X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fgui%2FJalview2XML_V1.java;h=b34786472757897c1fcc920118dbfdd0a3d12b22;hb=01a838156a865a61389825b3c5c968b6d8eee8f3;hp=a0369883103f2f119d3b20a3a56b76f004b5ea88;hpb=5e0c372a53e267a798bdb3e96fe7789a54b89109;p=jalview.git

diff --git a/src/jalview/gui/Jalview2XML_V1.java b/src/jalview/gui/Jalview2XML_V1.java
index a036988..b347864 100755
--- a/src/jalview/gui/Jalview2XML_V1.java
+++ b/src/jalview/gui/Jalview2XML_V1.java
@@ -80,7 +80,7 @@ public class Jalview2XML_V1
      *
      * @param file DOCUMENT ME!
      */
-    public AlignFrame LoadJalviewAlign(String file)
+    public AlignFrame LoadJalviewAlign(final String file)
     {
 
         jalview.gui.AlignFrame af = null;
@@ -132,39 +132,51 @@ public class Jalview2XML_V1
 
                     object = (JalviewModel) object.unmarshal(in);
 
-                    af = LoadFromObject(object);
+                    af = LoadFromObject(object, file);
                     entryCount++;
                 }
             }
             while (jarentry != null);
         }
-        catch(java.net.UnknownHostException ex)
+        catch (final java.net.UnknownHostException ex)
         {
           ex.printStackTrace();
-          System.err.println("Couldn't locate Jalview XML file : " +
-              ex + "\n");
-           JOptionPane.showInternalMessageDialog(Desktop.desktop,
-                                    "Couldn't locate " + file,
-                                    "URL not found",
-                                    JOptionPane.WARNING_MESSAGE);
+          javax.swing.SwingUtilities.invokeLater(new Runnable()
+          {
+            public void run()
+            {
 
+              System.err.println("Couldn't locate Jalview XML file : " +
+                                 ex + "\n");
+              JOptionPane.showInternalMessageDialog(Desktop.desktop,
+                                                    "Couldn't locate " + file,
+                                                    "URL not found",
+                                                    JOptionPane.WARNING_MESSAGE);
+            }
+          });
         }
         catch (Exception ex)
         {
           ex.printStackTrace();
-            System.err.println("Exception whilst loading jalview XML file : " +
-                ex + "\n");
-             JOptionPane.showInternalMessageDialog(Desktop.desktop,
-                                      "Error loading  " + file,
-                                      "Error loading Jalview file",
-                                      JOptionPane.WARNING_MESSAGE);
+          System.err.println("Exception whilst loading jalview XML file : " +
+                             ex + "\n");
+          javax.swing.SwingUtilities.invokeLater(new Runnable()
+          {
+            public void run()
+            {
 
+              JOptionPane.showInternalMessageDialog(Desktop.desktop,
+                  "Error loading  " + file,
+                  "Error loading Jalview file",
+                  JOptionPane.WARNING_MESSAGE);
+            }
+          });
         }
 
         return af;
     }
 
-    AlignFrame LoadFromObject(JalviewModel object)
+    AlignFrame LoadFromObject(JalviewModel object, String file)
     {
         Vector seqids = new Vector();
         SequenceSet vamsasSet = object.getVamsasModel().getSequenceSet(0);
@@ -182,7 +194,6 @@ public class Jalview2XML_V1
                     vamsasSeq[i].getSequence());
             jseqs[i].setStart(JSEQ[i].getStart());
             jseqs[i].setEnd(JSEQ[i].getEnd());
-            jseqs[i].setColor(new java.awt.Color(JSEQ[i].getColour()));
             seqids.add(jseqs[i]);
         }
 
@@ -269,6 +280,17 @@ public class Jalview2XML_V1
 
         AlignFrame af = new AlignFrame(al, view.getWidth(), view.getHeight());
 
+        af.setFileName(file, "Jalview");
+
+        for (int i = 0; i < JSEQ.length; i++)
+        {
+          af.viewport.setSequenceColour(
+              af.viewport.alignment.getSequenceAt(i),
+              new java.awt.Color(
+                  JSEQ[i].getColour()));
+        }
+
+
 
         //  af.changeColour() );
         /////////////////////////