From: Jim Procter <jprocter@issues.jalview.org>
Date: Tue, 27 Oct 2020 10:54:58 +0000 (+0000)
Subject: JAL-3700 JAL-3748 JAL-3763 don’t add stop codon via alignAs if guide peptide doesn... 
X-Git-Tag: Release_2_11_1_3~5^2~7
X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=commitdiff_plain;h=fd25ac2905528f9c2cf784317cc3d150c9167755

JAL-3700 JAL-3748 JAL-3763 don’t add stop codon via alignAs if guide peptide doesn’t include C terminus.
---

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(