X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fjws1%2FSeqSearchWSClient.java;h=92d17e869cc9604f4d0c22ffc5da65d27757cdd0;hb=0a7cea2df922f37196de9242fb7b02c180f7f828;hp=3a4bbd452e7edf860c7ee02e44a03a71b435fa51;hpb=2b34ad8d6c224117ca2a3199c237fd74d8137da6;p=jalview.git

diff --git a/src/jalview/ws/jws1/SeqSearchWSClient.java b/src/jalview/ws/jws1/SeqSearchWSClient.java
index 3a4bbd4..92d17e8 100644
--- a/src/jalview/ws/jws1/SeqSearchWSClient.java
+++ b/src/jalview/ws/jws1/SeqSearchWSClient.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.
  * 
@@ -20,6 +20,14 @@
  */
 package jalview.ws.jws1;
 
+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;
+
 import java.awt.Component;
 import java.awt.event.ActionEvent;
 import java.awt.event.ActionListener;
@@ -28,12 +36,12 @@ import java.util.Hashtable;
 import java.util.StringTokenizer;
 import java.util.Vector;
 
-import javax.swing.*;
+import javax.swing.JMenu;
+import javax.swing.JMenuItem;
 
-import ext.vamsas.*;
-import jalview.datamodel.*;
-import jalview.gui.*;
-import jalview.util.MessageManager;
+import ext.vamsas.SeqSearchServiceLocator;
+import ext.vamsas.SeqSearchServiceSoapBindingStub;
+import ext.vamsas.ServiceHandle;
 
 /**
  * DOCUMENT ME!
@@ -68,7 +76,7 @@ public class SeqSearchWSClient extends WS1Client
 
   public SeqSearchWSClient(ext.vamsas.ServiceHandle sh, String altitle,
           jalview.datamodel.AlignmentView msa, String db,
-          Alignment seqdataset, AlignFrame _alignFrame)
+          AlignmentI seqdataset, AlignFrame _alignFrame)
   {
     super();
     alignFrame = _alignFrame;
@@ -76,19 +84,23 @@ public class SeqSearchWSClient extends WS1Client
     // name to service client name
     if (!sh.getAbstractName().equals(this.getServiceActionKey()))
     {
-      JOptionPane.showMessageDialog(Desktop.desktop,
-    		  MessageManager.formatMessage("label.service_called_is_not_seq_search_service", new String[]{sh.getName()}),
-              MessageManager.getString("label.internal_jalview_error"), JOptionPane.WARNING_MESSAGE);
+      JvOptionPane.showMessageDialog(Desktop.desktop, MessageManager
+              .formatMessage(
+                      "label.service_called_is_not_seq_search_service",
+                      new String[] { sh.getName() }), MessageManager
+              .getString("label.internal_jalview_error"),
+              JvOptionPane.WARNING_MESSAGE);
 
       return;
     }
 
     if ((wsInfo = setWebService(sh)) == null)
     {
-      JOptionPane.showMessageDialog(Desktop.desktop,
-    		  MessageManager.formatMessage("label.seq_search_service_is_unknown", new String[]{sh.getName()}),
-              MessageManager.getString("label.internal_jalview_error"),
-              JOptionPane.WARNING_MESSAGE);
+      JvOptionPane.showMessageDialog(Desktop.desktop, MessageManager
+              .formatMessage("label.seq_search_service_is_unknown",
+                      new String[] { sh.getName() }), MessageManager
+              .getString("label.internal_jalview_error"),
+              JvOptionPane.WARNING_MESSAGE);
 
       return;
     }
@@ -115,7 +127,7 @@ public class SeqSearchWSClient extends WS1Client
   }
 
   private void startSeqSearchClient(String altitle, AlignmentView msa,
-          String db, Alignment seqdataset)
+          String db, AlignmentI seqdataset)
   {
     if (!locateWebService())
     {
@@ -160,8 +172,7 @@ public class SeqSearchWSClient extends WS1Client
 
     try
     {
-      this.server = (SeqSearchI) loc.getSeqSearchService(new java.net.URL(
-              WsURL));
+      this.server = loc.getSeqSearchService(new java.net.URL(WsURL));
       ((SeqSearchServiceSoapBindingStub) this.server).setTimeout(60000); // One
       // minute
       // timeout
@@ -208,13 +219,14 @@ public class SeqSearchWSClient extends WS1Client
     }
     if (!locateWebService())
     {
-      throw new Exception("Cannot contact service endpoint at " + WsURL);
+      throw new Exception(MessageManager.formatMessage(
+              "exception.cannot_contact_service_endpoint_at",
+              new String[] { WsURL }));
     }
     String database = server.getDatabase();
     if (database == null)
     {
-      dbParamsForEndpoint.put(WsURL, new String[]
-      {});
+      dbParamsForEndpoint.put(WsURL, new String[] {});
       return null;
     }
     StringTokenizer en = new StringTokenizer(database.trim(), ",| ");
@@ -227,6 +239,7 @@ public class SeqSearchWSClient extends WS1Client
     return dbs;
   }
 
+  @Override
   public void attachWSMenuEntry(JMenu wsmenu, final ServiceHandle sh,
           final AlignFrame af)
   {
@@ -267,6 +280,7 @@ public class SeqSearchWSClient extends WS1Client
     method.setToolTipText(sh.getEndpointURL());
     method.addActionListener(new ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
         // use same input gatherer as for secondary structure prediction
@@ -291,6 +305,7 @@ public class SeqSearchWSClient extends WS1Client
       final String searchdb = dbs[db];
       method.addActionListener(new ActionListener()
       {
+        @Override
         public void actionPerformed(ActionEvent e)
         {
           AlignmentView msa = af.gatherSeqOrMsaForSecStrPrediction();