JAL-3116 parse EMBL XML with JAXB (todo: update unit tests)

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

diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java
index 9285754..87b8d87 100644 (file)
--- a/src/jalview/gui/Jalview2XML.java
+++ b/src/jalview/gui/Jalview2XML.java
@@ -1102,13 +1102,13 @@ public class Jalview2XML
           {
             TreePanel tp = (TreePanel) frames[t];
 
-            if (tp.treeCanvas.av.getAlignment() == jal)
+            if (tp.getTreeCanvas().getViewport().getAlignment() == jal)
             {
               Tree tree = new Tree();
               tree.setTitle(tp.getTitle());
               tree.setCurrentTree((av.getCurrentTree() == tp.getTree()));
               tree.setNewick(tp.getTree().print());
-              tree.setThreshold(tp.treeCanvas.threshold);
+              tree.setThreshold(tp.getTreeCanvas().getThreshold());
 
               tree.setFitToWindow(tp.fitToWindow.getState());
               tree.setFontName(tp.getTreeFont().getName());
@@ -1247,7 +1247,7 @@ public class Jalview2XML
       {
         view.setComplementId(av.getCodingComplement().getViewId());
       }
-      view.setViewName(av.viewName);
+      view.setViewName(av.getViewName());
       view.setGatheredViews(av.isGatherViewsHere());
 
       Rectangle size = ap.av.getExplodedGeometry();
@@ -3763,11 +3763,11 @@ public class Jalview2XML
           tp.setTitle(tree.getTitle());
           tp.setBounds(new Rectangle(tree.getXpos(), tree.getYpos(),
                   tree.getWidth(), tree.getHeight()));
-          tp.av = av; // af.viewport; // TODO: verify 'associate with all
+          tp.setViewport(av); // af.viewport; // TODO: verify 'associate with all
           // views'
           // works still
-          tp.treeCanvas.av = av; // af.viewport;
-          tp.treeCanvas.ap = ap; // af.alignPanel;
+          tp.getTreeCanvas().setViewport(av); // af.viewport;
+          tp.getTreeCanvas().setAssociatedPanel(ap); // af.alignPanel;
 
         }
         if (tp == null)
@@ -3795,7 +3795,7 @@ public class Jalview2XML
         tp.showBootstrap(tree.getShowBootstrap());
         tp.showDistances(tree.getShowDistances());
 
-        tp.treeCanvas.threshold = tree.getThreshold();
+        tp.getTreeCanvas().setThreshold(tree.getThreshold());
 
         if (tree.getCurrentTree())
         {
@@ -4528,7 +4528,7 @@ public class Jalview2XML
 
     if (view.getViewName() != null)
     {
-      af.viewport.viewName = view.getViewName();
+      af.viewport.setViewName(view.getViewName());
       af.setInitialTabVisible();
     }
     af.setBounds(view.getXpos(), view.getYpos(), view.getWidth(),