Highlight from alignment

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

diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java
index c524b39..28840e7 100755 (executable)
--- a/src/jalview/gui/Jalview2XML.java
+++ b/src/jalview/gui/Jalview2XML.java
@@ -27,6 +27,7 @@ import java.io.*;
 import java.net.*;\r
 \r
 import java.util.*;\r
+\r
 import java.util.jar.*;\r
 \r
 import javax.swing.*;\r
@@ -156,7 +157,7 @@ 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 +222,11 @@ 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
@@ -390,7 +394,7 @@ public class Jalview2XML
         view.setShowBoxes(av.getShowBoxes());\r
         view.setShowColourText(av.getColourText());\r
         view.setShowConservation(av.showConservation);\r
-        view.setShowFullId(av.getShowFullId());\r
+        view.setShowFullId(av.getShowJVSuffix());\r
         view.setShowIdentity(av.showIdentity);\r
         view.setShowQuality(av.showQuality);\r
         view.setShowSequenceFeatures(av.showSequenceFeatures);\r
@@ -528,14 +532,25 @@ 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
@@ -686,8 +701,8 @@ public class Jalview2XML
         af.viewport.setConservationSelected(view.getConservationSelected());\r
         af.conservationMenuItem.setSelected(view.getConservationSelected());\r
 \r
-        af.viewport.setShowFullId(view.getShowFullId());\r
-        af.fullSeqId.setSelected(view.getShowFullId());\r
+        af.viewport.setShowJVSuffix(view.getShowFullId());\r
+        af.seqLimits.setSelected(view.getShowFullId());\r
 \r
         af.viewport.setFont(new java.awt.Font(view.getFontName(),\r
                 view.getFontStyle(), view.getFontSize()));\r
@@ -748,6 +763,7 @@ public class Jalview2XML
 \r
         if (view.getShowSequenceFeatures())\r
         {\r
+            af.featureSettings.setEnabled(true);\r
             af.viewport.showSequenceFeatures = true;\r
             af.sequenceFeatures.setSelected(true);\r
             new SequenceFeatureFetcher(al, af.alignPanel);\r
@@ -775,14 +791,20 @@ public class Jalview2XML
 \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