JAL-2023 CDS sequences added to / share alignment dataset

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

diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java
index 3f3e8f6..2799a7e 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];
@@ -2254,7 +2254,7 @@ public class Jalview2XML
     }
     if (frefedSequence == null)
     {
-      frefedSequence = new Vector();
+      frefedSequence = new Vector<Object[]>();
     }
 
     AlignFrame af = null, _af = null;
@@ -2850,7 +2850,7 @@ public class Jalview2XML
             {
               mapping = addMapping(maps[m].getMapping());
             }
-            if (dnaseq != null)
+            if (dnaseq != null && mapping.getTo() != null)
             {
               cf.addMap(dnaseq, mapping.getTo(), mapping.getMap());
             }