JAL-2617 omit stop codon from synthesized CDS sequence

[jalview.git] / src / jalview / analysis / AlignmentUtils.java

diff --git a/src/jalview/analysis/AlignmentUtils.java b/src/jalview/analysis/AlignmentUtils.java
index 2b9b9f9..311a9a3 100644 (file)
--- a/src/jalview/analysis/AlignmentUtils.java
+++ b/src/jalview/analysis/AlignmentUtils.java
@@ -2200,7 +2200,10 @@ public class AlignmentUtils
     {
       // assuming extra codon is for STOP and not in peptide
       codesForResidues--;
+      mappedDnaLength -= CODON_LENGTH;
+      MappingUtils.removeEndPositions(CODON_LENGTH, ranges);
     }
+
     if (codesForResidues == proteinLength)
     {
       proteinRange.add(new int[] { proteinStart, proteinEnd });
@@ -2211,7 +2214,7 @@ public class AlignmentUtils
 
   /**
    * Returns a list of CDS ranges found (as sequence positions base 1), i.e. of
-   * start/end positions of sequence features of type "CDS" (or a sub-type of
+   * [start, end] positions of sequence features of type "CDS" (or a sub-type of
    * CDS in the Sequence Ontology). The ranges are sorted into ascending start
    * position order, so this method is only valid for linear CDS in the same
    * sense as the protein product.