JAL-1620 version bump and release notes

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

diff --git a/src/jalview/gui/WsPreferences.java b/src/jalview/gui/WsPreferences.java
index de89241..d92cddb 100644 (file)
--- a/src/jalview/gui/WsPreferences.java
+++ b/src/jalview/gui/WsPreferences.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
@@ -33,6 +33,7 @@ import java.awt.Dimension;
 import java.awt.event.ActionEvent;
 import java.awt.event.ActionListener;
 import java.net.URL;
+import java.util.List;
 import java.util.Vector;
 
 import javax.swing.JLabel;
@@ -52,7 +53,9 @@ public class WsPreferences extends GWsPreferences
     initFromPreferences();
   }
 
-  Vector<String> wsUrls, oldUrls, rsbsUrls, oldRsbsUrls;
+  List<String> wsUrls;
+
+  Vector<String> oldUrls, rsbsUrls, oldRsbsUrls;
 
   private boolean needWsMenuUpdate;
 
@@ -62,8 +65,8 @@ public class WsPreferences extends GWsPreferences
   private void initFromPreferences()
   {
 
-    wsUrls = jalview.ws.jws2.Jws2Discoverer.getServiceUrls();
-    if (wsUrls != null)
+    wsUrls = Jws2Discoverer.getDiscoverer().getServiceUrls();
+    if (!wsUrls.isEmpty())
     {
       oldUrls = new Vector<String>(wsUrls);
     }
@@ -235,7 +238,7 @@ public class WsPreferences extends GWsPreferences
 
   private void updateServiceList()
   {
-    jalview.ws.jws2.Jws2Discoverer.setServiceUrls(wsUrls);
+    Jws2Discoverer.getDiscoverer().setServiceUrls(wsUrls);
   }
 
   private void updateRsbsServiceList()
@@ -256,7 +259,7 @@ public class WsPreferences extends GWsPreferences
     int sel = wsList.getSelectedRow();
     if (sel > -1)
     {
-      wsUrls.removeElementAt(sel);
+      wsUrls.remove(sel);
       update++;
       updateList();
     }
@@ -274,21 +277,22 @@ public class WsPreferences extends GWsPreferences
     int sel = wsList.getSelectedRow();
     if (sel > -1)
     {
-      String url = editUrl(wsUrls.elementAt(sel), MessageManager.getString("label.edit_jabaws_url"));
+      String url = editUrl(wsUrls.get(sel),
+              MessageManager.getString("label.edit_jabaws_url"));
       if (url != null)
       {
         int present = wsUrls.indexOf(url);
         if (present == -1)
         {
           update++;
-          wsUrls.setElementAt(url, sel);
+          wsUrls.set(sel, url);
           updateList();
         }
         else
         {
           if (present != sel)
           {
-            wsUrls.removeElementAt(sel);
+            wsUrls.remove(sel);
             updateList();
           }
         }
@@ -406,8 +410,8 @@ public class WsPreferences extends GWsPreferences
     if (p > -1 && p < wsUrls.size() - 1)
     {
       String t = wsUrls.get(p + 1);
-      wsUrls.setElementAt(wsUrls.elementAt(p), p + 1);
-      wsUrls.setElementAt(t, p);
+      wsUrls.set(p + 1, wsUrls.get(p));
+      wsUrls.set(p, t);
       updateList();
       wsList.getSelectionModel().setSelectionInterval(p + 1, p + 1);
       update++;
@@ -428,8 +432,8 @@ public class WsPreferences extends GWsPreferences
     if (p > 0)
     {
       String t = wsUrls.get(p - 1);
-      wsUrls.setElementAt(wsUrls.elementAt(p), p - 1);
-      wsUrls.setElementAt(t, p);
+      wsUrls.set(p - 1, wsUrls.get(p));
+      wsUrls.set(p, t);
       updateList();
       wsList.getSelectionModel().setSelectionInterval(p - 1, p - 1);
       update++;
@@ -487,7 +491,7 @@ public class WsPreferences extends GWsPreferences
 
       if (validate == JOptionPane.OK_OPTION)
       {
-        if (jalview.ws.jws2.Jws2Discoverer.testServiceUrl(foo))
+        if (Jws2Discoverer.testServiceUrl(foo))
         {
           return foo.toString();
         }
@@ -498,7 +502,7 @@ public class WsPreferences extends GWsPreferences
                           Desktop.desktop,
                           "The Server  '"
                                   + foo.toString()
-                                  + "' failed validation, do you want to proceed and add it anyway? ",
+                                  + "' failed validation,\ndo you want to add it anyway? ",
                           "Server Validation Failed",
                           JOptionPane.YES_NO_OPTION,
                           JOptionPane.INFORMATION_MESSAGE, null, null, null);
@@ -544,11 +548,11 @@ public class WsPreferences extends GWsPreferences
         int selind = wsList.getSelectedRow();
         if (selind > -1)
         {
-          wsUrls.insertElementAt(url, selind);
+          wsUrls.add(selind, url);
         }
         else
         {
-          wsUrls.addElement(url);
+          wsUrls.add(url);
         }
         update++;
         updateList();
@@ -651,8 +655,8 @@ public class WsPreferences extends GWsPreferences
   @Override
   protected void resetWs_actionPerformed(ActionEvent e)
   {
-    jalview.ws.jws2.Jws2Discoverer.setServiceUrls(null);
-    Vector nwsUrls = jalview.ws.jws2.Jws2Discoverer.getServiceUrls();
+    Jws2Discoverer.getDiscoverer().setServiceUrls(null);
+    List<String> nwsUrls = Jws2Discoverer.getDiscoverer().getServiceUrls();
     if (!wsUrls.equals(nwsUrls))
     {
       update++;