X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fws%2FAWSThread.java;h=7d174bc2953ded1796dc95c0eab56d84e31e4a6a;hb=23a5ed32b702d4d3682b8cdc8fd8e3f238202f7d;hp=11556b253c6385b9cc7f0492cef8ee4c05686300;hpb=153dd62dc91da13ae732600e6ea55ddbe15eab39;p=jalview.git
diff --git a/src/jalview/ws/AWSThread.java b/src/jalview/ws/AWSThread.java
index 11556b2..7d174bc 100644
--- a/src/jalview/ws/AWSThread.java
+++ b/src/jalview/ws/AWSThread.java
@@ -1,6 +1,6 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * 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.
*
@@ -34,47 +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()
{
@@ -202,7 +212,6 @@ public abstract class AWSThread extends Thread
}
}
-
public AWSThread()
{
super();
@@ -264,8 +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)
@@ -325,11 +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