JAL-1620 version bump and release notes

[jalview.git] / src / jalview / ws / jws1 / SeqSearchWSThread.java

diff --git a/src/jalview/ws/jws1/SeqSearchWSThread.java b/src/jalview/ws/jws1/SeqSearchWSThread.java
index 99a8d03..d920e37 100644 (file)
--- a/src/jalview/ws/jws1/SeqSearchWSThread.java
+++ b/src/jalview/ws/jws1/SeqSearchWSThread.java
@@ -1,19 +1,22 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
+ * Copyright (C) 2014 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;
 
@@ -24,32 +27,13 @@ import jalview.bin.*;
 import jalview.datamodel.*;
 import jalview.gui.*;
 import jalview.io.NewickFile;
+import jalview.util.MessageManager;
 import jalview.ws.AWsJob;
 import jalview.ws.JobStateSummary;
 import jalview.ws.WSClientI;
 import vamsas.objects.simple.MsaResult;
 import vamsas.objects.simple.SeqSearchResult;
 
-/**
- * <p>
- * Title:
- * </p>
- * 
- * <p>
- * Description:
- * </p>
- * 
- * <p>
- * Copyright: Copyright (c) 2004
- * </p>
- * 
- * <p>
- * Company: Dundee University
- * </p>
- * 
- * @author not attributable
- * @version 1.0
- */
 class SeqSearchWSThread extends JWS1Thread implements WSClientI
 {
   String dbs = null;
@@ -78,7 +62,7 @@ class SeqSearchWSThread extends JWS1Thread implements WSClientI
         subjobComplete = true;
         result = new MsaResult();
         result.setFinished(true);
-        result.setStatus("Job never ran - input returned to user.");
+        result.setStatus(MessageManager.getString("label.job_never_ran"));
       }
 
     }
@@ -101,8 +85,7 @@ class SeqSearchWSThread extends JWS1Thread implements WSClientI
       int nseqs = 0;
       if (minlen < 0)
       {
-        throw new Error(
-                "Implementation error: minlen must be zero or more.");
+          throw new Error(MessageManager.getString("error.implementation_error_minlen_must_be_greater_zero"));
       }
       for (int i = 0; i < seqs.length; i++)
       {
@@ -463,8 +446,7 @@ class SeqSearchWSThread extends JWS1Thread implements WSClientI
   {
     if (!(job instanceof SeqSearchWSJob))
     {
-      throw new Error("StartJob(MsaWSJob) called on a WSJobInstance "
-              + job.getClass());
+        throw new Error(MessageManager.formatMessage("error.implementation_error_msawbjob_called", new String[]{job.getClass().toString()}));
     }
     SeqSearchWSJob j = (SeqSearchWSJob) job;
     if (j.isSubmitted())
@@ -482,7 +464,7 @@ class SeqSearchWSThread extends JWS1Thread implements WSClientI
       j.setSubmitted(true);
       j.result = new MsaResult();
       j.result.setFinished(true);
-      j.result.setStatus("Empty Alignment Job");
+      j.result.setStatus(MessageManager.getString("label.empty_alignment_job"));
       ((MsaResult) j.result).setMsa(null);
     }
     try
@@ -501,10 +483,7 @@ class SeqSearchWSThread extends JWS1Thread implements WSClientI
       {
         if (jobsubmit == null)
         {
-          throw new Exception(
-                  "Server at "
-                          + WsUrl
-                          + " returned null object, it probably cannot be contacted. Try again later ?");
+          throw new Exception(MessageManager.formatMessage("exception.web_service_returned_null_try_later", new String[]{WsUrl}));
         }
 
         throw new Exception(jobsubmit.getJobId());
@@ -524,9 +503,7 @@ class SeqSearchWSThread extends JWS1Thread implements WSClientI
               WebserviceInfo.STATE_STOPPED_SERVERERROR);
       wsInfo.appendProgressText(
               j.getJobnum(),
-              "Failed to submit sequences for alignment.\n"
-                      + "It is most likely that there is a problem with the server.\n"
-                      + "Just close the window\n");
+              MessageManager.getString("info.failed_to_submit_sequences_for_alignment"));
 
       // e.printStackTrace(); // TODO: JBPNote DEBUG
     }
@@ -565,7 +542,7 @@ class SeqSearchWSThread extends JWS1Thread implements WSClientI
           if (valign != null)
           {
             wsInfo.appendProgressText(jobs[j].getJobnum(),
-                    "\nAlignment Object Method Notes\n");
+                    MessageManager.getString("info.alignment_object_method_notes"));
             String[] lines = valign.getMethod();
             for (int line = 0; line < lines.length; line++)
             {
@@ -665,7 +642,7 @@ class SeqSearchWSThread extends JWS1Thread implements WSClientI
               AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
       if (nf != null)
       {
-        af.ShowNewickTree(nf, "Tree from " + this.alTitle);
+        af.ShowNewickTree(nf, MessageManager.formatMessage("label.tree_from", new String[]{this.alTitle}));
       }
       // initialise with same renderer settings as in parent alignframe.
       af.getFeatureRenderer().transferSettings(this.featureSettings);