Trees aren't save in headless state in this version

diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java
index 403509d..70608c4 100755 (executable)
--- a/src/jalview/gui/Jalview2XML.java
+++ b/src/jalview/gui/Jalview2XML.java
@@ -134,6 +134,7 @@ public class Jalview2XML
         }\r
         catch (Exception ex)\r
         {\r
+          ex.printStackTrace();\r
         }\r
     }\r
 \r
@@ -199,38 +200,42 @@ public class Jalview2XML
         ///////////////////////////////////\r
         if (af.viewport.currentTree != null)\r
         {\r
-            // FIND ANY ASSOCIATED TREES\r
+          // FIND ANY ASSOCIATED TREES\r
+          // NOT IMPLEMENTED FOR HEADLESS STATE AT PRESENT\r
+          if (Desktop.desktop != null)\r
+          {\r
             JInternalFrame[] frames = Desktop.desktop.getAllFrames();\r
 \r
             for (int t = 0; t < frames.length; t++)\r
             {\r
-                if (frames[t] instanceof TreePanel)\r
-                {\r
-                    TreePanel tp = (TreePanel) frames[t];\r
+              if (frames[t] instanceof TreePanel)\r
+              {\r
+                TreePanel tp = (TreePanel) frames[t];\r
 \r
-                    if (tp.treeCanvas.av.alignment == jal)\r
-                    {\r
-                        Tree tree = new Tree();\r
-                        tree.setTitle(tp.getTitle());\r
-                        tree.setCurrentTree((af.viewport.currentTree == tp.getTree()));\r
-                        tree.setNewick(tp.getTree().toString());\r
-                        tree.setThreshold(tp.treeCanvas.threshold);\r
-\r
-                        tree.setFitToWindow(tp.fitToWindow.getState());\r
-                        tree.setFontSize(tp.treeCanvas.fontSize);\r
-                        tree.setMarkUnlinked(tp.placeholdersMenu.getState());\r
-                        tree.setShowBootstrap(tp.bootstrapMenu.getState());\r
-                        tree.setShowDistances(tp.distanceMenu.getState());\r
-\r
-                        tree.setHeight(tp.getHeight());\r
-                        tree.setWidth(tp.getWidth());\r
-                        tree.setXpos(tp.getX());\r
-                        tree.setYpos(tp.getY());\r
-\r
-                        jms.addTree(tree);\r
-                    }\r
+                if (tp.treeCanvas.av.alignment == jal)\r
+                {\r
+                  Tree tree = new Tree();\r
+                  tree.setTitle(tp.getTitle());\r
+                  tree.setCurrentTree( (af.viewport.currentTree == tp.getTree()));\r
+                  tree.setNewick(tp.getTree().toString());\r
+                  tree.setThreshold(tp.treeCanvas.threshold);\r
+\r
+                  tree.setFitToWindow(tp.fitToWindow.getState());\r
+                  tree.setFontSize(tp.treeCanvas.fontSize);\r
+                  tree.setMarkUnlinked(tp.placeholdersMenu.getState());\r
+                  tree.setShowBootstrap(tp.bootstrapMenu.getState());\r
+                  tree.setShowDistances(tp.distanceMenu.getState());\r
+\r
+                  tree.setHeight(tp.getHeight());\r
+                  tree.setWidth(tp.getWidth());\r
+                  tree.setXpos(tp.getX());\r
+                  tree.setYpos(tp.getY());\r
+\r
+                  jms.addTree(tree);\r
                 }\r
+              }\r
             }\r
+          }\r
         }\r
 \r
         //SAVE ANNOTATIONS\r