From b1fee2fba97963cc6ca71fd575dbb12004efc692 Mon Sep 17 00:00:00 2001 From: James Procter Date: Thu, 11 Jan 2024 17:16:28 +0000 Subject: [PATCH] JAL-4366 use dataset sequences for building the mapping --- src/jalview/analysis/AlignmentUtils.java | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/src/jalview/analysis/AlignmentUtils.java b/src/jalview/analysis/AlignmentUtils.java index af3669f..9675232 100644 --- a/src/jalview/analysis/AlignmentUtils.java +++ b/src/jalview/analysis/AlignmentUtils.java @@ -1479,19 +1479,23 @@ public class AlignmentUtils List thisSeqs = proteinAlignment.getSequences(); for (SequenceI aaSeq : thisSeqs) { + aaSeq = aaSeq.getDatasetSequence()!=null ? aaSeq.getDatasetSequence():null; boolean proteinMapped = false; AlignedCodonFrame acf = new AlignedCodonFrame(); for (SequenceI cdnaSeq : tdiAlignment.getSequences()) { + // resolve dataset sequences + cdnaSeq = cdnaSeq.getDatasetSequence()!=null ? cdnaSeq.getDatasetSequence():null; if (mappingExists(proteinAlignment.getCodonFrames(), - aaSeq.getDatasetSequence(), cdnaSeq.getDatasetSequence())) + aaSeq, cdnaSeq)) { mappingExistsOrAdded = true; } else { + if (canBuild3diMapping(aaSeq, cdnaSeq)) { MapList map = new MapList(new int[] { aaSeq.getStart(),aaSeq.getEnd()},new int[] { cdnaSeq.getStart(),cdnaSeq.getEnd()},1,1); -- 1.7.10.2