JAL-1355

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

diff --git a/src/jalview/ws/jws1/JPredThread.java b/src/jalview/ws/jws1/JPredThread.java
index 4fcba31..85969fc 100644 (file)
--- a/src/jalview/ws/jws1/JPredThread.java
+++ b/src/jalview/ws/jws1/JPredThread.java
@@ -6,14 +6,16 @@
  * 
  * 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;
@@ -138,8 +140,7 @@ class JPredThread extends JWS1Thread implements WSClientI
             if (!jalview.analysis.SeqsetUtils.deuniquify(
                     (Hashtable) SequenceInfo, sqs))
             {
-              throw (new Exception(
-                      "Couldn't recover sequence properties for alignment."));
+              throw (new Exception(MessageManager.getString("exception.couldnt_recover_sequence_properties_for_alignment")));
             }
           }
           FirstSeq = 0;
@@ -151,8 +152,7 @@ class JPredThread extends JWS1Thread implements WSClientI
         }
         else
         {
-          throw (new Exception("Unknown format " + format
-                  + " for file : \n" + result.getAligfile()));
+          throw (new Exception(MessageManager.formatMessage("exception.unknown_format_for_file", new String[]{format,result.getAligfile()})));
         }
       }
       else
@@ -166,14 +166,13 @@ class JPredThread extends JWS1Thread implements WSClientI
                   .getAlignmentAndColumnSelection(gc))[0];
           if (this.msaIndex >= sqs.length)
           {
-            throw new Error(
-                    "Implementation Error! Invalid msaIndex for JPredJob on parent MSA input object!");
+            throw new Error(MessageManager.getString("error.implementation_error_invalid_msa_index_for_job"));
           }
 
           // ///
           // Uses RemoveGapsCommand
           // ///
-          new jalview.commands.RemoveGapsCommand("Remove Gaps",
+          new jalview.commands.RemoveGapsCommand(MessageManager.getString("label.remove_gaps"),
                   new SequenceI[]
                   { sqs[msaIndex] }, currentView);
 
@@ -184,8 +183,7 @@ class JPredThread extends JWS1Thread implements WSClientI
         if (!jalview.analysis.SeqsetUtils.SeqCharacterUnhash(
                 al.getSequenceAt(FirstSeq), SequenceInfo))
         {
-          throw (new Exception(
-                  "Couldn't recover sequence properties for JNet Query sequence!"));
+          throw (new Exception(MessageManager.getString("exception.couldnt_recover_sequence_props_for_jnet_query")));
         }
         else
         {
@@ -355,9 +353,7 @@ class JPredThread extends JWS1Thread implements WSClientI
   {
     if (!(j instanceof JPredJob))
     {
-      throw new Error(
-              "Implementation error - StartJob(JpredJob) called on "
-                      + j.getClass());
+      throw new Error(MessageManager.formatMessage("error.implementation_error_startjob_called", new String[]{j.getClass().toString()}));
     }
     try
     {
@@ -378,7 +374,7 @@ class JPredThread extends JWS1Thread implements WSClientI
         {
           job.result = (vamsas.objects.simple.Result) new JpredResult();
           job.result.setInvalid(true);
-          job.result.setStatus("Submission " + job.getJobId());
+          job.result.setStatus(MessageManager.formatMessage("label.submission_params", new String[]{job.getJobId().toString()}));
           throw new Exception(job.getJobId());
         }
         else
@@ -390,7 +386,7 @@ class JPredThread extends JWS1Thread implements WSClientI
       }
       else
       {
-        throw new Exception("Server timed out - try again later\n");
+        throw new Exception(MessageManager.getString("exception.server_timeout_try_later"));
       }
     } catch (Exception e)
     {
@@ -414,9 +410,7 @@ class JPredThread extends JWS1Thread implements WSClientI
       {
         wsInfo.setStatus(j.getJobnum(), WebserviceInfo.STATE_STOPPED_ERROR);
         // JBPNote - this could be a popup informing the user of the problem.
-        wsInfo.appendProgressText(j.getJobnum(),
-                "Failed to submit the prediction:\n" + e.getMessage()
-                        + wsInfo.getProgressText());
+        wsInfo.appendProgressText(j.getJobnum(), MessageManager.formatMessage("info.failed_to_submit_prediction", new String[]{e.getMessage(),wsInfo.getProgressText()}));
 
         jalview.bin.Cache.log.debug(
                 "Failed Submission of job " + j.getJobnum(), e);
@@ -506,8 +500,7 @@ class JPredThread extends JWS1Thread implements WSClientI
             else
             {
               // do merge with other job results
-              throw new Error(
-                      "Multiple JNet subjob merging not yet implemented.");
+              throw new Error(MessageManager.getString("error.multiple_jnet_subjob_merge_not_implemented"));
             }
           } catch (Exception e)
           {
@@ -515,9 +508,7 @@ class JPredThread extends JWS1Thread implements WSClientI
                     "JNet Client: JPred Annotation Parse Error", e);
             wsInfo.setStatus(j.getJobnum(),
                     WebserviceInfo.STATE_STOPPED_ERROR);
-            wsInfo.appendProgressText(j.getJobnum(), OutputHeader + "\n"
-                    + j.result.getStatus()
-                    + "\nInvalid JNet job result data!\n" + e.getMessage());
+            wsInfo.appendProgressText(j.getJobnum(), MessageManager.formatMessage("info.invalid_jnet_job_result_data", new String[]{OutputHeader.toString(),j.result.getStatus(), e.getMessage() }));
             j.result.setBroken(true);
           }
         }
@@ -585,7 +576,7 @@ class JPredThread extends JWS1Thread implements WSClientI
 
   public void cancelJob()
   {
-    throw new Error("Implementation error!");
+    throw new Error(MessageManager.getString("error.implementation_error"));
   }
 
   public boolean canMergeResults()