JAL-2326 updated references of JOptionPane to JvOptionPane

[jalview.git] / src / jalview / gui / Jalview2XML_V1.java

diff --git a/src/jalview/gui/Jalview2XML_V1.java b/src/jalview/gui/Jalview2XML_V1.java
index f5eb1d6..2e6706c 100755 (executable)
--- a/src/jalview/gui/Jalview2XML_V1.java
+++ b/src/jalview/gui/Jalview2XML_V1.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
- * Copyright (C) 2015 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -155,11 +155,11 @@ public class Jalview2XML_V1
 
             System.err.println("Couldn't locate Jalview XML file : " + ex
                     + "\n");
-            JOptionPane.showInternalMessageDialog(Desktop.desktop,
+            JvOptionPane.showInternalMessageDialog(Desktop.desktop,
                     MessageManager.formatMessage("label.couldnt_locate",
                             new String[] { file }), MessageManager
                             .getString("label.url_not_found"),
-                    JOptionPane.WARNING_MESSAGE);
+                    JvOptionPane.WARNING_MESSAGE);
           }
         });
       }
@@ -176,12 +176,12 @@ public class Jalview2XML_V1
           public void run()
           {
 
-            JOptionPane.showInternalMessageDialog(Desktop.desktop,
+            JvOptionPane.showInternalMessageDialog(Desktop.desktop,
                     MessageManager.formatMessage(
                             "label.error_loading_file_params", new String[]
                             { file }), MessageManager
                             .getString("label.error_loading_jalview_file"),
-                    JOptionPane.WARNING_MESSAGE);
+                    JvOptionPane.WARNING_MESSAGE);
           }
         });
       }
@@ -359,8 +359,8 @@ public class Jalview2XML_V1
 
         if (groups[i].getConsThreshold() != 0)
         {
-          Conservation c = new Conservation("All", 3,
-                  sg.getSequences(null), 0, sg.getWidth() - 1);
+          Conservation c = new Conservation("All", sg.getSequences(null),
+                  0, sg.getWidth() - 1);
           c.calculate();
           c.verdict(false, 25);
           sg.cs.setConservation(c);