X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fviewmodel%2FAlignmentViewport.java;h=c1c88c1f203baac64bbf13a501706c01de1af8f4;hb=37de9310bec3501cbc6381e0c3dcb282fcaad812;hp=80319be8f00ed6209ad34a3181b6c109ee1d9514;hpb=2bd3c28fe234c6883bec5412db83a809ab8d1500;p=jalview.git

diff --git a/src/jalview/viewmodel/AlignmentViewport.java b/src/jalview/viewmodel/AlignmentViewport.java
index 80319be..c1c88c1 100644
--- a/src/jalview/viewmodel/AlignmentViewport.java
+++ b/src/jalview/viewmodel/AlignmentViewport.java
@@ -612,7 +612,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
     boolean recalc = false;
     if (cs != null)
     {
-      cs.setConservationApplied(recalc = getConservationSelected());
+      recalc = getConservationSelected();
       if (getAbovePIDThreshold() || cs instanceof PIDColourScheme
               || cs instanceof Blosum62ColourScheme)
       {
@@ -629,6 +629,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
         cs.setConsensus(hconsensus);
         cs.setConservation(hconservation);
       }
+      cs.setConservationApplied(getConservationSelected());
       cs.alignmentChanged(alignment, hiddenRepSequences);
     }
     if (getColourAppliesToAllGroups())
@@ -1573,7 +1574,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
   public boolean isHiddenRepSequence(SequenceI seq)
   {
     return (hiddenRepSequences != null && hiddenRepSequences
-                    .containsKey(seq));
+            .containsKey(seq));
   }
 
   /**
@@ -2796,8 +2797,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
   public void expandColSelection(SequenceGroup sg, boolean wholewidth)
   {
     int sgs, sge;
-    if (sg != null
-            && (sgs = sg.getStartRes()) >= 0
+    if (sg != null && (sgs = sg.getStartRes()) >= 0
             && sg.getStartRes() <= (sge = sg.getEndRes())
             && !this.hasSelectedColumns())
     {