Jalview-JS/JAL-3253-applet

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

diff --git a/src/jalview/gui/CrossRefAction.java b/src/jalview/gui/CrossRefAction.java
index 85f2498..cc2e0a9 100644 (file)
--- a/src/jalview/gui/CrossRefAction.java
+++ b/src/jalview/gui/CrossRefAction.java
@@ -276,15 +276,15 @@ public class CrossRefAction implements Runnable
       return;
     }
     
-    Set<String> ensemblDivisions = new EnsemblInfo().getDivisions();
+    Set<String> ensemblDivisions = EnsemblInfo.getDivisions();
     
     /*
      * first look for direct dbrefs from sequence to Ensembl
      */
     String[] divisionsArray = ensemblDivisions
             .toArray(new String[ensemblDivisions.size()]);
-    DBRefEntry[] seqRefs = seq.getDBRefs();
-    DBRefEntry[] directEnsemblRefs = DBRefUtils.selectRefs(seqRefs,
+    List<DBRefEntry> seqRefs = seq.getDBRefs();
+    List<DBRefEntry> directEnsemblRefs = DBRefUtils.selectRefs(seqRefs,
             divisionsArray);
     if (directEnsemblRefs != null)
     {
@@ -304,8 +304,8 @@ public class CrossRefAction implements Runnable
     {
       if (dbref.getMap() != null && dbref.getMap().getTo() != null)
       {
-        DBRefEntry[] dbrefs = dbref.getMap().getTo().getDBRefs();
-        DBRefEntry[] indirectEnsemblRefs = DBRefUtils.selectRefs(dbrefs,
+        List<DBRefEntry> dbrefs = dbref.getMap().getTo().getDBRefs();
+        List<DBRefEntry> indirectEnsemblRefs = DBRefUtils.selectRefs(dbrefs,
                 divisionsArray);
         if (indirectEnsemblRefs != null)
         {
@@ -437,7 +437,7 @@ public class CrossRefAction implements Runnable
             .setGapCharacter(alignFrame.viewport.getGapCharacter());
 
     StructureSelectionManager ssm = StructureSelectionManager
-            .getStructureSelectionManager(Desktop.instance);
+            .getStructureSelectionManager(Desktop.getInstance());
 
     /*
      * register any new mappings for sequence mouseover etc