From b028e684c807365decd0c6e6111aa4bf368a6fa8 Mon Sep 17 00:00:00 2001 From: James Procter Date: Thu, 11 Jan 2024 17:17:15 +0000 Subject: [PATCH] JAL-4366 fix reconstruction of peptide alignment... --- src/jalview/datamodel/Alignment.java | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java index 73ccdc5..6532a2d 100755 --- a/src/jalview/datamodel/Alignment.java +++ b/src/jalview/datamodel/Alignment.java @@ -1830,7 +1830,13 @@ public class Alignment implements AlignmentI, AutoCloseable { return AlignmentUtils.alignCdsAsProtein(this, al); } - return AlignmentUtils.alignAs(this, al); + else if (thatIsProtein && !thisIsNucleotide) + { + // honour sense we were called - align this according to al + return AlignmentUtils.alignAs(this, al); + } + // otherwise doing a DNA to DNA alignment - so use legacy obverse sense + return AlignmentUtils.alignAs(al, this); } /** -- 1.7.10.2