update author list in license for (JAL-826)

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

diff --git a/src/jalview/ws/AWSThread.java b/src/jalview/ws/AWSThread.java
index 4f60480..7d174bc 100644 (file)
--- 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()
   {
@@ -185,7 +212,6 @@ public abstract class AWSThread extends Thread
     }
   }
 
-
   public AWSThread()
   {
     super();
@@ -247,8 +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)
@@ -308,11 +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