JAL-1925 update source version in license

[jalview.git] / src / jalview / ws / jws2 / MsaWSThread.java

diff --git a/src/jalview/ws/jws2/MsaWSThread.java b/src/jalview/ws/jws2/MsaWSThread.java
index d0d0a6e..0ab38c7 100644 (file)
--- a/src/jalview/ws/jws2/MsaWSThread.java
+++ b/src/jalview/ws/jws2/MsaWSThread.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 2.9.0b2)
+ * Copyright (C) 2015 The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -125,7 +125,9 @@ class MsaWSThread extends AWS2Thread 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++)
       {
@@ -164,8 +166,7 @@ class MsaWSThread extends AWS2Thread implements WSClientI
                     .extractGaps(jalview.util.Comparison.GapChars,
                             seqs[i].getSequenceAsString());
           }
-          emptySeqs.add(new String[]
-          { newname, empty });
+          emptySeqs.add(new String[] { newname, empty });
         }
       }
       return valid;
@@ -296,8 +297,7 @@ class MsaWSThread extends AWS2Thread implements WSClientI
         jalview.analysis.AlignmentSorter.recoverOrder(alseqs);
         // account for any missing sequences
         jalview.analysis.SeqsetUtils.deuniquify(SeqNames, alseqs);
-        return new Object[]
-        { alseqs, msaorder };
+        return new Object[] { alseqs, msaorder };
       }
       return null;
     }
@@ -529,6 +529,7 @@ class MsaWSThread extends AWS2Thread implements WSClientI
   {
     return validInput;
   }
+
   public boolean isCancellable()
   {
     return true;
@@ -655,7 +656,9 @@ class MsaWSThread extends AWS2Thread implements WSClientI
     // boiler plate template
     if (!(job instanceof MsaWSJob))
     {
-      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() }));
     }
     MsaWSJob j = (MsaWSJob) job;
     if (j.isSubmitted())
@@ -701,28 +704,39 @@ class MsaWSThread extends AWS2Thread implements WSClientI
       }
       else
       {
-        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 }));
       }
     } catch (compbio.metadata.UnsupportedRuntimeException _lex)
     {
       lex = _lex;
-      wsInfo.appendProgressText(MessageManager.formatMessage("info.job_couldnt_be_run_server_doesnt_support_program", new String[]{_lex.getMessage()}));
-      wsInfo.warnUser(_lex.getMessage(), MessageManager.getString("warn.service_not_supported"));
+      wsInfo.appendProgressText(MessageManager.formatMessage(
+              "info.job_couldnt_be_run_server_doesnt_support_program",
+              new String[] { _lex.getMessage() }));
+      wsInfo.warnUser(_lex.getMessage(),
+              MessageManager.getString("warn.service_not_supported"));
       wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_SERVERERROR);
       wsInfo.setStatus(j.getJobnum(),
               WebserviceInfo.STATE_STOPPED_SERVERERROR);
     } catch (compbio.metadata.LimitExceededException _lex)
     {
       lex = _lex;
-      wsInfo.appendProgressText(MessageManager.formatMessage("info.job_couldnt_be_run_exceeded_hard_limit", new String[]{_lex.getMessage()}));
-      wsInfo.warnUser(_lex.getMessage(), MessageManager.getString("warn.input_is_too_big"));
+      wsInfo.appendProgressText(MessageManager.formatMessage(
+              "info.job_couldnt_be_run_exceeded_hard_limit",
+              new String[] { _lex.getMessage() }));
+      wsInfo.warnUser(_lex.getMessage(),
+              MessageManager.getString("warn.input_is_too_big"));
       wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);
       wsInfo.setStatus(j.getJobnum(), WebserviceInfo.STATE_STOPPED_ERROR);
     } catch (compbio.metadata.WrongParameterException _lex)
     {
       lex = _lex;
-      wsInfo.warnUser(_lex.getMessage(), MessageManager.getString("warn.invalid_job_param_set"));
-      wsInfo.appendProgressText(MessageManager.formatMessage("info.job_couldnt_be_run_incorrect_param_setting", new String[]{_lex.getMessage()}));
+      wsInfo.warnUser(_lex.getMessage(),
+              MessageManager.getString("warn.invalid_job_param_set"));
+      wsInfo.appendProgressText(MessageManager.formatMessage(
+              "info.job_couldnt_be_run_incorrect_param_setting",
+              new String[] { _lex.getMessage() }));
       wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);
       wsInfo.setStatus(j.getJobnum(), WebserviceInfo.STATE_STOPPED_ERROR);
     } catch (Error e)
@@ -755,8 +769,8 @@ class MsaWSThread extends AWS2Thread implements WSClientI
         // TODO: JBPNote catch timeout or other fault types explicitly
 
         j.setAllowedServerExceptions(0);
-        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"));
       }
     }
   }
@@ -764,7 +778,9 @@ class MsaWSThread extends AWS2Thread implements WSClientI
   public void parseResult()
   {
     long progbar = System.currentTimeMillis();
-    wsInfo.setProgressBar(MessageManager.getString("status.collecting_job_results"), progbar);
+    wsInfo.setProgressBar(
+            MessageManager.getString("status.collecting_job_results"),
+            progbar);
     int results = 0; // number of result sets received
     JobStateSummary finalState = new JobStateSummary();
     try
@@ -959,6 +975,7 @@ class MsaWSThread extends AWS2Thread implements WSClientI
     }
     else
     {
+      // TODO 2.9.x feature
       System.out.println("MERGE WITH OLD FRAME");
       // TODO: modify alignment in original frame, replacing old for new
       // alignment using the commands.EditCommand model to ensure the update can
@@ -987,17 +1004,24 @@ class MsaWSThread extends AWS2Thread implements WSClientI
       addSortByMenuItems(af, alorders);
     }
 
+    // TODO: refactor retrieve and show as new splitFrame as Desktop method
+
     /*
      * If alignment was requested from one half of a SplitFrame, show in a
      * SplitFrame with the other pane similarly aligned.
      */
     AlignFrame requestedBy = getRequestingAlignFrame();
-    if (requestedBy != null && requestedBy.getSplitViewContainer() != null)
+    if (requestedBy != null
+            && requestedBy.getSplitViewContainer() != null
+            && requestedBy.getSplitViewContainer().getComplement(
+                    requestedBy) != null)
     {
       AlignmentI complement = requestedBy.getSplitViewContainer()
               .getComplement(requestedBy);
       String complementTitle = requestedBy.getSplitViewContainer()
               .getComplementTitle(requestedBy);
+      // becomes null if the alignment window was closed before the alignment
+      // job finished.
       AlignmentI copyComplement = new Alignment(complement);
       copyComplement.alignAs(al);
       if (copyComplement.getHeight() > 0)