From a4b5b8219c60353fa9c0dbac0ff52c3beaf3c055 Mon Sep 17 00:00:00 2001 From: Jim Procter Date: Wed, 28 Oct 2020 22:56:38 +0000 Subject: [PATCH] JAL-3725 patch EMBL flat file to exclude stop codon from the mapping (for 2.11.1.3 - needs cherry-pick to 2.11.2) --- src/jalview/io/EmblFlatFile.java | 6 ++---- 1 file changed, 2 insertions(+), 4 deletions(-) diff --git a/src/jalview/io/EmblFlatFile.java b/src/jalview/io/EmblFlatFile.java index bfae4ed..21e66d2 100644 --- a/src/jalview/io/EmblFlatFile.java +++ b/src/jalview/io/EmblFlatFile.java @@ -841,11 +841,9 @@ public class EmblFlatFile extends AlignFile // FileParse int exonLength = MappingUtils.getLength(Arrays.asList(exon)); /* - * if exon length matches protein, or is shorter, or longer by the - * length of a stop codon (3 bases), then leave it unchanged + * if exon length matches protein, or is shorter, then leave it unchanged */ - if (expectedCdsLength >= exonLength - || expectedCdsLength == exonLength - 3) + if (expectedCdsLength >= exonLength) { return exon; } -- 1.7.10.2