Merge branch 'develop' into JAL-1705_trialMerge
[jalview.git] / src / jalview / gui / Jalview2XML.java
index fc96edc..3f3e8f6 100644 (file)
@@ -761,10 +761,11 @@ public class Jalview2XML
           if (sf[index].otherDetails != null)
           {
             String key;
-            Enumeration keys = sf[index].otherDetails.keys();
-            while (keys.hasMoreElements())
+            Iterator<String> keys = sf[index].otherDetails.keySet()
+                    .iterator();
+            while (keys.hasNext())
             {
-              key = keys.nextElement().toString();
+              key = keys.next();
               OtherData keyValue = new OtherData();
               keyValue.setKey(key);
               keyValue.setValue(sf[index].otherDetails.get(key).toString());
@@ -879,7 +880,7 @@ public class Jalview2XML
     // SAVE MAPPINGS
     if (jal.getCodonFrames() != null)
     {
-      Set<AlignedCodonFrame> jac = jal.getCodonFrames();
+      List<AlignedCodonFrame> jac = jal.getCodonFrames();
       for (AlignedCodonFrame acf : jac)
       {
         AlcodonFrame alc = new AlcodonFrame();
@@ -2178,6 +2179,7 @@ public class Jalview2XML
       {
         SwingUtilities.invokeAndWait(new Runnable()
         {
+          @Override
           public void run()
           {
             setLoadingFinishedForNewStructureViewers();