X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fgui%2FJalview2XML.java;h=9e319c1f38e2b6d581c4c4b5626b22bb0c73615b;hb=062ebc02980364930ceb26dd6c06448af971fe20;hp=b3572346b6413473df322dd8da0f87e54d12b4be;hpb=a181d953c856f070b327014888971670e2662ec1;p=jalview.git

diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java
index b357234..9e319c1 100644
--- a/src/jalview/gui/Jalview2XML.java
+++ b/src/jalview/gui/Jalview2XML.java
@@ -1084,7 +1084,7 @@ public class Jalview2XML
 
     // SAVE TREES
     // /////////////////////////////////
-    if (!storeDS && av.currentTree != null)
+    if (!storeDS && av.getCurrentTree() != null)
     {
       // FIND ANY ASSOCIATED TREES
       // NOT IMPLEMENTED FOR HEADLESS STATE AT PRESENT
@@ -1102,7 +1102,7 @@ public class Jalview2XML
             {
               Tree tree = new Tree();
               tree.setTitle(tp.getTitle());
-              tree.setCurrentTree((av.currentTree == tp.getTree()));
+              tree.setCurrentTree((av.getCurrentTree() == tp.getTree()));
               tree.setNewick(tp.getTree().print());
               tree.setThreshold(tp.treeCanvas.threshold);
 
@@ -4250,7 +4250,8 @@ public class Jalview2XML
       StructureData filedat = oldFiles.get(id);
       String pdbFile = filedat.getFilePath();
       SequenceI[] seq = filedat.getSeqList().toArray(new SequenceI[0]);
-      binding.getSsm().setMapping(seq, null, pdbFile, DataSourceType.FILE);
+      binding.getSsm().setMapping(seq, null, pdbFile, DataSourceType.FILE,
+              null);
       binding.addSequenceForStructFile(pdbFile, seq);
     }
     // and add the AlignmentPanel's reference to the view panel