X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fjws2%2FJws2Client.java;h=4166d3eb07b427a79b9254293b62b4c5082fb8bd;hb=62a585da2d97f93123b5482f2b5846fdac3bd97f;hp=e6b4cf577f68d448a0598ef2ac49f17b6c925560;hpb=c9df7697dacf668e97290c57d4d117ac8cc40bc8;p=jalview.git

diff --git a/src/jalview/ws/jws2/Jws2Client.java b/src/jalview/ws/jws2/Jws2Client.java
index e6b4cf5..4166d3e 100644
--- a/src/jalview/ws/jws2/Jws2Client.java
+++ b/src/jalview/ws/jws2/Jws2Client.java
@@ -1,13 +1,13 @@
 /*
- * 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
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
+ * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, 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 
@@ -45,8 +45,8 @@ public abstract class Jws2Client extends jalview.ws.WSClient
 
   protected List<Argument> paramset;
 
-  public Jws2Client(AlignFrame _alignFrame,
-          WsParamSetI preset, List<Argument> arguments)
+  public Jws2Client(AlignFrame _alignFrame, WsParamSetI preset,
+          List<Argument> arguments)
   {
     alignFrame = _alignFrame;
     this.preset = preset;
@@ -78,6 +78,7 @@ public abstract class Jws2Client extends jalview.ws.WSClient
   {
     return processParams(sh, editParams, false);
   }
+
   protected boolean processParams(Jws2Instance sh, boolean editParams,
           boolean adjustingExisting)
   {
@@ -89,7 +90,9 @@ public abstract class Jws2Client extends jalview.ws.WSClient
         sh.paramStore = new JabaParamStore(sh,
                 Desktop.getUserParameterStore());
       }
-      WsJobParameters jobParams = new WsJobParameters(sh, preset);
+      WsJobParameters jobParams = (preset == null && paramset != null && paramset
+              .size() > 0) ? new WsJobParameters(null, sh, null, paramset)
+              : new WsJobParameters(sh, preset);
       if (adjustingExisting)
       {
         jobParams.setName("Adjusting parameters for existing Calculation");
@@ -101,8 +104,9 @@ public abstract class Jws2Client extends jalview.ws.WSClient
       WsParamSetI prset = jobParams.getPreset();
       if (prset == null)
       {
-        paramset = JabaParamStore.getJabafromJwsArgs(jobParams
-                .getJobParams());
+        paramset = jobParams.isServiceDefaults() ? null : JabaParamStore
+                .getJabafromJwsArgs(jobParams.getJobParams());
+        this.preset = null;
       }
       else
       {