Merge branch 'develop' into feature/JAL-2759

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

diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java
index a64a475..c7ec757 100644 (file)
--- a/src/jalview/gui/Jalview2XML.java
+++ b/src/jalview/gui/Jalview2XML.java
@@ -1056,7 +1056,7 @@ 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
@@ -1074,7 +1074,7 @@ 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);
 
@@ -1389,9 +1389,10 @@ public class Jalview2XML
         }
         else
         {
-          ArrayList<int[]> hiddenRegions = hidden.getHiddenColumnsCopy();
-          for (int[] region : hiddenRegions)
+          Iterator<int[]> hiddenRegions = hidden.iterator();
+          while (hiddenRegions.hasNext())
           {
+            int[] region = hiddenRegions.next();
             HiddenColumns hc = new HiddenColumns();
             hc.setStart(region[0]);
             hc.setEnd(region[1]);
@@ -2267,6 +2268,7 @@ public class Jalview2XML
 
       jarInputStreamProvider jprovider = createjarInputStreamProvider(file);
       af = loadJalviewAlign(jprovider);
+      af.setMenusForViewport();
 
     } catch (MalformedURLException e)
     {
@@ -4221,7 +4223,8 @@ 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