X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FAAFrequency.java;h=57e00fedaf79737ff7ba1bd4e362801d56e517ee;hb=refs%2Fheads%2Ffeatures%2Fhmmer_statistics;hp=3cc57bf17c1eb4e4d9acd1d7c57f2926e7d56ae9;hpb=96356075a122b745936738f478a8ee33ac7e0f0a;p=jalview.git

diff --git a/src/jalview/analysis/AAFrequency.java b/src/jalview/analysis/AAFrequency.java
index 3cc57bf..57e00fe 100755
--- a/src/jalview/analysis/AAFrequency.java
+++ b/src/jalview/analysis/AAFrequency.java
@@ -107,6 +107,7 @@ public class AAFrequency
     }
   }
 
+
   /**
    * Calculate the consensus symbol(s) for each column in the given range.
    * 
@@ -762,7 +763,7 @@ public class AAFrequency
         value = hmm.getMatchEmissionProbability(column, symbol);
         double freq;
 
-        if (alph == AMINO && removeBelowBackground)
+        if (AMINO.equals(alph) && removeBelowBackground)
         {
           freq = ResidueProperties.aminoBackgroundFrequencies.get(symbol);
           if (value < freq)
@@ -770,7 +771,7 @@ public class AAFrequency
             value = 0d;
           }
         }
-        else if (alph == DNA && removeBelowBackground)
+        else if (DNA.equals(alph) && removeBelowBackground)
         {
           freq = ResidueProperties.nucleotideBackgroundFrequencies
                   .get(symbol);