X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=src%2Fjalview%2Fws%2FAWSThread.java;h=7d174bc2953ded1796dc95c0eab56d84e31e4a6a;hb=797df64fa2a0a30773d0f48f5494d4155e5a8be3;hp=4f604802d7a6d26633fba80790f5d1d2424bb4c1;hpb=add30afdc46a14e61ccf55881fa91b9ca9abfe80;p=jalview.git
diff --git a/src/jalview/ws/AWSThread.java b/src/jalview/ws/AWSThread.java
index 4f60480..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 .
+ */
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
- * codonframe
to al
- * TODO: refactor to datamodel
+ * codonframe
to al
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