X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fjws1%2FJPredClient.java;h=1e483e3094b9a1b6151aac36bd0b9f9b0baa053c;hb=8edebdd9789b2d93fb8f9db24b8be2c1e6317690;hp=e1a9e9429950c8bb7836a13782c80e18ac757c4e;hpb=a8f483d04205bb8273ee311c12968b7e86d205fa;p=jalview.git

diff --git a/src/jalview/ws/jws1/JPredClient.java b/src/jalview/ws/jws1/JPredClient.java
index e1a9e94..1e483e3 100644
--- a/src/jalview/ws/jws1/JPredClient.java
+++ b/src/jalview/ws/jws1/JPredClient.java
@@ -1,34 +1,48 @@
 /*
- * 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.
  * 
  * 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.analysis.SeqsetUtils;
+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.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 javax.swing.JOptionPane;
 
-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
 {
@@ -76,7 +90,7 @@ public class JPredClient extends WS1Client
    *          visible regions
    */
   private void startJPredClient(String title, boolean msa,
-          jalview.datamodel.AlignmentView alview, AlignFrame parentFrame,
+          AlignmentView alview, AlignFrame parentFrame,
           boolean viewonly)
   {
     AlignmentView input = alview;
@@ -115,8 +129,7 @@ public class JPredClient extends WS1Client
         aln[i] = msf[i].getSeq('-');
       }
 
-      Hashtable SequenceInfo = jalview.analysis.SeqsetUtils.uniquify(aln,
-              true);
+      Hashtable SequenceInfo = SeqsetUtils.uniquify(aln, true);
       if (viewonly)
       {
         // Remove hidden regions from sequence objects.
@@ -141,16 +154,14 @@ public class JPredClient extends WS1Client
     {
       if (!msa && msf.length > 1)
       {
-        throw new Error(
-                "Implementation Error! Multiple single sequence prediction jobs are not yet supported.");
+        throw new Error(MessageManager.getString("error.implementation_error_multiple_single_sequence_prediction_jobs_not_supported"));
       }
 
       String altitle = getPredictionName(WebServiceName) + " for "
               + (viewonly ? "visible " : "") + "sequence " + seq.getName()
               + " from " + title;
       String seqname = seq.getName();
-      Hashtable SequenceInfo = jalview.analysis.SeqsetUtils
-              .SeqCharacterHash(seq);
+      Hashtable SequenceInfo = SeqsetUtils.SeqCharacterHash(seq);
       if (viewonly)
       {
         // Remove hidden regions from input sequence
@@ -236,7 +247,7 @@ public class JPredClient extends WS1Client
       aln[i] = new jalview.datamodel.Sequence(msf[i]);
     }
 
-    Hashtable SequenceInfo = jalview.analysis.SeqsetUtils.uniquify(aln,
+    Hashtable SequenceInfo = SeqsetUtils.uniquify(aln,
             true);
 
     Jpred server = locateWebService();
@@ -264,8 +275,7 @@ public class JPredClient extends WS1Client
     String altitle = "JNet prediction for sequence " + seq.getName()
             + " from " + title;
 
-    Hashtable SequenceInfo = jalview.analysis.SeqsetUtils
-            .SeqCharacterHash(seq);
+    Hashtable SequenceInfo = SeqsetUtils.SeqCharacterHash(seq);
 
     Jpred server = locateWebService();
     if (server == null)
@@ -282,14 +292,14 @@ 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;
   }
@@ -309,12 +319,11 @@ 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",
+    		  MessageManager.formatMessage("label.secondary_structure_prediction_service_couldnt_be_located", new String[]{WebServiceName,WsURL}),
+    		  MessageManager.getString("label.internal_jalview_error"),
               JOptionPane.WARNING_MESSAGE);
-      wsInfo.setProgressText("Serious! " + WebServiceName
-              + " Service location failed\nfor URL :" + WsURL + "\n"
+      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);