add partial button fix to annotation and statistics output

[jalview.git] / src / jalview / analysis / AAFrequency.java

diff --git a/src/jalview/analysis/AAFrequency.java b/src/jalview/analysis/AAFrequency.java
index 3cc57bf..57e00fe 100755 (executable)
--- 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);