From 6a102719db960765b1e7111b7f51227248eaa802 Mon Sep 17 00:00:00 2001 From: gmungoc Date: Fri, 25 Jan 2019 09:19:31 +0000 Subject: [PATCH] JAL-3187 don't compute variant features on peptide, show on demand --- src/jalview/ext/ensembl/EnsemblSeqProxy.java | 4 ++-- src/jalview/io/vcf/VCFLoader.java | 4 ++-- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/src/jalview/ext/ensembl/EnsemblSeqProxy.java b/src/jalview/ext/ensembl/EnsemblSeqProxy.java index 7b448fd..648272c 100644 --- a/src/jalview/ext/ensembl/EnsemblSeqProxy.java +++ b/src/jalview/ext/ensembl/EnsemblSeqProxy.java @@ -332,8 +332,8 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient * copy exon features to protein, compute peptide variants from dna * variants and add as features on the protein sequence ta-da */ - AlignmentUtils.computeProteinFeatures(querySeq, proteinSeq, - mapList); + // JAL-3187 render on the fly instead + // AlignmentUtils.computeProteinFeatures(querySeq, proteinSeq, mapList); } } catch (Exception e) { diff --git a/src/jalview/io/vcf/VCFLoader.java b/src/jalview/io/vcf/VCFLoader.java index de2f18a..ff57d82 100644 --- a/src/jalview/io/vcf/VCFLoader.java +++ b/src/jalview/io/vcf/VCFLoader.java @@ -1,6 +1,5 @@ package jalview.io.vcf; -import jalview.analysis.AlignmentUtils; import jalview.analysis.Dna; import jalview.api.AlignViewControllerGuiI; import jalview.bin.Cache; @@ -563,7 +562,8 @@ public class VCFLoader /* * dna-to-peptide product mapping */ - AlignmentUtils.computeProteinFeatures(seq, mapTo, map); + // JAL-3187 render on the fly instead + // AlignmentUtils.computeProteinFeatures(seq, mapTo, map); } else { -- 1.7.10.2