X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fjws1%2FMsaWSClient.java;h=5ea553eaa7a02e0288da2334edada7f8475df527;hb=baee331692f533011f566ba30a7a711f3326320f;hp=17fccca22180d83d94d63bfcb1fc61493f31a961;hpb=838e4f91d4a53dd315640dbc9ff6ef7a815ee576;p=jalview.git

diff --git a/src/jalview/ws/jws1/MsaWSClient.java b/src/jalview/ws/jws1/MsaWSClient.java
index 17fccca..5ea553e 100644
--- a/src/jalview/ws/jws1/MsaWSClient.java
+++ b/src/jalview/ws/jws1/MsaWSClient.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
- * 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.
  * 
@@ -20,10 +20,11 @@
  */
 package jalview.ws.jws1;
 
-import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentI;
 import jalview.datamodel.AlignmentView;
 import jalview.gui.AlignFrame;
 import jalview.gui.Desktop;
+import jalview.gui.JvOptionPane;
 import jalview.gui.WebserviceInfo;
 import jalview.util.MessageManager;
 
@@ -32,9 +33,7 @@ import java.awt.event.ActionListener;
 
 import javax.swing.JMenu;
 import javax.swing.JMenuItem;
-import javax.swing.JOptionPane;
 
-import ext.vamsas.MuscleWS;
 import ext.vamsas.MuscleWSServiceLocator;
 import ext.vamsas.MuscleWSSoapBindingStub;
 import ext.vamsas.ServiceHandle;
@@ -72,29 +71,29 @@ public class MsaWSClient extends WS1Client
 
   public MsaWSClient(ext.vamsas.ServiceHandle sh, String altitle,
           jalview.datamodel.AlignmentView msa, boolean submitGaps,
-          boolean preserveOrder, Alignment seqdataset,
+          boolean preserveOrder, AlignmentI seqdataset,
           AlignFrame _alignFrame)
   {
     super();
     alignFrame = _alignFrame;
     if (!sh.getAbstractName().equals("MsaWS"))
     {
-      JOptionPane.showMessageDialog(Desktop.desktop, MessageManager
+      JvOptionPane.showMessageDialog(Desktop.desktop, MessageManager
               .formatMessage("label.service_called_is_not_msa_service",
                       new String[] { sh.getName() }), MessageManager
               .getString("label.internal_jalview_error"),
-              JOptionPane.WARNING_MESSAGE);
+              JvOptionPane.WARNING_MESSAGE);
 
       return;
     }
 
     if ((wsInfo = setWebService(sh)) == null)
     {
-      JOptionPane.showMessageDialog(Desktop.desktop, MessageManager
+      JvOptionPane.showMessageDialog(Desktop.desktop, MessageManager
               .formatMessage("label.msa_service_is_unknown",
                       new String[] { sh.getName() }), MessageManager
               .getString("label.internal_jalview_error"),
-              JOptionPane.WARNING_MESSAGE);
+              JvOptionPane.WARNING_MESSAGE);
 
       return;
     }
@@ -109,7 +108,7 @@ public class MsaWSClient extends WS1Client
   }
 
   private void startMsaWSClient(String altitle, AlignmentView msa,
-          boolean submitGaps, boolean preserveOrder, Alignment seqdataset)
+          boolean submitGaps, boolean preserveOrder, AlignmentI seqdataset)
   {
     if (!locateWebService())
     {
@@ -159,7 +158,7 @@ public class MsaWSClient extends WS1Client
 
     try
     {
-      this.server = (MuscleWS) loc.getMuscleWS(new java.net.URL(WsURL));
+      this.server = loc.getMuscleWS(new java.net.URL(WsURL));
       ((MuscleWSSoapBindingStub) this.server).setTimeout(60000); // One minute
       // timeout
     } catch (Exception ex)
@@ -201,6 +200,7 @@ public class MsaWSClient extends WS1Client
     return (WebServiceName.indexOf("lustal") > -1); // cheat!
   }
 
+  @Override
   public void attachWSMenuEntry(JMenu msawsmenu,
           final ServiceHandle serviceHandle, final AlignFrame alignFrame)
   {
@@ -209,6 +209,7 @@ public class MsaWSClient extends WS1Client
     method.setToolTipText(WsURL);
     method.addActionListener(new ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
         AlignmentView msa = alignFrame.gatherSequencesForAlignment();
@@ -228,6 +229,7 @@ public class MsaWSClient extends WS1Client
       methodR.setToolTipText(WsURL);
       methodR.addActionListener(new ActionListener()
       {
+        @Override
         public void actionPerformed(ActionEvent e)
         {
           AlignmentView msa = alignFrame.gatherSequencesForAlignment();