JAL-3725 patch EMBL flat file to exclude stop codon from the mapping (for 2.11.1...

diff --git a/src/jalview/io/EmblFlatFile.java b/src/jalview/io/EmblFlatFile.java
index bfae4ed..21e66d2 100644 (file)
--- a/src/jalview/io/EmblFlatFile.java
+++ b/src/jalview/io/EmblFlatFile.java
@@ -841,11 +841,9 @@ public class EmblFlatFile extends AlignFile // FileParse
     int exonLength = MappingUtils.getLength(Arrays.asList(exon));
 
     /*
-     * if exon length matches protein, or is shorter, or longer by the 
-     * length of a stop codon (3 bases), then leave it unchanged
+     * if exon length matches protein, or is shorter, then leave it unchanged
      */
-    if (expectedCdsLength >= exonLength
-            || expectedCdsLength == exonLength - 3)
+    if (expectedCdsLength >= exonLength)
     {
       return exon;
     }