JAL-1807 explicit imports (jalview.ws.*)

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

diff --git a/src/jalview/gui/WsPreferences.java b/src/jalview/gui/WsPreferences.java
index 876d157..39117d0 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 ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -24,6 +24,7 @@ import jalview.bin.Cache;
 import jalview.jbgui.GWsPreferences;
 import jalview.util.MessageManager;
 import jalview.ws.jws2.Jws2Discoverer;
+import jalview.ws.rest.RestClient;
 import jalview.ws.rest.RestServiceDescription;
 
 import java.awt.BorderLayout;
@@ -33,6 +34,7 @@ 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 +54,9 @@ 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 +66,8 @@ 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);
     }
@@ -75,7 +79,7 @@ public class WsPreferences extends GWsPreferences
     wsList.setDefaultRenderer(Integer.class, new JabaWSStatusRenderer());
     wsList.setAutoResizeMode(JTable.AUTO_RESIZE_ALL_COLUMNS);
     updateList();
-    rsbsUrls = jalview.ws.rest.RestClient.getRsbsDescriptions();
+    rsbsUrls = RestClient.getRsbsDescriptions();
     if (rsbsUrls != null)
     {
       oldRsbsUrls = new Vector<String>(rsbsUrls);
@@ -235,12 +239,12 @@ public class WsPreferences extends GWsPreferences
 
   private void updateServiceList()
   {
-    jalview.ws.jws2.Jws2Discoverer.setServiceUrls(wsUrls);
+    Jws2Discoverer.getDiscoverer().setServiceUrls(wsUrls);
   }
 
   private void updateRsbsServiceList()
   {
-    jalview.ws.rest.RestClient.setRsbsServices(rsbsUrls);
+    RestClient.setRsbsServices(rsbsUrls);
   }
 
   /*
@@ -256,7 +260,7 @@ public class WsPreferences extends GWsPreferences
     int sel = wsList.getSelectedRow();
     if (sel > -1)
     {
-      wsUrls.removeElementAt(sel);
+      wsUrls.remove(sel);
       update++;
       updateList();
     }
@@ -274,21 +278,22 @@ 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 +411,8 @@ 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 +433,8 @@ 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++;
@@ -484,18 +489,38 @@ public class WsPreferences extends GWsPreferences
                       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();
         }
         else
         {
-          JOptionPane
-                  .showInternalMessageDialog(
+          int opt = JOptionPane
+                  .showInternalOptionDialog(
                           Desktop.desktop,
-                          MessageManager.getString("warn.server_didnt_pass_validation"));
+                          "The Server  '"
+                                  + foo.toString()
+                                  + "' failed validation,\ndo you want to add it anyway? ",
+                          "Server Validation Failed",
+                          JOptionPane.YES_NO_OPTION,
+                          JOptionPane.INFORMATION_MESSAGE, null, null, null);
+          if (opt == JOptionPane.YES_OPTION)
+          {
+            return foo.toString();
+          }
+          else
+          {
+            JOptionPane
+                    .showInternalMessageDialog(
+                            Desktop.desktop,
+                            MessageManager
+                                    .getString("warn.server_didnt_pass_validation"));
+          }
+
+
         }
       }
       else
@@ -524,11 +549,11 @@ 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();
@@ -631,8 +656,8 @@ 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++;