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

[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 0fdc3ff..79c39b4 100644 (file)
--- a/src/jalview/ws/jws1/JPredThread.java
+++ b/src/jalview/ws/jws1/JPredThread.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
- * Copyright (C) 2014 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.
  * 
@@ -24,6 +24,7 @@ import jalview.analysis.AlignSeq;
 import jalview.bin.Cache;
 import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AlignmentI;
 import jalview.datamodel.AlignmentView;
 import jalview.datamodel.ColumnSelection;
 import jalview.datamodel.SequenceI;
@@ -103,7 +104,7 @@ class JPredThread extends JWS1Thread implements WSClientI
       {
         return null;
       }
-      Alignment al = null;
+      AlignmentI al = null;
       ColumnSelection alcsel = null;
       int FirstSeq = -1; // the position of the query sequence in Alignment al
 
@@ -146,10 +147,11 @@ class JPredThread extends JWS1Thread implements WSClientI
             {
               sqs[i] = al.getSequenceAt(i);
             }
-            if (!jalview.analysis.SeqsetUtils.deuniquify(
-                    SequenceInfo, sqs))
+            if (!jalview.analysis.SeqsetUtils.deuniquify(SequenceInfo, sqs))
             {
-              throw (new Exception(MessageManager.getString("exception.couldnt_recover_sequence_properties_for_alignment")));
+              throw (new Exception(
+                      MessageManager
+                              .getString("exception.couldnt_recover_sequence_properties_for_alignment")));
             }
           }
           FirstSeq = 0;
@@ -168,7 +170,9 @@ class JPredThread extends JWS1Thread implements WSClientI
         }
         else
         {
-          throw (new Exception(MessageManager.formatMessage("exception.unknown_format_for_file", new String[]{format,result.getAligfile()})));
+          throw (new Exception(MessageManager.formatMessage(
+                  "exception.unknown_format_for_file", new String[] {
+                      format, result.getAligfile() })));
         }
       }
       else
@@ -182,15 +186,17 @@ class JPredThread extends JWS1Thread implements WSClientI
                   .getAlignmentAndColumnSelection(gc)[0];
           if (this.msaIndex >= sqs.length)
           {
-            throw new Error(MessageManager.getString("error.implementation_error_invalid_msa_index_for_job"));
+            throw new Error(
+                    MessageManager
+                            .getString("error.implementation_error_invalid_msa_index_for_job"));
           }
 
           // ///
           // Uses RemoveGapsCommand
           // ///
-          new jalview.commands.RemoveGapsCommand(MessageManager.getString("label.remove_gaps"),
-                  new SequenceI[]
-                  { sqs[msaIndex] }, currentView);
+          new jalview.commands.RemoveGapsCommand(
+                  MessageManager.getString("label.remove_gaps"),
+                  new SequenceI[] { sqs[msaIndex] }, currentView);
 
           SequenceI profileseq = al.getSequenceAt(FirstSeq);
           profileseq.setSequence(sqs[msaIndex].getSequenceAsString());
@@ -199,7 +205,9 @@ class JPredThread extends JWS1Thread implements WSClientI
         if (!jalview.analysis.SeqsetUtils.SeqCharacterUnhash(
                 al.getSequenceAt(FirstSeq), SequenceInfo))
         {
-          throw (new Exception(MessageManager.getString("exception.couldnt_recover_sequence_props_for_jnet_query")));
+          throw (new Exception(
+                  MessageManager
+                          .getString("exception.couldnt_recover_sequence_props_for_jnet_query")));
         }
         else
         {
@@ -235,8 +243,7 @@ class JPredThread extends JWS1Thread implements WSClientI
                   alant.sequenceRef);
         }
       }
-      return new Object[]
-      { al, alcsel }; // , FirstSeq, noMsa};
+      return new Object[] { al, alcsel }; // , FirstSeq, noMsa};
     }
 
     /**
@@ -279,7 +286,7 @@ class JPredThread extends JWS1Thread implements WSClientI
      * @param al
      * @param profileseq
      */
-    private void alignToProfileSeq(Alignment al, SequenceI profileseq)
+    private void alignToProfileSeq(AlignmentI al, SequenceI profileseq)
     {
       char gc = al.getGapCharacter();
       int[] gapMap = profileseq.gapMap();
@@ -385,8 +392,7 @@ class JPredThread extends JWS1Thread implements WSClientI
     if (job.hasValidInput())
     {
       OutputHeader = wsInfo.getProgressText();
-      jobs = new WSJob[]
-      { job };
+      jobs = new WSJob[] { job };
       job.setJobnum(0);
     }
     else
@@ -404,8 +410,7 @@ class JPredThread extends JWS1Thread implements WSClientI
     JPredJob job = new JPredJob(SequenceInfo, msf, delMap);
     if (job.hasValidInput())
     {
-      jobs = new WSJob[]
-      { job };
+      jobs = new WSJob[] { job };
       OutputHeader = wsInfo.getProgressText();
       job.setJobnum(0);
     }
@@ -419,7 +424,9 @@ class JPredThread extends JWS1Thread implements WSClientI
   {
     if (!(j instanceof JPredJob))
     {
-      throw new Error(MessageManager.formatMessage("error.implementation_error_startjob_called", new String[]{j.getClass().toString()}));
+      throw new Error(MessageManager.formatMessage(
+              "error.implementation_error_startjob_called",
+              new String[] { j.getClass().toString() }));
     }
     try
     {
@@ -440,7 +447,9 @@ class JPredThread extends JWS1Thread implements WSClientI
         {
           job.result = new JpredResult();
           job.result.setInvalid(true);
-          job.result.setStatus(MessageManager.formatMessage("label.submission_params", new String[]{job.getJobId().toString()}));
+          job.result.setStatus(MessageManager.formatMessage(
+                  "label.submission_params", new String[] { job.getJobId()
+                          .toString() }));
           throw new Exception(job.getJobId());
         }
         else
@@ -452,7 +461,9 @@ class JPredThread extends JWS1Thread implements WSClientI
       }
       else
       {
-        throw new Exception(MessageManager.getString("exception.server_timeout_try_later"));
+        throw new Exception(
+                MessageManager
+                        .getString("exception.server_timeout_try_later"));
       }
     } catch (Exception e)
     {
@@ -476,7 +487,11 @@ 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(), MessageManager.formatMessage("info.failed_to_submit_prediction", new String[]{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);
@@ -566,7 +581,9 @@ class JPredThread extends JWS1Thread implements WSClientI
             else
             {
               // do merge with other job results
-              throw new Error(MessageManager.getString("error.multiple_jnet_subjob_merge_not_implemented"));
+              throw new Error(
+                      MessageManager
+                              .getString("error.multiple_jnet_subjob_merge_not_implemented"));
             }
           } catch (Exception e)
           {
@@ -574,7 +591,10 @@ 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(), MessageManager.formatMessage("info.invalid_jnet_job_result_data", new String[]{OutputHeader.toString(),j.result.getStatus(), 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);
           }
         }
@@ -585,6 +605,8 @@ class JPredThread extends JWS1Thread implements WSClientI
         if (newWindow)
         {
           AlignFrame af;
+          ((AlignmentI) res[0]).setSeqrep(((AlignmentI) res[0])
+                  .getSequenceAt(0));
           if (input == null)
           {
             if (res[1] != null)