From: jprocter <Jim Procter>
Date: Wed, 24 Jun 2009 08:22:47 +0000 (+0000)
Subject: take the average of the three consecutive codon sites when translating annotation... 
X-Git-Tag: Release_2_5~241
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=1e5fe67a3cfd5b0dbae0847d3cff7dc93c31f174;hp=b685f8d04ee267818d28c4377fe2ae4778082cd0;p=jalview.git

take the average of the three consecutive codon sites when translating annotation row scores from cDNA to protein.
---

diff --git a/src/jalview/analysis/Dna.java b/src/jalview/analysis/Dna.java
index ce13665..5ff6751 100644
--- a/src/jalview/analysis/Dna.java
+++ b/src/jalview/analysis/Dna.java
@@ -364,14 +364,44 @@ public class Dna
   {
     // Have a look at all the codon positions for annotation and put the first
     // one found into the translated annotation pos.
+    int contrib=0;
+    Annotation annot = null;
     for (int p = 0; p < 3; p++)
     {
       if (annotations[is[p]] != null)
       {
-        return new Annotation(annotations[is[p]]);
+        if (annot==null) {
+          annot = new Annotation(annotations[is[p]]);
+          contrib = 1;
+        } else {
+          // merge with last
+          Annotation cpy = new Annotation(annotations[is[p]]);
+          if (annot.colour==null)
+          {
+            annot.colour = cpy.colour;
+          }
+          if (annot.description==null || annot.description.length()==0)
+          {
+            annot.description = cpy.description;
+          }
+          if (annot.displayCharacter==null)
+          {
+            annot.displayCharacter = cpy.displayCharacter;
+          }
+          if (annot.secondaryStructure==0)
+          {
+            annot.secondaryStructure = cpy.secondaryStructure;
+          }
+          annot.value+=cpy.value;
+          contrib++;
+        }
       }
     }
-    return null;
+    if (contrib>1)
+    {
+      annot.value/=(float)contrib;
+    }
+    return annot;
   }
 
   /**