Merge branch 'develop' into features/JAL-2110_makeSenseOfCrossRef

[jalview.git] / src / jalview / gui / SequenceFetcher.java

diff --git a/src/jalview/gui/SequenceFetcher.java b/src/jalview/gui/SequenceFetcher.java
index e567d20..85ea20b 100755 (executable)
--- a/src/jalview/gui/SequenceFetcher.java
+++ b/src/jalview/gui/SequenceFetcher.java
@@ -407,6 +407,10 @@ public class SequenceFetcher extends JPanel implements Runnable
     this.add(jPanel2, java.awt.BorderLayout.NORTH);
     jScrollPane1.getViewport().add(textArea);
 
+    /*
+     * open the database tree
+     */
+    database.waitForInput();
   }
 
   private void pdbSourceAction()
@@ -813,10 +817,8 @@ public class SequenceFetcher extends JPanel implements Runnable
       Cache.log.info(
               "Error retrieving " + accession
               + " from " + proxy.getDbName(), e);
-    } finally
-    {
-      return success;
     }
+    return success;
   }
 
   /**
@@ -836,7 +838,6 @@ public class SequenceFetcher extends JPanel implements Runnable
 
     for (String q : queries)
     {
-      DBRefEntry[] found = null;
       DBRefEntry dbr = new DBRefEntry();
       dbr.setSource(proxy.getDbSource());
       dbr.setVersion(null);
@@ -847,8 +848,9 @@ public class SequenceFetcher extends JPanel implements Runnable
       {
         if (rs[r] != null)
         {
-          found = DBRefUtils.searchRefs(rs[r].getDBRefs(), accId);
-          if (found != null && found.length > 0)
+          List<DBRefEntry> found = DBRefUtils.searchRefs(rs[r].getDBRefs(),
+                  accId);
+          if (!found.isEmpty())
           {
             rfound = true;
             break;