3253-omnibus save

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

diff --git a/src/jalview/ext/ensembl/EnsemblFeatures.java b/src/jalview/ext/ensembl/EnsemblFeatures.java
index e4c4365..e28cc7f 100644 (file)
--- a/src/jalview/ext/ensembl/EnsemblFeatures.java
+++ b/src/jalview/ext/ensembl/EnsemblFeatures.java
@@ -27,7 +27,9 @@ import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceI;
 import jalview.io.gff.SequenceOntologyI;
 import jalview.util.JSONUtils;
+import jalview.util.Platform;
 
+import java.io.BufferedReader;
 import java.io.IOException;
 import java.net.MalformedURLException;
 import java.net.URL;
@@ -93,7 +95,10 @@ class EnsemblFeatures extends EnsemblRestClient
     List<String> queries = new ArrayList<>();
     queries.add(query);
     SequenceI seq = parseFeaturesJson(queries);
+    if (seq == null)
+       return null;
     return new Alignment(new SequenceI[] { seq });
+
   }
 
   /**
@@ -124,6 +129,7 @@ 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 phase = obj.get("phase");
           String alleles = JSONUtils
                   .arrayToStringList((List<Object>) obj.get("alleles"));
           String clinSig = JSONUtils
@@ -149,6 +155,10 @@ 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");