X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fext%2Fensembl%2FEnsemblFeatures.java;h=99ebc69a0349fa2d2ba1bfe8cc2423ca6fccc69b;hb=6a7ffd7997c11b84a81acbdd83e462cac76f124b;hp=a133381d51c7043ac54b5d8fd8b3a10031307851;hpb=cd268aa5e06c4327489110c59c987e3e071eb038;p=jalview.git

diff --git a/src/jalview/ext/ensembl/EnsemblFeatures.java b/src/jalview/ext/ensembl/EnsemblFeatures.java
index a133381..99ebc69 100644
--- a/src/jalview/ext/ensembl/EnsemblFeatures.java
+++ b/src/jalview/ext/ensembl/EnsemblFeatures.java
@@ -26,6 +26,7 @@ import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceI;
 import jalview.io.gff.SequenceOntologyI;
+import jalview.util.JSONUtils;
 
 import java.io.BufferedReader;
 import java.io.IOException;
@@ -129,15 +130,12 @@ class EnsemblFeatures extends EnsemblRestClient
           int end = Integer.parseInt(obj.get("end").toString());
           String source = obj.get("source").toString();
           String strand = obj.get("strand").toString();
-          Object value = obj.get("consequence_type");
-          value = obj.get("alleles");
-          JSONArray allelesArray = (JSONArray) value;
-          String alleles = allelesArray == null ? null
-                  : allelesArray.toString(); // todo need as a List?
-          value = obj.get("clinical_significance");
-          JSONArray clinSigArray = (JSONArray) value;
-          String clinSig = clinSigArray == null ? null
-                  : clinSigArray.toString();
+          Object phase = obj.get("phase");
+          String alleles = JSONUtils
+                  .arrayToList((JSONArray) obj.get("alleles"));
+          String clinSig = JSONUtils
+                  .arrayToList(
+                          (JSONArray) obj.get("clinical_significance"));
 
           /*
            * convert 'variation' to 'sequence_variant', and 'cds' to 'CDS'
@@ -158,6 +156,10 @@ class EnsemblFeatures extends EnsemblRestClient
           SequenceFeature sf = new SequenceFeature(type, desc, start, end,
                   source);
           sf.setStrand("1".equals(strand) ? "+" : "-");
+          if (phase != null)
+          {
+            sf.setPhase(phase.toString());
+          }
           setFeatureAttribute(sf, obj, "id");
           setFeatureAttribute(sf, obj, "Parent");
           setFeatureAttribute(sf, obj, "consequence_type");
@@ -179,7 +181,9 @@ class EnsemblFeatures extends EnsemblRestClient
   }
 
   /**
-   * Returns the first non-null attribute found (if any) as a string
+   * Returns the first non-null attribute found (if any) as a string, formatted
+   * suitably for display as feature description or tooltip. Answers null if
+   * none of the attribute keys is present.
    * 
    * @param obj
    * @param keys
@@ -194,7 +198,9 @@ class EnsemblFeatures extends EnsemblRestClient
       Object val = obj.get(key);
       if (val != null)
       {
-        String s = val.toString();
+        String s = val instanceof JSONArray
+                ? JSONUtils.arrayToList((JSONArray) val)
+                : val.toString();
         if (!s.isEmpty())
         {
           return s;