From fd25ac2905528f9c2cf784317cc3d150c9167755 Mon Sep 17 00:00:00 2001 From: Jim Procter Date: Tue, 27 Oct 2020 10:54:58 +0000 Subject: [PATCH] =?utf8?q?JAL-3700=20JAL-3748=20JAL-3763=20don=E2=80=99t=20a?= =?utf8?q?dd=20stop=20codon=20via=20alignAs=20if=20guide=20peptide=20doesn=E2?= =?utf8?q?=80=99t=20include=20C=20terminus.?= MIME-Version: 1.0 Content-Type: text/plain; charset=utf8 Content-Transfer-Encoding: 8bit --- src/jalview/analysis/AlignmentUtils.java | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) 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( -- 1.7.10.2