X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fjws2%2FMsaWSThread.java;h=a0cd0f4c4f41a9e0c4e180a563612cbfaeb9d7d9;hb=54ee3e95ec4f21a301e458f8b7f22876ae70a017;hp=c4fc66bbfb7801846c9e9bf29152cdef42e197bc;hpb=9a68d6293a1d0ded59716fa34826fb4af793c330;p=jalview.git

diff --git a/src/jalview/ws/jws2/MsaWSThread.java b/src/jalview/ws/jws2/MsaWSThread.java
index c4fc66b..a0cd0f4 100644
--- a/src/jalview/ws/jws2/MsaWSThread.java
+++ b/src/jalview/ws/jws2/MsaWSThread.java
@@ -38,6 +38,7 @@ import jalview.ws.AWsJob;
 import jalview.ws.JobStateSummary;
 import jalview.ws.WSClientI;
 import jalview.ws.jws2.dm.JabaWsParamSet;
+import jalview.ws.params.ArgumentI;
 import jalview.ws.params.WsParamSetI;
 
 import java.util.ArrayList;
@@ -70,7 +71,7 @@ class MsaWSThread extends AWS2Thread implements WSClientI
 
     WsParamSetI preset = null;
 
-    List<Argument> arguments = null;
+    List<ArgumentI> arguments = null;
 
     /**
      * input
@@ -385,7 +386,7 @@ class MsaWSThread extends AWS2Thread implements WSClientI
       }
       if (arguments != null && arguments.size() > 0)
       {
-        newargs.addAll(arguments);
+        newargs.addAll(JabaParamStore.getJabafromJwsArgs(arguments));
       }
       return newargs;
     }
@@ -402,7 +403,7 @@ class MsaWSThread extends AWS2Thread implements WSClientI
                 + "Preset: " + preset.getName());
         if (preset instanceof JabaWsParamSet)
         {
-          for (Argument opt : ((JabaWsParamSet) preset).getjabaArguments())
+          for (Argument opt : getJabaArguments())
           {
             jobProgress.append(
                     opt.getName() + " " + opt.getDefaultValue() + "\n");
@@ -413,7 +414,7 @@ class MsaWSThread extends AWS2Thread implements WSClientI
       {
         jobProgress.append("With custom parameters : \n");
         // merge arguments with preset's own arguments.
-        for (Argument opt : arguments)
+        for (Argument opt : getJabaArguments())
         {
           jobProgress.append(
                   opt.getName() + " " + opt.getDefaultValue() + "\n");
@@ -474,7 +475,7 @@ class MsaWSThread extends AWS2Thread implements WSClientI
    * @param seqset
    *          Alignment
    */
-  MsaWSThread(MsaWS server2, WsParamSetI preset, List<Argument> paramset,
+  MsaWSThread(MsaWS server2, WsParamSetI preset, List<ArgumentI> paramset,
           String wsUrl, WebserviceInfo wsinfo,
           jalview.gui.AlignFrame alFrame, String wsname, String title,
           AlignmentView _msa, boolean subgaps, boolean presorder,