JAL-3449 merge from develop

[jalview.git] / src / jalview / ext / ensembl / EnsemblSeqProxy.java

diff --git a/src/jalview/ext/ensembl/EnsemblSeqProxy.java b/src/jalview/ext/ensembl/EnsemblSeqProxy.java
index 5dc701d..b22b9c7 100644 (file)
--- a/src/jalview/ext/ensembl/EnsemblSeqProxy.java
+++ b/src/jalview/ext/ensembl/EnsemblSeqProxy.java
@@ -330,8 +330,8 @@ 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)
     {
@@ -724,18 +724,6 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient
     String comp = complement.toString();
     sf.setValue(Gff3Helper.ALLELES, comp);
     sf.setDescription(comp);
-
-    /*
-     * replace value of "alleles=" in sf.ATTRIBUTES as well
-     * so 'output as GFF' shows reverse complement alleles
-     */
-    String atts = sf.getAttributes();
-    if (atts != null)
-    {
-      atts = atts.replace(Gff3Helper.ALLELES + "=" + alleles,
-              Gff3Helper.ALLELES + "=" + comp);
-      sf.setAttributes(atts);
-    }
   }
 
   /**