Merge branch 'JAL-1422_srs_r281' into develop

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

diff --git a/src/jalview/gui/Preferences.java b/src/jalview/gui/Preferences.java
index ca8d5a4..c446f7f 100755 (executable)
--- a/src/jalview/gui/Preferences.java
+++ b/src/jalview/gui/Preferences.java
@@ -1,13 +1,13 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
+ * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
  * 
  * This file is part of Jalview.
  * 
  * Jalview is free software: you can redistribute it and/or
  * modify it under the terms of the GNU General Public License 
  * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- * 
+ *  
  * Jalview is distributed in the hope that it will be useful, but 
  * WITHOUT ANY WARRANTY; without even the implied warranty 
  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
@@ -28,7 +28,7 @@ import jalview.bin.*;
 import jalview.io.*;
 import jalview.jbgui.*;
 import jalview.schemes.*;
-import jalview.ws.EnfinEnvision2OneWay;
+import jalview.util.MessageManager;
 
 /**
  * DOCUMENT ME!
@@ -59,7 +59,7 @@ public class Preferences extends GPreferences
     String string = Cache
             .getDefault(
                     "SEQUENCE_LINKS",
-                    "SRS|http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-newId+(([uniprot-all:$SEQUENCE_ID$]))+-view+SwissEntry");
+                    "EMBL-EBI Search|http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$");
     sequenceURLLinks = new Vector();
 
     try
@@ -81,6 +81,18 @@ public class Preferences extends GPreferences
     {
       System.out.println(ex + "\nError parsing sequence links");
     }
+    {
+      // upgrade old SRS link
+      int srsPos = sequenceURLLinks
+              .indexOf("SRS|http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-newId+(([uniprot-all:$SEQUENCE_ID$]))+-view+SwissEntry");
+      if (srsPos > -1)
+      {
+        sequenceURLLinks.setElementAt(
+                "EMBL-EBI Search|http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$",
+                srsPos);
+      }
+    }
+
     /**
      * TODO: reformulate groupURL encoding so two or more can be stored in the
      * .properties file as '|' separated strings
@@ -554,7 +566,7 @@ public class Preferences extends GPreferences
     while (!valid)
     {
       if (JOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
-              "New sequence URL link", JOptionPane.OK_CANCEL_OPTION, -1,
+              MessageManager.getString("label.new_sequence_url_link"), JOptionPane.OK_CANCEL_OPTION, -1,
               null) == JOptionPane.OK_OPTION)
       {
         if (link.checkValid())
@@ -580,7 +592,7 @@ public class Preferences extends GPreferences
     if (index == -1)
     {
       JOptionPane.showInternalMessageDialog(Desktop.desktop,
-              "No link selected!", "No link selected",
+              MessageManager.getString("label.no_link_selected"), MessageManager.getString("label.no_link_selected"),
               JOptionPane.WARNING_MESSAGE);
       return;
     }
@@ -593,7 +605,7 @@ public class Preferences extends GPreferences
     {
 
       if (JOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
-              "New sequence URL link", JOptionPane.OK_CANCEL_OPTION, -1,
+              MessageManager.getString("label.new_sequence_url_link"), JOptionPane.OK_CANCEL_OPTION, -1,
               null) == JOptionPane.OK_OPTION)
       {
         if (link.checkValid())
@@ -618,7 +630,7 @@ public class Preferences extends GPreferences
     if (index == -1)
     {
       JOptionPane.showInternalMessageDialog(Desktop.desktop,
-              "No link selected!", "No link selected",
+              MessageManager.getString("label.no_link_selected"), MessageManager.getString("label.no_link_selected"),
               JOptionPane.WARNING_MESSAGE);
       return;
     }