X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2FAWSThread.java;h=7d174bc2953ded1796dc95c0eab56d84e31e4a6a;hb=797df64fa2a0a30773d0f48f5494d4155e5a8be3;hp=d49b245db6fd0a7afe04641fdb5fac9cbe13838c;hpb=fa129d373443b56d8a59fdec3a87f6f14b1771f3;p=jalview.git

diff --git a/src/jalview/ws/AWSThread.java b/src/jalview/ws/AWSThread.java
index d49b245..7d174bc 100644
--- a/src/jalview/ws/AWSThread.java
+++ b/src/jalview/ws/AWSThread.java
@@ -1,3 +1,20 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ * 
+ * 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/>.
+ */
 package jalview.ws;
 
 import jalview.bin.Cache;
@@ -17,47 +34,57 @@ public abstract class AWSThread extends Thread
    * view that this job was associated with
    */
   protected AlignmentI currentView = null;
+
   /**
    * feature settings from view that job was associated with
    */
   protected FeatureRendererSettings featureSettings = null;
+
   /**
    * metadata about this web service
    */
   protected WebserviceInfo wsInfo = null;
+
   /**
    * original input data for this job
    */
   protected AlignmentView input = null;
+
   /**
    * dataset sequence relationships to be propagated onto new results
    */
   protected AlignedCodonFrame[] codonframe = null;
+
   /**
    * are there jobs still running in this thread.
    */
   protected boolean jobComplete = false;
+
   /**
    * one or more jobs being managed by this thread.
    */
   protected AWsJob jobs[] = null;
+
   /**
    * full name of service
    */
   protected String WebServiceName = null;
+
   protected char defGapChar = '-';
+
   /**
    * header prepended to all output from job
    */
   protected String OutputHeader;
 
   /**
-   * only used when reporting a web service out of memory error - the job ID will be concatenated to the URL
+   * only used when reporting a web service out of memory error - the job ID
+   * will be concatenated to the URL
    */
   protected String WsUrl = null;
 
   /**
-   * generic web service job/subjob poll loop 
+   * generic web service job/subjob poll loop
    */
   public void run()
   {
@@ -97,7 +124,9 @@ public abstract class AWSThread extends Thread
                     + " Server exception!\n" + ex.getMessage());
             // always output the exception's stack trace to the log
             Cache.log.warn(WebServiceName + " job(" + jobs[j].jobnum
-                    + ") Server exception.",ex);
+                    + ") Server exception.");
+            // todo: could limit trace to cause if this is a SOAPFaultException.
+            ex.printStackTrace();
 
             if (jobs[j].allowedServerExceptions > 0)
             {
@@ -183,7 +212,6 @@ public abstract class AWSThread extends Thread
     }
   }
 
-
   public AWSThread()
   {
     super();
@@ -245,8 +273,8 @@ public abstract class AWSThread extends Thread
   /**
    * helper function to conserve dataset references to sequence objects returned
    * from web services 1. Propagates AlCodonFrame data from
-   * <code>codonframe</code> to <code>al</code>
-   * TODO: refactor to datamodel
+   * <code>codonframe</code> to <code>al</code> TODO: refactor to datamodel
+   * 
    * @param al
    */
   public void propagateDatasetMappings(Alignment al)
@@ -306,11 +334,11 @@ public abstract class AWSThread extends Thread
   }
 
   /**
-   * 
+   * Extracts additional info from alignment view's context.
    * @param alframe
    *          - reference for copying mappings and display styles across
    * @param wsinfo2
-   *          - gui attachment point
+   *          - gui attachment point - may be null
    * @param alview
    *          - input data for the calculation
    * @param wsurl2