fixed jalview 2.3 bug where gapped aligned codons were always translated as inserted...

diff --git a/src/jalview/analysis/Dna.java b/src/jalview/analysis/Dna.java
index 5096ae8..48d03b3 100644 (file)
--- a/src/jalview/analysis/Dna.java
+++ b/src/jalview/analysis/Dna.java
@@ -116,6 +116,7 @@ public class Dna {
                 newSeq[sq].insertCharAt(aspos, gapCharacter);\r
               }\r
               System.arraycopy(codons, aspos, codons, aspos+1, aslen-aspos);\r
                 newSeq[sq].insertCharAt(aspos, gapCharacter);\r
               }\r
               System.arraycopy(codons, aspos, codons, aspos+1, aslen-aspos);\r

+              codons[aspos]=null; // clear so new codon position can be marked.\r

               findpos=false;\r
               break;\r
             case +1:\r
               findpos=false;\r
               break;\r
             case +1:\r