Next active Frame losing focus bug fixed

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

diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java
index ffa837d..9ab6419 100755 (executable)
--- a/src/jalview/gui/Jalview2XML.java
+++ b/src/jalview/gui/Jalview2XML.java
@@ -18,8 +18,6 @@
  */\r
 package jalview.gui;\r
 \r
-import jalview.binding.*;\r
-\r
 import jalview.io.*;\r
 \r
 import jalview.schemes.*;\r
@@ -33,6 +31,8 @@ import java.util.jar.*;
 \r
 import javax.swing.*;\r
 \r
+import jalview.binding.*;\r
+\r
 \r
 /**\r
  * DOCUMENT ME!\r
@@ -156,7 +156,7 @@ public class Jalview2XML
         AlignViewport av = af.viewport;\r
 \r
         JalviewModel object = new JalviewModel();\r
-        object.setVamsasModel(new VamsasModel());\r
+        object.setVamsasModel(new jalview.binding.VamsasModel());\r
 \r
         object.setCreationDate(new java.util.Date(timeStamp));\r
         object.setVersion(jalview.bin.Cache.getProperty("VERSION"));\r
@@ -221,8 +221,11 @@ public class Jalview2XML
                   tree.setThreshold(tp.treeCanvas.threshold);\r
 \r
                   tree.setFitToWindow(tp.fitToWindow.getState());\r
-                  tree.setFontSize(tp.treeCanvas.fontSize);\r
+                  tree.setFontName(tp.getTreeFont().getName());\r
+                  tree.setFontSize(tp.getTreeFont().getSize());\r
+                  tree.setFontStyle(tp.getTreeFont().getStyle());\r
                   tree.setMarkUnlinked(tp.placeholdersMenu.getState());\r
+\r
                   tree.setShowBootstrap(tp.bootstrapMenu.getState());\r
                   tree.setShowDistances(tp.distanceMenu.getState());\r
 \r
@@ -528,14 +531,25 @@ public class Jalview2XML
             }\r
             while (jarentry != null);\r
         }\r
+        catch(java.net.UnknownHostException ex)\r
+        {\r
+          ex.printStackTrace();\r
+          System.err.println("Couldn't locate Jalview XML file : " +\r
+              ex + "\n");\r
+           JOptionPane.showInternalMessageDialog(Desktop.desktop,\r
+                                    "Couldn't locate " + file,\r
+                                    "URL not found",\r
+                                    JOptionPane.WARNING_MESSAGE);\r
+\r
+        }\r
         catch (Exception ex)\r
         {\r
           ex.printStackTrace();\r
             System.err.println("Exception whilst loading jalview XML file : " +\r
                 ex + "\n");\r
              JOptionPane.showInternalMessageDialog(Desktop.desktop,\r
-                                      "Couldn't locate " + file,\r
-                                      "URL not found",\r
+                                      "Error loading  " + file,\r
+                                      "Error loading Jalview file",\r
                                       JOptionPane.WARNING_MESSAGE);\r
 \r
         }\r
@@ -754,6 +768,9 @@ public class Jalview2XML
             al.featuresAdded = true;\r
         }\r
 \r
+        Desktop.addInternalFrame(af, view.getTitle(),\r
+             view.getWidth(), view.getHeight());\r
+\r
         //LOAD TREES\r
         ///////////////////////////////////////\r
         if (jms.getTreeCount() > 0)\r
@@ -762,24 +779,30 @@ public class Jalview2XML
             {\r
                 for (int t = 0; t < jms.getTreeCount(); t++)\r
                 {\r
+\r
                     Tree tree = jms.getTree(t);\r
 \r
                     TreePanel tp = af.ShowNewickTree(new jalview.io.NewickFile(\r
-                                tree.getNewick()), tree.getTitle());\r
-\r
-                    tp.setBounds(tree.getXpos(), tree.getYpos(),\r
-                        tree.getWidth(), tree.getHeight());\r
+                                tree.getNewick()), tree.getTitle(),\r
+                                tree.getWidth(), tree.getHeight(),\r
+                                tree.getXpos(), tree.getYpos());\r
 \r
                     tp.fitToWindow.setState(tree.getFitToWindow());\r
                     tp.fitToWindow_actionPerformed(null);\r
-                    tp.treeCanvas.fontSize = tree.getFontSize();\r
-                    tp.fontSize.setText("Font Size - " + tree.getFontSize());\r
-                    tp.placeholdersMenu.setState(tree.getMarkUnlinked());\r
-                    tp.placeholdersMenu_actionPerformed(null);\r
-                    tp.bootstrapMenu.setState(tree.getShowBootstrap());\r
-                    tp.bootstrapMenu_actionPerformed(null);\r
-                    tp.distanceMenu.setState(tree.getShowDistances());\r
-                    tp.distanceMenu_actionPerformed(null);\r
+\r
+                    if(tree.getFontName()!=null)\r
+                      tp.setTreeFont(new java.awt.Font(tree.getFontName(),\r
+                                          tree.getFontStyle(),\r
+                                          tree.getFontSize()));\r
+                    else\r
+                      tp.setTreeFont(new java.awt.Font(view.getFontName(),\r
+                                            view.getFontStyle(),\r
+                                            tree.getFontSize()));\r
+\r
+                    tp.showPlaceholders(tree.getMarkUnlinked());\r
+                    tp.showBootstrap(tree.getShowBootstrap());\r
+                    tp.showDistances(tree.getShowDistances());\r
+\r
                     tp.treeCanvas.threshold = tree.getThreshold();\r
 \r
                     if (tree.getCurrentTree())\r
@@ -794,9 +817,6 @@ public class Jalview2XML
 \r
         }\r
 \r
-        Desktop.addInternalFrame(af, view.getTitle(),\r
-             AlignFrame.NEW_WINDOW_WIDTH, AlignFrame.NEW_WINDOW_HEIGHT);\r
-\r
         return af;\r
     }\r
 }\r