X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=blobdiff_plain;f=src%2Fjalview%2Fio%2FEmblFlatFile.java;h=21e66d2eb60e847f1aed4da87b8e5f139d4327a4;hp=bfae4ed37eb64a446967420e9bfd40fbe8315aa9;hb=a4b5b8219c60353fa9c0dbac0ff52c3beaf3c055;hpb=c6018dc0dc12720e13b75850a5303279ac7094b7

diff --git a/src/jalview/io/EmblFlatFile.java b/src/jalview/io/EmblFlatFile.java
index bfae4ed..21e66d2 100644
--- 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;
     }