JAL-4392 Merging consensus secondary structure

[jalview.git] / src / jalview / gui / AlignViewport.java

diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index a8bc815..037f120 100644 (file)
--- a/src/jalview/gui/AlignViewport.java
+++ b/src/jalview/gui/AlignViewport.java
@@ -281,7 +281,9 @@ 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);
@@ -314,6 +316,7 @@ public class AlignViewport extends AlignmentViewport
     if (residueShading != null)
     {
       residueShading.setConsensus(hconsensus);
+      residueShading.setSsConsensus(hSSConsensus);
     }
     setColourAppliesToAllGroups(true);
   }