JAL-2505 use constructors to set (what will be) final fields in

[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 d32933a..2d0e3fe 100644 (file)
--- a/src/jalview/ext/ensembl/EnsemblSeqProxy.java
+++ b/src/jalview/ext/ensembl/EnsemblSeqProxy.java
@@ -214,7 +214,7 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient
       EnsemblFeatureType[] features = getFeaturesToFetch();
       AlignmentI geneFeatures = gffFetcher.getSequenceRecords(accId,
               features);
-      if (geneFeatures.getHeight() > 0)
+      if (geneFeatures != null && geneFeatures.getHeight() > 0)
       {
         genomicSequence = geneFeatures.getSequenceAt(0);
       }
@@ -658,13 +658,15 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient
 
     if (mappedRange != null)
     {
-      SequenceFeature copy = new SequenceFeature(sf);
-      copy.setBegin(Math.min(mappedRange[0], mappedRange[1]));
-      copy.setEnd(Math.max(mappedRange[0], mappedRange[1]));
-      if (".".equals(copy.getFeatureGroup()))
+      String group = sf.getFeatureGroup();
+      if (".".equals(group))
       {
-        copy.setFeatureGroup(getDbSource());
+        group = getDbSource();
       }
+      int newBegin = Math.min(mappedRange[0], mappedRange[1]);
+      int newEnd = Math.max(mappedRange[0], mappedRange[1]);
+      SequenceFeature copy = new SequenceFeature(sf, newBegin, newEnd,
+              group);
       targetSequence.addSequenceFeature(copy);
 
       /*