X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FAlignmentUtils.java;fp=src%2Fjalview%2Fanalysis%2FAlignmentUtils.java;h=d04d810e3c102a12aea5c1e7c30c925bf7b1e91c;hp=d8c1cdff513f4bd63ec26f58c1d18a1e134941c6;hb=fd25ac2905528f9c2cf784317cc3d150c9167755;hpb=ca4805d04d23cb913e80363023d1e75cee4972be

diff --git a/src/jalview/analysis/AlignmentUtils.java b/src/jalview/analysis/AlignmentUtils.java
index d8c1cdf..d04d810 100644
--- a/src/jalview/analysis/AlignmentUtils.java
+++ b/src/jalview/analysis/AlignmentUtils.java
@@ -979,10 +979,10 @@ public class AlignmentUtils
                   .getFromRanges());
           int mappedToLength = MappingUtils
                   .getLength(mapList.getToRanges());
-          boolean addStopCodon = (cdsLength == mappedFromLength
+          boolean addStopCodon = peptide.getDatasetSequence().getEnd()==peptide.getEnd() && ((cdsLength == mappedFromLength
                   * CODON_LENGTH + CODON_LENGTH)
                   || (peptide.getDatasetSequence()
-                          .getLength() == mappedFromLength - 1);
+                          .getLength() == mappedFromLength - 1));
           if (cdsLength != mappedToLength && !addStopCodon)
           {
             System.err.println(String.format(