JAL-1645 Version-Rel Version 2.9 Year-Rel 2015 Licensing glob

[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 5d44ddd..bf791e2 100644 (file)
--- a/src/jalview/ws/jws1/SeqSearchWSThread.java
+++ b/src/jalview/ws/jws1/SeqSearchWSThread.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
- * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -20,17 +20,23 @@
  */
 package jalview.ws.jws1;
 
-import java.util.*;
-
-import jalview.analysis.*;
-import jalview.bin.*;
-import jalview.datamodel.*;
-import jalview.gui.*;
+import jalview.analysis.AlignSeq;
+import jalview.bin.Cache;
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentView;
+import jalview.datamodel.SequenceI;
+import jalview.gui.AlignFrame;
+import jalview.gui.Desktop;
+import jalview.gui.WebserviceInfo;
 import jalview.io.NewickFile;
 import jalview.util.MessageManager;
 import jalview.ws.AWsJob;
 import jalview.ws.JobStateSummary;
 import jalview.ws.WSClientI;
+
+import java.util.Hashtable;
+import java.util.Vector;
+
 import vamsas.objects.simple.MsaResult;
 import vamsas.objects.simple.SeqSearchResult;
 
@@ -85,7 +91,9 @@ class SeqSearchWSThread extends JWS1Thread implements WSClientI
       int nseqs = 0;
       if (minlen < 0)
       {
-          throw new Error(MessageManager.getString("error.implementation_error_minlen_must_be_greater_zero"));
+        throw new Error(
+                MessageManager
+                        .getString("error.implementation_error_minlen_must_be_greater_zero"));
       }
       for (int i = 0; i < seqs.length; i++)
       {
@@ -126,8 +134,7 @@ class SeqSearchWSThread extends JWS1Thread implements WSClientI
                     .extractGaps(jalview.util.Comparison.GapChars,
                             seqs[i].getSequenceAsString());
           }
-          emptySeqs.add(new String[]
-          { newname, empty });
+          emptySeqs.add(new String[] { newname, empty });
         }
       }
       if (submitGaps)
@@ -259,8 +266,7 @@ class SeqSearchWSThread extends JWS1Thread implements WSClientI
          * trigger a 'fetchDBids' to annotate sequences with database ids...
          */
 
-        return new Object[]
-        { al, nf };
+        return new Object[] { al, nf };
       }
       return null;
     }
@@ -446,7 +452,9 @@ class SeqSearchWSThread extends JWS1Thread implements WSClientI
   {
     if (!(job instanceof SeqSearchWSJob))
     {
-        throw new Error(MessageManager.formatMessage("error.implementation_error_msawbjob_called", new String[]{job.getClass().toString()}));
+      throw new Error(MessageManager.formatMessage(
+              "error.implementation_error_msawbjob_called",
+              new String[] { job.getClass().toString() }));
     }
     SeqSearchWSJob j = (SeqSearchWSJob) job;
     if (j.isSubmitted())
@@ -464,7 +472,8 @@ class SeqSearchWSThread extends JWS1Thread implements WSClientI
       j.setSubmitted(true);
       j.result = new MsaResult();
       j.result.setFinished(true);
-      j.result.setStatus(MessageManager.getString("label.empty_alignment_job"));
+      j.result.setStatus(MessageManager
+              .getString("label.empty_alignment_job"));
       ((MsaResult) j.result).setMsa(null);
     }
     try
@@ -483,7 +492,9 @@ class SeqSearchWSThread extends JWS1Thread implements WSClientI
       {
         if (jobsubmit == null)
         {
-          throw new Exception(MessageManager.formatMessage("exception.web_service_returned_null_try_later", new String[]{WsUrl}));
+          throw new Exception(MessageManager.formatMessage(
+                  "exception.web_service_returned_null_try_later",
+                  new String[] { WsUrl }));
         }
 
         throw new Exception(jobsubmit.getJobId());
@@ -501,9 +512,8 @@ class SeqSearchWSThread extends JWS1Thread implements WSClientI
       wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_SERVERERROR);
       wsInfo.setStatus(j.getJobnum(),
               WebserviceInfo.STATE_STOPPED_SERVERERROR);
-      wsInfo.appendProgressText(
-              j.getJobnum(),
-              MessageManager.getString("info.failed_to_submit_sequences_for_alignment"));
+      wsInfo.appendProgressText(j.getJobnum(), MessageManager
+              .getString("info.failed_to_submit_sequences_for_alignment"));
 
       // e.printStackTrace(); // TODO: JBPNote DEBUG
     }
@@ -541,8 +551,8 @@ class SeqSearchWSThread extends JWS1Thread implements WSClientI
                   .getAlignment();
           if (valign != null)
           {
-            wsInfo.appendProgressText(jobs[j].getJobnum(),
-                    MessageManager.getString("info.alignment_object_method_notes"));
+            wsInfo.appendProgressText(jobs[j].getJobnum(), MessageManager
+                    .getString("info.alignment_object_method_notes"));
             String[] lines = valign.getMethod();
             for (int line = 0; line < lines.length; line++)
             {
@@ -642,7 +652,8 @@ class SeqSearchWSThread extends JWS1Thread implements WSClientI
               AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
       if (nf != null)
       {
-        af.ShowNewickTree(nf, MessageManager.formatMessage("label.tree_from", new String[]{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);