X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fappletgui%2FAlignViewport.java;h=ff3fe55524efcbf49e79c500a97dc24ba14e232a;hb=1d534b200f4a912f02f869c9d860f462511ea46f;hp=85c8ab56a299ac46c62c2954fc3f04c6c8b1c213;hpb=ca79e93cac909fb78e5f6143906e7b635d9bdc35;p=jalview.git

diff --git a/src/jalview/appletgui/AlignViewport.java b/src/jalview/appletgui/AlignViewport.java
index 85c8ab5..ff3fe55 100755
--- a/src/jalview/appletgui/AlignViewport.java
+++ b/src/jalview/appletgui/AlignViewport.java
@@ -559,7 +559,7 @@ public class AlignViewport
 
         hconsensus = new Hashtable[aWidth];
         AAFrequency.calculate(alignment.getSequencesArray(), 0, alignment
-                .getWidth(), hconsensus, includeAllConsensusSymbols);
+                .getWidth(), hconsensus, true); // always calculate the full profile
         AAFrequency.completeConsensus(consensus, hconsensus, 0, aWidth,
                 ignoreGapsInConsensusCalculation,
                 includeAllConsensusSymbols);