X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FHiddenMarkovModel.java;h=5331f3d7c5da0336db9c7258732f9331639d907b;hb=293afc4e4e080e8d48cfa99760667b2b1dfe1da0;hp=e2143732c90af84d5fe4aff230ed822c966890d5;hpb=d70c093b72754e026fc6df06e3e13464d6330408;p=jalview.git

diff --git a/src/jalview/datamodel/HiddenMarkovModel.java b/src/jalview/datamodel/HiddenMarkovModel.java
index e214373..5331f3d 100644
--- a/src/jalview/datamodel/HiddenMarkovModel.java
+++ b/src/jalview/datamodel/HiddenMarkovModel.java
@@ -290,7 +290,7 @@ public class HiddenMarkovModel
     int symbolIndex;
     int nodeIndex;
     Double probability;
-    if (symbol == '-')
+    if (!symbolIndexLookup.containsKey(symbol))
     {
       return 0d;
     }
@@ -322,7 +322,7 @@ public class HiddenMarkovModel
     int symbolIndex;
     int nodeIndex;
     Double probability;
-    if (symbol == '-')
+    if (!symbolIndexLookup.containsKey(symbol))
     {
       return 0d;
     }