X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fjws1%2FJPredClient.java;h=65847e6db6a06e2d9f80ed70fde474f5c8997295;hb=76caf07872d92bdc21faaa9278d9cccd7609d9b8;hp=c62b282a26fc683d61e35f5a00bba95ae0d151ba;hpb=59d682209891099d46b960509907c79e3fb276fe;p=jalview.git

diff --git a/src/jalview/ws/jws1/JPredClient.java b/src/jalview/ws/jws1/JPredClient.java
index c62b282..65847e6 100644
--- a/src/jalview/ws/jws1/JPredClient.java
+++ b/src/jalview/ws/jws1/JPredClient.java
@@ -1,33 +1,47 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
  * Jalview is free software: you can redistribute it and/or
  * modify it under the terms of the GNU General Public License 
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
  *  
  * Jalview is distributed in the hope that it will be useful, but 
  * WITHOUT ANY WARRANTY; without even the implied warranty 
  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
  * PURPOSE.  See the GNU General Public License for more details.
  * 
- * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 package jalview.ws.jws1;
 
+import jalview.analysis.AlignSeq;
+import jalview.bin.Cache;
+import jalview.datamodel.AlignmentView;
+import jalview.datamodel.SeqCigar;
+import jalview.datamodel.SequenceI;
+import jalview.gui.AlignFrame;
+import jalview.gui.Desktop;
+import jalview.gui.JvOptionPane;
+import jalview.gui.WebserviceInfo;
+import jalview.util.MessageManager;
+
 import java.awt.event.ActionEvent;
 import java.awt.event.ActionListener;
-import java.util.*;
+import java.util.Hashtable;
 
-import javax.swing.*;
+import javax.swing.JMenu;
+import javax.swing.JMenuItem;
 
-import ext.vamsas.*;
-import jalview.analysis.*;
-import jalview.bin.*;
-import jalview.datamodel.*;
-import jalview.gui.*;
+import ext.vamsas.Jpred;
+import ext.vamsas.JpredServiceLocator;
+import ext.vamsas.JpredSoapBindingStub;
+import ext.vamsas.ServiceHandle;
 
 public class JPredClient extends WS1Client
 {
@@ -141,7 +155,8 @@ public class JPredClient extends WS1Client
       if (!msa && msf.length > 1)
       {
         throw new Error(
-                "Implementation Error! Multiple single sequence prediction jobs are not yet supported.");
+                MessageManager
+                        .getString("error.implementation_error_multiple_single_sequence_prediction_jobs_not_supported"));
       }
 
       String altitle = getPredictionName(WebServiceName) + " for "
@@ -223,7 +238,7 @@ public class JPredClient extends WS1Client
 
     SequenceI seq = msf[0];
 
-    String altitle = "JNet prediction on " + seq.getName()
+    String altitle = "JPred prediction on " + seq.getName()
             + " using alignment from " + title;
 
     wsInfo.setProgressText("Job details for MSA based prediction (" + title
@@ -260,7 +275,7 @@ public class JPredClient extends WS1Client
     wsInfo.setProgressText("Job details for prediction on sequence :\n>"
             + seq.getName() + "\n"
             + AlignSeq.extractGaps("-. ", seq.getSequenceAsString()) + "\n");
-    String altitle = "JNet prediction for sequence " + seq.getName()
+    String altitle = "JPred prediction for sequence " + seq.getName()
             + " from " + title;
 
     Hashtable SequenceInfo = jalview.analysis.SeqsetUtils
@@ -281,14 +296,15 @@ public class JPredClient extends WS1Client
   private WebserviceInfo setWebService()
   {
     WebServiceName = "JNetWS";
-    WebServiceJobTitle = "JNet secondary structure prediction";
+    WebServiceJobTitle = MessageManager
+            .getString("label.jnet_secondary_structure_prediction");
     WebServiceReference = "\"Cuff J. A and Barton G.J (2000) Application of "
             + "multiple sequence alignment profiles to improve protein secondary structure prediction, "
             + "Proteins 40:502-511\".";
     WsURL = "http://www.compbio.dundee.ac.uk/JalviewWS/services/jpred";
 
     WebserviceInfo wsInfo = new WebserviceInfo(WebServiceJobTitle,
-            WebServiceReference);
+            WebServiceReference, true);
 
     return wsInfo;
   }
@@ -307,14 +323,21 @@ public class JPredClient extends WS1Client
 
     } catch (Exception ex)
     {
-      JOptionPane.showMessageDialog(Desktop.desktop,
-              "The Secondary Structure Prediction Service named "
-                      + WebServiceName + " at " + WsURL
-                      + " couldn't be located.", "Internal Jalview Error",
-              JOptionPane.WARNING_MESSAGE);
-      wsInfo.setProgressText("Serious! " + WebServiceName
-              + " Service location failed\nfor URL :" + WsURL + "\n"
-              + ex.getMessage());
+      JvOptionPane
+              .showMessageDialog(
+                      Desktop.desktop,
+                      MessageManager
+                              .formatMessage(
+                                      "label.secondary_structure_prediction_service_couldnt_be_located",
+                                      new String[] { WebServiceName, WsURL }),
+                      MessageManager
+                              .getString("label.internal_jalview_error"),
+                      JvOptionPane.WARNING_MESSAGE);
+      wsInfo.setProgressText(MessageManager
+              .formatMessage(
+                      "label.secondary_structure_prediction_service_couldnt_be_located",
+                      new String[] { WebServiceName, WsURL })
+              + "\n" + ex.getMessage());
       wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_SERVERERROR);
 
     }
@@ -322,6 +345,7 @@ public class JPredClient extends WS1Client
     return server;
   }
 
+  @Override
   public void attachWSMenuEntry(JMenu wsmenu, final ServiceHandle sh,
           final AlignFrame af)
   {
@@ -329,6 +353,7 @@ public class JPredClient extends WS1Client
     method.setToolTipText(sh.getEndpointURL());
     method.addActionListener(new ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
         AlignmentView msa = af.gatherSeqOrMsaForSecStrPrediction();