X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FDna.java;h=5096ae82bf269fd24d797afd08b1970f20c858bc;hb=ff385fde554b8fe517dbb734ca687ef7552f2350;hp=836c39ef2f9a96462ce454a7d7ed4efec1af9785;hpb=4484ac6bdcc92f0e0e430f64d3587f026fafb476;p=jalview.git

diff --git a/src/jalview/analysis/Dna.java b/src/jalview/analysis/Dna.java
index 836c39e..5096ae8 100644
--- a/src/jalview/analysis/Dna.java
+++ b/src/jalview/analysis/Dna.java
@@ -197,28 +197,36 @@ public class Dna {
         if (annotations[i].autoCalculated) {
           continue;
         }
-
-        aSize = aslen; // aa alignment width.
-        jalview.datamodel.Annotation[] anots =
-          new jalview.datamodel.Annotation[aSize];
         
-        for (a = 0; a < aSize; a++)
+        aSize = aslen; // aa alignment width.
+        jalview.datamodel.Annotation[] anots = 
+          (annotations[i].annotations==null) 
+          ? null :
+            new jalview.datamodel.Annotation[aSize];
+        if (anots!=null)
         {
-          // process through codon map.
-          if (codons[a]!=null && codons[a][0]==(codons[a][2]-2))
+          for (a = 0; a < aSize; a++)
           {
-            pos = codons[a][0];
-            if (annotations[i].annotations[pos] == null
-                || annotations[i].annotations[pos] == null)
-              continue;
+            // process through codon map.
+            if (codons[a]!=null && codons[a][0]==(codons[a][2]-2))
+            {
+              pos = codons[a][0];
+              if (annotations[i].annotations[pos] == null
+                      || annotations[i].annotations[pos] == null)
+                continue;
             
-            anots[a] = new Annotation(annotations[i].annotations[pos]);
+              anots[a] = new Annotation(annotations[i].annotations[pos]);
+            }
           }
         }
 
         jalview.datamodel.AlignmentAnnotation aa
         = new jalview.datamodel.AlignmentAnnotation(annotations[i].label,
             annotations[i].description, anots);
+        if (annotations[i].hasScore)
+        {
+          aa.setScore(annotations[i].getScore());
+        }
         al.addAnnotation(aa);
       }
     }