JAL-3285 change method declaration in AAFrequency to match develop

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

diff --git a/src/jalview/analysis/AAFrequency.java b/src/jalview/analysis/AAFrequency.java
index 1553021..1fef08e 100755 (executable)
--- a/src/jalview/analysis/AAFrequency.java
+++ b/src/jalview/analysis/AAFrequency.java
@@ -385,8 +385,8 @@ public class AAFrequency
       String description = isNaN ? null
               : String.format("%.4f bits", value);
       information.annotations[column] = new Annotation(
-              Character.toString(Character
-                      .toUpperCase(hmm.getConsensusAtAlignColumn(column))),
+              Character.toString(
+                      Character.toUpperCase(hmmSeq.getCharAt(column))),
               description, ' ', value);
     }
 
@@ -406,7 +406,7 @@ public class AAFrequency
    * @param endCol
    *          end column (exclusive)
    */
-  public static void completeOccupancyAnnot(AlignmentAnnotation occupancy,
+  public static void completeGapAnnot(AlignmentAnnotation occupancy,
           ProfilesI profiles, int startCol, int endCol, long nseq)
   {
     if (occupancy == null || occupancy.annotations == null