flag to indicate if errors are raised as warning dialog boxes or not.

diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java
index 4f76445..9a56150 100755 (executable)
--- a/src/jalview/gui/Jalview2XML.java
+++ b/src/jalview/gui/Jalview2XML.java
@@ -52,6 +52,14 @@ public class Jalview2XML
   Hashtable seqRefIds = null;
 
   Vector frefedSequence = null;
+  boolean raiseGUI = true; // whether errors are raised in dialog boxes or not
+  public Jalview2XML()
+  {
+  }
+  public Jalview2XML(boolean raiseGUI)
+  {
+    this.raiseGUI = raiseGUI;
+  }
 
   public void resolveFrefedSequences()
   {
@@ -1227,8 +1235,18 @@ public class Jalview2XML
     } catch (Exception ex)
     {
       //Is Version 1 Jar file?
-      af = new Jalview2XML_V1().LoadJalviewAlign(file);
+      try {
+        af = new Jalview2XML_V1(raiseGUI).LoadJalviewAlign(file);
+      } catch (Exception ex2) {
+        System.err.println("Exception whilst loading as jalviewXMLV1:");
+        ex2.printStackTrace();
+        af = null;
+      }
 
+      if (Desktop.instance != null)
+      {
+        Desktop.instance.stopLoading();
+      }
       if (af != null)
       {
         System.out.println("Successfully loaded archive file");
@@ -1254,15 +1272,20 @@ public class Jalview2XML
     if (errorMessage != null)
     {
       final String finalErrorMessage = errorMessage;
-      javax.swing.SwingUtilities.invokeLater(new Runnable()
-      {
-        public void run()
+      if (raiseGUI)
+        {
+        javax.swing.SwingUtilities.invokeLater(new Runnable()
+        {
+          public void run()
         {
           JOptionPane.showInternalMessageDialog(Desktop.desktop,
                   finalErrorMessage, "Error loading Jalview file",
                   JOptionPane.WARNING_MESSAGE);
         }
       });
+        } else {
+          System.err.println("Problem loading Jalview file: "+errorMessage);
+        }
     }
 
     return af;

diff --git a/src/jalview/gui/Jalview2XML_V1.java b/src/jalview/gui/Jalview2XML_V1.java
index d8e79ce..fe17dff 100755 (executable)
--- a/src/jalview/gui/Jalview2XML_V1.java
+++ b/src/jalview/gui/Jalview2XML_V1.java
@@ -37,6 +37,14 @@ import jalview.schemes.*;
  */\r
 public class Jalview2XML_V1\r
 {\r
+  boolean raiseGUI=true;\r
+  public Jalview2XML_V1() {\r
+    \r
+  };\r
+  public Jalview2XML_V1(boolean raiseGUI) {\r
+    this.raiseGUI = raiseGUI;\r
+  };\r
+  \r
   jalview.schemes.UserColourScheme GetUserColourScheme(\r
       JalviewModelSequence jms, String id)\r
   {\r
@@ -131,7 +139,8 @@ public class Jalview2XML_V1
     catch (final java.net.UnknownHostException ex)\r
     {\r
       ex.printStackTrace();\r
-      javax.swing.SwingUtilities.invokeLater(new Runnable()\r
+      if (raiseGUI)\r
+        {javax.swing.SwingUtilities.invokeLater(new Runnable()\r
       {\r
         public void run()\r
         {\r
@@ -143,14 +152,14 @@ public class Jalview2XML_V1
                                                 "URL not found",\r
                                                 JOptionPane.WARNING_MESSAGE);\r
         }\r
-      });\r
+      });};\r
     }\r
     catch (Exception ex)\r
     {\r
+      System.err.println("Exception whilst loading jalview XML file : ");\r
       ex.printStackTrace();\r
-      System.err.println("Exception whilst loading jalview XML file : " +\r
-                         ex + "\n");\r
-      javax.swing.SwingUtilities.invokeLater(new Runnable()\r
+      if (raiseGUI)\r
+      {  javax.swing.SwingUtilities.invokeLater(new Runnable()\r
       {\r
         public void run()\r
         {\r
@@ -161,6 +170,7 @@ public class Jalview2XML_V1
                                                 JOptionPane.WARNING_MESSAGE);\r
         }\r
       });\r
+      }\r
     }\r
 \r
     return af;\r