From: Jim Procter Date: Wed, 28 Oct 2020 22:56:38 +0000 (+0000) Subject: JAL-3725 patch EMBL flat file to exclude stop codon from the mapping (for 2.11.1... X-Git-Tag: Release_2_11_1_3~5^2~2 X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=commitdiff_plain;h=a4b5b8219c60353fa9c0dbac0ff52c3beaf3c055;hp=c6018dc0dc12720e13b75850a5303279ac7094b7 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) --- 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; }