X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FJalview2XML.java;h=2799a7e2921d5867352c63a98e0fe635b57ce2d7;hb=39d0e8bf8f541357c21ca322b939835b9f5e5561;hp=96abf81aaef44c08f79fc4c17679dce257fa9bc8;hpb=51f05d7903402a5dec8e915fbe5e49ce913d069a;p=jalview.git

diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java
index 96abf81..2799a7e 100644
--- 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];
@@ -1949,16 +1949,16 @@ public class Jalview2XML
     if (jds.getDatasetSequence() != null)
     {
       vamsasSeq.setDsseqid(seqHash(jds.getDatasetSequence()));
-      if (jds.getDatasetSequence().getDBRef() != null)
+      if (jds.getDatasetSequence().getDBRefs() != null)
       {
-        dbrefs = jds.getDatasetSequence().getDBRef();
+        dbrefs = jds.getDatasetSequence().getDBRefs();
       }
     }
     else
     {
       vamsasSeq.setDsseqid(id); // so we can tell which sequences really are
       // dataset sequences only
-      dbrefs = jds.getDBRef();
+      dbrefs = jds.getDBRefs();
     }
     if (dbrefs != null)
     {
@@ -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());
             }