JAL-2023 fix for CDS shared dataset, robust load of split frame project

[jalview.git] / src / jalview / gui / Jalview2XML.java

diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java
index 6fea041..ce8d2dd 100644 (file)
--- a/src/jalview/gui/Jalview2XML.java
+++ b/src/jalview/gui/Jalview2XML.java
@@ -163,7 +163,7 @@ public class Jalview2XML
    */
   Map<String, SequenceI> seqRefIds = null;
 
-  Vector frefedSequence = null;
+  Vector<Object[]> frefedSequence = null;
 
   boolean raiseGUI = true; // whether errors are raised in dialog boxes or not
 
@@ -258,7 +258,7 @@ public class Jalview2XML
       int r = 0, rSize = frefedSequence.size();
       while (r < rSize)
       {
-        Object[] ref = (Object[]) frefedSequence.elementAt(r);
+        Object[] ref = frefedSequence.elementAt(r);
         if (ref != null)
         {
           String sref = (String) ref[0];
@@ -2178,6 +2178,7 @@ public class Jalview2XML
       {
         SwingUtilities.invokeAndWait(new Runnable()
         {
+          @Override
           public void run()
           {
             setLoadingFinishedForNewStructureViewers();
@@ -2252,7 +2253,7 @@ public class Jalview2XML
     }
     if (frefedSequence == null)
     {
-      frefedSequence = new Vector();
+      frefedSequence = new Vector<Object[]>();
     }
 
     AlignFrame af = null, _af = null;
@@ -2848,7 +2849,7 @@ public class Jalview2XML
             {
               mapping = addMapping(maps[m].getMapping());
             }
-            if (dnaseq != null)
+            if (dnaseq != null && mapping.getTo() != null)
             {
               cf.addMap(dnaseq, mapping.getTo(), mapping.getMap());
             }
@@ -5088,7 +5089,7 @@ public class Jalview2XML
     }
     if (this.frefedSequence == null)
     {
-      frefedSequence = new Vector();
+      frefedSequence = new Vector<Object[]>();
     }
 
     viewportsAdded.clear();