Merge remote-tracking branch

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

diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java
index 962dc0d..6361caf 100644 (file)
--- a/src/jalview/gui/Jalview2XML.java
+++ b/src/jalview/gui/Jalview2XML.java
@@ -1107,7 +1107,7 @@ public class Jalview2XML
               Tree tree = new Tree();
               tree.setTitle(tp.getTitle());
               tree.setCurrentTree((av.currentTree == tp.getTree()));
-              tree.setNewick(tp.getTree().toString());
+              tree.setNewick(tp.getTree().print());
               tree.setThreshold(tp.treeCanvas.threshold);
 
               tree.setFitToWindow(tp.fitToWindow.getState());
@@ -1415,16 +1415,16 @@ public class Jalview2XML
       {
         jalview.datamodel.HiddenColumns hidden = av.getAlignment()
                 .getHiddenColumns();
-        if (hidden == null || hidden.getListOfCols() == null)
+        if (hidden == null || hidden.getHiddenRegions() == null)
         {
           warn("REPORT BUG: avoided null columnselection bug (DMAM reported). Please contact Jim about this.");
         }
         else
         {
-          for (int c = 0; c < hidden.getListOfCols()
+          for (int c = 0; c < hidden.getHiddenRegions()
                   .size(); c++)
           {
-            int[] region = hidden.getListOfCols()
+            int[] region = hidden.getHiddenRegions()
                     .get(c);
             HiddenColumns hc = new HiddenColumns();
             hc.setStart(region[0]);
@@ -3681,7 +3681,7 @@ public class Jalview2XML
         TreePanel tp = (TreePanel) retrieveExistingObj(tree.getId());
         if (tp == null)
         {
-          tp = af.ShowNewickTree(
+          tp = af.showNewickTree(
                   new jalview.io.NewickFile(tree.getNewick()),
                   tree.getTitle(), tree.getWidth(), tree.getHeight(),
                   tree.getXpos(), tree.getYpos());