From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Fri, 25 Jan 2019 09:19:31 +0000 (+0000)
Subject: JAL-3187 don't compute variant features on peptide, show on demand
X-Git-Tag: Release_2_11_1_0~66
X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=commitdiff_plain;h=6a102719db960765b1e7111b7f51227248eaa802

JAL-3187 don't compute variant features on peptide, show on demand
---

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
       {