Merge branch 'develop' into feature/JAL-3187linkedFeatures

[jalview.git] / src / jalview / io / vcf / VCFLoader.java

diff --git a/src/jalview/io/vcf/VCFLoader.java b/src/jalview/io/vcf/VCFLoader.java
index 04c73b5..1ac9ad7 100644 (file)
--- 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;
@@ -382,6 +381,8 @@ public class VCFLoader
   {
     if (reference == null)
     {
+      Cache.log.error("No VCF ##reference found, defaulting to "
+              + DEFAULT_REFERENCE + ":" + DEFAULT_SPECIES);
       reference = DEFAULT_REFERENCE; // default to GRCh37 if not specified
     }
     reference = reference.toLowerCase();
@@ -652,7 +653,8 @@ 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
       {
@@ -735,7 +737,7 @@ public class VCFLoader
     String species = seqCoords.getSpeciesId();
     String chromosome = seqCoords.getChromosomeId();
     String seqRef = seqCoords.getAssemblyId();
-    MapList map = seqCoords.getMap();
+    MapList map = seqCoords.getMapping();
 
     // note this requires the configured species to match that
     // returned with the Ensembl sequence; todo: support aliases?