JAL-1503 update version in GPL header

[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 893482a..108a586 100644 (file)
--- a/src/jalview/ws/jws1/SeqSearchWSThread.java
+++ b/src/jalview/ws/jws1/SeqSearchWSThread.java
@@ -1,19 +1,20 @@
 /*
- * 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 2.8.1)
+ * 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.
- * 
+ *  
  * 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/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 package jalview.ws.jws1;
 
@@ -30,26 +31,6 @@ 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;
@@ -124,8 +105,8 @@ class SeqSearchWSThread extends JWS1Thread implements WSClientI
         // for
         // any
         // subjob
-        SeqNames.put(newname, jalview.analysis.SeqsetUtils
-                .SeqCharacterHash(seqs[i]));
+        SeqNames.put(newname,
+                jalview.analysis.SeqsetUtils.SeqCharacterHash(seqs[i]));
         if (valid && seqs[i].getEnd() - seqs[i].getStart() > minlen - 1)
         {
           seqarray[n] = new vamsas.objects.simple.Sequence();
@@ -140,8 +121,8 @@ class SeqSearchWSThread extends JWS1Thread implements WSClientI
           if (seqs[i].getEnd() >= seqs[i].getStart())
           {
             empty = (submitGaps) ? seqs[i].getSequenceAsString() : AlignSeq
-                    .extractGaps(jalview.util.Comparison.GapChars, seqs[i]
-                            .getSequenceAsString());
+                    .extractGaps(jalview.util.Comparison.GapChars,
+                            seqs[i].getSequenceAsString());
           }
           emptySeqs.add(new String[]
           { newname, empty });
@@ -374,9 +355,8 @@ class SeqSearchWSThread extends JWS1Thread implements WSClientI
         }
         if (njobs > 0)
         {
-          wsinfo
-                  .setProgressName("region " + jobs[j].getJobnum(),
-                          jobs[j].getJobnum());
+          wsinfo.setProgressName("region " + jobs[j].getJobnum(),
+                  jobs[j].getJobnum());
         }
         wsinfo.setProgressText(jobs[j].getJobnum(), OutputHeader);
       }
@@ -430,7 +410,8 @@ class SeqSearchWSThread extends JWS1Thread implements WSClientI
             cancelledMessage += ("\nProblems cancelling the job : Exception received...\n"
                     + exc + "\n");
             Cache.log.warn(
-                    "Exception whilst cancelling " + jobs[job].getJobId(), exc);
+                    "Exception whilst cancelling " + jobs[job].getJobId(),
+                    exc);
           }
           wsInfo.setProgressText(jobs[job].getJobnum(), OutputHeader
                   + cancelledMessage + "\n");
@@ -447,17 +428,16 @@ class SeqSearchWSThread extends JWS1Thread implements WSClientI
     {
       if (!jobComplete)
       {
-        wsInfo
-                .setProgressText(OutputHeader
-                        + "Server cannot cancel this job because it has not been submitted properly. just close the window.\n");
+        wsInfo.setProgressText(OutputHeader
+                + "Server cannot cancel this job because it has not been submitted properly. just close the window.\n");
       }
     }
   }
 
   public void pollJob(AWsJob job) throws Exception
   {
-    ((SeqSearchWSJob) job).result = server
-            .getResult(((SeqSearchWSJob) job).getJobId());
+    ((SeqSearchWSJob) job).result = server.getResult(((SeqSearchWSJob) job)
+            .getJobId());
   }
 
   public void StartJob(AWsJob job)
@@ -488,8 +468,8 @@ class SeqSearchWSThread extends JWS1Thread implements WSClientI
     }
     try
     {
-      vamsas.objects.simple.WsJobId jobsubmit = server.search(j.seqs
-              .getSeqs()[0], dbArg);
+      vamsas.objects.simple.WsJobId jobsubmit = server.search(
+              j.seqs.getSeqs()[0], dbArg);
 
       if ((jobsubmit != null) && (jobsubmit.getStatus() == 1))
       {
@@ -521,13 +501,13 @@ class SeqSearchWSThread extends JWS1Thread implements WSClientI
                       + e.toString() + "\n");
       j.setAllowedServerExceptions(0);
       wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_SERVERERROR);
-      wsInfo.setStatus(j.getJobnum(), 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");
+      wsInfo.setStatus(j.getJobnum(),
+              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");
 
       // e.printStackTrace(); // TODO: JBPNote DEBUG
     }
@@ -541,8 +521,8 @@ class SeqSearchWSThread extends JWS1Thread implements WSClientI
 
     for (int i = 0, j = seqs.length; i < j; i++)
     {
-      msa[i] = new jalview.datamodel.Sequence(seqs[i].getId(), seqs[i]
-              .getSeq());
+      msa[i] = new jalview.datamodel.Sequence(seqs[i].getId(),
+              seqs[i].getSeq());
     }
 
     return msa;
@@ -561,7 +541,7 @@ class SeqSearchWSThread extends JWS1Thread implements WSClientI
                 && jobs[j].hasResults())
         {
           results++;
-          vamsas.objects.simple.Alignment valign = ((SeqSearchResult) ((SeqSearchWSJob)jobs[j]).result)
+          vamsas.objects.simple.Alignment valign = ((SeqSearchResult) ((SeqSearchWSJob) jobs[j]).result)
                   .getAlignment();
           if (valign != null)
           {
@@ -570,7 +550,8 @@ class SeqSearchWSThread extends JWS1Thread implements WSClientI
             String[] lines = valign.getMethod();
             for (int line = 0; line < lines.length; line++)
             {
-              wsInfo.appendProgressText(jobs[j].getJobnum(), lines[line] + "\n");
+              wsInfo.appendProgressText(jobs[j].getJobnum(), lines[line]
+                      + "\n");
             }
             // JBPNote The returned files from a webservice could be
             // hidden behind icons in the monitor window that,