X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=blobdiff_plain;f=src%2Fjalview%2Fio%2FEMBLLikeFlatFile.java;h=8fba76c53dfd89473725ec77f3ee62ebbbfff543;hp=9e8cff6c7b32cc08117d2a890ae4e8774d06bc27;hb=56b18f65d6718fc6cfd7eeae53fdec97fdc7a360;hpb=a1984b1c8c273ed33c7ce9283039f4027dcae2de

diff --git a/src/jalview/io/EMBLLikeFlatFile.java b/src/jalview/io/EMBLLikeFlatFile.java
index 9e8cff6..8fba76c 100644
--- a/src/jalview/io/EMBLLikeFlatFile.java
+++ b/src/jalview/io/EMBLLikeFlatFile.java
@@ -83,8 +83,7 @@ public abstract class EMBLLikeFlatFile extends AlignFile
 
   /**
    * Truncates (if necessary) the exon intervals to match 3 times the length of
-   * the protein; also accepts 3 bases longer (for stop codon not included in
-   * protein)
+   * the protein(including truncation for stop codon included in exon)
    * 
    * @param proteinLength
    * @param exon
@@ -102,11 +101,9 @@ public abstract class EMBLLikeFlatFile extends AlignFile
     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;
     }