JAL-1619 AlignedCodonFrame in new alignment should references realigned

[jalview.git] / src / jalview / ws / AWSThread.java

diff --git a/src/jalview/ws/AWSThread.java b/src/jalview/ws/AWSThread.java
index 0167690..7f05e90 100644 (file)
--- a/src/jalview/ws/AWSThread.java
+++ b/src/jalview/ws/AWSThread.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;
@@ -25,8 +27,9 @@ import jalview.datamodel.AlignmentI;
 import jalview.datamodel.AlignmentView;
 import jalview.datamodel.SequenceI;
 import jalview.gui.AlignFrame;
-import jalview.gui.WebserviceInfo;
 import jalview.gui.FeatureRenderer.FeatureRendererSettings;
+import jalview.gui.WebserviceInfo;
+import jalview.util.MessageManager;
 
 public abstract class AWSThread extends Thread
 {
@@ -121,8 +124,8 @@ public abstract class AWSThread extends Thread
           } catch (Exception ex)
           {
             // Deal with Transaction exceptions
-            wsInfo.appendProgressText(jobs[j].jobnum, "\n" + WebServiceName
-                    + " Server exception!\n" + ex.getMessage());
+            wsInfo.appendProgressText(jobs[j].jobnum, 
+                       MessageManager.formatMessage("info.server_exception", new String[]{WebServiceName,ex.getMessage()}));
             // always output the exception's stack trace to the log
             Cache.log.warn(WebServiceName + " job(" + jobs[j].jobnum
                     + ") Server exception.");
@@ -187,7 +190,7 @@ public abstract class AWSThread extends Thread
       Cache.log
               .debug("WebServiceJob poll loop finished with no jobs created.");
       wsInfo.setStatus(wsInfo.STATE_STOPPED_ERROR);
-      wsInfo.appendProgressText("No jobs ran.");
+      wsInfo.appendProgressText(MessageManager.getString("info.no_jobs_ran"));
       wsInfo.setFinishedNoResults();
     }
   }
@@ -294,10 +297,11 @@ public abstract class AWSThread extends Thread
       {
         for (int i = 0; i < codonframe.length; i++)
         {
-          if (codonframe[i] != null
-                  && codonframe[i].involvesSequence(alignment[sq]))
+          AlignedCodonFrame acf = codonframe[i];
+          final SequenceI seq = alignment[sq];
+          if (acf != null && acf.involvesSequence(seq))
           {
-            al.addCodonFrame(codonframe[i]);
+            al.addCodonFrame(new AlignedCodonFrame(acf, alignment));
             codonframe[i] = null;
             break;
           }