residueShading != null)
     {
       residueShading.setConsensus(hconsensus);
+      residueShading.setSsConsensus(hSSConsensus);
     }
     setColourAppliesToAllGroups(true);
   }
@@ -998,7 +1002,7 @@ public class AlignViewport extends AlignmentViewport
    */
   protected boolean noReferencesTo(AlignedCodonFrame acf)
   {
-    AlignFrame[] frames = Desktop.getAlignFrames();
+    AlignFrame[] frames = Desktop.getDesktopAlignFrames();
     if (frames == null)
     {
       return true;