X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FAAFrequency.java;h=fb495419d2573bbf56ade3e0c21ca46c42ad933e;hb=37de9310bec3501cbc6381e0c3dcb282fcaad812;hp=3a7995913b3110ae210806a277d9a3250c3fe82a;hpb=17e77c3f2949a0729322b4a8d907f3f34b6a9914;p=jalview.git

diff --git a/src/jalview/analysis/AAFrequency.java b/src/jalview/analysis/AAFrequency.java
index 3a79959..fb49541 100755
--- a/src/jalview/analysis/AAFrequency.java
+++ b/src/jalview/analysis/AAFrequency.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
- * Copyright (C) 2015 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -32,7 +32,6 @@ import jalview.util.QuickSort;
 import java.util.Arrays;
 import java.util.Hashtable;
 import java.util.List;
-import java.util.Set;
 
 /**
  * Takes in a vector or array of sequences and column start and column end and
@@ -520,7 +519,7 @@ public class AAFrequency
           Hashtable[] hconsensus)
   {
     final char gapCharacter = alignment.getGapCharacter();
-    Set<AlignedCodonFrame> mappings = alignment.getCodonFrames();
+    List<AlignedCodonFrame> mappings = alignment.getCodonFrames();
     if (mappings == null || mappings.isEmpty())
     {
       return;
@@ -541,12 +540,16 @@ public class AAFrequency
         {
           continue;
         }
-        char[] codon = MappingUtils.findCodonFor(seq, col, mappings);
-        int codonEncoded = CodingUtils.encodeCodon(codon);
-        if (codonEncoded >= 0)
+        List<char[]> codons = MappingUtils
+                .findCodonsFor(seq, col, mappings);
+        for (char[] codon : codons)
         {
-          codonCounts[codonEncoded + 2]++;
-          ungappedCount++;
+          int codonEncoded = CodingUtils.encodeCodon(codon);
+          if (codonEncoded >= 0)
+          {
+            codonCounts[codonEncoded + 2]++;
+            ungappedCount++;
+          }
         }
       }
       codonCounts[1] = ungappedCount;
@@ -621,8 +624,11 @@ public class AAFrequency
       String modalCodon = String.valueOf(CodingUtils
               .decodeCodon(modalCodonEncoded));
       if (sortedCodonCounts.length > 1
-              && sortedCodonCounts[codons.length - 2] == modalCodonEncoded)
+              && sortedCodonCounts[codons.length - 2] == sortedCodonCounts[codons.length - 1])
       {
+        /*
+         * two or more codons share the modal count
+         */
         modalCodon = "+";
       }
       float pid = sortedCodonCounts[sortedCodonCounts.length - 1] * 100