JAL-1925 update source version in license

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

diff --git a/src/jalview/gui/WsPreferences.java b/src/jalview/gui/WsPreferences.java
index 0674352..0e94d4b 100644 (file)
--- a/src/jalview/gui/WsPreferences.java
+++ b/src/jalview/gui/WsPreferences.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
+ * Copyright (C) 2015 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);
     }
@@ -125,7 +128,8 @@ public class WsPreferences extends GWsPreferences
     }
 
     wsList.setModel(new WsUrlTableModel(tdat));
-    wsList.getColumn(MessageManager.getString("label.status")).setMinWidth(10);
+    wsList.getColumn(MessageManager.getString("label.status")).setMinWidth(
+            10);
   }
 
   private class JabaWSStatusRenderer extends JPanel implements
@@ -184,8 +188,10 @@ public class WsPreferences extends GWsPreferences
   {
 
     private Object[][] data;
-    private String[] columnNames = new String[]
-    { MessageManager.getString("label.service_url"), MessageManager.getString("label.status") };
+
+    private String[] columnNames = new String[] {
+        MessageManager.getString("label.service_url"),
+        MessageManager.getString("label.status") };
 
     public WsUrlTableModel(Object[][] tdat)
     {
@@ -201,7 +207,7 @@ public class WsPreferences extends GWsPreferences
     @Override
     public String getColumnName(int column)
     {
-        return columnNames[column];
+      return columnNames[column];
     }
 
     @Override
@@ -235,7 +241,7 @@ public class WsPreferences extends GWsPreferences
 
   private void updateServiceList()
   {
-    jalview.ws.jws2.Jws2Discoverer.setServiceUrls(wsUrls);
+    Jws2Discoverer.getDiscoverer().setServiceUrls(wsUrls);
   }
 
   private void updateRsbsServiceList()
@@ -256,7 +262,7 @@ public class WsPreferences extends GWsPreferences
     int sel = wsList.getSelectedRow();
     if (sel > -1)
     {
-      wsUrls.removeElementAt(sel);
+      wsUrls.remove(sel);
       update++;
       updateList();
     }
@@ -274,21 +280,22 @@ 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 +413,8 @@ 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 +435,8 @@ 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++;
@@ -479,15 +486,14 @@ public class WsPreferences extends GWsPreferences
     }
     if (valid && resp == JOptionPane.OK_OPTION)
     {
-      int validate = JOptionPane
-              .showInternalConfirmDialog(
-                      Desktop.desktop,
-                      MessageManager.getString("info.validate_jabaws_server"),
-                      MessageManager.getString("label.test_server"), JOptionPane.YES_NO_OPTION);
+      int validate = JOptionPane.showInternalConfirmDialog(Desktop.desktop,
+              MessageManager.getString("info.validate_jabaws_server"),
+              MessageManager.getString("label.test_server"),
+              JOptionPane.YES_NO_OPTION);
 
       if (validate == JOptionPane.OK_OPTION)
       {
-        if (jalview.ws.jws2.Jws2Discoverer.testServiceUrl(foo))
+        if (Jws2Discoverer.testServiceUrl(foo))
         {
           return foo.toString();
         }
@@ -515,7 +521,6 @@ public class WsPreferences extends GWsPreferences
                                     .getString("warn.server_didnt_pass_validation"));
           }
 
-
         }
       }
       else
@@ -536,7 +541,8 @@ public class WsPreferences extends GWsPreferences
   @Override
   protected void newWsUrl_actionPerformed(ActionEvent e)
   {
-    String url = editUrl(null, MessageManager.getString("label.add_jabaws_url"));
+    String url = editUrl(null,
+            MessageManager.getString("label.add_jabaws_url"));
     if (url != null)
     {
       if (!wsUrls.contains(url))
@@ -544,11 +550,11 @@ 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();
@@ -621,8 +627,8 @@ public class WsPreferences extends GWsPreferences
         public void run()
         {
           long ct = System.currentTimeMillis();
-          Desktop.instance.setProgressBar(MessageManager.getString("status.refreshing_web_service_menus"),
-                  ct);
+          Desktop.instance.setProgressBar(MessageManager
+                  .getString("status.refreshing_web_service_menus"), ct);
           if (lastrefresh != update)
           {
             lastrefresh = update;
@@ -651,8 +657,8 @@ 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++;